From 86d10ba4fe075b958c41e79805825cdba8d4ac95 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Sun, 17 Nov 2024 14:26:59 +0100 Subject: [PATCH] Update citations (#1301) Co-authored-by: bgruening --- _bibliography/citations-eu.bib | 1023 +++++++++++++++++++++++++++++++- 1 file changed, 1019 insertions(+), 4 deletions(-) diff --git a/_bibliography/citations-eu.bib b/_bibliography/citations-eu.bib index e796dd35..106f2f36 100644 --- a/_bibliography/citations-eu.bib +++ b/_bibliography/citations-eu.bib @@ -363,6 +363,24 @@ @article{alcaraz_development_2021 year = {2021} } +@incollection{ali_bioinformatics_2024, + abstract = {Bioinformatics and computational biology integrate computer science, molecular biology, statistics, mathematics, and engineering to collect, manage, and analyze biological data. This interdisciplinary synergy has led to innovative advances in our understanding of plant diseases and the development of effective strategies for disease management. Bioinformatics plays a diverse and influential role in addressing the fundamental challenges faced by plant pathologists. Bioinformatics in plant pathology is vital for analyzing pathogen genomes, achieved through DNA sequencing and annotation. Comparative genomics involves comparing different pathogen genomes to identify commonalities and differences, shedding light on the genetic basis of pathogenicity, virulence, drug resistance, and evolutionary relationships. Bioinformatics also aids in studying pathogen evolution, reconstructing their history, and tracking new variants, essential for predicting disease outbreaks and developing mitigation strategies. Additionally, bioinformatics contributes to advanced diagnostic tools, detecting specific genetic markers for rapid and accurate disease identification, crucial for minimizing crop losses and ensuring food security. This chapter introduces and uses different bioinformatics tools and resources used to study plant pathogens. Moreover, applications and methods of the tools involved in BLAST, multiple sequence alignment, phylogenetics, gene structure analysis, protein domain and motif, gene localization on the chromosome, protein expression analysis, and molecular docking and interaction networks are also discussed.}, + address = {Singapore}, + author = {Ali, Muhammad Amjad and Zahoor, Adil and Niaz, Zeenat and Jabran, Muhammad and Anas, Muhammad and Shafique, Ikhlas and Ahmad, Hafiz Muhammad and Usama, Muhammad and Abbas, Amjad}, + booktitle = {Trends in {Plant} {Biotechnology}}, + doi = {10.1007/978-981-97-0814-7_10}, + editor = {Ijaz, Siddra and Ul Haq, Imran and Mohamed Ali, Hayssam}, + isbn = {978-981-9708-14-7}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + pages = {281--334}, + publisher = {Springer Nature}, + title = {Bioinformatics and {Computational} {Biology}}, + url = {https://doi.org/10.1007/978-981-97-0814-7_10}, + urldate = {2024-11-17}, + year = {2024} +} + @article{ali_characterization_2021, author = {Ali, Renee and Jayaraman, Jayaraj and Mohammed, Azad and Chinnaraja, Chinnadurai and Carrington, Christine V. F. and Severson, David W. and Ramsubhag, Adesh}, doi = {10.21203/rs.3.rs-380784/v1}, @@ -822,6 +840,27 @@ @article{asiri_-silico_2024 year = {2024} } +@article{atac_identification_2024, + abstract = {The proneural transcription factor atonal basic helix–loop–helix transcription factor 7 (ATOH7) is expressed in early progenitors in the developing neuroretina. In vertebrates, this is crucial for the development of retinal ganglion cells (RGCs), as mutant animals show an almost complete absence of RGCs, underdeveloped optic nerves, and aberrations in retinal vessel development. Human mutations are rare and result in autosomal recessive optic nerve hypoplasia (ONH) or severe vascular changes, diagnosed as autosomal recessive persistent hyperplasia of the primary vitreous (PHPVAR). To better understand the role of ATOH7 in neuroretinal development, we created ATOH7 knockout and eGFP-expressing ATOH7 reporter human induced pluripotent stem cells (hiPSCs), which were differentiated into early-stage retinal organoids. Target loci regulated by ATOH7 were identified by Cleavage Under Targets and Release Using Nuclease with sequencing (CUT\&RUN-seq) and differential expression by RNA sequencing (RNA-seq) of wildtype and mutant organoid-derived reporter cells. Additionally, single-cell RNA sequencing (scRNA-seq) was performed on whole organoids to identify cell type-specific genes. Mutant organoids displayed substantial deficiency in axon sprouting, reduction in RGCs, and an increase in other cell types. We identified 469 differentially expressed target genes, with an overrepresentation of genes belonging to axon development/guidance and Notch signaling. Taken together, we consolidate the function of human ATOH7 in guiding progenitor competence by inducing RGC-specific genes while inhibiting other cell fates. Furthermore, we highlight candidate genes responsible for ATOH7-associated optic nerve and retinovascular anomalies, which sheds light to potential future therapy targets for related disorders.}, + author = {Atac, David and Maggi, Kevin and Feil, Silke and Maggi, Jordi and Cuevas, Elisa and Sowden, Jane C. and Koller, Samuel and Berger, Wolfgang}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/cells13131142}, + issn = {2073-4409}, + journal = {Cells}, + keywords = {{\textgreater}UseGalaxy.eu, ATOH7, CUT\&RUN sequencing, RNA sequencing, retinal development, retinal ganglion cells, retinal organoids, retinal progenitor cells, scRNA sequencing}, + language = {en}, + month = {January}, + note = {Number: 13 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {13}, + pages = {1142}, + title = {Identification and {Characterization} of {ATOH7}-{Regulated} {Target} {Genes} and {Pathways} in {Human} {Neuroretinal} {Development}}, + url = {https://www.mdpi.com/2073-4409/13/13/1142}, + urldate = {2024-11-17}, + volume = {13}, + year = {2024} +} + @article{bafna_dynamic_2023, abstract = {The mammalian suprachiasmatic nucleus (SCN), located in the ventral hypothalamus, synchronizes and maintains daily cellular and physiological rhythms across the body, in accordance with environmental and visceral cues. Consequently, the systematic regulation of spatiotemporal gene transcription in the SCN is vital for daily timekeeping. So far, the regulatory elements assisting circadian gene transcription have only been studied in peripheral tissues, lacking the critical neuronal dimension intrinsic to the role of the SCN as central brain pacemaker. By using histone-ChIP-seq, we identified SCN-enriched gene regulatory elements that associated with temporal gene expression. Based on tissue-specific H3K27ac and H3K4me3 marks, we successfully produced the first-ever SCN gene-regulatory map. We found that a large majority of SCN enhancers not only show robust 24-h rhythmic modulation in H3K27ac occupancy, peaking at distinct times of day, but also possess canonical E-box (CACGTG) motifs potentially influencing downstream cycling gene expression. To establish enhancer–gene relationships in the SCN, we conducted directional RNA-seq at six distinct times across the day and night, and studied the association between dynamically changing histone acetylation and gene transcript levels. About 35\% of the cycling H3K27ac sites were found adjacent to rhythmic gene transcripts, often preceding the rise in mRNA levels. We also noted that enhancers encompass noncoding, actively transcribing enhancer RNAs (eRNAs) in the SCN, which in turn oscillate, along with cyclic histone acetylation, and correlate with rhythmic gene transcription. Taken together, these findings shed light on genome-wide pretranscriptional regulation operative in the central clock that confers its precise and robust oscillation necessary to orchestrate daily timekeeping in mammals.}, author = {Bafna, Akanksha and Banks, Gareth and Hastings, Michael H. and Nolan, Patrick M.}, @@ -914,6 +953,25 @@ @article{baker_no_2020 year = {2020} } +@article{balcke_coordinated_2024, + abstract = {In plants, exposure to high light irradiation induces various stress responses, which entail complex metabolic rearrangements. To explore these dynamics, we conducted time-course experiments spanning 2 min to 72 h with Arabidopsis thaliana under high and control light. Comparative metabolomics, transcriptomics, redox proteomics, and stable isotope labeling on leaf rosettes identified a series of synchronous and successive responses that provide a deeper insight into well-orchestrated mechanisms contributing to high-light acclimation. We observed transient transcriptome downregulation related to light harvesting and electron flow before the profound remodeling of the photosynthetic apparatus. Throughout the entire time course, redox homeostasis is tightly balanced between downregulation of production and enhanced transformation of NADPH accompanied by redistribution of reducing equivalents across several subcellular compartments. In both light conditions, C4 acids such as malate and fumarate are produced via anaplerosis. In carbon units, their accumulation in vacuoles surpasses plastidic levels of starch and intensifies notably under high light. In parallel, citrate synthesis from pyruvate is significantly hindered diurnally. Isotopic labeling in 2-oxoglutarate and glutamate suggests a moderate de novo synthesis of C5 acids from a vacuolar citrate reservoir during the light phase while they are largely renewed during the night. In the absence of a diurnal clockwise flow through the tricarboxylic acid (TCA) cycle, increased oxidation of photorespiratory glycine takes over as a source of reductants to fuel mitochondrial ATP production. These findings, along with previous research, contribute to a model integrating redox balance and linking increased carbon assimilation and nitrogen metabolism, especially in the context of an incomplete TCA cycle.}, + author = {Balcke, Gerd Ulrich and Vahabi, Khabat and Giese, Jonas and Finkemeier, Iris and Tissier, Alain}, + copyright = {© 2024 The Author(s). The Plant Journal published by Society for Experimental Biology and John Wiley \& Sons Ltd.}, + doi = {10.1111/tpj.16992}, + issn = {1365-313X}, + journal = {The Plant Journal}, + keywords = {{\textgreater}UseGalaxy.eu, acclimation, anaplerosis, excess light, malate valve, metabolism, metabolomics, photosystem, regulation, stress, transcriptomics, vacuole}, + language = {de}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.16992}, + number = {1}, + pages = {387--405}, + title = {Coordinated metabolic adaptation of {Arabidopsis} thaliana to high light}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.16992}, + urldate = {2024-11-17}, + volume = {120}, + year = {2024} +} + @phdthesis{baldwin_evaluating_2019, abstract = {Chlorpyrifos (CPF) is an organophosphate pesticide used extensively in Canada and around the world. Due to its highly conserved mechanism of action involving inhibition of acetylcholinesterase (AChE), CPF has the ability to exert toxicity on non-target species in aquatic systems. In fish species, exposure to CPF has been associated with a range of adverse effects across physiological endpoints including abnormal development, inhibition of AChE, immunomodulation, and molecular level effects such as altered expression of specific genes and global transcriptomes. However, the literature on amphibians exposed to CPF is not as extensive despite the known global declines of amphibian species and the hypothesized links between these declines and anthropogenic pesticide contamination of aquatic systems worldwide. The overall objective of this thesis was to gain a better understanding of the sub-lethal effects of CPF exposure on the model amphibian, Xenopus laevis, across levels of biological organization from molecular to whole animal. The first study (Chapter 2) examined the molecular toxicity pathways and mechanisms of toxicity after short-term exposure of early life-stage (ELS) X. laevis to CPF using whole body transcriptome analyses. The ELS transcriptomic responses were then compared to apical outcomes of chronic exposure to CPF to determine if identified dysregulated pathways could provide early indicators of these adverse outcomes. Post-hatch individuals were exposed to nominal CPF concentrations of 0.4, 2, or 10 μg L-1. A subset of individuals were sampled at 96 hours (h) for whole-body transcriptomic analysis and remaining individuals were transferred to tanks for long-term exposure through to metamorphic climax ({\textasciitilde} 75 days). Pathway analysis revealed dysregulated pathways that were related to outcomes known to be associated with exposure to CPF such as altered serine hydrolase activity, impacted metabolic processes, and immune-related outcomes. Other dysregulated pathways with less precedence in the literature included vasculature development and sensory perception of light stimulus. Apical outcomes of chronic CPF exposure included inhibition of AChE activity, increased relative liver weight, and a decrease in percentage of individuals that reached metamorphic climax. Dysregulation of serine hydrolase associated pathways after ELS CPF exposure is in agreeance with the decrease in AChE (a serine hydrolase enzyme) activity observed in the brains of individuals at metamorphic climax. Additionally, an increase in relative liver weight after chronic CPF exposure could be related to dysregulation of ELS pathways associated with metabolic processes and immune function. In fact, several pathways related to immune function were depleted. @@ -1007,6 +1065,43 @@ @article{barragan-rosillo_genome_2021 year = {2021} } +@mastersthesis{barreira_predictability_2024, + abstract = {Predicting genomic evolution, which is influenced by selection, genetic drift, and population +history, is a central question in evolutionary biology. This study investigates the genetic basis of +adaptation in Drosophila subobscura populations that were initially collected from two +contrasting European latitudes and years, and subsequently underwent independent lab +adaptation. The goal was to test the predictability of evolution at the genomic level, +complementing previous research done on phenotypic changes of those populations. +First approach, I utilised the latest tools and reference genome to recreate existing analysis +pipelines. I observed some evidence of convergent and parallel evolution, distinct from the +major signal composed of drift and divergence. No common candidate SNPs were observed +between populations indicating low repeatability of changes at such level. I also noted major +genomic changes likely due to selection pressures acting on chromosomal inversion frequencies +(CIF) across populations. +After that analysis, I developed custom analysis tools, CAR (coverage adjusted rho) and CDD +(convergence divergence detection), which analyse more nucleotide data points and differentiate +between parallel, convergent, and divergent selection. This approach confirmed indication of +changes in CIF and identified selection peaks across populations, even though the peak regions +could not be functionally annotated. Most notably, I observed large genomic regions showing +convergence - likely associated with inversions - while divergence was widespread across the +genome, likely as a result of genetic drift. I also used these algorithms to successfully detect a +component of parallel evolution, when comparing populations. +An ontological functional analysis of candidate regions did not reveal similar motifs across +populations, suggesting that predictability in evolution might be partially limited to larger +structures like inversions. Future research with higher coverage data and more comprehensive +genomic annotation may provide deeper insights into the underlying mechanisms of genomic +evolution, thereby enhancing the predictability of such changes.}, + author = {Barreira, Elias Miguel da Costa}, + copyright = {openAccess}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + note = {Accepted: 2024-04-12T17:16:39Z}, + title = {Predictability of genomic evolution of populations with contrasting initial history}, + url = {https://repositorio.ul.pt/handle/10451/64228}, + urldate = {2024-11-17}, + year = {2024} +} + @article{bartas_changes_2021, author = {Bartas, Martin and Brázda, Václav and Volná, Adriana and Červeň, Jiří and Pečinka, Petr and Zawacka-Pankau, Joanna E.}, doi = {10.3390/ijms22168512}, @@ -1327,7 +1422,7 @@ @article{berlanga_biodiversity_2024 doi = {10.3389/fevo.2024.1412124}, issn = {2296-701X}, journal = {Frontiers in Ecology and Evolution}, - keywords = {{\textgreater}UseGalaxy.eu, Bacterial community diversity, Endorheic saline lagoons, bacterial community functionality, biofilm-sediment biotope, water column biotope}, + keywords = {{\textgreater}UseGalaxy.eu, Bacterial community diversity, Endorheic saline lagoons, bacterial community diversity, bacterial community functionality, biofilm-sediment biotope, endorheic saline lagoons, water column biotope}, language = {English}, month = {July}, note = {Publisher: Frontiers}, @@ -1504,6 +1599,23 @@ @incollection{boeckman_phage_2024 year = {2024} } +@article{bogguri_biphasic_2024, + abstract = {{\textless}p{\textgreater}Organophosphorus nerve agents (OPNA) are hazardous environmental exposures to the civilian population and have been historically weaponized as chemical warfare agents (CWA). OPNA exposure can lead to several neurological, sensory, and motor symptoms that can manifest into chronic neurological illnesses later in life. There is still a large need for technological advancement to better understand changes in brain function following OPNA exposure. The human-relevant {\textless}italic{\textgreater}in vitro{\textless}/italic{\textgreater} multi-electrode array (MEA) system, which combines the MEA technology with human stem cell technology, has the potential to monitor the acute, sub-chronic, and chronic consequences of OPNA exposure on brain activity. However, the application of this system to assess OPNA hazards and risks to human brain function remains to be investigated. In a concentration-response study, we have employed a human-relevant MEA system to monitor and detect changes in the electrical activity of engineered neural networks to increasing concentrations of the sarin surrogate 4-nitrophenyl isopropyl methylphosphonate (NIMP). We report a biphasic response in the spiking (but not bursting) activity of neurons exposed to low (i.e., 0.4 and 4 μM) versus high concentrations (i.e., 40 and 100 μM) of NIMP, which was monitored during the exposure period and up to 6 days post-exposure. Regardless of the NIMP concentration, at a network level, communication or coordination of neuronal activity decreased as early as 60 min and persisted at 24 h of NIMP exposure. Once NIMP was removed, coordinated activity was no different than control (0 μM of NIMP). Interestingly, only in the high concentration of NIMP did coordination of activity at a network level begin to decrease again at 2 days post-exposure and persisted on day 6 post-exposure. Notably, cell viability was not affected during or after NIMP exposure. Also, while the catalytic activity of AChE decreased during NIMP exposure, its activity recovered once NIMP was removed. Gene expression analysis suggests that human iPSC-derived neurons and primary human astrocytes resulted in altered genes related to the cell’s interaction with the extracellular environment, its intracellular calcium signaling pathways, and inflammation, which could have contributed to how neurons communicated at a network level.{\textless}/p{\textgreater}}, + author = {Bogguri, Chandrakumar and George, Vivek Kurien and Amiri, Beheshta and Ladd, Alexander and Hum, Nicholas R. and Sebastian, Aimy and Enright, Heather A. and Valdez, Carlos A. and Mundhenk, T. Nathan and Cadena, Jose and Lam, Doris}, + doi = {10.3389/fncel.2024.1378579}, + issn = {1662-5102}, + journal = {Frontiers in Cellular Neuroscience}, + keywords = {{\textgreater}UseGalaxy.eu, Acute exposure, Human Induced Pluripotent Stem Cells, Microphysiological systems, Multi-Electrode Array, human neuronal activity, nerve agent, organophosphate}, + language = {English}, + month = {September}, + note = {Publisher: Frontiers}, + title = {Biphasic response of human {iPSC}-derived neural network activity following exposure to a sarin-surrogate nerve agent}, + url = {https://www.frontiersin.org/journals/cellular-neuroscience/articles/10.3389/fncel.2024.1378579/full}, + urldate = {2024-11-17}, + volume = {18}, + year = {2024} +} + @article{bohlender_stable_2020, abstract = {Recombinantly produced proteins are indispensable tools for medical applications. Since the majority of them are glycoproteins, their N-glycosylation profiles are major determinants for their activity, structural properties and safety. For therapeutical applications, a glycosylation pattern adapted to product and treatment requirements is advantageous. Physcomitrium patens (Physcomitrella, moss) is able to perform highly homogeneous complex-type N-glycosylation. Additionally, it has been glyco-engineered to eliminate plant-specific sugar residues by knock-out of the β1,2-xylosyltransferase and α1,3-fucosyltransferase genes (Δxt/ft). Furthermore, Physcomitrella meets wide-ranging biopharmaceutical requirements such as GMP compliance, product safety, scalability and outstanding possibilities for precise genome engineering. However, all plants, in contrast to mammals, lack the capability to perform N-glycan sialylation. Since sialic acids are a common terminal modification on human N glycans, the property to perform N-glycan sialylation is highly desired within the plant-based biopharmaceutical sector. In this study, we present the successful achievement of protein N-glycan sialylation in stably transformed Physcomitrella. The sialylation ability was achieved in a Δxt/ft moss line by stable expression of seven mammalian coding sequences combined with targeted organelle-specific localization of the encoded enzymes responsible for the generation of β1,4 galactosylated acceptor N glycans as well as the synthesis, activation, transport and transfer of sialic acid. Production of free (Neu5Ac) and activated (CMP-Neu5Ac) sialic acid was proven. The glycosidic anchor for the attachment of terminal sialic acid was generated by the introduction of a chimeric human β1,4 galactosyltransferase gene under the simultaneous knock-out of the gene encoding the endogenous β1,3 galactosyltransferase. Functional complex-type N-glycan sialylation was confirmed via mass spectrometric analysis of a stably co-expressed recombinant human protein.}, author = {Bohlender, Lennard L. and Parsons, Juliana and Hoernstein, Sebastian N. W. and Rempfer, Christine and Ruiz-Molina, Natalia and Lorenz, Timo and Rodríguez Jahnke, Fernando and Figl, Rudolf and Fode, Benjamin and Altmann, Friedrich and Reski, Ralf and Decker, Eva L.}, @@ -1573,6 +1685,24 @@ @article{boneva_mace_2020 year = {2020} } +@article{boneva_multifaceted_2024, + abstract = {Despite great advances in proliferative diabetic retinopathy (PDR) therapy over the last decades, one third of treated patients continue to lose vision. While resident vitreous macrophages called hyalocytes have been implicated in the pathophysiology of vitreoretinal proliferative disease previously, little is known about their exact role in PDR. In this study, we address molecular and cellular alterations in the vitreous of PDR patients as a means towards assessing the potential contribution of hyalocytes to disease pathogenesis.}, + author = {Boneva, Stefaniya K. and Wolf, Julian and Jung, Malte and Prinz, Gabriele and Chui, Toco Y. P. and Jauch, Jacqueline and Drougard, Anne and Pospisilik, J. Andrew and Schlecht, Anja and Bucher, Felicitas and Rosen, Richard B. and Agostini, Hansjürgen and Schlunck, Günther and Lange, Clemens A. K.