Article
Biology
Daphne Z. Hoh, Hsin-Han Lee, Naohisa Wada, Wei-An Liu, Min R. Lu, Cheng-Kuo Lai, Huei-Mien Ke, Pei-Feng Sun, Sen-Lin Tang, Wen-Hsin Chung, Ying-Lien Chen, Chia-Lin Chung, Isheng Jason Tsai
Summary: This study investigates the genome diversity and transcriptome responses of the Fusarium solani species complex (FSSC), which includes fungal pathogens responsible for mortality in animals and plants. The study provides insights into the evolution of FSSC chromosomes and establishes an animal model for fungal pathogens.
Article
Biochemistry & Molecular Biology
Silvia Zanini, Ena Secic, Tobias Busche, Matteo Galli, Ying Zheng, Joern Kalinowski, Karl-Heinz Kogel
Summary: The study investigated gene regulation mechanisms in the fungal pathogen Magnaporthe oryzae and the model plant Brachypodium distachyon during infection, identifying differentially expressed genes and sRNAs, and highlighting the importance of RNAi genes for fungal virulence.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Avishek Paul, Jingyi Huang, Yanxiao Han, Xintong Yang, Lela Vukovic, Petr Kral, Lifei Zheng, Andreas Herrmann
Summary: This study presents a novel light-responsive ribo-switch controlled by small photo-switchable signaling molecules, demonstrating photochemically controlled expression of two different genes with high spatiotemporal resolution. The modular design of this system is believed to provide a powerful platform for controlling the expression of other functional proteins using light as a stimulus.
Review
Microbiology
Sabine Brantl, Peter Mueller
Summary: sRNAs act as abundant posttranscriptional regulators in all three kingdoms of life, with various methods being used to study chromosome-encoded sRNAs in bacteria over the past 20 years; while improved bioinformatics tools can predict potential sRNA targets, experimental confirmation remains challenging; known sRNAs in B. subtilis have defined targets and regulatory mechanisms.
Review
Biology
Xia Meng, Mengping He, Pengpeng Xia, Jinqiu Wang, Heng Wang, Guoqiang Zhu
Summary: This article reviews the functions of sRNAs during Salmonella infection of host cells. sRNAs play important roles in helping Salmonella resist acidic environmental stress, regulate virulent genes for adhesion and invasion, adapt to oxidative stress within host cells, and promote survival within macrophages. By regulating gene expression, sRNAs contribute to the pathogenic mechanism of Salmonella.
Article
Biology
Sarah Lauren Svensson, Cynthia Mira Sharma
Summary: Bacterial small RNAs (sRNAs) play important roles as post-transcriptional regulators in stress responses and virulence. RNase III is involved in processing a pair of cis-encoded sRNAs in Campylobacter jejuni, where CJnc190 and CJnc180 interact with each other and impact the regulation of the colonization factor PtmG.
Article
Genetics & Heredity
Zhaochong Tan, Limeng Wu, Yan Fang, Pingshan Chen, Rong Wan, Yang Shen, Jianping Hu, Zhenhong Jiang, Kui Hong
Summary: This study analyzed the expression pattern of nuclear-encoded mitochondrial genes in HCM and identified 316 differentially expressed NMGenes. Pathway enrichment analysis and protein-protein interaction network construction revealed the dysregulation of energy metabolism-related pathways and identified potential transcription factors regulating the expression of DE-NMGenes. Furthermore, a mouse model was used to validate the upregulation of certain genes in HCM.
FRONTIERS IN GENETICS
(2021)
Article
Biology
Jonas Birkelund Nilsson, Saghar Kaabinejadian, Hooman Yari, Bjoern Peters, Carolina Barra, Loren Gragert, William Hildebrand, Morten Nielsen
Summary: This study addresses the prediction of HLA-DQ antigen presentation and the contribution of trans-only variants in shaping the HLA-DQ immunopeptidome. By integrating immunoinformatics data mining models with mass spectrometry immunopeptidomics data, the study demonstrates improved predictive power and molecular coverage for models trained with novel HLA-DQ data. The study also reveals the limited contribution of trans-only HLA-DQ variants to the overall HLA-DQ immunopeptidome.
