Article
Biochemistry & Molecular Biology
Charles Coluzzi, Martin Guillemet, Fanny Mazzamurro, Marie Touchon, Maxime Godfroid, Guillaume Achaz, Philippe Glaser, Eduardo P. C. Rocha
Summary: Horizontal gene transfer has a significant impact on the evolution of core genes, with mutations providing resistance to antibiotics and shaping the emergence of adaptive mutations. The rapid accumulation of these mutations increases the acquisition rate of other antibiotic resistances, leading to multidrug resistance.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Huiting Zhang, Eric K. Wafula, Jon Eilers, Alex E. Harkess, Paula E. Ralph, Prakash Raj Timilsena, Claude W. dePamphilis, Jessica M. Waite, Loren A. Honaas
Summary: The lack of direct experimental evidence connecting genes to important agronomic traits in non-model plants remains a challenge. This study presents a workflow using bioinformatic tools to curate deeply conserved gene families of interest across plant genomes. The researchers applied this workflow to study tree architecture genes in European pear and other rosaceous species, identifying issues in the genome assembly and improving the gene models. Additionally, the global gene family classification provides a valuable resource for the Rosaceae research community.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Lan Jiang, Tingting Fan, Lihu Wang, Lin Zhang, Jun Xu
Summary: This study identified and analyzed the flowering-related genes in Euphorbiaceae species, providing insights into the mechanisms of flowering in these plants. The findings have implications for marker-assisted breeding and improving variety quality.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Beibei Liu, Aiko Iwata-Otsubo, Diya Yang, Robert L. Baker, Chun Liang, Scott A. Jackson, Shengyi Liu, Jianxin Ma, Meixia Zhao
Summary: In this study, it was found that the TNP2-like transposase genes of Bot1 transposable elements in Brassica oleracea retain three AT-rich introns, while these introns were lost in the majority of the Bot1 elements in Brassica rapa. Additionally, a recent burst of transposition of Bot1 was observed in B. oleracea, but not in B. rapa. Analysis of small RNAs showed different populations in B. oleracea compared to B. rapa, indicating the differential activity and silencing of the Bot1 family in the two closely related Brassica species.
Article
Computer Science, Theory & Methods
Aymen Al-Saadi, Ioannis Paraskevakos, Bento Collares Goncalves, Heather J. Lynch, Shantenu Jha, Matteo Turilli
Summary: This paper investigates the use of High Resolution satellite and aerial imagery for monitoring ecological systems and the application of Convolutional Neural Networks for image analysis. Three task-parallel, data-driven workflow designs are studied to support imagery analysis pipelines, with experimental results determining which design is best suited for scientific pipelines.
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE
(2021)
Article
Infectious Diseases
Vincenzo Pennone, Miguel Prieto, Avelino Alvarez-Ordonez, Jose F. Cobo-Diaz
Summary: This study analyzed publicly available genomes of Staphylococcus aureus and identified different antimicrobial resistance genes (ARGs) in chromosomes and plasmids. Differences in the distribution of ARGs and clonal complexes (CC) were observed among continents. Temporal changes over the past 20 years showed a decrease in MRSA and macrolide resistance occurrence in plasmids, while the occurrence of ARGs associated with aminoglycoside resistance increased.
Article
Microbiology
Albert Rene, Elisabet Alacid, Rachele Gallisai, Aurelie Chambouvet, Alan D. Fernandez-Valero, Esther Garces
Summary: Perkinsea is a phylogenetic group of protists that includes parasites of distantly related hosts. Two new parasitoid species infecting dinoflagellates were reported in this study, with one clustering within Parviluciferaceae and the other in a distinct branch. Laboratory cross-infection experiments showed that the parasitoid host range is restricted to dinoflagellates, even across different genera.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Medicine, General & Internal
Yanfeng Wang, Qian Ma, Zhenghao Huo
Summary: Bioinformatic analysis was used to identify a large number of SLE-related DEGs in the GEO database, with potential key genes identified as potential biomarkers for the diagnosis and treatment of SLE.
Article
Virology
Hugo de Paula Oliveira, Ethiane R. dos Santos, Robert L. Harrison, Bergmann Morais Ribeiro, Daniel M. P. Ardisson-Araujo
Summary: In this study, a large-scale in silico search was conducted to identify putative tRNA genes in baculovirus genomes. The analysis revealed diverse tRNA genes with variations in structure, location, and anti-codon identity. Some genes showed a bias for the codons specified by the tRNAs present in their genomes. Additionally, evidence of transcription and modification of viral tRNA genes was found through analysis of small RNA deep sequencing data. Further research is required to understand the expression and functionality of these viral tRNAs.