}, + doi = {10.1186/s12974-024-03291-5}, + issn = {1742-2094}, + journal = {Journal of Neuroinflammation}, + keywords = {{\textgreater}UseGalaxy.eu, Angiomodulation, Erythrophagocytosis, Hyalocytes, Inflammation, Proliferative diabetic retinopathy, RNA-Sequencing, Vitreous macrophages}, + month = {November}, + number = {1}, + pages = {297}, + shorttitle = {The multifaceted role of vitreous hyalocytes}, + title = {The multifaceted role of vitreous hyalocytes: {Orchestrating} inflammation, angiomodulation and erythrophagocytosis in proliferative diabetic retinopathy}, + url = {https://doi.org/10.1186/s12974-024-03291-5}, + urldate = {2024-11-17}, + volume = {21}, + year = {2024} +} + @article{boneva_transcriptional_2020, abstract = {To decipher the transcriptional signature of macrophages of the human vitreous, also known as hyalocytes, and compare it to the profiles of other myeloid cell populations including human blood-derived monocytes, macrophages and brain microglia. This study involves a total of 13 patients of advanced age with disorders of the vitreoretinal interface undergoing vitrectomy at the University Eye Hospital Freiburg between 2018 and 2019. Vitreal hyalocytes were analyzed by fluorescence-activated cell sorting (FACS) and isolated as CD45+CD11b+CX3CR1+Mat-Mac+ cells using a FACS-based sorting protocol. RNA extraction, library preparation and RNA sequencing were performed and the sequencing data was analyzed using the Galaxy web platform. The transcriptome of human hyalocytes was compared to the transcriptional profile of human blood-derived monocytes, macrophages and brain microglia obtained from public databases. Protein validation for selected factors was performed by immunohistochemistry on paraffin sections from three human donor eyes. On average, 383 ± 233 hyalocytes were isolated per patient, resulting in 128 pg/µl ± 76 pg/µl total RNA per sample. RNA sequencing revealed that SPP1, FTL, CD74 and HLA-DRA are among the most abundantly expressed genes in hyalocytes, which was confirmed by immunofluorescence for CD74, FTL and HLA-DRA. Gene ontology (GO) enrichment analysis showed that biological processes such as “humoral immune response”, “leukocyte migration” and “antigen processing and presentation of peptide antigen” (adjusted p \< 0.001) are dominating in vitreal hyalocytes. While the comparison of the gene expression profiles of hyalocytes and other myeloid cell populations showed an overall strong similarity (R2 \> 0.637, p \< 0.001), hyalocytes demonstrated significant differences with respect to common leukocyte-associated factors. In particular, transcripts involved in the immune privilege of the eye, such as POMC, CD46 and CD86, were significantly increased in hyalocytes compared to other myeloid cell subsets. Human hyalocytes represent a unique and distinct innate immune cell population specialized and adapted for the tissue-specific needs in the human vitreous. Vitreal hyalocytes are characterized by a strong expression of genes related to antigen processing and presentation as well as immune modulation. Thus, hyalocytes may represent an underestimated mediator in vitreoretinal disease and for the immune privilege of the eye.}, author = {Boneva, Stefaniya Konstantinova and Wolf, Julian and Rosmus, Dennis-Dominik and Schlecht, Anja and Prinz, Gabriele and Laich, Yannik and Boeck, Myriam and Zhang, Peipei and Hilgendorf, Ingo and Stahl, Andreas and Reinhard, Thomas and Bainbridge, James and Schlunck, Günther and Agostini, Hansjürgen and Wieghofer, Peter and Lange, Clemens A. K.}, @@ -1829,6 +1959,19 @@ @article{breidenbach_microcystin-lr_2022 year = {2022} } +@mastersthesis{brink_identification_2024, + abstract = {Cardiomyopathy is one of the major causes of heart failure that affects approximately 26 million patients worldwide. In a healthy situation, the heart depends on fatty acid oxidation (FAO) to maintain its energy demand. In failing hearts, the heart reverts to a fetal-like metabolic state in which FAO is downregulated and the heart switches to glucose metabolism. Peroxisome proliferator-activated receptor alpha (PPARA), a regulator of FAO, has recently been found to be hypoacetylated and its downstream effectors downregulated in dilated cardiomyopathy. However, the exact mechanisms remain largely unknown. The main purpose of this internship was to identify the specific FAO expression patterns in a large heterogenic patient cohort and investigate the involvement of PPARA regulation. The secondary goal was to set up a transcriptomic pipeline within Galaxy, a user-friendly bioinformatics platform, and test whether this platform can be used in diagnostics in the future. Differential expression analysis and gene enrichment of RNA-sequencing data show a type-specific FAO expression pattern of DCM and LVH versus HCM and confirm a downregulation of FAO related processes. Public RNA-sequencing data after the use of a bezafibrate, a PPARA agonist, which has been integrated, shows the upregulation of genes that are downregulated in our data. Combined, the results confirm the downregulation of FAO, but indicate a disease-type-specific FAO expression pattern. The results from the Galaxy pipeline show that this pipeline is suitable for transcriptomic analyses. Furthermore, we highlight the potential therapeutic role of bezafibrate in cardiomyopathy.}, + author = {Brink, Alyssa van den}, + copyright = {CC-BY-NC-ND}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {EN}, + note = {Accepted: 2024-01-01T01:02:24Z}, + title = {Identification of the {Expression} {Patterns} of {Fatty} {Acid} {Oxidation} {Genes} in a {Heterogenic} {Cardiomyopathy} {Patient} {Cohort}}, + url = {https://studenttheses.uu.nl/handle/20.500.12932/45733}, + urldate = {2024-11-17}, + year = {2024} +} + @article{broche_genome-wide_2021, abstract = {Chromatin properties are regulated by complex networks of epigenome modifications. Currently, it is unclear how these modifications interact and if they control downstream effects such as gene expression. We employed promiscuous chromatin binding of a zinc finger fused catalytic domain of DNMT3A to introduce DNA methylation in HEK293 cells at many CpG islands (CGIs) and systematically investigated the dynamics of the introduced DNA methylation and the consequent changes of the epigenome network. We observed efficient methylation at thousands of CGIs, but it was unstable at about 90\% of them, highlighting the power of genome-wide molecular processes that protect CGIs against DNA methylation. Partially stable methylation was observed at about 1000 CGIs, which showed enrichment in H3K27me3. Globally, the introduced DNA methylation strongly correlated with a decrease in gene expression indicating a direct effect. Similarly, global but transient reductions in H3K4me3 and H3K27ac were observed after DNA methylation but no changes were found for H3K9me3 and H3K36me3. Our data provide a global and time-resolved view on the network of epigenome modifications, their connections with DNA methylation and the responses triggered by artificial DNA methylation revealing a direct repressive effect of DNA methylation in CGIs on H3K4me3, histone acetylation, and gene expression.}, author = {Broche, Julian and Kungulovski, Goran and Bashtrykov, Pavel and Rathert, Philipp and Jeltsch, Albert}, @@ -2137,6 +2280,22 @@ @article{capitani_genome-based_2023 year = {2023} } +@article{capitani_vivo_2024, + author = {Capitani, Valerio and Arcari, Gabriele and Ambrosi, Cecilia and Scribano, Daniela and Ceparano, Mariateresa and Polani, Riccardo and De Francesco, Alice and Raponi, Giammarco and Ceccarelli, Giancarlo and Villari, Paolo and Palamara, Anna Teresa and Marzuillo, Carolina and Carattoli, Alessandra}, + doi = {10.1128/msphere.00423-24}, + journal = {mSphere}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + note = {Publisher: American Society for Microbiology}, + number = {9}, + pages = {e00423--24}, + title = {In vivo evolution to hypermucoviscosity and ceftazidime/avibactam resistance in a liver abscess caused by {Klebsiella} pneumoniae sequence type 512}, + url = {https://journals.asm.org/doi/full/10.1128/msphere.00423-24}, + urldate = {2024-11-17}, + volume = {9}, + year = {2024} +} + @article{capra_cpg_2023, abstract = {During epididymal transit spermatozoa acquire specific morphological features which enhance their ability to swim in a progressive manner and interact with the oocytes. At the same time, sperm cells undergo specific molecular rearrangements essential for the fertilizing sperm to drive a correct embryo development. To assess epigenetic sperm changes during epididymal maturation, the caput, corpus and cauda epididymis sperm tracts were isolated from eight bulls and characterized for different sperm quality parameters and for CpG DNA methylation using Reduced Representation Bisulfite Sequencing (RRBS) able to identify differentially methylated regions (DMRs) in higher CpG density regions.}, author = {Capra, Emanuele and Turri, F. and Lazzari, B. and Biffani, S. and Lange Consiglio, A. and Ajmone Marsan, P. and Stella, A. and Pizzi, F.}, @@ -2198,6 +2357,20 @@ @article{carvalho_genomics_2024 year = {2024} } +@article{casal_plant_2024, + abstract = {Plants are exposed to temperature conditions that fluctuate over different time scales, including those inherent to global warming. In the face of these variations, plants sense temperature to adjust their functions and minimize the negative consequences. Transcriptome responses underlie changes in growth, development, and biochemistry (thermomorphogenesis and acclimation to extreme temperatures). We are only beginning to understand temperature sensation by plants. Multiple thermosensors convey complementary temperature information to a given signaling network to control gene expression. Temperature-induced changes in protein or transcript structure and/or in the dynamics of biomolecular condensates are the core sensing mechanisms of known thermosensors, but temperature impinges on their activities via additional indirect pathways. The diversity of plant responses to temperature anticipates that many new thermosensors and eventually novel sensing mechanisms will be uncovered soon.}, + author = {Casal, Jorge J. and Murcia, Germán and Bianchimano, Luciana}, + doi = {10.1146/annurev-genet-111523-102327}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {July}, + note = {Publisher: Annual Reviews}, + title = {Plant {Thermosensors}}, + url = {https://www.annualreviews.org/content/journals/10.1146/annurev-genet-111523-102327}, + urldate = {2024-11-17}, + year = {2024} +} + @article{castellana_pannonibacter_2024, abstract = {This study describes two cases of bacteraemia sustained by a new putative Pannonibacter species isolated at the U.O.C. of Microbiology and Virology of the Policlinico of Bari (Bari, Italy) from the blood cultures of two patients admitted to the Paediatric Oncohaematology Unit. Pannonibacter spp. is an environmental Gram-negative bacterium not commonly associated with nosocomial infections. Species identification was performed using Sanger sequencing of the 16S rRNA gene and Whole-Genome Sequencing (WGS) for both strains. Genomic analyses for the two isolates, BLAST similarity search, and phylogeny for the 16S rDNA sequences lead to an assignment to the species Pannonibacter phragmitetus. However, by performing ANIb, ANIm, tetranucleotide correlation, and DNA-DNA digital hybridization, analyses of the two draft genomes showed that they were very different from those of the species P. phragmitetus. MALDI-TOF analysis, assessment of antimicrobial susceptibility by E-test method, and Analytical Profile Index (API) tests were also performed. This result highlights how environmental bacterial species can easily adapt to the human host and, especially in nosocomial environments, also gain pathogenic potential through antimicrobial resistance.}, author = {Castellana, Stefano and De Laurentiis, Vittoriana and Bianco, Angelica and Del Sambro, Laura and Grassi, Massimo and De Leonardis, Francesco and Derobertis, Anna Maria and De Carlo, Carmen and Sparapano, Eleonora and Mosca, Adriana and Stolfa, Stefania and Ronga, Luigi and Santacroce, Luigi and Chironna, Maria and Parisi, Michela and Capozzi, Loredana and Parisi, Antonio}, @@ -2273,6 +2446,21 @@ @article{chanama_comparative_2023 year = {2023} } +@article{chatti_genome-wide_2024, + abstract = {The R2R3-MYB transcription factor (TF) family is crucial for regulating plant growth, stress response, and fruit ripening. Although this TF family has been examined in a multitude of plants, the R2R3-MYB TFs in Ficus carica, a Mediterranean fruit species, have yet to be characterized. This study identified and classified 63 R2R3-MYB genes (FcMYB1 to FcMYB63) in the F. carica genome. We analyzed these genes for physicochemical properties, conserved motifs, phylogenetic relationships, gene architecture, selection pressure, and gene expression profiles and networks. The genes were classified into 29 clades, with members of the same clade showing similar exon–intron structures and motif compositions. Of the 54 orthologous gene pairs shared with mulberry (Morus notabilis), 52 evolved under negative selection, while two pairs (FcMYB55/MnMYB20 and FcMYB59/MnMYB31) experienced diversifying selection. RNA-Seq analysis showed that FcMYB26, FcMYB33, and FcMYB34 were significantly overexpressed in fig fruit peel during maturation phase III. Weighted gene co-expression network analysis (WGCNA) indicated that these genes are part of an expression module associated with the anthocyanin pathway. RT-qPCR validation confirmed these findings and revealed that the Tunisian cultivars 'Zidi' and 'Soltani' have cultivar-specific R2R3-FcMYB genes highly overexpressed during the final stage of fruit maturation and color acquisition. These genes likely influence cultivar-specific pigment synthesis. This study provides a comprehensive overview of the R2R3-MYB TF family in fig, offering a framework for selecting genes related to fruit peel color in breeding programs.}, + author = {Chatti, Khaled and Kmeli, Narjes and Bettaieb, Inchirah and Hamdi, Jihen and Gaaied, Sonia and Mlouka, Rania and Mars, Messaoud and Bouktila, Dhia}, + doi = {10.1007/s10528-024-10960-w}, + issn = {1573-4927}, + journal = {Biochemical Genetics}, + keywords = {{\textgreater}UseGalaxy.eu, Expression profile, Fig tree, Fruit pigmentation, Functional plant omics, Gene family, R2R3-MYB, Transcription factor}, + language = {en}, + month = {November}, + title = {Genome-{Wide} {Analysis} of the {Common} {Fig} ({Ficus} carica {L}.) {R2R3}-{MYB} {Genes} {Reveals} {Their} {Structure}, {Evolution}, and {Roles} in {Fruit} {Color} {Variation}}, + url = {https://doi.org/10.1007/s10528-024-10960-w}, + urldate = {2024-11-17}, + year = {2024} +} + @article{chen_first_2021, author = {Chen, Dong-Bin and Zhang, Ru-Song and Jin, Xiang-Dong and Yang, Jian and Li, Peng and Liu, Yan-Qun}, doi = {10.1017/s0007485321000808}, @@ -2361,6 +2549,28 @@ @article{chetverikov_molecular_2024 year = {2024} } +@article{chiappa_potential_2024, + abstract = {Venomous marine gastropods of the superfamily Conoidea possess a rich arsenal of toxins, including neuroactive toxins. Venom adaptations might have played a fundamental role in the radiation of conoideans; nevertheless, there is still no knowledge about the venom of the most diversified family of the group: Raphitomidae Bellardi, 1875. In this study, transcriptomes were produced from the carcase, salivary glands, and proximal and distal venom ducts of the northeastern Atlantic species Raphitoma purpurea (Montagu, 1803). Using a gut barcoding approach, we were also able to report, for the first time, molecular evidence of a vermivorous diet for the genus. Transcriptomic analyses revealed over a hundred putative venom components (PVC), including 69 neurotoxins. Twenty novel toxin families, including some with high levels of expansion, were discovered. No significant difference was observed between the distal and proximal venom duct secretions. Peptides related to cone snail toxins (Cerm06, Pgam02, and turritoxin) and other venom-related proteins (disulfide isomerase and elevenin) were retrieved from the salivary glands. These salivary venom components may constitute ancestral adaptations for venom production in conoideans. Although often neglected, salivary gland secretions are of extreme importance for understanding the evolutionary history of conoidean venom.}, + author = {Chiappa, Giacomo and Fassio, Giulia and Modica, Maria Vittoria and Oliverio, Marco}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/toxins16080348}, + issn = {2072-6651}, + journal = {Toxins}, + keywords = {{\textgreater}UseGalaxy.eu, Raphitomidae, conotoxin, salivary glands, transcriptome, trophic ecology, venom duct, venom evolution}, + language = {en}, + month = {August}, + note = {Number: 8 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {8}, + pages = {348}, + shorttitle = {Potential {Ancestral} {Conoidean} {Toxins} in the {Venom} {Cocktail} of the {Carnivorous} {Snail} {Raphitoma} purpurea ({Montagu}, 1803) ({Neogastropoda}}, + title = {Potential {Ancestral} {Conoidean} {Toxins} in the {Venom} {Cocktail} of the {Carnivorous} {Snail} {Raphitoma} purpurea ({Montagu}, 1803) ({Neogastropoda}: {Raphitomidae})}, + url = {https://www.mdpi.com/2072-6651/16/8/348}, + urldate = {2024-11-17}, + volume = {16}, + year = {2024} +} + @article{chiara_next_2021, abstract = {Various next generation sequencing (NGS) based strategies have been successfully used in the recent past for tracing origins and understanding the evolution of infectious agents, investigating the spread and transmission chains of outbreaks, as well as facilitating the development of effective and rapid molecular diagnostic tests and contributing to the hunt for treatments and vaccines. The ongoing COVID-19 pandemic poses one of the greatest global threats in modern history and has already caused severe social and economic costs. The development of efficient and rapid sequencing methods to reconstruct the genomic sequence of SARS-CoV-2, the etiological agent of COVID-19, has been fundamental for the design of diagnostic molecular tests and to devise effective measures and strategies to mitigate the diffusion of the pandemic.Diverse approaches and sequencing methods can, as testified by the number of available sequences, be applied to SARS-CoV-2 genomes. However, each technology and sequencing approach has its own advantages and limitations. In the current review, we will provide a brief, but hopefully comprehensive, account of currently available platforms and methodological approaches for the sequencing of SARS-CoV-2 genomes. We also present an outline of current repositories and databases that provide access to SARS-CoV-2 genomic data and associated metadata. Finally, we offer general advice and guidelines for the appropriate sharing and deposition of SARS-CoV-2 data and metadata, and suggest that more efficient and standardized integration of current and future SARS-CoV-2-related data would greatly facilitate the struggle against this new pathogen. We hope that our ‘vademecum’ for the production and handling of SARS-CoV-2-related sequencing data, will contribute to this objective.}, author = {Chiara, Matteo and D’Erchia, Anna Maria and Gissi, Carmela and Manzari, Caterina and Parisi, Antonio and Resta, Nicoletta and Zambelli, Federico and Picardi, Ernesto and Pavesi, Giulio and Horner, David S and Pesole, Graziano}, @@ -2677,6 +2887,41 @@ @article{de_jesus_bertani_whole_2023 year = {2023} } +@article{de_melo_mitochondrial_2024, + abstract = {Syagrus coronata (Mart.) Becc. belongs to the Arecaceae family. It is a species native to Brazil of ecological, social, and economic importance. To date, there are few mitochondrial genomes in Arecaceae (Cocos nucifera and Phoenix dactylifera L.), and studies of the mitochondrial genome are essential to understand the evolution of the Arecaceae family. This study reports and compares the newly sequenced genome of S. coronata. Single-end and paired-end reads were used to obtain de novo contigs. The mitochondrial contigs were selected using C. nucifera as a reference and were merged using mate paired-end reads. The mitochondrial genome showed 642,817 bp, circular structure, containing 73 predicted functional genes, including four ribosomal RNA (rRNA) genes, 27 transfer RNA (tRNA) genes, and 42 coding protein genes. Large chloroplast genomic fragments were identified in the mitochondrial genome, and large DNA repetitive fragments were into intergenic space regions. Arecaceae mitochondrial genomes showed partial similarities in size, genome structure, and gene content. However, they exhibited numerous rearrangements. In summary, (1) we sequenced the mitochondrial genome of S. coronata and compared with other mitogenomes of Arecaceae. (2) Genomic rearrangements and gene transfer have been identified from the chloroplast genome to the mitochondrial genome. (3) The mitochondrial genome of Arecareae showed similarities in size, structure, and gene content. (4) The expansion of intergenic space size occurs due to the insertion of genes originating from the nucleus.}, + author = {de Melo, Suzyanne Morais Firmino and Marques, André and Almeida, Cícero}, + doi = {10.1007/s11295-024-01643-z}, + issn = {1614-2950}, + journal = {Tree Genetics \& Genomes}, + keywords = {{\textgreater}UseGalaxy.eu, Arecaceae, Mitogenome, Ouricuri}, + language = {en}, + month = {March}, + number = {2}, + pages = {10}, + title = {The mitochondrial genome sequence of {Syagrus} coronata ({Mart}.) {Becc}. ({Arecaceae}) is characterized by gene insertion within intergenic spaces}, + url = {https://doi.org/10.1007/s11295-024-01643-z}, + urldate = {2024-11-17}, + volume = {20}, + year = {2024} +} + +@article{de_oliveira_apoplastomes_2024, + abstract = {{\textless}p{\textgreater}Witches’ broom disease (WBD) affects cocoa trees ({\textless}italic{\textgreater}Theobroma cacao{\textless}/italic{\textgreater} L.) and is caused by the fungus {\textless}italic{\textgreater}Moniliophthora perniciosa{\textless}/italic{\textgreater} that grows in the apoplast in its biotrophic phase and later progresses into the tissues, causing serious losses in the production of cocoa beans. Therefore, the apoplast of {\textless}italic{\textgreater}T. cacao{\textless}/italic{\textgreater} can provide important defense responses during the interaction with {\textless}italic{\textgreater}M. perniciosa{\textless}/italic{\textgreater}. In this work, the protein profile of the apoplast of the {\textless}italic{\textgreater}T. cacao{\textless}/italic{\textgreater} genotypes Catongo, susceptible to WBD, and CCN-51, resistant one, was evaluated. The leaves of {\textless}italic{\textgreater}T. cacao{\textless}/italic{\textgreater} were collected from asymptomatic plants grown in a greenhouse (GH) and from green witches’ brooms grown under field (FD) conditions for extraction of apoplastic washing fluid (AWF). AWF was used in proteomic and enzymatic analysis. A total of 14 proteins were identified in Catongo GH and six in Catongo FD, with two proteins being common, one up-accumulated, and one down-accumulated. In CCN-51, 19 proteins were identified in the GH condition and 13 in FD, with seven proteins being common, one up-accumulated, and six down-accumulated. Most proteins are related to defense and stress in both genotypes, with emphasis on pathogenesis-related proteins (PR): PR-2 (β-1,3-glucanases), PR-3 and PR-4 (chitinases), PR-5 (thaumatine), PR-9 (peroxidases), and PR-14 (lipid transfer proteins). Furthermore, proteins from microorganisms were detected in the AWF. The enzymatic activities of PR-3 showed a significant increase (p \< 0.05) in Catongo GH and PR-2 activity (p \< 0.01) in CCN-51 FD. The protein profile of the {\textless}italic{\textgreater}T. cacao{\textless}/italic{\textgreater} apoplastome offers insight into the defense dynamics that occur in the interaction with the fungus {\textless}italic{\textgreater}M. perniciosa{\textless}/italic{\textgreater} and offers new insights in exploring future WBD control strategies.{\textless}/p{\textgreater}}, + author = {De Oliveira, Ivina Barbosa and Alves, Saline dos Santos and Ferreira, Monaliza Macêdo and Santos, Ariana Silva and Farias, Keilane Silva and Assis, Elza Thaynara Cardoso de Menezes and Mora-Ocampo, Irma Yuliana and Muñoz, Jonathan Javier Mucherino and Costa, Eduardo Almeida and Gramacho, Karina Peres and Pirovani, Carlos Priminho}, + doi = {10.3389/fpls.2024.1387153}, + issn = {1664-462X}, + journal = {Frontiers in Plant Science}, + keywords = {{\textgreater}UseGalaxy.eu, Apoplast, Moniliophthora perniciosa, apoplastic washing fluid, defense proteins, theobroma cacao}, + language = {English}, + month = {May}, + note = {Publisher: Frontiers}, + title = {Apoplastomes of contrasting cacao genotypes to witches’ broom disease reveals differential accumulation of {PR} proteins}, + url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1387153/full}, + urldate = {2024-11-17}, + volume = {15}, + year = {2024} +} + @article{de_souza_mitochondrial_2024, abstract = {Plant mitochondrial genomes are characterized by high homologous recombination, extensive intergenic spacers, conservation in DNA sequences, and gene content. The Hancornia genus belongs to the Apocynaceae family, with H. speciosa Gomes being the sole species in the genus. It is an siganificant commercial fruit crop; however, only a number of studies have been conducted. In this study, we present the mitochondrial genome of H. speciosa and compare it with other mitochondrial genomes within the Apocynaceae family.