COMMUNICATIONS BIOLOGY
(2023)
Article
Plant Sciences
Junpeng Zhan, Lily O'Connor, D. Blaine Marchant, Chong Teng, Virginia Walbot, Blake C. Meyers
Summary: The phased, small interfering RNAs (phasiRNAs) enriched in anthers play essential roles in maintaining male fertility in grass species. This study identified coexpression networks associated with anther development in maize and found two modules highly enriched for the phasiRNA loci. It revealed the timing of transcription factors (TFs) in phasiRNA biogenesis and showed that certain TFs can activate phasiRNA pathway genes but not specific PHAS loci.
Article
Plant Sciences
Weitao Jia, Kangqi Lin, Tengxue Lou, Juanjuan Feng, Sulian Lv, Ping Jiang, Ze Yi, Xuan Zhang, Duoliya Wang, Zijing Guo, Yetao Tang, Rongliang Qiu, Yinxin Li
Summary: Key miRNAs were identified to be involved in the regulation of Cd accumulation and tolerance in sweet sorghum. Differential expressions of miRNAs and their targets were observed between high-Cd accumulation and low-Cd accumulation genotypes. Potential regulatory roles of miRNAs in response to Cd stress were revealed, providing references for developing high-Cd accumulation or high Cd-resistant germplasm for phytoremediation purposes.
Article
Plant Sciences
Kyu Tae Park, SeonJoo Park
Summary: The study characterized the complete chloroplast genomes of Hepatica, identifying unique gene features and selection pressures. Comparative analyses revealed insights into the phylogenetic relationships of Hepatica and its relatives through multiple comparisons and gene loss events.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Biochemical Research Methods
Mariella Bonomo, Raffaele Giancarlo, Daniele Greco, Simona E. Rombo
Summary: This study compares and analyzes nine topological measures based on the ranking results they induce on biological networks. The goal is to evaluate their ability to correctly position nodes/edges according to the functional knowledge encoded in the networks.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Microbiology
Alena Aliashkevich, Matthew Howell, Pamela J. B. Brown, Felipe Cava
Summary: This study investigated the chemical editing of bacterial cell wall by canavanine in Pseudomonas putida, uncovering its impact on other organisms in the same niche. The findings demonstrate that canavanine dramatically alters the PG structure of Rhizobiales bacteria, affecting cell division. Furthermore, experiments with Agrobacterium tumefaciens revealed that the detrimental effect of canavanine can be suppressed by a single amino acid substitution in a cell division-related protein.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Computer Science, Information Systems
A. Ram, Clair A. Kronk, Jacob R. Eleazer, Joseph L. Goulet, Cynthia A. Brandt, Karen H. Wang
Summary: Transgender individuals often face harassment and harm in healthcare settings, with gender-related terminology in electronic health records potentially exacerbating harm and failing to accommodate nonbinary patients.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2021)
Article
Biotechnology & Applied Microbiology
Hassan Zafar, Milton H. Saier
Summary: The study analyzed the transportomes of nine bifidobacterial species, finding similarities in pore-forming toxins and drug exporters among them that may play roles in pathogenesis. Bifidobacteria have larger transportomes, preferring primary active transport systems, and some species have limited interactions with host cells and other gut microbes.