}, author = {de Souza, Fernanda Danielle and Marques, André and Almeida, Cícero}, @@ -3229,6 +3474,25 @@ @article{emser_mitochondrial_2023 year = {2023} } +@article{epihov_iron_2024, + abstract = {Enhanced rock weathering (EW) is an emerging atmospheric carbon dioxide removal (CDR) strategy being scaled up by the commercial sector. Here, we combine multiomics analyses of belowground microbiomes, laboratory-based dissolution studies, and incubation investigations of soils from field EW trials to build the case for manipulating iron chelators in soil to increase EW efficiency and lower costs. Microbial siderophores are high-affinity, highly selective iron (Fe) chelators that enhance the uptake of Fe from soil minerals into cells. Applying RNA-seq metatranscriptomics and shotgun metagenomics to soils and basalt grains from EW field trials revealed that microbial communities on basalt grains significantly upregulate siderophore biosynthesis gene expression relative to microbiomes of the surrounding soil. Separate in vitro laboratory incubation studies showed that micromolar solutions of siderophores and high-affinity synthetic chelator (ethylenediamine-N,N′-bis-2-hydroxyphenylacetic acid, EDDHA) accelerate EW to increase CDR rates. Building on these findings, we develop a potential biotechnology pathway for accelerating EW using the synthetic Fe-chelator EDDHA that is commonly used in agronomy to alleviate the Fe deficiency in high pH soils. Incubation of EW field trial soils with potassium-EDDHA solutions increased potential CDR rates by up to 2.5-fold by promoting the abiotic dissolution of basalt and upregulating microbial siderophore production to further accelerate weathering reactions. Moreover, EDDHA may alleviate potential Fe limitation of crops due to rising soil pH with EW over time. Initial cost-benefit analysis suggests potassium-EDDHA could lower EW-CDR costs by up to U.S. \$77 t CO2 ha–1 to improve EW’s competitiveness relative to other CDR strategies.}, + author = {Epihov, Dimitar Z. and Banwart, Steven A. and McGrath, Steve P. and Martin, David P. and Steeley, Isabella L. and Cobbold, Vicky and Kantola, Ilsa B. and Masters, Michael D. and DeLucia, Evan H. and Beerling, David J.}, + doi = {10.1021/acs.est.3c10146}, + issn = {0013-936X}, + journal = {Environmental Science \& Technology}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {July}, + note = {Publisher: American Chemical Society}, + number = {27}, + pages = {11970--11987}, + shorttitle = {Iron {Chelation} in {Soil}}, + title = {Iron {Chelation} in {Soil}: {Scalable} {Biotechnology} for {Accelerating} {Carbon} {Dioxide} {Removal} by {Enhanced} {Rock} {Weathering}}, + url = {https://doi.org/10.1021/acs.est.3c10146}, + urldate = {2024-11-17}, + volume = {58}, + year = {2024} +} + @article{ercole_unveiling_2024, abstract = {Stenotrophomonas species are recognized as rhizobacteria that play a pivotal role in promoting plant growth by making substantial contributions to enhanced soil fertility, nutrient recycling, and phytopathogen control. Employing them as bioinputs constitutes an environmentally sound strategy, particularly within the rhizospheric community. This study revealed the draft genome sequence of Stenotrophomonas geniculata LGMB417, which was originally isolated from root samples of maize (Zea mays L.). This research assessed the potential of a bacterial strain at the molecular level through genome mining, aiming to identify genes with biotechnological significance for promoting plant growth and protection. The assembly findings indicate that strain LGMB417 possesses a genome size of 4,654,011 bp, with a G + C content of 66.50\%. The draft genome sequence revealed the presence of gene clusters responsible for the synthesis of secondary metabolites and carbohydrate active enzymes (CAZymes), glycoside hydrolases (23), glycosyltransferases (18), carbohydrate esterases (5), polysaccharide lyases (2), carbohydrate-binding modules (2), and auxiliary activities (1). Several genes related to growth promotion were found in the genome, including those associated with phosphate transport and solubilization, nitrogen metabolism, siderophore production and iron transport, hormonal modulation, stress responses (such as to drought, temperature fluctuations, osmotic challenges, and oxidative conditions), and volatile organic compounds (VOCs). Subsequent phases will encompass investigations utilizing gene expression methodologies, with future explorations concentrating on facets pertinent to agricultural production, including comprehensive field studies.}, author = {Ercole, Tairine Graziella and Kava, Vanessa Merlo and Petters-Vandresen, Desirrê Alexia Lourenço and Ribeiro, Renan Augusto and Hungria, Mariangela and Galli, Lygia Vitoria}, @@ -3662,6 +3926,39 @@ @phdthesis{fernandes_guavadb_2020 year = {2020} } +@mastersthesis{fernandes_lama2-cmd_2024, + abstract = {In skeletal muscle tissue, the basement membrane lining the sarcolemma coats and protects myofibers +from contraction-induced damage. A key component of this specialized structure is the Laminin-211 +(LN211). Pathogenic mutations in the LAMA2 gene, which encodes the α2-chain of laminin-211, trigger +a life-threatening and currently incurable disease, LAMA2-muscular dystrophy (LAMA2-MD). However, +the classical gene therapy approaches are not feasible due to the size of the LAMA2 gene, which exceeds +the packaging capacity of one of the most used viral vectors, the recombinant adeno-associated virus +(rAAV). Instead of introducing the complete gene sequence into the cells, homology-directed repair +(HDR) can theoretically correct the majority of pathogenic point mutations responsible for LAMA2-MD. +Using the CRISPR/Cas9 system, we have established two C2C12 myoblast cell lines that carry point +mutations in Lama2, which recapitulate the ones found in the dy2J/dy2J and dynmf417/dynmf417 mouse +models for LAMA2-MD. Furthermore, the obtained single-cell clones were confirmed by nextgeneration sequencing (NGS) to be heterozygous for the intended mutations. The established cell lines +were then characterized and had an impairment in myoblast differentiation and fusion into myotubes. +The single-cell clone carrying the dynmf417 mutation was used to evaluate the reversion of the specific +mutation with all-in-one rAAV vectors by HDR. The engineered vector encoded a smaller version of +Cas9 from Neisseria meningitidis, Nme2Cas9, a single sgRNA and the HDR donor template. The rAAV +production was also optimized and the AAV1 serotype was selected as the most suitable for the +transduction of the C2C12 cells. The muscle-specific rAAV9:HDR system was not able to edit and +revert the specific mutation in the Lama2 gene but gave critical insights into the best rAAV design +strategies. This project will contribute to the development of a new therapeutic strategy targeting +LAMA2-MD that will be preceded by the in vivo studies using the dy2J/dy2J mice.}, + author = {Fernandes, Diogo Rodrigues}, + copyright = {openAccess}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + note = {Accepted: 2024-02-21T18:31:44Z}, + shorttitle = {{LAMA2}-{CMD}}, + title = {{LAMA2}-{CMD}: establishment of a new gene therapy strategy using an in vitro model}, + url = {https://repositorio.ul.pt/handle/10451/62797}, + urldate = {2024-11-17}, + year = {2024} +} + @article{fernandez-diaz_draft_2023, abstract = {This study presents a draft genome sequence of a Newcastle disease virus (NDV) strain (VFAR-136) isolated from a fighting cock (Gallus gallus) in the south of Peru. Strain VFAR-136 is a new report of NDV genotype VII circulating in Peru.}, author = {Fernández-Díaz, Manolo and Montalván-Avalos, Angela and Isasi-Rivas, Gisela and Villanueva-Pérez, Doris and Quiñones-Garcia, Stefany and Tataje-Lavanda, Luis and Rios-Matos, Dora and Lulo-Vargas, Milagros and Fernández-Sánchez, Manolo and Guevara-Sarmiento, Luis A. and Zimic, Mirko and Rojas-Neyra, Aldo and Calderón, Katherine}, @@ -3867,6 +4164,21 @@ @article{foll_moving_2021 year = {2021} } +@article{fonseca_mineracao_2024, + abstract = {The Amazon, with its vast biodiversity, harbors a complex network of ecosystems interconnected by rivers such as the Negro and Solimões. This unique dynamic favors the emergence and diversification of microbial lineages, rendering the region a hotspot for the discovery of innovative biological solutions. Within this context, this thesis investigated the biotechnological potential of 36 bacteria isolated from Amazonian river sediments, focusing on applications in phytopathogen biocontrol and plant growth promotion. The bacterial isolates were evaluated in vitro against agriculturally significant phytopathogens, including Corynespora cassiicola, Colletotrichum siamense, Rhizoctonia solani, and Ralstonia solanacearum. This initial screening gave rise to two main chapters: the first investigates the biocontrol of R. solanacearum, while the second examines the genomic potential and agricultural applications of Alcaligenes nematophilus SOL 109. In Chapter 1, three isolates - Priestia aryabhattai RN 11, Streptomyces sp. RN 24, and Kitasatospora sp. SOL 195 - demonstrated remarkable efficacy against R. solanacearum, with in vitro inhibition of 87-100\%, reduction of disease incidence by 40-90\% in tomato seedlings, and promotion of plant growth. Phylogenomic analyses based on ANI and dDDH revealed that RN 11 belongs to the species Priestia aryabhattai (ANI: 98.61\%, dDDH: 88.3\%), while RN 24 and SOL 195 presented values below the cut-off points for new species, potentially representing novel species within the genera Streptomyces and Kitasatospora, respectively. Chapter 2 elucidates the multifaceted potential of A. nematophilus SOL 109, demonstrating in vitro inhibition ranging from 74 to 93\% against phytopathogenic fungi. Under greenhouse conditions, evaluations indicate that the SOL 109 effectively controlled the pathogen R. solani and promoted growth in tomato plants. Genomic and chemical analyses of SOL 109 identified unique and shared biosynthetic gene clusters (BGCs) within the genus Alcaligenes, genes conferring resistance to antibiotics and heavy metals, and metabolites with antimicrobial properties. The results of this thesis highlight the unexplored potential of Amazonian aquatic microorganisms, revealing new actinobacterial species (RN 24 and SOL 195) and reporting for the first time the occurrence of A. nematophilus in Brazil. This study significantly contributes to the development of sustainable plant disease management strategies, offers valuable insights into the secondary metabolism of the genus Alcaligenes, and opens new perspectives for biotechnological applications in agriculture, reinforcing the importance of conservation and study of Amazonian microbial biodiversity.}, + author = {Fonseca, Jennifer Salgado da}, + copyright = {https://creativecommons.org/licenses/by-nc-nd/4.0/}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {por}, + month = {September}, + note = {Accepted: 2024-11-06T15:09:43Z +Publisher: Universidade Federal do Amazonas}, + title = {Mineração genômica e identificação de moléculas com potencial biotecnológico da microbiota amazônica}, + url = {https://tede.ufam.edu.br/handle/tede/10467}, + urldate = {2024-11-17}, + year = {2024} +} + @article{formenti_gfastats_2022, abstract = {With the current pace at which reference genomes are being produced, the availability of tools that can reliably and efficiently generate genome assembly summary statistics has become critical. Additionally, with the emergence of new algorithms and data types, tools that can improve the quality of existing assemblies through automated and manual curation are required.We sought to address both these needs by developing gfastats, as part of the Vertebrate Genomes Project (VGP) effort to generate high-quality reference genomes at scale. Gfastats is a standalone tool to compute assembly summary statistics and manipulate assembly sequences in FASTA, FASTQ or GFA [.gz] format. Gfastats stores assembly sequences internally in a GFA-like format. This feature allows gfastats to seamlessly convert FAST* to and from GFA [.gz] files. Gfastats can also build an assembly graph that can in turn be used to manipulate the underlying sequences following instructions provided by the user, while simultaneously generating key metrics for the new sequences.Gfastats is implemented in C++. Precompiled releases (Linux, MacOS, Windows) and commented source code for gfastats are available under MIT licence at https://github.com/vgl-hub/gfastats. Examples of how to run gfastats are provided in the GitHub. Gfastats is also available in Bioconda, in Galaxy (https://assembly.usegalaxy.eu) and as a MultiQC module (https://github.com/ewels/MultiQC). An automated test workflow is available to ensure consistency of software updates.Supplementary data are available at Bioinformatics online.}, author = {Formenti, Giulio and Abueg, Linelle and Brajuka, Angelo and Brajuka, Nadolina and Gallardo-Alba, Cristóbal and Giani, Alice and Fedrigo, Olivier and Jarvis, Erich D}, @@ -4401,20 +4713,19 @@ @article{godbole_multiomic_2024 year = {2024} } -@article{goglio_performance_2025, +@article{goglio_performance_2024, abstract = {This work studied the performances of two ad hoc biochar-based cathode materials: one obtained from pyrolysis of the organic fraction of municipal solid waste (OW) and the other of wood chips (WC), in the context of three different bio-electrochemical reactors’ scope: MFC, MEC and MES. Cathodes were characterized through composition, pH, specific surface area and infrared spectroscopy; then production of electricity, methane (CH4), and volatile fatty acids (VFAs) from carbon dioxide (CO2) was described, and finally the microbial community was explored through 16S rRNA gene sequencing. WC-based electrodes performed better than OW-based ones. WC (200 ± 25 mV) generated twice the amount of electricity compared to OW (100 ± 10 mV) in MFC modality. In MEC modality, WC achieved both higher CH4 production and concentration (3.6 ± 0.7 mL per day, 73.2 ± 3.9 \% v/v, respectively) than OW (3.0 ± 0.3 mL per day, 70 ± 8 \% v/v, respectively). In MES modality, WC produced ten times more acetic acid (0.3 ± 0.13 g L−1 per day) than OW (0.03 ± 0.04 g L−1 per day). The better performance of the WC-biochar cathode was attributed to its higher Brunauer–Emmett–Teller (BET) value and its carbonaceous graphite-like structure. NGS analysis highlighted the presence of specific genera of microorganisms leading to the differential functioning of the systems.}, author = {Goglio, Andrea and Carrara, Arianna and Elboghdady, Hager Galal Elsayed and Cucina, Mirko and Clagnan, Elisa and Soggia, Gabriele and De Nisi, Patrizia and Adani, Fabrizio}, doi = {10.1016/j.jpowsour.2024.235623}, issn = {0378-7753}, journal = {Journal of Power Sources}, keywords = {{\textgreater}UseGalaxy.eu, Biochar-based electrode, CO electro-recycling, Microbial electrolysis cell, Microbial electrosynthesis, Microbial fuel cell, Organic wastes}, - month = {January}, pages = {235623}, title = {The performance of biochar waste-derived electrodes in different bio-electrochemical applications}, url = {https://www.sciencedirect.com/science/article/pii/S0378775324015751}, urldate = {2024-11-02}, volume = {625}, - year = {2025} + year = {2024} } @article{goossens_obligate_2023, @@ -4593,6 +4904,22 @@ @article{gu_galaxy-ml_2021 year = {2021} } +@inproceedings{gu_proswats_2024, + abstract = {It is time-consuming and knowledge-intensive for scientists to find practical workflows from the massive number of scientific workflow models. Currently, the retrieval approaches are mainly based on text matching between natural language queries and the descriptions of candidate workflows. Notably, the workflow structure also provides essential semantics, but the challenge lies in effectively matching these two pieces of heterogeneous information. To address this issue, we propose a Proxy-based Scientific workflow retrieval approach, ProSwats, which selects a workflow as the Proxy for each text query to bridge the gap between textual and structural semantics. ProSwats consists of two stages: workflow pre-selection based on text similarity and workflow ranking based on a matching degree prediction model. The textual and structural features are integrated by the proxy in this model, which is used to predict and rank the degree of semantic matching between the user query and candidate workflows. Crucially, ProSwats incorporates a confidence-aware learning mechanism to adapt to the varying reliability of proxies, enhancing generalizability. Extensive experimental results on two real-world datasets demonstrate that ProSwats outperforms state-of-the-art methods with statistical significance.}, + author = {Gu, Yang and Cao, Jian and Qian, Shiyou and Zhu, Nengjun and Guan, Wei}, + booktitle = {2024 {IEEE} {International} {Conference} on {Web} {Services} ({ICWS})}, + doi = {10.1109/ICWS62655.2024.00111}, + keywords = {{\textgreater}UseGalaxy.eu, Adaptation models, Bridges, Confidence-aware Learning, Learning systems, Natural languages, Predictive models, Proxy Mechanism, Quality of service, Reliability, Scientific Workflow Retrieval, Semantic Gap, Semantics, Services Composition, Training, Web services}, + month = {July}, + note = {ISSN: 2836-3868}, + pages = {932--943}, + shorttitle = {{ProSwats}}, + title = {{ProSwats}: {A} {Proxy}-based {Scientific} {Workflow} {Retrieval} {Approach} by {Bridging} the {Gap} between {Textual} and {Structural} {Semantics}}, + url = {https://ieeexplore.ieee.org/abstract/document/10707449?casa_token=6EMmhIm15zsAAAAA:ebcpnJVSk9Kf3uXJvbOC_nQHOs_rF9FRNcgXLl_f_D-lRSMgFfr4YySCkUsH2IFlrfwH4JgwCg}, + urldate = {2024-11-17}, + year = {2024} +} + @article{guendel_group_2020, abstract = {Solitary intestinal lymphoid tissues such as cryptopatches (CPs) and isolated lymphoid follicles (ILFs) constitute steady-state activation hubs containing group 3 innate lymphoid cells (ILC3) that continuously produce interleukin (IL)-22. The outer surface of CPs and ILFs is demarcated by a poorly characterized population of CD11c+ cells. Using genome-wide single-cell transcriptional profiling of intestinal mononuclear phagocytes and multidimensional flow cytometry, we found that CP- and ILF-associated CD11c+ cells were a transcriptionally distinct subset of intestinal cDCs, which we term CIA-DCs. CIA-DCs required programming by CP- and ILF-resident CCR6+ ILC3 via lymphotoxin-β receptor signaling in cDCs. CIA-DCs differentially expressed genes associated with immunoregulation and were the major cellular source of IL-22 binding protein (IL-22BP) at steady state. Mice lacking CIA-DC-derived IL-22BP exhibited diminished expression of epithelial lipid transporters, reduced lipid resorption, and changes in body fat homeostasis. Our findings provide insight into the design principles of an immunoregulatory checkpoint controlling nutrient absorption.}, author = {Guendel, Fabian and Kofoed-Branzk, Michael and Gronke, Konrad and Tizian, Caroline and Witkowski, Mario and Cheng, Hung-Wei and Heinz, Gitta Anne and Heinrich, Frederik and Durek, Pawel and Norris, Paula S. and Ware, Carl F. and Ruedl, Christiane and Herold, Susanne and Pfeffer, Klaus and Hehlgans, Thomas and Waisman, Ari and Becher, Burkhard and Giannou, Anastasios D. and Brachs, Sebastian and Ebert, Karolina and Tanriver, Yakup and Ludewig, Burkhard and Mashreghi, Mir-Farzin and Kruglov, Andrey A. and Diefenbach, Andreas}, @@ -4646,6 +4973,27 @@ @article{guindo_tetragenococcus_2022 year = {2022} } +@article{guo_mitogenome-based_2024, + abstract = {Heptageniidae are known for their flat heads and bodies and are divided into three subfamilies. Despite the extensive diversity within this group and considerable efforts made to understand their evolutionary history, the internal classifications and origin time of Heptageniidae remains controversial. In this study, we newly sequenced 17 complete mitogenomes of Heptageniidae to reconstruct their phylogenetic positions within this family. Because of the ambiguous time of origin, our study also estimated the divergence time within Heptageniidae based on five fossil calibration points. The results of BI and ML trees all highly supported the monophyly of Heptageniidae and three subfamilies. The phylogenetic relationship of Rhithrogeninae + (Ecdyonurinae + Heptageniinae) was also recovered. The divergence time showed that Heptageniidae originated from 164.38 Mya (95\% HPD, 150.23–181.53 Mya) in the mid-Jurassic, and Rhithrogeninae originated from 95.54 Mya (95\% HPD, 73.86–120.19 Mya) in the mid-Cretaceous. Ecdyonurinae and Heptageniinae began to diverge at 90.08 Mya (95\% HPD, 68.81–113.16 Mya) in the middle Cretaceous. After morphological identification, analysis of the mitogenome’s composition, genetic distance calculation, phylogenetic analysis, and divergence time calculation, we suggest that two different populations of Epeorus montanus collected from Aksu, Xinjiang Uygur Autonomous Region (40°16′ N, 80°26′ E) and Xinyuan, Xinjiang Uygur Autonomous Region (43°20′ N, 83°43′ E) in China are cryptic species of E. montanus, but further detailed information on their morphological characteristics is needed to fully identify them.}, + author = {Guo, Zhi-Qiang and Shen, Chen-Yang and Cheng, Hong-Yi and Chen, Yu-Xin and Wu, Hui-Yuan and Storey, Kenneth B. and Yu, Dan-Na and Zhang, Jia-Yong}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/insects15100745}, + issn = {2075-4450}, + journal = {Insects}, + keywords = {{\textgreater}UseGalaxy.eu, Heptageniidae, cryptic species, divergence time, mitogenomes, phylogenetic relationship}, + language = {en}, + month = {October}, + note = {Number: 10 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {10}, + pages = {745}, + title = {Mitogenome-{Based} {Phylogeny} with {Divergence} {Time} {Estimates} {Revealed} the {Presence} of {Cryptic} {Species} within {Heptageniidae} ({Insecta}, {Ephemeroptera})}, + url = {https://www.mdpi.com/2075-4450/15/10/745}, + urldate = {2024-11-17}, + volume = {15}, + year = {2024} +} + @article{gussak_precision_2023, abstract = {Streptococcussuis is an important zoonotic pathogen that causes severe invasive disease in pigs and humans. Current methods for genome engineering of S. suis rely on the insertion of antibiotic resistance markers, which is time-consuming and labor-intensive and does not allow the precise introduction of small genomic mutations. Here we developed a system for CRISPR-based genome editing in S. suis, utilizing linear DNA fragments for homologous recombination (HR) and a plasmid-based negative selection system for bacteria not edited by HR. To enable the use of this system in other bacteria, we engineered a broad-host-range replicon in the CRISPR plasmid. We demonstrated the utility of this system to rapidly introduce multiple gene deletions in successive rounds of genome editing and to make precise nucleotide changes in essential genes. Furthermore, we characterized a mechanism by which S. suis can escape killing by a targeted Cas9-sgRNA complex in the absence of HR. A characteristic of this new mechanism is the presence of very slow-growing colonies in a persister-like state that may allow for DNA repair or the introduction of mutations, alleviating Cas9 pressure. This does not impact the utility of CRISPR-based genome editing because the escape colonies are easily distinguished from genetically edited clones due to their small colony size. Our CRISPR-based editing system is a valuable addition to the genetic toolbox for engineering of S. suis, as it accelerates the process of mutant construction and simplifies the removal of antibiotic markers between successive rounds of genome editing.}, author = {Gussak, Alex and Ferrando, Maria Laura and Schrama, Mels and van Baarlen, Peter and Wells, Jerry Mark}, @@ -4788,6 +5136,25 @@ @article{hardtner_comparative_2023 year = {2023} } +@article{hashempour_reverse_2024, + abstract = {Substantial advances have been made in the development of promising HIV vaccines to eliminate HIV-1 infection. For the first time, one hundred of the most submitted HIV subtypes and CRFs were retrieved from the LANL database, and the consensus sequences of the eleven HIV proteins were obtained to design vaccines for human and mouse hosts. By using various servers and filters, highly qualified B-cell epitopes, as well as HTL and CD8 + epitopes that were common between mouse and human alleles and were also located in the conserved domains of HIV proteins, were considered in the vaccine constructs. With 90\% coverage worldwide, the human vaccine model covers a diverse allelic population, making it widely available. Codon optimization and in silico cloning in prokaryotic and eukaryotic vectors guarantee high expression of the vaccine models in human and E. coli hosts. Molecular dynamics confirmed the stable interaction of the vaccine constructs with TLR3, TLR4, and TLR9, leading to a substantial immunogenic response to the designed vaccine. Vaccine models effectively target the humoral and cellular immune systems in humans and mice; however, experimental validation is needed to confirm these findings in silico.}, + author = {Hashempour, Ava and Khodadad, Nastaran and Akbarinia, Shokufeh and Ghasabi, Farzane and Ghasemi, Younes and Nazar, Mohamad Matin Karbalaei Ali and Falahi, Shahab}, + doi = {10.1186/s12879-024-09775-2}, + issn = {1471-2334}, + journal = {BMC Infectious Diseases}, + keywords = {{\textgreater}UseGalaxy.eu, Bioinformatic, HIV, Main HIV subtypes and CRF, Molecular dynamic, TLR, Vaccine}, + language = {en}, + month = {August}, + number = {1}, + pages = {873}, + shorttitle = {Reverse vaccinology approaches to design a potent multiepitope vaccine against the {HIV} whole genome}, + title = {Reverse vaccinology approaches to design a potent multiepitope vaccine against the {HIV} whole genome: immunoinformatic, bioinformatics, and molecular dynamics approaches}, + url = {https://doi.org/10.1186/s12879-024-09775-2}, + urldate = {2024-11-17}, + volume = {24}, + year = {2024} +} + @article{hassan_genome-wide_2023, author = {Hassan, Zarqa and Abbas, Amjad and Shafique, Ikhlas}, doi = {10.22194/pdc/3.1017}, @@ -4804,6 +5171,24 @@ @article{hassan_genome-wide_2023 year = {2023} } +@article{he_novel_2024, + abstract = {The holothurians, commonly known as sea cucumbers, are marine organisms that possess significant dietary, nutritional, and medicinal value. However, the National Center for Biotechnology Information (NCBI) currently possesses only approximately 70 complete mitochondrial genome datasets of Holothurioidea, which poses limitations on conducting comprehensive research on their genetic resources and evolutionary patterns. In this study, a novel species of sea cucumber belonging to the genus Benthodytes, was discovered in the western Pacific Ocean. The genomic DNA of the novel sea cucumber was extracted, sequenced, assembled and subjected to thorough analysis.}, + author = {He, Yingying and Zhao, Hancheng and Wang, Yongxin and Qu, Changfeng and Gao, Xiangxing and Miao, Jinlai}, + doi = {10.1186/s12864-024-10607-5}, + issn = {1471-2164}, + journal = {BMC Genomics}, + keywords = {{\textgreater}UseGalaxy.eu, Benthodytes sp. Gxx-2023, Bioinformatics analysis, Mitogenome, Phylogenetic evolution, Sea cucumber}, + language = {en}, + month = {July}, + number = {1}, + pages = {689}, + title = {A novel deep-benthic sea cucumber species of {Benthodytes} ({Holothuroidea}, {Elasipodida}, {Psychropotidae}) and its comprehensive mitochondrial genome sequencing and evolutionary analysis}, + url = {https://doi.org/10.1186/s12864-024-10607-5}, + urldate = {2024-11-17}, + volume = {25}, + year = {2024} +} + @misc{hecht_quantum_2024, abstract = {There is a lack of experimental electron ionization high-resolution mass spectra available to assist compound identification. The in silico generation of mass spectra by quantum chemistry can aid annotation workflows, in particular to support the identification of compounds that lack experimental reference spectra, such as environmental chemicals. We present an open-source, semi-automated workflow for the in silico prediction of electron ionization high-resolution mass spectra based on the QCxMS software. The workflow was applied to predict the spectra of 367 environmental chemicals and accuracy evaluated by comparison to experimental reference spectra acquired. The molecular flexibility, number of rotatable bonds and number of electronegative atoms of a compound were negatively correlated with prediction accuracy. Few analytes are predicted to sufficient accuracy for the direct application of predicted spectra in spectral matching workflows. The m/z values of the top 5 most abundant ions of predicted spectra rarely match ions in experimental spectra, evidencing the disconnect between simulated fragmentation pathways and empirical reaction mechanisms.}, author = {Hecht, Helge and Rojas, Wudmir Y. and Ahmad, Zargham and Křenek, Aleš and Klánová, Jana and Price, Elliott J.}, @@ -5200,6 +5585,27 @@ @article{howard_complete_2023 year = {2023} } +@article{huang_rs1347093_2024, + abstract = {Background +Single nucleotide polymorphism (SNP) rs1347093 shows statistically significant association with lung cancer risk, but there is no further rs1347093 expression quantitative trait loci (eQTL) effect information. SNP rs1347093 is located in microRNA-216/-217 (miR-216/-217) locus. In addition, miR-216/-217 have pancreas-enriched expressions. In this study, we examined a potential miR-216/-217 promoter region, and investigated the effect of rs1347093-A allele on the miR-216/-217 promoter activity. +Methods +Bioinformatics analysis, quantitative real-time PCR, luciferase reporter assay, Western blotting, and cell counting kit-8 (CCK-8) assay were performed. +Results +The miR-216/-217 expressions are down-regulated in pancreatic cancer. In pancreatic cancer patients carrying the rs1347093-A allele, miR-216/-217 expressions were more largely suppressed. We identified a potential promoter region in miR-216/-217 locus and further showed that rs1347093-A allele resulted in significantly reduced promoter activity in pancreatic cancer cells, which could be mediated by MEF2C activities. In terms of mechanism in the pathogenesis of pancreatic cancer, miR-216b-5p expression was down-regulated, thereby preventing it from interacting with beclin-1 mRNA while promoting the survival of pancreatic cancer cells. +Conclusions +This study may reveal the biological relevance underlying rs1347093-A allele with an increase in pancreatic cancer risk. SNP rs1347093 could be meaningful as a novel biomarker for pancreatic cancer risk.}, + author = {Huang, Hsin-Hung and Shiu, Tzu-Yue and Chan, De-Chuan and Chang, Chao-Feng and Lin, Hsuan-Hwai and Lin, Jung-Chun and Chen, Peng-Jen and Shih, Yu-Lueng and Chang, Wei-Kuo and Hsieh, Tsai-Yuan}, + doi = {10.1016/j.pan.2024.10.004}, + issn = {1424-3903}, + journal = {Pancreatology}, + keywords = {{\textgreater}UseGalaxy.eu, Beclin-1, Pancreatic cancer, Single nucleotide polymorphism, miR-216b-5p}, + month = {October}, + title = {Rs1347093 regulates {microRNA}-216/-217 expression and is associated with pancreatic cancer risk}, + url = {https://www.sciencedirect.com/science/article/pii/S1424390324007543}, + urldate = {2024-11-17}, + year = {2024} +} + @article{huang_translational_2023, abstract = {Ethylene plays essential roles in rice growth, development and stress adaptation. Translational control of ethylene signaling remains unclear in rice. Here, through analysis of an ethylene-response mutant mhz9, we identified a glycine-tyrosine-phenylalanine (GYF) domain protein MHZ9, which positively regulates ethylene signaling at translational level in rice. MHZ9 is localized in RNA processing bodies. The C-terminal domain of MHZ9 interacts with OsEIN2, a central regulator of rice ethylene signaling, and the N-terminal domain directly binds to the OsEBF1/2 mRNAs for translational inhibition, allowing accumulation of transcription factor OsEIL1 to activate the downstream signaling. RNA-IP seq and CLIP-seq analyses reveal that MHZ9 associates with hundreds of RNAs. Ribo-seq analysis indicates that MHZ9 is required for the regulation of {\textasciitilde} 90\% of genes translationally affected by ethylene. Our study identifies a translational regulator MHZ9, which mediates translational regulation of genes in response to ethylene, facilitating stress adaptation and trait improvement in rice.}, author = {Huang, Yi-Hua and Han, Jia-Qi and Ma, Biao and Cao, Wu-Qiang and Li, Xin-Kai and Xiong, Qing and Zhao, He and Zhao, Rui and Zhang, Xun and Zhou, Yang and Wei, Wei and Tao, Jian-Jun and Zhang, Wan-Ke and Qian, Wenfeng and Chen, Shou-Yi and Yang, Chao and Yin, Cui-Cui and Zhang, Jin-Song}, @@ -5221,6 +5627,24 @@ @article{huang_translational_2023 year = {2023} } +@article{humphrey_genomic_2024, + abstract = {Genome sequencing of Clostridium clostridioforme strain LM41 revealed the presence of an atypically high proportion of mobile genetic elements for this species, with a particularly high abundance of prophages. Bioinformatic analysis of prophage sequences sought to characterize these elements and identify prophage-linked genes contributing to enhanced fitness of the host bacteria in the dysbiotic gut. Using PHASTER, PhageScope and manual curation, this work has identified 15 prophages: 4 predicted to be intact, 2 predicted to be defective and 9 which are unclassified. Quantitative PCR (qPCR) analysis revealed spontaneous release of four of the LM41 prophages (φ1, φ2, φ4 and φ10) into the culture supernatant, with virion-like particles visualized using transmission electron microscopy. The majority (12/14) of these particles had morphology akin to podoviruses, which is consistent with morphology predictions for φ1 and φ4. We observed diversity in the lysogeny mechanisms utilized by the prophages, with examples of the classical λ-like CI/Cro system, the ICEBs1 ImmR/ImmA-like system and the Mu-like C/Ner system. Classical morons, such as toxins or immune evasion factors, were not observed. We did, however, identify a variety of genes with roles in mediating restriction modification and genetic diversity, as well as some candidate genes with potential roles in host adaptation. Despite being the most abundant entities in the intestine, there is a dearth of information about phages associated with members of the microbiome. This work begins to shed light on the contribution of these elements to the lifestyle of C. clostridioforme LM41.}, + author = {Humphrey, Suzanne and Marouli, Angeliki and Thümmler, Katja and Mullin, Margaret and Pritchard, Leighton and Wall, Daniel M.}, + doi = {10.1099/mic.0.001486}, + issn = {1465-2080}, + journal = {Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + note = {Publisher: Microbiology Society,}, + number = {8}, + pages = {001486}, + shorttitle = {Genomic characterization of prophage elements in {Clostridium} clostridioforme}, + title = {Genomic characterization of prophage elements in {Clostridium} clostridioforme: an understudied component of the intestinal microbiome}, + url = {https://www.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.001486}, + urldate = {2024-11-17}, + volume = {170}, + year = {2024} +} + @article{huszarik_external_2023, abstract = {DNA metabarcoding is increasingly used to analyze the diet of arthropods, including spiders. However, high sensitivity to DNA contamination makes it difficult to apply to organisms obtained from mass-sampling methods such as pitfall traps. An alternative is to hand-sample spiders, but it is unclear how effectively this prevents external contamination, especially with new knowledge showing the wide spread of eDNA in the environment. Protocols using bleach to remove external DNA have been tested on several invertebrates, though testing with both mass-sampling methods and spiders is lacking. Here, we used wolf spiders (Lycosidae) to assess the risk of external DNA contamination from pitfall trapping and hand sampling, and the efficacy of bleach decontamination. We first conducted a contamination experiment where we placed spiders in pitfall traps containing trapping medium and a nonprey insect species to simulate external DNA contamination. We also compared sampling methods by collecting spiders using pitfall traps and hand sampling. Spiders from the contamination experiment and sampling method comparison were either bleached or untreated, then metabarcoded using multiple primer pairs. The contamination experiment resulted in the contamination of almost all spiders from pitfall traps, which was successfully eliminated with bleaching. Interestingly, there was no difference in the number of amplicon sequence variants (ASVs) detected per spider between pitfall trapping and hand sampling but bleaching resulted in significantly fewer ASV detections for both methods. Additionally, bleaching, but not sampling method, affected the taxonomic diet composition for both hand-sampled and pitfall-trapped spiders, indicating similar levels of external contamination. Our results are the first to confirm that DNA metabarcoding can be used together with bleaching for spiders sampled from pitfall traps, and that hand sampling does not necessarily exclude external DNA contamination. Thus, diet studies using metabarcoding should address the risk of external contamination with field-sampled arthropods, regardless of sampling method.}, author = {Huszarik, Maike and Röder, Nina and Eberhardt, Linda and Kennedy, Susan and Krehenwinkel, Henrik and Schwenk, Klaus and Entling, Martin H.}, @@ -5278,6 +5702,26 @@ @article{ilikkan_laktik_2023 year = {2023} } +@article{imre_epigenetic_2024, + abstract = {H2A.Z-nucleosomes are present in both euchromatin and heterochromatin and it has proven difficult to interpret their disparate roles in the context of their stability features. Using an in situ assay of nucleosome stability and DT40 cells expressing engineered forms of the histone variant we show that native H2A.Z, but not C-terminally truncated H2A.Z (H2A.Z∆C), is released from nucleosomes of peripheral heterochromatin at unusually high salt concentrations. H2A.Z and H3K9me3 landscapes are reorganized in H2A.Z∆C-nuclei and overall sensitivity of chromatin to nucleases is increased. These tail-dependent differences are recapitulated upon treatment of HeLa nuclei with the H2A.Z-tail-peptide (C9), with MNase sensitivity being increased genome-wide. Fluorescence correlation spectroscopy revealed C9 binding to reconstituted nucleosomes. When introduced into live cells, C9 elicited chromatin reorganization, overall nucleosome destabilization and changes in gene expression. Thus, H2A.Z-nucleosomes influence global chromatin architecture in a tail-dependent manner, what can be modulated by introducing the tail-peptide into live cells.}, + author = {Imre, László and Nánási, Péter and Benhamza, Ibtissem and Enyedi, Kata Nóra and Mocsár, Gábor and Bosire, Rosevalentine and Hegedüs, Éva and Niaki, Erfaneh Firouzi and Csóti, Ágota and Darula, Zsuzsanna and Csősz, Éva and Póliska, Szilárd and Scholtz, Beáta and Mező, Gábor and Bacsó, Zsolt and Timmers, H. T. Marc and Kusakabe, Masayuki and Balázs, Margit and Vámosi, György and Ausio, Juan and Cheung, Peter and Tóth, Katalin and Tremethick, David and Harata, Masahiko and Szabó, Gábor}, + copyright = {2024 The Author(s)}, + doi = {10.1038/s41467-024-53514-9}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Epigenetics, Gene regulation, Nuclear organization}, + language = {en}, + month = {October}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {9171}, + title = {Epigenetic modulation via the {C}-terminal tail of {H2A}.{Z}}, + url = {https://www.nature.com/articles/s41467-024-53514-9}, + urldate = {2024-11-17}, + volume = {15}, + year = {2024} +} + @article{iniesta-pallares_changes_2023, abstract = {The Doñana wetlands comprise an emblematic Mediterranean landscape protected as a UNESCO World Heritage Site. Some parts of these wetlands have been transformed into intensive rice cultivation areas, which are currently the most productive rice-growing areas in Europe. We examined the bacterial communities in these domesticated soils as they are key for plant health and productivity and have a strong influence on biochemical cycles. To identify the bacteria, we used metabarcoding analysis coupled with metabolic predictions and co-occurrence networks. This analysis was performed in the bulk and rhizosphere soils during different stages in the growing season. These soil compartments had a greater effect on the bacterial communities than the plant phenological stages. The diversity and richness of the bacterial population inhabiting the rhizosphere was much lower than that in the bulk soil, comprising taxa that were significantly more represented in this soil compartment, such as bacteria from the genus Hydrogenophaga, three genera from the order Rhizobiales, and unclassified genera from the families Desulfocapsaceae and Actinobacteria. Rhizosphere co-occurrence networks revealed a high number of negative connections, indicating unstable bacterial communities that may be highly influenced by biotic and abiotic factors. Rhizosphere networks mostly rely on two taxa belonging to the phyla Proteobacteria and Cyanobacteria, which are the predicted network hubs in this soil compartment. The bulk soil conserved high bacterial diversity and richness that was stable throughout the growth period of rice. Anaerobic bacteria from genera Marmoricola, the uncultured Gemmatimonadota bacteria SDR1034 terrestrial group, Anaerolinea, and the sulphur oxidizer, Thiobacillus were highly represented. This analysis provides valuable information for understanding bacterial diversity in the rhizosphere of rice cultivated in this region, which is critical for enhancing plant growth and productivity.}, author = {Iniesta-Pallarés, Macarena and Brenes-Álvarez, Manuel and Lasa, Ana V. and Fernández-López, Manuel and Álvarez, Consolación and Molina-Heredia, Fernando P. and Mariscal, Vicente}, @@ -5656,6 +6100,22 @@ @article{jude_draft_2019 year = {2019} } +@article{kaari_integrated_2024, + abstract = {Ralstonia solanacearum is one of the most destructive soil-borne pathogen, causing bacterial wilt to the solanaceae vegetables. Streptomyces sp. UP1A-1 isolated from healthy solanaceae rhizosphere soil, exhibited the lowest disease incidence and increased fruit yield of solanaceae vegetables. However, the genomic and functional properties of UP1A-1 are unclear. Therefore, we conducted the present study to elucidate the genomic characteristics of UP1A-1 by whole genome sequencing. The results indicate that the genome of Streptomyces sp. UP1A-1 consists of 8,252,902 bp and contains 72.42 \% G + C. We identified the genes that confer plant growth promoting (PGP) function, which include those involved in siderophore production, indole-3-acetic acid biosynthesis, phosphate solubilization, nitrogen metabolism, and potassium metabolism. We also identified several other genes, such as chitinase, peroxidase, superoxide dismutase, catalase, proline biosynthesis, and glucose dehydrogenase, which are believed to be involved in the control of wilt disease. These genes revealed that the strain UP1A-1 has physiologically adapted to varied environmental conditions and could potentially control both abiotic and biotic stresses.}, + author = {Kaari, Manigundan and Manikkam, Radhakrishnan and Joseph, Jerrine and Krishnan, Sakthivel and Annamalai, Kishore Kumar and Khan, Abujunaid and Rajput, Vinay and Dastager, Syed Gulam and Dharne, Mahesh S. and Umar, Md and Venugopal, Gopikrishnan and Alexander, Balamurugan}, + doi = {10.1016/j.genrep.2024.102012}, + issn = {2452-0144}, + journal = {Gene Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Bacterial wilt, Biocontrol genes, Plant growth, Whole genome sequencing}, + month = {December}, + pages = {102012}, + title = {Integrated genomic and functional analysis of \textit{{Streptomyces}} sp. {UP1A}-1 for bacterial wilt control and solanaceae yield increase}, + url = {https://www.sciencedirect.com/science/article/pii/S2452014424001353}, + urldate = {2024-11-17}, + volume = {37}, + year = {2024} +} + @article{kahraman-ilikkan_comparative_2024, abstract = {Lactic acid bacteria (LAB) can be used as a probiotic or starter culture in dairy, meat, and vegetable fermentation. Therefore, their isolation and identification are essential. Recent advances in omics technologies and high-throughput sequencing have made the identification and characterization of bacteria. This study firstly aimed to demonstrate the sensitivity of the Vitek MS (MALDI-TOF) system in the identification of lactic acid bacteria and, secondly, to characterize bacteria using various bioinformatics approaches. Probiotic potency-related genes and secondary metabolite biosynthesis gene clusters were examined. The Vitek MS (MALDI-TOF) system was able to identify all of the bacteria at the genus level. According to whole genome sequencing, the bacteria were confirmed to be Lentilactobacillus buchneri, Levilactobacillus brevis, Lactiplantibacillus plantarum, Levilactobacillus namurensis. Bacteria had most of the probiotic potency-related genes, and different toxin-antitoxin systems such as PemIK/MazEF, Hig A/B, YdcE/YdcD, YefM/YoeB. Also, some of the secondary metabolite biosynthesis gene clusters, some toxic metabolite-related genes, and antibiotic resistance-related genes were detected. In addition, Lentilactobacillus buchneri Egmn17 had a type II-A CRISPR/Cas system. Lactiplantibacillus plantarum Gmze16 had a bacteriocin, plantaricin E/F.}, author = {Kahraman-Ilıkkan, Özge}, @@ -5720,6 +6180,22 @@ @article{kalnytska_sorcs2_2024 year = {2024} } +@article{kamajian_identification_2024, + abstract = {Spot blotch disease, caused by the fungal pathogen Bipolaris sorokiniana, poses a significant threat to global production particularly wheat, and barley due to substantial yield losses. Similar to many fungal pathogens, the infection of host plants heavily depends on the pathogen's ability to secrete effector proteins, which manipulate host defenses and aid disease progression. However, a critical knowledge gap exists in the comprehensive identification and characterization of effector candidates (ECs) in B. sorokiniana, requiring further research efforts. Therefore, study aimed to systematically identify and characterize ECs in B. sorokiniana by conducting pathogenicity tests to confirm disease symptoms on wheat leaves, utilizing a rigorous bioinformatics approach to predict ECs through sequence analysis and structural similarities, and validating effector expression profiles during infection using RNA sequencing (RNA-Seq) and quantitative real-time polymerase chain reaction (qRT-PCR). Pathogenicity testing confirmed the typical symptoms of spot blotch disease upon inoculation with B. sorokiniana. Through bioinformatics analysis, 81 ECs were identified, showing dynamic expression patterns during infection stages. Among these ECs, genes such as Cocsa1{\textbar}129517, Cocsa1{\textbar}141231, and Cocsa1{\textbar}193443 stood out due to their different expression patterns and structural similarities, indicating their potential roles as effectors. This study offers new novel insights into the effector repertoire of B. sorokiniana and its implications for spot blotch disease management. The identified ECs present promising targets for further investigation to clarify their specific roles in fungal virulence and host immune modulation.}, + author = {Kamajian, Mahla and Soorni, Aboozar and Mehrabi, Rahim}, + doi = {10.1016/j.pmpp.2024.102343}, + issn = {0885-5765}, + journal = {Physiological and Molecular Plant Pathology}, + keywords = {{\textgreater}UseGalaxy.eu, Effector proteins, Gene expression, Spot blotch, Structural similarity}, + month = {September}, + pages = {102343}, + title = {Identification of effector candidates in \textit{{Bipolaris} sorokiniana} and their expression profile analysis during pathogen-wheat interactions}, + url = {https://www.sciencedirect.com/science/article/pii/S0885576524001279}, + urldate = {2024-11-17}, + volume = {133}, + year = {2024} +} + @article{kandinov_azithromycin_2023, abstract = {The aim of this work was to study the resistance to macrolides (azithromycin) in the modern Russian population of N. gonorrhoeae with the analysis of genetic resistance determinants. Azithromycin is not used to treat gonococcal infection in Russia. However, among 162 isolates collected in 2020–2021, 22 isolates (13.6\%) were phenotypically resistant to azithromycin. Mutations in 23S rRNA genes were found only in two isolates; erm and mefA genes were absent. Azithromycin resistance was shown to be predominantly associated with mutations in the mtrR and mtrD genes of the MtrCDE efflux pump and their mosaic alleles which may have formed due to a horizontal transfer from N. meningitidis. A total of 30 types of mtrR alleles and 10 types of mtrD alleles were identified including mosaic variants. Matching between the mtrR and mtrD alleles was revealed to indicate the cooperative molecular evolution of these genes. A link between the mtrR and mtrD alleles and NG-MAST types was found only for NG-MAST 228 and 807, typical of N. gonorrhoeae in Russia. The high level of resistance to azithromycin in Russia may be related to the spread of multiple transferable resistance to antimicrobials regardless of their use in the treatment of gonococcal infection.