MICROBIAL PHYSIOLOGY
(2022)
Article
Microbiology
Elizaveta Krol, Hamish C. L. Yau, Marcus Lechner, Simon Schaeper, Gert Bange, Waldemar Vollmer, Anke Becker
Article
Biochemistry & Molecular Biology
Delia Casas-Pastor, Raphael Rene Mueller, Sebastian Jaenicke, Karina Brinkrolf, Anke Becker, Mark Buttner, Carol Gross, Thorsten Mascher, Alexander Goesmann, Georg Fritz
Summary: Extracytoplasmic function sigma factors (ECFs) play a major role in bacterial signal transduction mechanisms, with our comprehensive phylogenetic analysis identifying numerous new ECF groups and expanding classification efforts. This detailed description of the phylogenetic distribution of the ECF family will serve as a powerful tool for guiding future research in the field.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Elizaveta Krol, Lisa Stuckenschneider, Joana M. Kastle Silva, Peter L. Graumann, Anke Becker
Summary: In Rhizobiales bacteria, such as Sinorhizobium meliloti, cell elongation specifically occurs at new cell poles generated by cell division. The FtsN-like protein RgsS and peptidoglycan amidase AmiC play crucial roles in reliable selection of the new cell pole as the cell elongation zone. Absence of these components can lead to inverted growth polarity and incomplete chromosome segregation.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Francisco J. Albicoro, Walter O. Draghi, Maria C. Martini, Maria E. Salas, G. A. Torres Tejerizo, Mauricio J. Lozano, Jose L. Lopez, Carolina Vacca, Juan H. Cafiero, Mariano Pistorio, Hanna Bednarz, Doreen Meier, Antonio Lagares, Karsten Niehaus, Anke Becker, M. F. Del Papa
Summary: The study identified adaptive mutations of RR proteins in Sinorhizobium meliloti under acidic conditions, indicating the significance of these proteins for optimal symbiosis development.
JOURNAL OF BIOTECHNOLOGY
(2021)
Article
Microbiology
Michelle A. Williams, Alena Aliashkevich, Elizaveta Krol, Erkin Kuru, Jacob M. Bouchier, Jonathan Rittichier, Yves V. Brun, Michael S. VanNieuwenhze, Anke Becker, Felipe Cava, Pamela J. B. Brown
Summary: The study investigated cell wall synthesis enzymes in Rhizobiales bacteria, revealing the essential role of a class A penicillin-binding protein in polar peptidoglycan synthesis. Additionally, an alternative mode of cell wall synthesis requiring LD-transpeptidase activity was identified. The findings suggest potential targets for biocontrol of pathogenic Rhizobiales by focusing on penicillin-binding proteins and LD-transpeptidases driving unipolar growth.
Article
Microbiology
Sofya Kuzmich, Patrick Blumenkamp, Doreen Meier, Dobromir Szadkowski, Alexander Goesmann, Anke Becker, Lotte Sgaard-Andersen
Summary: The second messenger c-di-GMP plays an important role in both stages of Myxococcus xanthus' nutrient-regulated biphasic life cycle, with the formation of predatory swarms in the presence of nutrients and spore-filled fruiting bodies in the absence of nutrients. However, different enzymes are involved in c-di-GMP synthesis and degradation during distinct life cycle stages.
Article
Multidisciplinary Sciences
Vera Bettenworth, Simon van Vliet, Bartosz Turkowyd, Annika Bamberger, Heiko Wendt, Matthew McIntosh, Wieland Steinchen, Ulrike Endesfelder, Anke Becker
Summary: In quorum sensing, bacteria use frequency-modulated pulsing mechanism to make collective decisions. Each cell's physiological state and behavioral needs are encoded in the pulse frequency of autoinducer synthase gene expression, and the integration of pulse frequencies with other cells determines the initiation of collective behavior.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Daniel Stukenberg, Josef Hoff, Anna Faber, Anke Becker
Summary: The bacterium Vibrio natriegens has gained attention for its potential in genetic research and biotechnology. This article presents a method called NT-CRISPR, which combines natural transformation with CRISPR-Cas9 counterselection to achieve efficient genome editing and cell killing. This method allows for scarless, markerless edits with single-base precision.
COMMUNICATIONS BIOLOGY
(2022)
Article
Engineering, Biomedical
Chisom Ezekannagha, Anke Becker, Dominik Heider, Georges Hattab
Summary: DNA is increasingly being used as a long-term archival data storage medium due to its high capacity, high storage density, and ability to store data for thousands of years. The performance of DNA under different processing and storage conditions significantly affects the capabilities of the data storage system. Design considerations for a DNA storage system include error reduction, robustness, and reliability.