}, author = {Kandinov, Ilya and Shaskolskiy, Boris and Kravtsov, Dmitry and Vinokurova, Alexandra and Gorshkova, Sofya and Kubanov, Alexey and Solomka, Victoria and Shagabieva, Julia and Deryabin, Dmitry and Dementieva, Ekaterina and Gryadunov, Dmitry}, @@ -5932,6 +6408,26 @@ @article{khine_comparative_2023 year = {2023} } +@article{kifle_shotgun_2024, + abstract = {Antibiotic resistance is a worldwide problem that imposes a devastating effect on developing countries and requires immediate interventions. Initially, most of the antibiotic drugs were identified by culturing soil microbes. However, this method is prone to discovering the same antibiotics repeatedly. The present study employed a shotgun metagenomics approach to investigate the taxonomic diversity, functional potential, and biosynthetic capacity of microbiomes from two natural agricultural farmlands located in Bekeka and Welmera Choke Kebelle in Ethiopia for the first time. Analysis of the small subunit rRNA revealed bacterial domain accounting for 83.33\% and 87.24\% in the two selected natural farmlands. Additionally, the analysis showed the dominance of Proteobacteria representing 27.27\% and 28.79\% followed by Actinobacteria making up 12.73\% and 13.64\% of the phyla composition. Furthermore, the analysis revealed the presence of unassigned bacteria in the studied samples. The metagenome functional analysis showed 176,961 and 104, 636 number of protein-coding sequences (pCDS) from the two samples found a match with 172,655 and 102, 275 numbers of InterPro entries, respectively. The Genome ontology annotation suggests the presence of 5517 and 3293 pCDS assigned to the “biosynthesis process”. Numerous Kyoto Encyclopedia of Genes and Genomes modules (KEGG modules) involved in the biosynthesis of terpenoids and polyketides were identified. Furthermore, both known and novel Biosynthetic gene clusters, responsible for the production of secondary metabolites, such as polyketide synthases, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptides (Ripp), and Terpene, were discovered. Generally, from the results it can be concluded that the microbiomes in the selected sampling sites have a hidden functional potential for the biosynthesis of secondary metabolites. Overall, this study can serve as a strong preliminary step in the long journey of bringing new antibiotics to the market.}, + author = {Kifle, Bezayit Amare and Sime, Amsale Melkamu and Gemeda, Mesfin Tafesse and Woldesemayat, Adugna Abdi}, + copyright = {2024 The Author(s)}, + doi = {10.1038/s41598-024-63254-x}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Biotechnology, Computational biology and bioinformatics}, + language = {en}, + month = {July}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {15096}, + title = {Shotgun metagenomic insights into secondary metabolite biosynthetic gene clusters reveal taxonomic and functional profiles of microbiomes in natural farmland soil}, + url = {https://www.nature.com/articles/s41598-024-63254-x}, + urldate = {2024-11-17}, + volume = {14}, + year = {2024} +} + @article{kim_complete_2022, abstract = {Metabacillus litoralis is part of the newly proposed genus Metabacillus. The bacterium was first isolated from a Yellow Sea tidal flat in 2005. As of May 2022, there are five genomic assemblies deposited in GenBank. We report the 5.2-Mbp genome sequence of M. litoralis strain NCTR108, from commercial tattoo ink.}, author = {Kim, Sung Guk and Summage-West, Christine V. and Reyna, Mariela and Kim, Seong-Jae and Foley, Steven L.}, @@ -6778,6 +7274,23 @@ @article{lenz_denervated_2023 year = {2023} } +@article{lenz_transcriptomic_2024, + abstract = {Understanding the mechanisms of synaptic plasticity is crucial for elucidating how the brain adapts to internal and external stimuli. A key objective of plasticity is maintaining physiological activity states during perturbations by adjusting synaptic transmission through negative feedback mechanisms. However, identifying and characterizing novel molecular targets orchestrating synaptic plasticity remains a significant challenge. This study investigated the effects of tetrodotoxin (TTX)-induced synaptic plasticity within organotypic entorhino-hippocampal tissue cultures, offering insights into the functional, transcriptomic, and proteomic changes associated with network inhibition via voltage-gated sodium channel blockade. Our experiments demonstrate that TTX treatment induces substantial functional plasticity of excitatory synapses, as evidenced by increased miniature excitatory postsynaptic current (mEPSC) amplitudes and frequencies in both dentate granule cells and CA1 pyramidal neurons. Correlating transcriptomic and proteomic data, we identified novel targets for future research into homeostatic plasticity, including cytoglobin, SLIT-ROBO Rho GTPase Activating Protein 3, Transferrin receptor, and 3-Hydroxy-3-Methylglutaryl-CoA Synthase 1. These data provide a valuable resource for future studies aiming to understand the orchestration of homeostatic plasticity by metabolic pathways in distinct cell types of the central nervous system.}, + author = {Lenz, Maximilian and Turko, Paul and Kruse, Pia and Eichler, Amelie and Chen, Zhuo Angel and Rappsilber, Juri and Vida, Imre and Vlachos, Andreas}, + doi = {10.1186/s13041-024-01153-y}, + issn = {1756-6606}, + journal = {Molecular Brain}, + keywords = {{\textgreater}UseGalaxy.eu, homeostatic synaptic plasticity, organotypic tissue culture, proteomics, transcriptome}, + month = {November}, + number = {1}, + pages = {78}, + title = {Transcriptomic and de novo proteomic analyses of organotypic entorhino-hippocampal tissue cultures reveal changes in metabolic and signaling regulators in {TTX}-induced synaptic plasticity}, + url = {https://doi.org/10.1186/s13041-024-01153-y}, + urldate = {2024-11-17}, + volume = {17}, + year = {2024} +} + @article{lezameta_draft_2020, abstract = {Providencia stuartii is an opportunistic pathogen of the Enterobacteriales order. Here, we report the 4,594,658-bp draft genome sequence of a New Delhi metallo-β-lactamase (NDM-1)-producing Providencia stuartii strain that was isolated from an emergency patient in a private clinic in Lima, Peru.}, author = {Lezameta, Lizet and Cuicapuza, Diego and Dávila-Barclay, Alejandra and Torres, Susan and Salvatierra, Guillermo and Tsukayama, Pablo and Tamariz, Jesús}, @@ -6898,6 +7411,22 @@ @article{liang_reciprocal_2020 year = {2020} } +@article{lin_characteristics_2024, + abstract = {This study sequenced and assembled the mitochondrial genome of the rare dragonfly species Libellula melli, and submitted the results to the NCBI GenBank database, obtaining the accession number PP588458. The mitochondrial genome spans a total length of 15,149 bp, encompassing 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a control region or D-loop. Of these, 25 genes and segments are located on the heavy strand (H-strand), while the remaining 13 reside on the light strand (L-strand). The nucleotide composition of the L. melli mitochondrial genome exhibits a prominent AT bias (AT = 73.3 \%), with T, C, A, and G bases comprising 34.5 \%, 15.6 \%, 38.8 \%, and 11.1 \% respectively, displaying a positive AT skew of 0.059. Among the 13 PCGs, the primary start codons are ATT, ATG, and TTG, while the primary stop codons are TAA, with instances of TA(C) and T(AT) also observed. RSCU analysis reveals that the most frequently used codon is UUA, with an RSCU value of 3.75, encoding leucine (Leu). The secondary structures of the proteins encoded by the 13 PCGs generally exhibit a trend of α-helix {\textgreater} random coil {\textgreater} extended strand {\textgreater} β-turn. Phylogenetic analysis uncovers the phylogenetic relationships of L. melli within the reported Libellulidae species, revealing (((((((L. melli + L. quadrimaculata) + L. angelina) + ((O. chrysis + O. glaucum) + O. albistylum)) + ((C. servilia servilia + T. virginia) + N. fulvia) + (L. albifrons + S. eroticum)) + (P. flavescens + T. aurora)) + (D. phaon + H. croceus)) + (B. contaminate + P. zonata)). This study provides insights into the mitochondrial genome and its characteristics of this rare dragonfly species, contributing to our understanding of the intricate evolutionary relationships within the Odonata order. The data obtained serve as a foundation for further exploration of the complex phylogenetic relationships among dragonfly insects.}, + author = {Lin, Binquan and Chen, Hao and Li, Jiayu and Liao, Jian}, + doi = {10.1016/j.genrep.2024.101986}, + issn = {2452-0144}, + journal = {Gene Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Dragonfly, Mitogenomes, Phylogeny, Protein-coding genes}, + month = {September}, + pages = {101986}, + title = {Characteristics and phylogenetic implications of the mitochondrial genome of a rare species, \textit{{Libellula} melli}}, + url = {https://www.sciencedirect.com/science/article/pii/S2452014424001092}, + urldate = {2024-11-17}, + volume = {36}, + year = {2024} +} + @phdthesis{link_characterization_2024, abstract = {{\textless}em{\textgreater}T. halophilus{\textless}/em{\textgreater} and {\textless}em{\textgreater}D. hansenii{\textless}/em{\textgreater} are key players in the fermentation of lupine moromi. Comparative genomic analyses and transcriptomic profiling of {\textless}em{\textgreater}T. halophilus{\textless}/em{\textgreater} strains isolated from lupine moromi led to the identification of genes beneficial in this environment. Further, the competitiveness of isolated {\textless}em{\textgreater}T. halophilus{\textless}/em{\textgreater} strains in a lupine moromi model fermentation was investigated. The {\textless}em{\textgreater}D. hansenii{\textless}/em{\textgreater} strain that dominated the lupine moromi fermentation was fully sequenced and genomically analyzed.}, author = {Link, Tobias}, @@ -7315,6 +7844,24 @@ @article{martin_selection_2022 year = {2022} } +@article{martineau_unravelling_2024, + abstract = {Mycoplasma spp. are wall-less bacteria with small genomes (usually 0.5–1.5 Mb). Many Mycoplasma (M.) species are known to colonize the respiratory tract of both humans and livestock animals, where they act as primary pathogens or opportunists. M. equirhinis was described for the first time in 1975 in horses but has been poorly studied since, despite regular reports of around 14\% prevalence in equine respiratory disorders. We recently showed that M. equirhinis is not a primary pathogen but could play a role in co-infections of the respiratory tract. This study was a set up to propose the first genomic characterization to better our understanding of the M. equirhinis species.}, + author = {Martineau, Matthieu and Ambroset, Chloé and Lefebvre, Stéphanie and Kokabi, Éléna and Léon, Albertine and Tardy, Florence}, + doi = {10.1186/s12864-024-10789-y}, + issn = {1471-2164}, + journal = {BMC Genomics}, + keywords = {{\textgreater}UseGalaxy.eu, Diversity, Genome, Mobile genetic elements, Mycoplasma, Virulence}, + language = {en}, + month = {September}, + number = {1}, + pages = {886}, + title = {Unravelling the main genomic features of {Mycoplasma} equirhinis}, + url = {https://doi.org/10.1186/s12864-024-10789-y}, + urldate = {2024-11-17}, + volume = {25}, + year = {2024} +} + @article{martinez-fabregas_cdk8_2020, abstract = {Cytokines are highly pleiotropic ligands that regulate the immune response. Here, using interleukin-6 (IL-6) as a model system, we perform detailed phosphoproteomic and transcriptomic studies in human CD4+ T helper 1 (Th-1) cells to address the molecular bases defining cytokine functional pleiotropy. We identify CDK8 as a negative regulator of STAT3 transcriptional activities, which interacts with STAT3 upon IL-6 stimulation. Inhibition of CDK8 activity, using specific small molecule inhibitors, reduces the IL-6-induced phosphoproteome by 23\% in Th-1 cells, including STAT3 S727 phosphorylation. STAT3 binding to target DNA sites in the genome is increased upon CDK8 inhibition, which results in a concomitant increase in STAT3-mediated transcriptional activity. Importantly, inhibition of CDK8 activity under Th-17 polarizing conditions results in an enhancement of Th-17 differentiation. Our results support a model where CDK8 regulates STAT3 transcriptional processivity by modulation of its gene loci resident time, critically contributing to diversification of IL-6 responses.}, author = {Martinez-Fabregas, Jonathan and Wang, Luopin and Pohler, Elizabeth and Cozzani, Adeline and Wilmes, Stephan and Kazemian, Majid and Mitra, Suman and Moraga, Ignacio}, @@ -7887,6 +8434,39 @@ @article{mohebifar_construction_2023 year = {2023} } +@article{molina_valencia_anotacion_2024, + abstract = {The lack of complete genetic information on the pitaya (Hylocereus spp.) genome and the absence of annotations in biological databases hinder the precise identification of genes expressed under stress conditions. To address this challenge, this study focused on annotating genes involved in the biosynthesis of phenolic compounds in pitaya under biotic (pathogen infection) and abiotic (flowering induction with supplementary light) stress conditions. Using various bioinformatic techniques, transcriptomic data were analyzed to assemble de novo sequences from raw reads for each stress condition. The quality of these assemblies was rigorously evaluated, and a consensus sequence was generated to analyze its homology with related species. Structural and functional annotation of the assemblies was conducted using ab initio and de novo prediction tools, resulting in annotations in GFF3 format that detail both the structure and biological functions of the predicted genes. Subsequently, a differential expression analysis (DEG) was performed to identify genes expressed in the biosynthesis of phenolic compounds under different stress conditions. The results revealed nine key enzymes involved in the metabolic pathways of phenylpropanoids, flavonoids, and anthocyanins. Additionally, a MYB transcription factor that regulates gene expression in these pathways was identified. This research underscores the complexity of pitaya's adaptive mechanisms in response to stress, highlighting its activation of specific biosynthetic processes that enhance antioxidant capacity and adaptive ability under adverse conditions.}, + author = {Molina Valencia, Erick Santiago}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {spa}, + month = {August}, + note = {Publisher: Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología}, + title = {Anotación genómica de genes expresados en la biosíntesis de compuestos fenólicos en pitahaya ({Hylocereus} spp.) expuesta a condiciones de estrés}, + url = {https://repositorio.uta.edu.ec/handle/123456789/42325}, + urldate = {2024-11-17}, + year = {2024} +} + +@article{molla_harnessing_2024, + abstract = {The biodegradable and renewable nature of lignocellulosic biomass (LCB) has gained significant interest in recent years. This study explores the lignocellulolytic and electrogenic potential of Shewanella oneidensis MR-1, Cellulomonas fimi ATCC 484, and Cellulomonas biazotea NBRC 12680 on LCB. Two strategies were tested: assessing strains LCB degradation ability under non-electrochemical and electrochemical conditions. Strain selection was based on literature, and bioinformatical analyses were conducted to predict CAZymes and carbohydrate degradation pathways. Cellulomonas strains have a potential to degrade LCB due to high CAZyme count and specific metabolic pathways. Strains growth capacity on LCB was evaluated by culturing without electrodes on LCB for 12 days, showing superior growth on wheat bran compared to wheat straw. Enzymatic assays indicate laccase activity in all strains, highest in C. biazotea NBRC 12680 (11.66 IU). The strains ability to form electrogenic biofilms on carbon cloth anodes polarized at +0.2 V (vs Ag/AgCl) was evaluated. The results indicate that bioanodes can function with wheat bran (max current density: 14.92 mA m−2), with voltammograms showing redox activities. Attenuated total reflection Fourier transform infrared spectroscopy shows lignin and protein degradation in both electrochemical and non-electrochemical experiments. These findings suggest potential use of these strains in electro-microbial systems with LCB.}, + author = {Molla, Animut Assefa and Mishyn, Vladyslav and Bernet, Nicolas and Bouchez, Théodore and Besaury, Ludovic and Abdellaoui, Sofiene}, + doi = {10.1149/1945-7111/ad7909}, + issn = {1945-7111}, + journal = {Journal of The Electrochemical Society}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {September}, + note = {Publisher: IOP Publishing}, + number = {9}, + pages = {095501}, + shorttitle = {Harnessing {Lignocellulolytic} and {Electrogenic} {Potential}}, + title = {Harnessing {Lignocellulolytic} and {Electrogenic} {Potential}: {Insights} from {Shewanella} oneidensis {MR}-1 and {Cellulomonas} {Strains} on {Lignocellulosic} {Biomass}}, + url = {https://dx.doi.org/10.1149/1945-7111/ad7909}, + urldate = {2024-11-17}, + volume = {171}, + year = {2024} +} + @article{mootapally_sediment_2021, abstract = {Plasmidomes have become the research area of interest for ecologists exploring bacteria rich ecosystems. Marine environments are among such niche that host a huge number of microbes and have a complex environment which pose the need to study these bacterial indicators of horizontal gene transfer events for survival and stability. The plasmid content of the metagenomics data from 8 sediment samples of the Gulfs of Kathiawar and an open Arabian Sea sample was screened. The reads corresponding to hits against the plasmid database were assembled and studied for diversity using Kraken and functional content using MG-RAST. The sequences were also checked for resistome and virulence factors. The replicon hosts were overall dominated by Proteobacteria, Firmicutes, and Actinobacteria while red algae specific to the Kutch samples. The genes encoded were dominant in the flagella motility and type VI secretion systems. Overall, results from the study confirmed that the plasmids encoded traits for metal, antibiotic, and phage resistance along with virulence systems, and these would be conferring benefit to the hosts. The study throws insights into the environmental role of the plasmidome in adaptation of the microbes in the studied sites to the environmental stresses.}, author = {Mootapally, Chandrashekar and Mahajan, Mayur S. and Nathani, Neelam M.}, @@ -8191,6 +8771,28 @@ @article{naimi_direct_2021 year = {2021} } +@article{naorem_immunoinformatics_2024, + abstract = {Dental caries, a persistent oral health challenge primarily linked to Streptococcus mutans, extends its implications beyond dental decay, affecting over 4 billion individuals globally. Despite its historical association with childhood, dental caries often persists into adulthood with prevalence rates ranging from 60 to 90\% in children and 26 to 85\% in adults. Currently, there is a dearth of multiepitope vaccines (MEVs) specifically designed to combat S. mutans. To address this gap, we employed an immunoinformatics approach for MEV design, identifying five promising vaccine candidates (PBP2X, PBP2b, MurG, ATP-F, and AGPAT) based on antigenicity and conservation using several tools including CELLO v.2.5, Vaxign, v2.0, ANTIGENpro, and AllerTop v2.0 tools. Subsequent identification of linear B-cell and T-cell epitopes by SVMTrip and NetCTL/NetMHC II tools, respectively, guided the construction of a MEV comprising 10 Cytotoxic T Lymphocyte (CTL) epitopes, 5 Helper T Lymphocyte (HTL) epitopes, and 5 linear B-cell epitopes, interconnected by suitable linkers. The resultant MEV demonstrated high antigenicity, solubility, and structural stability. In silico immune simulations showcased the MEV’s potential to elicit robust humoral and cell-mediated immune responses. Molecular docking studies revealed strong interactions between the MEV construct and Toll-Like Receptors (TLRs) and Major Histocompatibility Complex (MHC) molecules. Remarkably, the MEV–TLR-4 complexes exhibited a low energy score, high binding affinity, and a low dissociation constant. The Molecular Dynamic (MD) simulation analysis suggested that MEV–TLR-4 complexes had the highest stability and minimal conformational changes indicating equilibrium within 40 nanosecond time frames. Comprehensive computational analyses strongly support the potential of the proposed MEV to combat dental caries and associated infections. The study’s computational assays yielded promising results, but further validation through in vitro and in vivo experiments is needed to assess its efficacy and safety.}, + author = {Naorem, Romen Singh and Pangabam, Bandana Devi and Bora, Sudipta Sankar and Fekete, Csaba and Teli, Anju Barhai}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/pathogens13100916}, + issn = {2076-0817}, + journal = {Pathogens}, + keywords = {\textit{Streptococcus mutans}, {\textgreater}UseGalaxy.eu, dental caries, immunoinformatics, molecular docking simulation, molecular dynamic simulation, multiepitope vaccine}, + language = {en}, + month = {October}, + note = {Number: 10 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {10}, + pages = {916}, + shorttitle = {Immunoinformatics {Design} of a {Multiepitope} {Vaccine} ({MEV}) {Targeting} {Streptococcus} mutans}, + title = {Immunoinformatics {Design} of a {Multiepitope} {Vaccine} ({MEV}) {Targeting} {Streptococcus} mutans: {A} {Novel} {Computational} {Approach}}, + url = {https://www.mdpi.com/2076-0817/13/10/916}, + urldate = {2024-11-17}, + volume = {13}, + year = {2024} +} + @article{napoli_absence_2022, abstract = {Despite the increasing interest in using microbial-based technologies to support human space exploration, many unknowns remain not only on bioprocesses but also on microbial survivability and genetic stability under non-Earth conditions. Here the desert cyanobacterium Chroococcidiopsis sp. CCMEE 029 was investigated for robustness of the repair capability of DNA lesions accumulated under Mars-like conditions (UV radiation and atmosphere) simulated in low Earth orbit using the EXPOSE-R2 facility installed outside the International Space Station. Genomic alterations were determined in a space-derivate of Chroococcidiopsis sp. CCMEE 029 obtained upon reactivation on Earth of the space-exposed cells. Comparative analysis of whole-genome sequences showed no increased variant numbers in the space-derivate compared to triplicates of the reference strain maintained on the ground. This result advanced cyanobacteria-based technologies to support human space exploration.}, author = {Napoli, Alessandro and Micheletti, Diego and Pindo, Massimo and Larger, Simone and Cestaro, Alessandro and de Vera, Jean-Pierre and Billi, Daniela}, @@ -8310,6 +8912,25 @@ @misc{nguionza_development_2024 year = {2024} } +@article{nguyen_genomic_2024, + abstract = {Previous studies have reported the functional role, biochemical features and synthesis pathway of podophyllotoxin (PTOX) in plants. In this study, we employed combined morphological and molecular techniques to identify an endophytic fungus and extract PTOX derivatives. Based on the analysis of ITS sequences and the phylogenetic tree, the isolate was classified as Penicillium herquei HGN12.1C, with a sequence identity of 98.58\%. Morphologically, the HGN12.1C strain exhibits white colonies, short-branched mycelia and densely packed hyphae. Using PacBio sequencing at an average read depth of 195×, we obtained a high-quality genome for the HGN12.1C strain, which is 34.9 Mb in size, containing eight chromosomes, one mitochondrial genome and a GC content of 46.5\%. Genome analysis revealed 10 genes potentially involved in PTOX biosynthesis. These genes include VdtD, Pinoresinollariciresinol reductase (PLR), Secoisolariciresinol dehydrogenase (SDH), CYP719A23, CYP71BE54, O-methyltransferase 1 (OMT1), O-methyltransferase 3 (OMT3), 2-ODD, CYP71CU and CYP82D61. Notably, the VdtD gene in fungi shares functional similarities with the DIR gene found in plants. Additionally, we identified peltatin, a PTOX derivative, in the HGN12.1C extract. Docking analysis suggests a potential role for the 2-ODD enzyme in converting yatein to deoxypodophyllotoxin. These findings offer invaluable insights into the synthesis mechanism of PTOX in fungi, shedding light on the relationship between host plants and endophytes.}, + author = {Nguyen, Duong Huy and Tran, Quang Ho and Le, Lam Tung and Nguyen, Ha Hong Thi and Tran, Hoa Thi and Do, Thuy Phuong and Ho, Anh Ngoc and Tran, Quang Hong and Thu, Hien Thi Nguyen and Bui, Van Ngoc and Chu, Hoang Ha and Pham, Ngoc Bich}, + copyright = {© 2024 The Author(s). Microbial Biotechnology published by John Wiley \& Sons Ltd.}, + doi = {10.1111/1751-7915.70007}, + issn = {1751-7915}, + journal = {Microbial Biotechnology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1751-7915.70007}, + number = {9}, + pages = {e70007}, + title = {Genomic characterization and identification of candidate genes for putative podophyllotoxin biosynthesis pathway in {Penicillium} herquei {HGN12}.{1C}}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1751-7915.70007}, + urldate = {2024-11-17}, + volume = {17}, + year = {2024} +} + @article{nicholson_contribution_2024, abstract = {{\textless}p{\textgreater}{\textless}italic{\textgreater}Bordetella bronchiseptica{\textless}/italic{\textgreater} is a highly contagious respiratory bacterial veterinary pathogen. In this study the contribution of the transcriptional regulators BvgR, RisA, RisS, and the phosphorylation of RisA to global gene regulation, intracellular cyclic-di-GMP levels, motility, and biofilm formation were evaluated. Next Generation Sequencing (RNASeq) was used to differentiate the global gene regulation of both virulence-activated and virulence-repressed genes by each of these factors. The BvgAS system, along with BvgR, RisA, and the phosphorylation of RisA served in cyclic-di-GMP degradation. BvgR and unphosphorylated RisA were found to temporally regulate motility. Additionally, BvgR, RisA, and RisS were found to be required for biofilm formation.{\textless}/p{\textgreater}}, author = {Nicholson, Tracy L. and Waack, Ursula and Fleming, Damarius S. and Chen, Qing and Miller, Laura C. and Merkel, Tod J. and Stibitz, Scott}, @@ -8398,6 +9019,24 @@ @article{noauthor_characterization_2023 year = {2023} } +@misc{noauthor_draft_2024, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Draft genome sequence of {Streptomyces} poriferorum {RTGN2}, a bacterial endophyte isolated from {Alnus} glutinosa root nodules {\textbar} {Microbiology} {Resource} {Announcements}}, + url = {https://journals.asm.org/doi/full/10.1128/mra.00486-23}, + urldate = {2024-11-17}, + year = {2024} +} + +@misc{noauthor_effect_2024, + abstract = {Explore millions of resources from scholarly journals, books, newspapers, videos and more, on the ProQuest Platform.}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {de}, + title = {The {Effect} of {Methamphetamine} on {NeuroHIV}, {Alzheimer}’s {Disease}, and {Alzheimer}’s {Disease} {Related} {Dementias} - {ProQuest}}, + url = {https://www.proquest.com/openview/4f248f86ae7ffd53c71632627e9c1298/1?pq-origsite=gscholar&cbl=18750&diss=y}, + urldate = {2024-11-17}, + year = {2024} +} + @misc{noauthor_effect_2024, keywords = {{\textgreater}UseGalaxy.eu}, month = {January}, @@ -8455,6 +9094,22 @@ @article{noauthor_proceedings_2023 year = {2023} } +@misc{noauthor_repositorio_2024, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Repositório {Institucional} da {UnB}: {Estudo} sobre bactérias degradadoras de polietileno : descrição de uma potencial nova espécie bacteriana e caracterização de uma enzima peroxirredoxina}, + url = {http://icts.unb.br/jspui/handle/10482/50754}, + urldate = {2024-11-17}, + year = {2024} +} + +@misc{noauthor_whole-genome_2024, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Whole-genome long-read sequencing to unveil {Enterococcus} antimicrobial resistance in dairy cattle farms exposed a widespread occurrence of {Enterococcus} lactis {\textbar} {Microbiology} {Spectrum}}, + url = {https://journals.asm.org/doi/full/10.1128/spectrum.03672-23}, + urldate = {2024-11-17}, + year = {2024} +} + @article{nugroho_transcriptome_2024, abstract = {Sengon (Falcataria falcata) is an economically important legume tree widely cultivated in community forests, especially in Java Island. However, attacks of gall rust disease by Uromycladium falcatariae is difficult to manage. Understanding sengon genes expressions when artificially infected with gall rust fungi can help unravel its resistance mechanisms. Total RNA was extracted from sengon seedlings samples inoculated with U. falcatariae fungi at 7, 21, and 35 days after inoculation (DAI) and from the control group. Total RNA sequencing was performed using the PCR-cDNA Sequencing protocol (SQK-PCB109) from Oxford Nanopore Technologies. The RNA-Seq obtained varies from 1.3 million to 1.9 million total reads. The assembled full-length transcript was constructed using the RATTLE program, resulting in 21,819 transcripts. The TransDecoder program used to define open reading frames (ORFs) generated 2,342 transcripts, of which 34.15\% were 5′prime\_partial, 8.15\% were 3′prime\_partial, 8.5\% were internal, and 49.14\% were complete. Analysis of differentially expressed genes (DEGs) between resistant and susceptible seedlings, found that 1,013 genes that were up-regulated and 1,130 genes that were down-regulated in the resistant lines. The transcriptome data discussed in this article have been deposited in the DDBJ with accession number DRA015681.}, author = {Nugroho, Aditya and Siregar, Iskandar Zulkarnaen and Matra, Deden Derajat and Siregar, Ulfah Juniarti}, @@ -8724,6 +9379,30 @@ @article{ostrovsky_using_2021 year = {2021} } +@article{ou_differences_2024, + abstract = {Much of the profound interspecific variation in genome content has been attributed to transposable elements (TEs). To explore the extent of TE variation within species, we developed an optimized open-source algorithm, panEDTA, to de novo annotate TEs in a pangenome context. We then generated a unified TE annotation for a maize pangenome derived from 26 reference-quality genomes, which reveals an excess of 35.1 Mb of TE sequences per genome in tropical maize relative to temperate maize. A small number (n = 216) of TE families, mainly LTR retrotransposons, drive these differences. Evidence from the methylome, transcriptome, LTR age distribution, and LTR insertional polymorphisms reveals that 64.7\% of the variability is contributed by LTR families that are young, less methylated, and more expressed in tropical maize, whereas 18.5\% is driven by LTR families with removal or loss in temperate maize. Additionally, we find enrichment for Young LTR families adjacent to nucleotide-binding and leucine-rich repeat (NLR) clusters of varying copy number across lines, suggesting TE activity may be associated with disease resistance in maize.}, + author = {Ou, Shujun and Scheben, Armin and Collins, Tyler and Qiu, Yinjie and Seetharam, Arun S. and Menard, Claire C. and Manchanda, Nancy and Gent, Jonathan I. and Schatz, Michael C. and Anderson, Sarah N. and Hufford, Matthew B. and Hirsch, Candice N.}, + doi = {10.1101/gr.278131.123}, + issn = {1088-9051, 1549-5469}, + journal = {Genome Research}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {August}, + note = {Company: Cold Spring Harbor Laboratory Press +Distributor: Cold Spring Harbor Laboratory Press +Institution: Cold Spring Harbor Laboratory Press +Label: Cold Spring Harbor Laboratory Press +Publisher: Cold Spring Harbor Lab}, + number = {8}, + pages = {1140--1153}, + pmid = {39251347}, + title = {Differences in activity and stability drive transposable element variation in tropical and temperate maize}, + url = {https://genome.cshlp.org/content/34/8/1140}, + urldate = {2024-11-17}, + volume = {34}, + year = {2024} +} + @article{owen_rna-sequencing_2019, abstract = {High-throughput, massively parallel sequence analysis has revolutionized the way that researchers design and execute scientific investigations. Vast amounts of sequence data can be generated in short periods of time. Regarding ophthalmology and vision research, extensive interrogation of patient samples for underlying causative DNA mutations has resulted in the discovery of many new genes relevant to eye disease. However, such analysis remains functionally limited. RNA-sequencing accurately snapshots thousands of genes, capturing many subtypes of RNA molecules, and has become the gold standard for transcriptome gene expression quantification. RNA-sequencing has the potential to advance our understanding of eye development and disease; it can reveal new candidates to improve our molecular diagnosis rates and highlight therapeutic targets for intervention. But with a wide range of applications, the design of such experiments can be problematic, no single optimal pipeline exists, and therefore, several considerations must be undertaken for optimal study design. We review the key steps involved in RNA-sequencing experimental design and the downstream bioinformatic pipelines used for differential gene expression. We provide guidance on the application of RNAsequencing to ophthalmology and sources of open-access eye-related data sets.}, author = {Owen, Nicholas and Moosajee, Mariya}, @@ -9540,6 +10219,21 @@ @article{qiu_smcyp71d373_2024 year = {2024} } +@mastersthesis{rabbas_surveillance_2024, + abstract = {The discovery of antibiotics has radically changed the treatment of bacterial infections, making the increasing antibiotic resistance one of the top ten greatest threats to the global health. The main focus of antibiotic resistance research has, until recently, been focused on clinical settings and human and veterinary aspects. It has become more evident that the environment plays a vital role in the evolution, dissemination and prevalence of antibiotic resistant bacteria and genes. Aquatic ecosystems are a known mixing ground for clinical and environmental bacteria and can be a source and reservoir for resistance genes. The transfer of resistance between environmental and clinically important bacteria occurs, and surveillance of the environment is therefore important to better understand this flow of resistance. + +The purpose of this thesis was to investigate the occurrence of antibiotic resistant bacteria and genes in aquatic environments in Ås and Nordre Follo municipalities in Norway. Water samples were collected from three different locations was filtered and plated out on Brilliance™ ESBL and CRE chromogenic agar plates selecting for Extended spectrum β-lactamase (ESBL) producing and carbapenem resistant bacteria. Bacterial colonies were isolated, and DNA was extracted, followed by 16S PCR and identification by Sanger sequencing. Multiplex and Singelplex PCR with ESBL-specific primers were utilized to screen for specific ESBL-genes, which were confirmed by sequencing. Selected bacterial strains were chosen for antimicrobial susceptibility testing using five different classes of antibiotics. Illumina MiSeq was utilized for whole genome sequencing (WGS) for three selected bacteria, followed by screening for antibiotic resistance and virulence genes, multidrug efflux pumps and metal resistance genes. Several bacteria genera were detected by selective agar plates and identified by 16S rRNA, including the genera Pseudomonas, Serratia, Herbaspirillum, Aeromonas, Shewanella, Chitinophaga and Pandoraea. The susceptibility testing revealed a high amount of resistance to Penicillins and four different Multidrug resistant (MDR) isolates. The bacteria showing the highest amount of resistance was Pandoraea sp., which demonstrated clinical resistance to five out of seven antibiotics tested. The screening for resistance in the three WGS bacteria, Pseudomonas aeruginosa, Chitinophaga silvatica and Pandoraea sp., revealed several β-lactamases. This included the class D β-lactamases blaOXA-50, blaOXA-158 and two bla genes, and the class C β-lactamases blaPDC-202 and blaPAO. Several genes conferring metal resistance and genes for multidrug efflux pumps were also discovered. Together, the results obtained in this work indicate an occurrence of antibiotic resistant bacteria and resistance genes, including several blaOXA-variants, in the aquatic environments in Ås and Nordre-Follo municipalities.}, + author = {Rabbås, Hanne Brænd}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + note = {Accepted: 2024-08-23T16:27:53Z}, + school = {Norwegian University of Life Sciences}, + title = {Surveillance and detection of multidrug resistant bacterial strains and {blaOXA} genes in aquatic environments in Ås and {Nordre} {Follo} municipalities}, + url = {https://nmbu.brage.unit.no/nmbu-xmlui/handle/11250/3147945}, + urldate = {2024-11-17}, + year = {2024} +} + @article{ragot_edna_2022, author = {Ragot, Rose and Villemur, Richard}, journal = {Environmental monitoring and assessment}, @@ -9831,6 +10525,25 @@ @article{richter_genome_2024 year = {2024} } +@article{richter_genomic_2024, + abstract = {Escherichia coli, both commensal and pathogenic, can colonize plants and persist in various environments. It indicates fecal contamination in water and food and serves as a marker of antimicrobial resistance. In this context, 61 extended-spectrum β-lactamase (ESBL)-producing E. coli from irrigation water and fresh produce from previous studies were characterized using whole genome sequencing (Illumina MiSeq). The Center for Genomic Epidemiology and Galaxy platforms were used to determine antimicrobial resistance genes, virulence genes, plasmid typing, mobile genetic elements, multilocus sequence typing (MLST), and pathogenicity prediction. In total, 19 known MLST groups were detected among the 61 isolates. Phylogroup B1 (ST58) and Phylogroup E (ST9583) were the most common sequence types. The six ST10 (serotype O101:H9) isolates carried the most resistance genes, spanning eight antibiotic classes. Overall, 95.1\% of the isolates carried resistance genes from three or more classes. The blaCTX-M-1, blaCTX-M-14, and blaCTX-M-15 ESBL genes were associated with mobile genetic elements, and all of the E. coli isolates showed a {\textgreater}90\% predicted probability of being a human pathogen. This study provided novel genomic information on environmental multidrug-resistant ESBL-producing E. coli from fresh produce and irrigation water, highlighting the environment as a reservoir for multidrug-resistant strains and emphasizing the need for ongoing pathogen surveillance within a One Health context.}, + author = {Richter, Loandi and Duvenage, Stacey and du Plessis, Erika Margarete and Msimango, Thabang and Dlangalala, Manana and Mathavha, Muneiwa Tshidino and Molelekoa, Tintswalo and Kgoale, Degracious Moloko and Korsten, Lise}, + doi = {10.1021/acs.est.4c02431}, + issn = {0013-936X}, + journal = {Environmental Science \& Technology}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + note = {Publisher: American Chemical Society}, + number = {32}, + pages = {14421--14438}, + shorttitle = {Genomic {Evaluation} of {Multidrug}-{Resistant} {Extended}-{Spectrum} β-{Lactamase} ({ESBL})-{Producing} {Escherichia} coli from {Irrigation} {Water} and {Fresh} {Produce} in {South} {Africa}}, + title = {Genomic {Evaluation} of {Multidrug}-{Resistant} {Extended}-{Spectrum} β-{Lactamase} ({ESBL})-{Producing} {Escherichia} coli from {Irrigation} {Water} and {Fresh} {Produce} in {South} {Africa}: {A} {Cross}-{Sectional} {Analysis}}, + url = {https://doi.org/10.1021/acs.est.4c02431}, + urldate = {2024-11-17}, + volume = {58}, + year = {2024} +} + @article{riediger_analysis_2020, author = {Riediger, Matthias and Spät, Philipp and Bilger, Raphael and Voigt, Karsten and Maček, Boris and Hess, Wolfgang R.}, doi = {10.1093/plcell/koaa017}, @@ -9903,6 +10616,18 @@ @article{robson_environmental_2024 year = {2024} } +@article{rodrigues_alves_barbosa_phenotypic_2024, + abstract = {Essential genes are deemed crucial for survival and/or reproductive success, hence, their loss of function leads to lethality. However, gene essentiality is not static, but dependent on multiple factors, including the genetic background. The genetic background affects gene essentiality through genetic modifiers, second-site variants capable of interacting with the primary variant and altering phenotype. Genetic modifiers can act as suppressors, alleviating the phenotype, or enhancers, exacerbating the phenotype. The plasticity (modification) of gene essentiality caused by genetic modifiers has been shown in multiple species. In Caenorhabditis elegans, recent evidence shows phenotypic variability for knock-down of essential genes in two natural isolates: N2 and CB4856. N2 represents the laboratory-cultivated strain, while CB4856 is one of the strains with most diverse genome in comparison to N2. Much has been explored for these two genetic backgrounds, but little is known about the plasticity of gene essentiality in other C. elegans wild isolates. Thus, I here explore the effect of the genetic background on the plasticity of two genes, known as essential in the N2 background, but potentially dispensable in CB4856: the Metaphase-to-Anaphase Transition Defect gene (mat-1), and the Conserved Germline Helicase (cgh-1). These are involved in cell division and posttranscriptional regulation, respectively. Here, I further investigate the plasticity of mat-1 and cgh-1 in N2 and CB4856 backgrounds, and also include four other wild isolate backgrounds from diverse geographical locations (GXW1, KR314, JU1400, and AB1). Using hatch rate and propagation assays, I explored the phenotype of mat-1 and cgh-1 knockdowns across the six natural isolates using temperature-sensitive alleles and uncovered phenotypic variability for the embryonic lethal phenotype, suggestively due to influence of each genetic background. Next, bioinformatics and genomics tools were utilized for identification of candidate genetic modifiers for mat-1 and cgh-1 and led to prioritization of eight extragenic variants. Out of these, none showed notable modifying activity when studied in isolation. Importantly, this work shows the challenges associated with identifying true genetic modifiers in genomes with substantial variation. Undeniably, understanding more about a gene and its phenotype under different conditions and genetic backgrounds may be fundamental for elucidating fixed and plastic genetic interactions.}, + author = {Rodrigues Alves Barbosa, Victoria}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {March}, + title = {Phenotypic variability in {C}. elegans natural isolates reveals plasticity of gene essentiality for mat-1 and cgh-1}, + url = {https://hdl.handle.net/1880/118237}, + urldate = {2024-11-17}, + year = {2024} +} + @article{rogg_srgap1_2021, author = {Rogg, Manuel and Maier, Jasmin I. and Dotzauer, Robert and Artelt, Nadine and Kretz, Oliver and Helmstädter, Martin and Abed, Ahmed and Sammarco, Alena and Sigle, August and Sellung, Dominik and Dinse, Patrick and Reiche, Karoline and Yasuda-Yamahara, Mako and Biniossek, Martin L. and Walz, Gerd and Werner, Martin and Endlich, Nicole and Schilling, Oliver and Huber, Tobias B. and Schell, Christoph}, doi = {10.1681/asn.2020081126}, @@ -10017,6 +10742,24 @@ @article{royaux_genetic_2024 year = {2024} } +@article{rukminiati_first_2024, + abstract = {Recent spoligotyping results in the island nation of Indonesia had revealed the existence of Mycobacterium tuberculosis complex lineage 3 (MTBC L3) or Central Asian (CAS) strains. In this work, whole-genome sequencing (WGS) – based methods were used to search for the presence of MTBC L3.}, + author = {Rukminiati, Yuni and Mesak, Felix and Lolong, Dina and Sudarmono, Pratiwi}, + doi = {10.1186/s13104-024-06825-5}, + issn = {1756-0500}, + journal = {BMC Research Notes}, + keywords = {{\textgreater}UseGalaxy.eu, Phylogenomic, Tuberculosis, Whole genome sequencing}, + language = {en}, + month = {June}, + number = {1}, + pages = {176}, + title = {First {Indonesian} report of {WGS}-based {MTBC} {L3} discovery}, + url = {https://doi.org/10.1186/s13104-024-06825-5}, + urldate = {2024-11-17}, + volume = {17}, + year = {2024} +} + @article{russo_excrete_2024, abstract = {Extracellular proteins play a significant role in shaping microbial communities which, in turn, can impact ecosystem function, human health, and biotechnological processes. Yet, for many ubiquitous microbes, there is limited knowledge regarding the identity and function of secreted proteins. Here, we introduce EXCRETE (enhanced exoproteome characterization by mass spectrometry), a workflow that enables comprehensive description of microbial exoproteomes from minimal starting material. Using cyanobacteria as a case study, we benchmark EXCRETE and show a significant increase over current methods in the identification of extracellular proteins. Subsequently, we show that EXCRETE can be miniaturized and adapted to a 96-well high-throughput format. Application of EXCRETE to cyanobacteria from different habitats (Synechocystis sp. PCC 6803, Synechococcus sp. PCC 11901, and Nostoc punctiforme PCC 73102), and in different cultivation conditions, identified up to 85\% of all potentially secreted proteins. Finally, functional analysis reveals that cell envelope maintenance and nutrient acquisition are central functions of the predicted cyanobacterial secretome. Collectively, these findings challenge the general belief that cyanobacteria lack secretory proteins and suggest that multiple functions of the secretome are conserved across freshwater, marine, and terrestrial species.}, author = {Russo, David A. and Oliinyk, Denys and Pohnert, Georg and Meier, Florian and Zedler, Julie A. Z.}, @@ -10231,6 +10974,19 @@ @incollection{saleh_nascent_2021 year = {2021} } +@book{salerno_metaproteomics_2024, + abstract = {This volume provides references for methods about the proteomics of microbial communities, also called metaproteomics. Chapters guide readers first through specific protein extractions from different environments and/or ecological niches crowded by heterogeneous microbial communities, then deepening the possible complete metaproteomic workflows in several situations or conditions. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Metaproteomics: Methods and Protocols aims to ensure successful results in the further study of this vital field.}, + author = {Salerno, Carlo}, + isbn = {978-1-07-163910-8}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + note = {Google-Books-ID: GisREQAAQBAJ}, + publisher = {Springer Nature}, + shorttitle = {Metaproteomics}, + title = {Metaproteomics: {Methods} and {Protocols}}, + year = {2024} +} + @article{sanchez-leon_heteroresistance_2023, abstract = {Heteroresistance to colistin can be defined as the presence of resistant subpopulations in an isolate that is susceptible to this antibiotic. Colistin resistance in Gram-negative bacteria is more frequently related to chromosomal mutations and insertions. This work aimed to study heteroresistance in nine clinical isolates of Klebsiella pneumoniae producing OXA-48 and to describe genomic changes in mutants with acquired resistance in vitro. Antimicrobial susceptibility was determined by broth microdilution (BMD) and heteroresistance by population analysis profiling (PAP). The proteins related to colistin resistance were analyzed for the presence of mutations. Additionally, PCR of the mgrB gene was performed to identify the presence of insertions. In the nine parental isolates, the PAP method showed colistin heteroresistance of colonies growing on plates with concentrations of up to 64 mg/L, corresponding to stable mutant subpopulations. The MICs of some mutants from the PAP plate containing 4×MIC of colistin had absolute values of ≤2 mg/L that were higher than the parental MICs and were defined as persistent variants. PCR of the mgrB gene identified an insertion sequence that inactivated the gene in 21 mutants. Other substitutions in the investigated mutants were found in PhoP, PhoQ, PmrB, PmrC, CrrA and CrrB proteins. Colistin heteroresistance in K. pneumoniae isolates was attributed mainly to insertions in the mgrB gene and point mutations in colistin resistance proteins. The results of this study will improve understanding regarding the mechanisms of colistin resistance in mutants of K. pneumoniae producing OXA-48.