MATERIALS TODAY BIO
(2022)
Article
Multidisciplinary Sciences
Marco Guedes Salgado, Irina Demina, Pooja Jha Maity, Anurupa Nagchowdhury, Andrea Caputo, Elizaveta Krol, Christoph Loderer, Gunther Muth, Anke Becker, Katharina Pawlowski
Summary: Datisca glomerata is an actinorhizal plant that forms root nodules in symbiosis with actinobacteria. In this study, a highly expressed gene family encoding nodule-specific defensin-like peptides was investigated. The results showed that the defensin domain of DgDef1 has cytotoxic effects and can induce the expression of oxidative stress-related genes. These findings suggest that nodule-specific defensin-like peptides were part of the original toolkit for root nodule formation and have been maintained in actinorhizal lineages.
Article
Biotechnology & Applied Microbiology
Mauricio J. Lozano, Ezequiel G. Mogro, M. Eugenia Salas, Sofia A. Erdozain, Nicolas E. Zuber, Anke Becker, Antonio Lagares
Summary: Through genome-wide screening of Ensifer meliloti mutants, it was found that persistence in peat inoculants involves a complex phenotype connected to diverse cellular activities, mainly related to satisfying bacterial nutrition requirements and coping with specific stresses. These results provide a base knowledge that could be used to understand the survival mechanisms used by rhizobia during the maturation of peat-based inoculants and to improve inoculant formulations.
JOURNAL OF BIOTECHNOLOGY
(2023)
Article
Immunology
Stefanie M. Herbel, Lambert Moyon, Marvin Christ, Eslam M. Elsayed, Brian E. Caffrey, Silke Malmsheimer, Iwan Grin, Kerstin Hoffmann, Kristin Surmann, Sascha Blankenburg, Anna Lena Jung, Christina E. Herkt, Marco Borso, Beyza Bozdag, Axel Imhof, Anke Becker, Samuel Wagner, Gert Bange, Uwe Voelker, Wilhelm Bertrams, Annalisa Marsico, Bernd Schmeck
Summary: Legionella pneumophila is a common pathogen that causes pneumonia and it acquires eukaryote-like protein motifs that contribute to its pathogenicity. The study identified a bacterial factor, Smh1, with histone deacetylase activity that moderates host gene expression and promotes bacterial replication.
Article
Microbiology
Laura Werel, Neda Farmani, Elizaveta Krol, Javier Serrania, Lars-Oliver Essen, Anke Becker
Summary: In bacteria, the receptor proteins of cAMP and cGMP are found among transcription factors of the Crp-Fnr superfamily. The prototypic Escherichia coli CAP can bind cAMP and cGMP, whereas Sinorhizobium meliloti Clr can activate transcription with both cyclic nucleotides. Crystal structures of Clr-cAMP and Clr-cGMP bound to the DNA binding site reveal similar active conformations induced by the cyclic nucleotides. Clr shows similar affinities for cAMP and cGMP in the presence of DNA, but different affinities in their absence.
Article
Multidisciplinary Sciences
Marius Welzel, Peter Michael Schwarz, Hannah F. Loechel, Tolganay Kabdullayeva, Sandra Clemens, Anke Becker, Bernd Freisleben, Dominik Heider
Summary: The extensive information capacity of DNA and decreasing costs for DNA synthesis and sequencing make it an attractive alternative to traditional data storage. DNA-Aeon is a concatenated coding scheme for DNA data storage that supports the generation of variable-sized encoded sequences with user-defined constraints.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Natalia I. Garcia-Tomsig, Fernando M. Garcia-Rodriguez, Sabina K. Guedes-Garcia, Vicenta Millan, Anke Becker, Marta Robledo, Jose I. Jimenez-Zurdo
Summary: The N status transduced by the NtrBC system is an important signaling cue in the root nodule endosymbiosis, and the sRNA NfeR1 influences the symbiotic performance of Sinorhizobium meliloti by fine-tuning NtrBC output.