}, author = {Sánchez-León, Irene and García-Martínez, Teresa and Diene, Seydina M. and Pérez-Nadales, Elena and Martínez-Martínez, Luis and Rolain, Jean-Marc}, @@ -10252,6 +11008,20 @@ @article{sanchez-leon_heteroresistance_2023 year = {2023} } +@article{sanchez-leon_heterorresistencia_2024, + abstract = {La heterorresistencia (HR) puede ser definida como la presencia de subpoblaciones resistentes en un aislado que es sensible a un antibiótico. En este trabajo se evalúa la HR a colistina en diversas cepas de Klebsiella pneumoniae con fenotipo silvestre (Kp-WT) y productoras de la carbapenemasa OXA-48 (Kp-OXA48). Para ello, la sensibilidad a colistina se determinó mediante microdilución en caldo (BMD) y la HR mediante análisis de perfil de población (PAP). Los mutantes resistentes se caracterizaron a nivel molecular mediante el análisis del genoma completo y PCR del gen mgrB para identificar la presencia de mutaciones en genes relacionados con la síntesis del lipopolisacárido. La BMD determino que todas las cepas estudiadas fueron sensibles a colistina y el método PAP mostro que las CMIs de algunos mutantes de la placa PAP que contenía 4×MIC de colistina tenían valores absolutos similares a las CMIs parentales y se definieron como variantes persistentes mientras que la HR a colistina de las colonias que crecían en placas con concentraciones de hasta 32-64 mg/L, correspondieron a subpoblaciones mutantes estables. La PCR del gen mgrB identifico diversas secuencias de inserción que inactivaba el gen en 14 mutantes de Kp-WT y en 21 mutantes de Kp-OXA48 pertenecientes principalmente a la familia IS1 (ISKpn14) and IS5 (ISKpn74). En los mutantes de Kp- WT se identificaron mutaciones puntuales en proteínas relacionadas con la síntesis del lipopolisacárido (MgrB, PhoP, PhoQ, PmrB, CrrA y CrrB). En los mutantes de Kp- OXA48 se identificaron también mutaciones puntuales en estas proteínas; la HR a colistina en estos aislados se atribuyó fundamentalmente a las inserciones y mutaciones puntuales detectadas. Los resultados de este estudio podrían mejorar la comprensión de los mecanismos de resistencia a colistina en mutantes de Kp-WT y Kp-OXA48.}, + author = {Sánchez-León, Irene}, + copyright = {https://creativecommons.org/licenses/by-nc-nd/4.0/}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {spa}, + note = {Accepted: 2024-10-29T12:08:23Z +Publisher: Universidad de Córdoba, UCOPress}, + title = {Heterorresistencia a colistina en aislados clínicos de {Klebsiella} pneumoniae con fenotipo de resistencia silvestre o productores de la carbapenemasa {OXA}-48}, + url = {http://helvia.uco.es/xmlui/handle/10396/29757}, + urldate = {2024-11-17}, + year = {2024} +} + @article{sanchez_pathwaymatcher_2019, abstract = {AbstractBackground. Mapping biomedical data to functional knowledge is an essential task in bioinformatics and can be achieved by querying identifiers (e.g., g}, author = {Sánchez, Luis Francisco Hernández and Burger, Bram and Horro, Carlos and Fabregat, Antonio and Johansson, Stefan and Njølstad, Pål Rasmus and Barsnes, Harald and Hermjakob, Henning and Vaudel, Marc}, @@ -10342,6 +11112,23 @@ @article{sauriol_modeling_2020 year = {2020} } +@phdthesis{schafer_algorithms_2024, + abstract = {RNA-RNA intra- and intermolecular interactions are fundamental for numerous biological processes. While there are reasonable approaches to map RNA secondary structures genome-wide, understanding how different RNAs interact to carry out their regulatory functions requires mapping of intermolecular base pairs. RNA-RNA interaction prediction algorithms alone are not capable to consider all biological factors, thus, they suffer from low accuracy. Recently, different strategies to detect RNA-RNA duplexes in living cells, so called direct duplex detection (DDD) methods, have been developed. Common to all is the psoralen-mediated in vivo RNA crosslinking followed by RNA Proximity Ligation to join the two interacting RNA strands. Sequencing of the RNA via classical RNA-Seq and subsequent specialised bioinformatic analyses, which results in the prediction of intra- and intermolecular RNA-RNA interactions. Existing approaches adapt standard RNA-seq analysis pipelines but often neglect inherent features of RNA-RNA interactions that are useful for filtering and statistical assessment. In this work, RNAnue is presented, a general pipeline for the inference of RNA-RNA interactions from DDD experiments that takes into account hybridisation potential and statistical significance to improve prediction accuracy. RNAnue was applied to data from different DDD studies, and the results were compared to those of the original methods. This showed that RNAnue performs better in terms of prediction quantity and quality.}, + author = {Schäfer, Richard A.}, + copyright = {info:eu-repo/semantics/openAccess}, + doi = {10.18419/opus-14990}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + note = {Accepted: 2024-10-01T08:49:19Z +ISBN: 9781903881606 +Journal Abbreviation: Algorithmen zur globalen Abbildung von RNA-RNA Interaktomen}, + title = {Algorithms for the global mapping of {RNA}-{RNA} interactomes}, + type = {{doctoralThesis}}, + url = {http://elib.uni-stuttgart.de/handle/11682/15009}, + urldate = {2024-11-17}, + year = {2024} +} + @article{schafer_glassgo_2020, abstract = {AbstractMotivation. The correct prediction of bacterial sRNA homologs is a prerequisite for many downstream analyses based on comparative genomics, but it is f}, author = {Schäfer, Richard A. and Lott, Steffen C. and Georg, Jens and Grüning, Björn A. and Hess, Wolfgang R. and Voß, Björn}, @@ -10630,6 +11417,25 @@ @article{sethi_ezsinglecell_2024 year = {2024} } +@article{shaikh_stcdf1_2024, + abstract = {Transcription factors of the CYCLING DOF FACTOR (CDF) family activate in potato the SP6A FT tuberization signal in leaves. In modern cultivars, truncated StCDF1.2 alleles override strict SD control by stabilizing the StCDF1 protein, which leads to StCOL1 suppression and impaired activation of the antagonic SP5G paralog. By using DAP-seq and RNA-seq studies, we here show that StCDF1 not only acts as an upstream regulator of the day length pathway but also directly regulates several N assimilation and transport genes. StCDF1 directly represses expression of NITRATE REDUCTASE (NR/NIA), which catalyses the first reduction step in nitrate assimilation, and is encoded by a single potato locus. StCDF1 knock-down lines performed better in N-limiting conditions, and this phenotype correlated with derepressed StNR expression. Also, deletion of the StNR DAP-seq region abolished repression by StCDF1, while it did not affect NLP7-dependent activation of the StNR promoter. We identified multiple nucleotide polymorphisms in the DAP-seq region in potato cultivars with early StCDF1 alleles, suggesting that this genetic variation was selected as compensatory mechanism to the negative impact of StCDF1 stabilization. Thereby, directed modification of the StCDF1-recognition elements emerges as a promising strategy to enhance limiting StNR activity in potato.}, + author = {Shaikh, Maroof Ahmed and Ramírez-Gonzales, Lorena and Franco-Zorrilla, José M. and Steiner, Evyatar and Oortwijn, Marian and Bachem, Christian W. B. and Prat, Salomé}, + copyright = {© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.}, + doi = {10.1111/nph.20186}, + issn = {1469-8137}, + journal = {New Phytologist}, + keywords = {{\textgreater}UseGalaxy.eu, DAP-seq, Solanum tuberosum L., StCDF1 transcription factor, nitrate reductase, promoter polymorphism}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.20186}, + number = {n/a}, + shorttitle = {{StCDF1}}, + title = {{StCDF1}: {A} ‘jack of all trades’ clock output with a central role in regulating potato nitrate reduction activity}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.20186}, + urldate = {2024-11-17}, + volume = {n/a}, + year = {2024} +} + @article{shankar_structure_2023, abstract = {Tea, a widely consumed aromatic beverage, is often adulterated with dyes such as Bismarck brown Y (C.I. 21000) (BBY), Prussian blue, and Plumbago, which pose potential health risks. The objective of this study is to analyze how the food dye BBY interacts with serum protein, bovine serum albumin (BSA). This study investigated the BBY-BSA interaction at the molecular level. Fluorescence spectroscopy results showed that the quenching of BSA by BBY is carried out by dynamic quenching mechanism. The displacement assay and molecular docking studies revealed that BBY binds at the flavanone binding site of BSA with hydrophobic interactions. Circular Dichroism results indicate the structural stability of the protein upon BBY binding. Molecular dynamics simulations demonstrated the stability of the complex in a dynamic solvent system, and quantum mechanics calculations showed slight conformational changes of the diaminophenyl ring due to increased hydrophobic interaction. The energetics of gas phase optimized and stable MD structures of BBY indicated similar values which further confirmed that the conformational changes were minor, and it also exhibited a moderate binding with BSA as shown by the MM/PBSA results. This study enhances our understanding of the molecular-level interactions between BBY and BSA, emphasizing the critical role of hydrophobic interactions.}, author = {Shankar, Manwi and Rani, Majji Sai Sudha and Gopi, Priyanka and P, Arsha and Pandya, Prateek}, @@ -10741,6 +11547,24 @@ @article{shi_recapitulating_2022 year = {2022} } +@article{shipman_combined_2024, + abstract = {Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense (Foc), is a serious disease that threatens banana production worldwide. It is a long-standing problem in Hawaii, but previously, there was little knowledge of the causal pathogen. We isolated a strain of Foc, named Foc-UH, from a field experiencing the disease epidemic in Hawaii. Infection assays of a diverse panel of 26 banana clones, including varieties used for differentiating pathogen races and fruit production, revealed that Foc-UH has a race 1 pathogenic phenotype with an intermediate race 2 virulence and revealed the differential resistance of varieties to infection. Separate phylogenetic analyses using the barcoding regions of three nuclear genes, seven complete nuclear genes, and single-nucleotide polymorphisms within conserved whole-genome protein coding sequences placed Foc-UH into recently proposed taxonomic frameworks relevant to Foc and the F. oxysporum species complex. Screening of the 99.7\% complete draft genome identified five secreted in xylem (SIX) gene homologs: SIX1d, SIX1f, SIX9a, SIX9b, and SIX13a. This profile is similar to that of several race 1 isolates except for the absence of SIX4 and SIX6. Foc-UH was morphologically dissimilar to the nearest related isolates. Altogether, this study identified a unique isolate that causes banana Fusarium wilt, which represents the first characterization of the causal pathogen in Hawaii. The findings and genomic resources generated in this study are expected to guide banana breeding and cultivar deployment in Hawaii and beyond and contribute to further understanding of the pathogenicity and evolutionary systematics of Foc.}, + author = {Shipman, Aaron and Tian, Miaoying}, + doi = {10.1094/PHYTO-07-23-0257-R}, + issn = {0031-949X}, + journal = {Phytopathology®}, + keywords = {{\textgreater}UseGalaxy.eu, Fusarium oxysporum f. sp. cubense, Fusarium oxysporum species complex, Fusarium wilt, banana, secreted in xylem (SIX)}, + month = {June}, + note = {Publisher: Scientific Societies}, + number = {6}, + pages = {1305--1319}, + title = {Combined {Use} of {Phenotype}-{Based} and {Genome}-{Informed} {Approaches} {Identified} a {Unique} {Fusarium} oxysporum f. sp. cubense {Isolate} in {Hawaii}}, + url = {https://apsjournals.apsnet.org/doi/abs/10.1094/PHYTO-07-23-0257-R}, + urldate = {2024-11-17}, + volume = {114}, + year = {2024} +} + @article{siatra_return_2023, abstract = {The single curative measure for heart failure patients is a heart transplantation, which is limited due to a shortage of donors, the need for immunosuppression and economic costs. Therefore, there is an urgent unmet need for identifying cell populations capable of cardiac regeneration that we will be able to trace and monitor. Injury to the adult mammalian cardiac muscle, often leads to a heart attack through the irreversible loss of a large number of cardiomyocytes, due to an idle regenerative capability. Recent reports in zebrafish indicate that Tbx5a is a vital transcription factor for cardiomyocyte regeneration. Preclinical data underscore the cardioprotective role of Tbx5 upon heart failure. Data from our earlier murine developmental studies have identified a prominent unipotent Tbx5-expressing embryonic cardiac precursor cell population able to form cardiomyocytes, in vivo, in vitro and ex vivo. Using a developmental approach to an adult heart injury model and by employing a lineage-tracing mouse model as well as the use of single-cell RNA-seq technology, we identify a Tbx5-expressing ventricular cardiomyocyte-like precursor population, in the injured adult mammalian heart. The transcriptional profile of that precursor cell population is closer to that of neonatal than embryonic cardiomyocyte precursors. Tbx5, a cardinal cardiac development transcription factor, lies in the center of a ventricular adult precursor cell population, which seems to be affected by neurohormonal spatiotemporal cues. The identification of a Tbx5-specific cardiomyocyte precursor-like cell population, which is capable of dedifferentiating and potentially deploying a cardiomyocyte regenerative program, provides a clear target cell population for translationally-relevant heart interventional studies.}, author = {Siatra, Panagiota and Vatsellas, Giannis and Chatzianastasiou, Athanasia and Balafas, Evangelos and Manolakou, Theodora and Papapetropoulos, Andreas and Agapaki, Anna and Mouchtouri, Eleni-Taxiarchia and Ruchaya, Prashant J. and Korovesi, Artemis G. and Mavroidis, Manolis and Thanos, Dimitrios and Beis, Dimitris and Kokkinopoulos, Ioannis}, @@ -10762,6 +11586,22 @@ @article{siatra_return_2023 year = {2023} } +@misc{silar_fungani_2024, + abstract = {There is presently no easy-to-use program calculating the Average Nucleotide Identity (ANI) between two fungal genomes that can be used by mycologists having limited access to bioinformatic facilities. Here, we present FungANI, a customizable BLAST-based program that calculate ANI between genomes. The program runs on the latest Windows, macOS and Linux 64-Bit operating systems as a standalone desktop application. It was tested with various publicly-available genomes from species belonging to the Sordariales order. It proved efficient to differentiate closely related species and retrace their possible phylogenetic relationships. However, FungANI did not perform well for phylogenetic reconstruction on a broader evolutionary scale such as inferring relationships between distant genera. The program is freely available at https://github.com/podo-gec/fungani.}, + address = {Rochester, NY}, + author = {Silar, Philippe and Lalanne, Christophe}, + doi = {10.2139/ssrn.4952315}, + keywords = {{\textgreater}UseGalaxy.eu, Average Nucleotide Identity (ANI), FungANI, Genome Sequence, Phylogeny, Sordariales}, + language = {en}, + month = {September}, + publisher = {Social Science Research Network}, + title = {Fungani, a {Blast}-{Based} {Program} for {Analyzing} {Average} {Nucleotide} {Identity} ({Ani}) between {Two} {Fungal} {Genomes}, {Enables} {Easy} {Fungal} {Species} {Delimitation}}, + type = {{SSRN} {Scholarly} {Paper}}, + url = {https://papers.ssrn.com/abstract=4952315}, + urldate = {2024-11-17}, + year = {2024} +} + @article{silva_comparative_2024, abstract = {We explored the metabolic integration of Blattella germanica and its obligate endosymbiont Blattabacterium cuenoti by the transcriptomic analysis of the fat body of quasi-aposymbiotic cockroaches, where the endosymbionts were almost entirely removed with rifampicin. Fat bodies from quasi-aposymbiotic insects displayed large differences in gene expression compared to controls. In quasi-aposymbionts, the metabolism of phenylalanine and tyrosine involved in cuticle sclerotization and pigmentation increased drastically to compensate for the deficiency in the biosynthesis of these amino acids by the endosymbionts. On the other hand, the uricolytic pathway and the biosynthesis of uric acid were severely decreased, probably because the reduced population of endosymbionts was unable to metabolize urea to ammonia. Metabolite transporters that could be involved in the endosymbiosis process were identified. Immune system and antimicrobial peptide (AMP) gene expression was also reduced in quasi-aposymbionts, genes encoding peptidoglycan-recognition proteins, which may provide clues for the maintenance of the symbiotic relationship, as well as three AMP genes whose involvement in the symbiotic relationship will require additional analysis. Finally, a search for AMP-like factors that could be involved in controlling the endosymbiont identified two orphan genes encoding proteins smaller than 200 amino acids underexpressed in quasi-aposymbionts, suggesting a role in the host–endosymbiont relationship.}, author = {Silva, Francisco J. and Domínguez-Santos, Rebeca and Latorre, Amparo and García-Ferris, Carlos}, @@ -10783,6 +11623,24 @@ @article{silva_comparative_2024 year = {2024} } +@article{sime_microbial_2024, + abstract = {The global over-reliance on non-renewable fossil fuels has led to the emission of greenhouse gases, creating a critical global environmental challenge. There is an urgent need for alternative solutions like biofuels. Advanced biofuel is a renewable sustainable energy generated from lignocellulosic plant materials, which can significantly contribute to mitigating CO2 emissions. Microbial Carbohydrate Active Enzymes (CAZymes) are the most crucial enzymes for the generation of sustainable biofuel energy. The present study designed shotgun metagenomics approaches to assemble, predict, and annotate, aiming to gain an insight into the taxonomic diversity, annotate CAZymes, and identify carbohydrate hydrolyzing CAZymes from microbiomes in Menagesha suba forest soil for the first time.}, + author = {Sime, Amsale Melkamu and Kifle, Bezayit Amare and Woldesemayat, Adugna Abdi and Gemeda, Mesfin Tafesse}, + doi = {10.1186/s12866-024-03436-9}, + issn = {1471-2180}, + journal = {BMC Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, CAZyme genes, Carbohydrate-active enzyme, Forest soil, Shotgun metagenomic sequencing}, + language = {en}, + month = {August}, + number = {1}, + pages = {285}, + title = {Microbial carbohydrate active enzyme ({CAZyme}) genes and diversity from {Menagesha} {Suba} natural forest soils of {Ethiopia} as revealed by shotgun metagenomic sequencing}, + url = {https://doi.org/10.1186/s12866-024-03436-9}, + urldate = {2024-11-17}, + volume = {24}, + year = {2024} +} + @article{simon-chica_novel_2021, abstract = {Macrophages (MΦ), known for immunological roles such as phagocytosis and antigen presentation, have been found to electrotonically couple to cardiomyocytes (CM) of the atrio-ventricular node via Cx43, affecting cardiac conduction in isolated mouse hearts. Here, we characterise passive and active electrophysiological properties of murine cardiac resident MΦ, and model their potential electrophysiological relevance for CM.We combined classic electrophysiological approaches with 3 D florescence imaging, RNA-sequencing, pharmacological interventions and computer simulations. We used Cx3cr1eYFP/+ mice wherein cardiac MΦ were fluorescently labelled. FACS-purified fluorescent MΦ from mouse hearts were studied by whole-cell patch-clamp. MΦ electrophysiological properties include: membrane resistance 2.2 ± 0.1 GΩ (all data mean±SEM), capacitance 18.3 ± 0.1 pF, resting membrane potential -39.6 ± 0.3 mV, and several voltage-activated, outward or inwardly-rectifying potassium currents. Using ion channel blockers (barium, TEA, 4-AP, margatoxin, XEN-D0103, DIDS), flow cytometry, immuno-staining and RNA-sequencing, we identified Kv1.3, Kv1.5 and Kir2.1 as channels contributing to observed ion currents. MΦ displayed four patterns for outward and two for inward-rectifier potassium currents. Additionally, MΦ showed surface expression of Cx43, a prerequisite for homo- and/or heterotypic electrotonic coupling. Experimental results fed into development of an original computational model to describe cardiac MΦ electrophysiology. Computer simulations to quantitatively assess plausible effects of MΦ on electrotonically coupled CM showed that MΦ can depolarise resting CM, shorten early and prolong late action potential duration, with effects depending on coupling strength and individual MΦ electrophysiological properties, in particular resting membrane potential and presence/absence of Kir2.1.Our results provide a first electrophysiological characterisation of cardiac resident MΦ, and a computational model to quantitatively explore their relevance in the heterocellular heart. Future work will be focussed at distinguishing electrophysiological effects of MΦ–CM coupling on both cell types during steady-state and in patho-physiological remodelling, when immune cells change their phenotype, proliferate, and/or invade from external sources.Cardiac tissue contains resident macrophages (MΦ) which, beyond immunological and housekeeping roles, have been found to electrotonically couple via connexins to cardiomyocytes (CM), stabilising atrio-ventricular conduction at high excitation rates. Here, we characterise structure and electrophysiological function of murine cardiac MΦ and provide a computational model to quantitatively probe the potential relevance of MΦ-CM coupling for cardiac electrophysiology. We find that MΦ are unlikely to have major electrophysiological effects in normal tissue, where they would hasten early and slow late CM-repolarisation. Further work will address potential arrhythmogenicity of MΦ in patho-physiologically remodelled tissue containing elevated MΦ-numbers, incl. non-resident recruited cells.}, author = {Simon-Chica, Ana and Fernández, Marbely C and Wülfers, Eike M and Lother, Achim and Hilgendorf, Ingo and Seemann, Gunnar and Ravens, Ursula and Kohl, Peter and Schneider-Warme, Franziska}, @@ -10975,6 +11833,17 @@ @article{soriano-sexto_identification_2022 year = {2022} } +@phdthesis{souza_effect_2024, + abstract = {In this thesis, we investigated the relationship between increasing plant richness and the diversity and composition of soil and endophytic microbiome and its importance to stress response. We made use of a plant richness diversity gradient established in a long-term biodiversity experiment (the Jena experiment) to access the changes on seed microbiome of a model plant, Plantago lanceolata and the effect of this diversity gradient on the soil bacterial community after long term drought stress.}, + author = {Souza, De and Alves, Yuri Pinheiro}, + keywords = {{\textgreater}UseGalaxy.eu}, + school = {Technische Universität München}, + title = {The effect of increasing plant species richness on soil and seed microbiome and its importance to stress response}, + url = {https://mediatum.ub.tum.de/1738650}, + urldate = {2024-11-17}, + year = {2024} +} + @mastersthesis{soyland_mapping_2024, abstract = {The last few decades have seen a massive use of antibiotics worldwide, in all from human health care and veterinary use to agriculture and aquaculture. This has led to a rise in emergence of antibiotic resistant bacteria (ARB), where bacteria harbouring genes for extended-spectrum β-lactamases (ESBL) and carbapenem resistance are of particular concern. Infectious diseases caused by these bacteria can be very challenging to treat, and a staggering number of deaths every year result directly or indirectly from antibiotic resistance. With no measurements taken to stop the ARB spread, this problem will only keep on growing. @@ -11031,6 +11900,46 @@ @article{spano_comparative_2023 year = {2023} } +@article{spano_overview_2024, + abstract = {Plant tissue in vitro culture is increasingly used in agriculture to improve crop production, nutritional quality, and commercial value. In plant virology, the technique is used as sanitation protocol to produce virus-free plants. Sanitized (S) artichokes show increased vigour compared to their non-sanitized (NS) counterparts, because viral infections lead to a decline of growth and development. To investigate mechanisms that control the complex traits related to morphology, growth, and yield in S artichokes compared to NS plants, RNAseq analysis and phenotyping by imaging were used. The role of peroxidases (POD) was also investigated to understand their involvement in sanitized plant development. Results showed that virus infection affected regulation of cell cycle, gene expression and signal transduction modulating cellular response to stimulus/stress. Moreover, primary metabolism and photosynthesis were also influenced, contributing to explain the main morphological differences observed between S and NS artichokes. Sanitized artichokes are also characterized by higher POD activity, probably associated with increased plant growth, rather than strengthening of cell walls. Overall, results show that the differences in development of S artichokes may be derived from the in vitro culture stressor, as well as through pathogen elimination, which, in turn, improve qualitative and quantitative artichoke production.}, + author = {Spanò, R. and Petrozza, A. and Summerer, S. and Fortunato, S. and de Pinto, M. C. and Cellini, F. and Mascia, T.}, + copyright = {© 2024 The Author(s). Plant Biology published by John Wiley \& Sons Ltd on behalf of German Society for Plant Sciences, Royal Botanical Society of the Netherlands.}, + doi = {10.1111/plb.13675}, + issn = {1438-8677}, + journal = {Plant Biology}, + keywords = {{\textgreater}UseGalaxy.eu, RNAseq analysis, lignin, peroxidase, plant phenotyping, sanitation protocol, virus infection}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/plb.13675}, + number = {5}, + pages = {715--726}, + title = {Overview of transcriptome changes and phenomic profile of sanitized artichoke vis-à-vis non-sanitized plants}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/plb.13675}, + urldate = {2024-11-17}, + volume = {26}, + year = {2024} +} + +@article{spano_spotlight_2024, + abstract = {Globe artichoke (Cynara cardunculus L. subsp. scolymus) is an important crop of the Mediterranean basin characterized by many properties, like hepatoprotective, anticarcinogenic, antioxidant, antibacterial, and beneficial to human health. The high bioactive compounds (BACs) content, as polyphenols, has attracted the research interest in artichoke extracts. We analysed the changes in polyphenol transcriptome profile between sanitized (S) virus-free and non-sanitized (NS) artichoke plants, focusing on genes involved in phenylpropanoid metabolic pathway and flavonoid biosynthesis. A total of 2458 upregulated and 2154 downregulated differentially expressed genes (DEGs) were functionally characterized. Among them, 31 and 35 KEGG orthology entries characterized by upregulated and downregulated DEGs, respectively, were involved in the biosynthesis of other secondary metabolites. A downregulation of PAL, C4H, 4CL, HST/HQT, C3′H, CCoAMT, CCR1, and F5H, was observed in S artichoke compared to NS one, whereas the CSE, CHS, and CHI genes were upregulated in S samples. Transcriptome results were compared to the polyphenols accumulation in S and NS artichoke leaves. A higher content of total polyphenols was observed in older leaves of NS samples, compared to extracts obtained from young leaves or from S plants, and this result was associated with the presence of viral infections in NS plants. In all the conditions tested, the most represented compound was chlorogenic acid, followed by luteolin-7-O-glucoside. The different composition of each extract was evaluated by a polyphenol dose–response treatment on the rodent hepatoma FaO cell line to the accumulation of reactive oxygen species (ROS). A significant reduction in ROS content ranging between −40\% and −48\% was observed when 10–20 mg/L of polyphenols from NS or S plants were used, characterized by a specific profile of compounds. To reduce MetOH residues in polyphenol extracts, a supercritical fluid CO2 extraction was evaluated to propose a sustainable green extraction.}, + author = {Spanò, Roberta and Gena, Patrizia and Linsalata, Vito and Sini, Valeria and D’Antuono, Isabella and Cardinali, Angela and Cotugno, Pietro and Calamita, Giuseppe and Mascia, Tiziana}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/antiox13070852}, + issn = {2076-3921}, + journal = {Antioxidants}, + keywords = {{\textgreater}UseGalaxy.eu, RNAseq analysis, anti-inflammatory effects, antioxidant and antimicrobial effects, artichoke, polyphenol extracts, supercritical fluid extraction, virus infection, virus sanitation protocol}, + language = {en}, + month = {July}, + note = {Number: 7 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {7}, + pages = {852}, + title = {Spotlight on {Secondary} {Metabolites} {Produced} by an {Early}-{Flowering} {Apulian} {Artichoke} {Ecotype} {Sanitized} from {Virus} {Infection} by {Meristem}-{Tip}-{Culture} and {Thermotherapy}}, + url = {https://www.mdpi.com/2076-3921/13/7/852}, + urldate = {2024-11-17}, + volume = {13}, + year = {2024} +} + @article{spradling_mitochondrial_2021, author = {Spradling, Theresa A. and Place, Alexandra C. and Campbell, Ashley L. and Demastes, James W.}, doi = {10.1371/journal.pone.0254138}, @@ -11582,6 +12491,22 @@ @article{thompson_draft_2023 } @article{thompson_draft_2024, + author = {Thompson, Ryan Michael and Fox, Edward M. and Montero-Calasanz, Maria del Carmen}, + doi = {10.1128/mra.01131-23}, + journal = {Microbiology Resource Announcements}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {February}, + note = {Publisher: American Society for Microbiology}, + number = {3}, + pages = {e01131--23}, + title = {Draft genome sequences of two {Micromonospora} strains isolated from the root nodules of {Alnus} glutinosa}, + url = {https://journals.asm.org/doi/full/10.1128/mra.01131-23}, + urldate = {2024-11-17}, + volume = {13}, + year = {2024} +} + +@article{thompson_draft_2024-1, author = {Thompson, Ryan Michael and Fox, Edward M. and Montero-Calasanz, Maria del Carmen}, doi = {10.1128/mra.01132-23}, journal = {Microbiology Resource Announcements}, @@ -11615,6 +12540,20 @@ @article{thongbunrod_potential_2024 year = {2024} } +@phdthesis{tiwari_innate_2024, + abstract = {The age-related decline in the nervous system's capacity to regenerate impairs functional recovery after demyelinating injury. When damage or inflammation occurs in the brain, microglia are the first line of defense. Recovery from demyelinating injury is hindered by age-related changes in the phenotype of microglia. There is evidence that microglial metabolic capacity is overwhelmed by myelin debris in the aged subjects, preventing tissue regeneration, but the mechanisms underlying this effect are not well understood. Many genes that are inefficiently activated in aged microglia/macrophages in a model of demyelination were found to have epigenetic modifications associated with decreased chromatin accessibility. The ability of aged mice to re-myelinate damaged tissue was restored by selectively deleting two class I histone deacetylases in microglia/macrophages. We used Bacillus Calmette-Guerin (BCG), a live-attenuated vaccine, to train the innate immune system, and detected epigenetic reprogramming of brain-resident myeloid cells and functional restoration of myelin debris clearance and lesion recovery. Further, trained microglia showed enhanced activation and improved myelin lipid metabolism in response to demyelinating injury, a process mediated at least in part by histone deacetylases. Our results provide insight into aging-associated decline in myeloid function and how this decay can be prevented by innate immune system reprogramming. In conclusion, we demonstrate that epigenetically mediated innate immune training of microglia can serve as strategy to convert microglia into pro-reparative state following demyelinating injury.}, + author = {Tiwari, Vini}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {de}, + month = {February}, + school = {Ludwig-Maximilians-Universität München}, + title = {Innate immune training restores pro-reparative myeloid functions for remyelination in aged central nervous system}, + type = {Text.{PhDThesis}}, + url = {https://edoc.ub.uni-muenchen.de/33226/}, + urldate = {2024-11-17}, + year = {2024} +} + @article{tiwari_innate_2024, abstract = {{\textless}h2{\textgreater}Summary{\textless}/h2{\textgreater}{\textless}p{\textgreater}The reduced ability of the central nervous system to regenerate with increasing age limits functional recovery following demyelinating injury. Previous work has shown that myelin debris can overwhelm the metabolic capacity of microglia, thereby impeding tissue regeneration in aging, but the underlying mechanisms are unknown. In a model of demyelination, we found that a substantial number of genes that were not effectively activated in aged myeloid cells displayed epigenetic modifications associated with restricted chromatin accessibility. Ablation of two class I histone deacetylases in microglia was sufficient to restore the capacity of aged mice to remyelinate lesioned tissue. We used Bacillus Calmette-Guerin (BCG), a live-attenuated vaccine, to train the innate immune system and detected epigenetic reprogramming of brain-resident myeloid cells and functional restoration of myelin debris clearance and lesion recovery. Our results provide insight into aging-associated decline in myeloid function and how this decay can be prevented by innate immune reprogramming.{\textless}/p{\textgreater}}, author = {Tiwari, Vini and Prajapati, Bharat and Asare, Yaw and Damkou, Alkmini and Ji, Hao and Liu, Lu and Naser, Nawraa and Gouna, Garyfallia and Leszczyńska, Katarzyna B. and Mieczkowski, Jakub and Dichgans, Martin and Wang, Qing and Kawaguchi, Riki and Shi, Zechuan and Swarup, Vivek and Geschwind, Daniel H. and Prinz, Marco and Gokce, Ozgun and Simons, Mikael}, @@ -11839,6 +12778,25 @@ @article{umpeleva_identification_2024 year = {2024} } +@article{urrutia-angulo_unravelling_2024, + abstract = {Mastitis, inflammation of the mammary gland, is a major disease of dairy cattle and the main cause for antimicrobial use. Although mainly caused by bacterial infections, the aetiological agent often remains unidentified by conventional microbiological culture methods. The aim of this study was to test whether shifts in the bovine mammary gland microbiota can result in initiation or progression of mastitis.}, + author = {Urrutia-Angulo, Leire and Ocejo, Medelin and Oporto, Beatriz and Aduriz, Gorka and Lavín, José Luís and Hurtado, Ana}, + doi = {10.1186/s42523-024-00345-0}, + issn = {2524-4671}, + journal = {Animal Microbiome}, + keywords = {{\textgreater}UseGalaxy.eu, Dairy cattle, Enterotyping, Full-length 16S-metabarcoding, Long-read sequencing, Mastitis, Milk microbiome}, + language = {en}, + month = {October}, + number = {1}, + pages = {58}, + shorttitle = {Unravelling the complexity of bovine milk microbiome}, + title = {Unravelling the complexity of bovine milk microbiome: insights into mastitis through enterotyping using full-length {16S}-metabarcoding}, + url = {https://doi.org/10.1186/s42523-024-00345-0}, + urldate = {2024-11-17}, + volume = {6}, + year = {2024} +} + @article{valadez-moctezuma_first_2023, abstract = {Although Opuntia is one of the most emblematic and promising crops in Mexico, no extensive genomic resources are available. Herein, we present the first transcriptomic datasets of three species of Opuntia. Comparative transcriptome profiling provides insights into the molecular and physiological functions between species and tissues. Total RNA from young cladodes and developing fruits of O. ficus-indica, O. robusta and O. joconostle was purified and sequenced by Massive Analysis of cDNA Ends technology, an RNA-seq variant. A total of 8383, 7890, and 5300 transcripts and GC content of 40.1, 39.9 and 40.1\% were obtained for the de novo assembly of O. ficus-indica, O. robusta and O. joconostle, respectively. For annotations, about 22.2–23.7\% of transcripts had matches in the UniProtKB/Swiss-Prot database. Moreover, the enriched 21 COG categories, 282 KEGG pathways and 2793 GO terms revealed that the transcriptomes obtained included functionally diverse genes in Opuntia. Differentially expressed transcripts (DETs) between fruit and cladode resulted in the enrichment of 13 significant KEGG pathways and 80 GO terms, where some genes viz. FULL, CYP75B1, and CMB1 were upregulated in the fruits of the three species. Between species, the most enriched GOs fell into the category of “Cellular Components”, which would explain the morphological and physiological differences between the three species. Moreover, DETs comparisons between fruit types and between cladodes were also reported. Overall, the transcriptomic data generated in this study provide the initial resources to understand the biology of Opuntia, offering new insight to understand its morphology, systematic and adaptation.}, author = {Valadez-Moctezuma, Ernestina and Samah, Samir and Mascorro-Gallardo, J. Oscar and Marbán-Mendoza, Nahum and Aranda-Osorio, Gilberto and Flores-Girón, Emmanuel and Brito-Nájera, Guadalupe and Rodríguez de la O, José Luis}, @@ -11908,6 +12866,22 @@ @article{vaquero-sedas_epigenetic_2022 year = {2022} } +@article{vecchi_mitogenome_2024, + abstract = {Ramazzottius is a widespread genus of tardigrades with extreme cryptobiotic capabilities. Thanks to its ability to survive desiccation and freezing, this genus is usually recorded from harsh habitats such as exposed mosses and lichens and rock pools. In the last years, research focused on both describing Ramazzottius diversity and revealing the molecular mechanisms behind their cryptobiotic capabilities. Despite the research efforts in these fields, much still remains to be discovered. Here we describe a new Ramazzottius species from an Italian rock pool by means of integrative taxonomy (morphology, morphometry, and DNA sequencing) and sequenced its genome with Nanopore technology to provide an assembled mitogenome and annotate its Temperature and Desiccation Resistance Proteins (TDPR) repertoire. The new gonochoric species is phylogenetically close to the parthenogenetic R. varieornatus, a strain of which (YOKOZUNA-1) has been adopted as model organism for the study of cryptobiosis. The mitogenome of the new species shows perfect synteny with R. varieornatus and shares with it most of the TDPR genes. The relative genetic similarity of the new species to the model R. varieornatus, combined with unique biological traits (for example the difference in reproductive mode and the unique habitat it colonizes), makes the new species a potential new addition to the range of model tardigrade species.}, + author = {Vecchi, Matteo and Stec, Daniel}, + doi = {10.1007/s13127-024-00662-x}, + issn = {1618-1077}, + journal = {Organisms Diversity \& Evolution}, + keywords = {{\textgreater}UseGalaxy.eu, Anhydrobiosis, Mitogenome, Nanopore, New species, Ramazzottius}, + language = {en}, + month = {October}, + shorttitle = {Mitogenome of a new {Ramazzottius} species ({Tardigrada}}, + title = {Mitogenome of a new {Ramazzottius} species ({Tardigrada}: {Eutardigrada}: {Ramazzottiidae}) discovered in rock pools along with its temperature and desiccation-related proteins repertoire}, + url = {https://doi.org/10.1007/s13127-024-00662-x}, + urldate = {2024-11-17}, + year = {2024} +} + @article{vergata_how_2023, abstract = {Phylloremediation for the reduction of air particulate matter (PM) is an interesting opportunity to significantly contribute to improve the air quality of urban environment. The aim of this study was to: 1) gain insight into the gene regulatory networks modulating leaf responses to polluted air, 2) identify possible changes in the leaf microbiome due to particulate matter in the real urban environment. The leaf transcriptome and microbiome were analyzed for Photinia x fraseri L. plants cultivated for three months in pots in two close-by areas under different levels of air PMs (low and high). PCA and heat map analysis showed that 28 differentially expressed genes in common between the three pairwise comparisons were able to clearly discriminate plants under higher PM levels. The pollutants were mainly sensed by plants through a restructuring modification of cell wall and membrane due to the main repression of lipid desaturases. In addition, high PMs showed a clear repression of genes belonging to primary metabolism pathways involved in C assimilation. Microbiome analysis showed no significant changes in taxonomic diversity indexes for the bacterial communities, whereas fungi belonging to the genera Epicoccum and Dioszegia were differently affected by the different exposure to PM levels. A model of transcriptional regulation to air PMs in plants has been proposed.}, author = {Vergata, Chiara and Contaldi, Felice and Baccelli, Ivan and Basso, Marcos Fernando and Santini, Alberto and Pecori, Francesco and Buti, Matteo and Mengoni, Alessio and Vaccaro, Francesca and Moura, Barbara Basso and Ferrini, Francesco and Martinelli, Federico}, @@ -13043,6 +14017,26 @@ @article{yol_high-density_2021 year = {2021} } +@article{yong_complete_2024, + abstract = {Bactrocera (Bulladacus) cinnabaria and B. (Bactrocera) propinqua are tephritid fruit flies of the subfamily Dacinae, tribe Dacini. The whole mitogenomes of these two species (first report for the subgenus Bulladacus) possess 37 genes (13 protein-coding genes – PCGs, 2 rRNA and 22 tRNA genes). The mitogenome of B. cinnabaria (15,225 bp) is shorter than that of B. propinqua (15,927 bp), mainly due to the smaller size of the control region and intergenic spacers in B. cinnabaria. Molecular phylogeny based on mitochondrial genes (mt-genes) reveals two clades of the genus Bactrocera: one comprising the subgenus Bactrocera and the other comprising the subgenera Bulladacus, Daculus, Tetradacus and unassigned Bactrocera sp. ‘yunnanensis’. The subgenera represented by two or more taxa are monophyletic. B. (Bulladacus) cinnabaria forms a sister group with the subgenus Tetradacus (B. minax and B. tsuneonis) and B. sp. ‘yunnanensis’, in a clade containing also the basal sister lineage of the subgenus Daculus (B. oleae and B. biguttula). B. propinqua forms a sister group with B. ritsemai and B. limbifera in a subclade containing also B. umbrosa, B. curvifera and B. moluccensis of the monophyletic subgenus Bactrocera. The present study supports the synonymy of B. ruiliensis with B. thailandica. It also shows a high genetic similarity between (a) B. melastomatos and B. rubigina, (b) B. papayae and B. philippinensis, (c) B. dorsalis and B. invadens, (d) B. tryoni and B. neohumeralis, and (e) B. cheni and B. tuberculata; and B. cheni is distinct from and not a synonym of B. tsuneonis or B. lombokensis.}, + author = {Yong, Hoi-Sen and Song, Sze-Looi and Chua, Kah-Ooi and Liew, Yvonne Jing Mei and Chan, Kok-Gan and Lim, Phaik-Eem and Eamsobhana, Praphathip}, + copyright = {2024 Hoi-Sen Yong, Sze-Looi Song, Kah-Ooi Chua, Yvonne Jing Mei Liew, Kok-Gan Chan, Phaik-Eem Lim, Praphathip Eamsobhana}, + doi = {10.3897/asp.82.e115954}, + issn = {1864-8312}, + journal = {Arthropod Systematics \& Phylogeny}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {July}, + note = {Publisher: Senckenberg Gesellschaft für Naturforschung}, + pages = {515--526}, + shorttitle = {Complete mitochondrial genomes of {Bactrocera} ({Bulladacus}) cinnabaria and {B}. ({Bactrocera}) propinqua ({Diptera}}, + title = {Complete mitochondrial genomes of {Bactrocera} ({Bulladacus}) cinnabaria and {B}. ({Bactrocera}) propinqua ({Diptera}: {Tephritidae}) and their phylogenetic relationships with other congeners}, + url = {https://arthropod-systematics.arphahub.com/article/115954/}, + urldate = {2024-11-17}, + volume = {82}, + year = {2024} +} + @article{yoshida_dataset_2020, abstract = {In this article, we report the first de novo transcriptome assembly of the African bullfrog Pyxicephalus adspersus. In this data, 75,320,390 raw reads were acquired from African bullfrog mRNA using Illumina paired-end sequencing platform. De novo assembly resulted in a total of 136,958 unigenes. In the obtained unigenes, 30,039 open reading frames (ORFs) were detected. This dataset provides basic information for molecular level analysis of this species, which undergoes a state of dormancy under dry conditions at ordinary temperatures called estivation.}, author = {Yoshida, Naoki and Kaito, Chikara}, @@ -13276,6 +14270,27 @@ @article{zerouki_whole-genome_2023 year = {2023} } +@article{zhan_comparison_2024, + abstract = {Continual climate change strongly influences temperature conditions worldwide, making ectothermic animals as suitable species for studying the potential impact of climate change on global biodiversity. However, the study of how lizards distributed at different latitudes respond to climate change at the transcriptome level is still insufficient. According to the Climatic Variability Hypothesis (CVH), the range of climate fluctuations experienced by terrestrial animals throughout the year increases with latitude, so individuals at higher latitudes should exhibit greater thermal plasticity to cope with fluctuating environments. Mitochondria, as the energy center of vertebrate cells, may indicate species’ plasticity through the sensitivity of gene expression. In this study, we focused on the changes in transcript levels of liver mitochondrial protein-coding genes (PCGs) in skinks from the genus Plestiodon (P. capito and P. elegans) and the genus Scincella (S. modesta and S. reevesii) under low-temperature conditions of 8 °C, compared to the control group at 25 °C. Species within the same genus of skinks exhibit different latitudinal distribution patterns. We found that the two Plestiodon species, P. elegans and P. capito, employ a metabolic depression strategy (decreased transcript levels) to cope with low temperatures. In contrast, the two Scincella species show markedly different patterns: S. modesta exhibits significant increases in the transcript levels of six genes (metabolic compensation), while in S. reevesii, only two mitochondrial genes are downregulated (metabolic depression) compared to the control group. We also found that P. capito and S. modesta, which live at mid-to-high latitudes, exhibit stronger adaptive responses and plasticity at the mitochondrial gene level compared to P. elegans and S. reevesii, which live at lower latitudes. We suggest that this enhanced adaptability corresponds to more significant changes in a greater number of genes (plasticity genes).}, + author = {Zhan, Lemei and He, Jingyi and Ding, Lingyi and Storey, Kenneth B. and Zhang, Jiayong and Yu, Danna}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ijms251910637}, + issn = {1422-0067}, + journal = {International Journal of Molecular Sciences}, + keywords = {\textit{RT}-qPCR, {\textgreater}UseGalaxy.eu, latitudinal pattern, low-temperature stress, mitochondrial genome expression, skink}, + language = {en}, + month = {January}, + note = {Number: 19 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {19}, + pages = {10637}, + title = {Comparison of {Mitochondrial} {Genome} {Expression} {Differences} among {Four} {Skink} {Species} {Distributed} at {Different} {Latitudes} under {Low}-{Temperature} {Stress}}, + url = {https://www.mdpi.com/1422-0067/25/19/10637}, + urldate = {2024-11-17}, + volume = {25}, + year = {2024} +} + @article{zhang_complete_2024, abstract = {There has been debate about whether individuals with different color phenotypes should have different taxonomic status. In order to determine whether the different color phenotypes of Nedyopus patrioticus require separate taxonomic status or are simply synonyms, here, the complete mitochondrial genomes (mitogenomes) of two different colored N. patrioticus, i.e., red N. patrioticus and white N. patrioticus, are presented. The two mitogenomes were 15,781 bp and 15,798 bp in length, respectively. Each mitogenome contained 13 PCGs, 19 tRNAs, 2 rRNAs, and 1 CR, with a lack of trnI, trnL2, and trnV compared to other Polydesmida species. All genes were located on a single strand in two mitogenomes. Mitochondrial DNA analyses revealed that red N. patrioticus and white N. patrioticus did not show clear evolutionary differences. Furthermore, no significant divergence was discovered by means of base composition analysis. As a result, we suggest that white N. patrioticus might be regarded as a synonym for red N. patrioticus. The current findings confirmed the existence of color polymorphism in N. patrioticus, which provides exciting possibilities for future research. It is necessary to apply a combination of molecular and morphological methods in the taxonomy of millipedes.}, author = {Zhang, Gaoji and Xu, Tangjun and Chen, Yukun and Xu, Wei and Wang, Yinuo and Li, Yuanyuan and Zhu, Fuyuan and Liu, Hongyi and Ruan, Honghua},