Article
Cell Biology
Junjie Jiang, Jiao Yuan, Zhongyi Hu, Youyou Zhang, Tianli Zhang, Mu Xu, Meixiao Long, Yi Fan, Janos L. Tanyi, Kathleen T. Montone, Omid Tavana, Robert H. Vonderheide, Ho Man Chan, Xiaowen Hu, Lin Zhang
Summary: By integrating multiple druggable genome resources, researchers identified a group of potential druggable genes and analyzed their expression, genomic alterations, cancer dependencies, and therapeutic potentials. The study revealed a significant number of reliably expressed potential druggable genes in major adult cancers, including some understudied genes, providing new opportunities for cancer treatment.
Review
Microbiology
Juan Sebastian Andrade-Martinez, Laura Carolina Camelo Valera, Luis Alberto Chica Cardenas, Laura Forero-Junco, Gamaliel Lopez-Leal, J. Leonardo Moreno-Gallego, Guillermo Rangel-Pineros, Alejandro Reyes
Summary: Over a century of bacteriophage research has uncovered fundamental aspects of their biology, ecology, and evolution. The introduction of community-level studies through metagenomics has revealed unprecedented insights on the impact that phages have on ecological and physiological processes. The availability of computational tools has greatly contributed to our knowledge of phage diversity and ecology, but the ongoing surge in software programs makes it challenging to keep up with them.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2022)
Review
Clinical Neurology
Ibitayo Abigail Ademuwagun, Solomon Oladapo Rotimi, Steffen Syrbe, Yvonne Ukamaka Ajamma, Ezekiel Adebiyi
Summary: Genetic epilepsy can be caused by mutations in a single gene or an interplay of different genes, particularly in ion channel genes. Voltage gated sodium channel genes play a crucial role in action potentials in neurons, with inherited and de novo mutations linked to various forms of epilepsy. Understanding these channel mutations may guide effective treatment decisions in patient management.
FRONTIERS IN NEUROLOGY
(2021)
Article
Biology
P. Ferreira, G. T. Kwan, S. Haldorson, J. L. Rummer, F. Tashiro, L. F. C. Castro, M. Tresguerres, J. M. Wilson
Summary: Puffer and porcupine fishes have the ability to inflate themselves by swallowing seawater to defend against predation, but this mechanism leads to the loss of stomach function. Through studying the stomach phenotype and genotype of four different fish species, it was found that this inflation mechanism is only present in Tetraodontiformes and is not a selective pressure for stomach loss in other gastric inflating fishes.
Article
Biotechnology & Applied Microbiology
Qiao Sun, Lin Bai, Shaopin Zhu, Lu Cheng, Yang Xu, Yu-Dong Cai, Hui Chen, Jian Zhang
Summary: This study utilized gene ontology and KEGG pathway analyses to identify lymphoma-associated genes and determine their biological processes. Features were selected and ranked using various methods, and a decision tree model was used to extract classification rules. The predicted features were consistent with recent publications and provide a new perspective for understanding the molecular mechanisms of lymphoma.
BIOMED RESEARCH INTERNATIONAL
(2022)
Article
Microbiology
Fatemah Almalki, Madhusudan Choudhary, Rajeev K. K. Azad
Summary: Since the discovery of second chromosomes in Rhodobacter sphaeroides 2.4.1 in 1989, multipartite genomes have been observed in over three hundred bacterial species under nine different phyla. However, the mechanisms underlying the emergence and evolution of multipartite genomes in bacteria, as well as the genetic factors that differentiate them from single-chromosome genomes, remain poorly understood. In this study, comparative evolutionary and functional genomics analyses were conducted to identify molecular factors that distinguish multipartite from unipartite bacteria. The findings reveal the potential roles of secondary chromosomes in assisting bacteria with multipartite genomes to adapt to specialized environments or growth conditions.
ARCHIVES OF MICROBIOLOGY
(2023)
Article
Neurosciences
Tigran P. Norekian, Leonid L. Moroz
JOURNAL OF COMPARATIVE NEUROLOGY
(2019)
Article
Neurosciences
Tigran P. Norekian, Leonid L. Moroz
JOURNAL OF COMPARATIVE NEUROLOGY
(2020)
Article
Neurosciences
Tigran P. Norekian, Leonid L. Moroz
JOURNAL OF COMPARATIVE NEUROLOGY
(2020)
Article
Biochemistry & Molecular Biology
Leonid L. Moroz, Dosung Sohn, Daria Y. Romanova, Andrea B. Kohn
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2020)
Article
Anatomy & Morphology
Gabrielle C. Winters, Gianluca Polese, Anna Di Cosmo, Leonid L. Moroz
JOURNAL OF MORPHOLOGY
(2020)
Article
Multidisciplinary Sciences
Leonid L. Moroz, Daria Y. Romanova, Mikhail A. Nikitin, Dosung Sohn, Andrea B. Kohn, Emilie Neveu, Frederique Varoqueaux, Dirk Fasshauer
SCIENTIFIC REPORTS
(2020)
Article
Biochemistry & Molecular Biology
Daria Y. Romanova, Ivan Smirnov, Mikhail A. Nikitin, Andrea B. Kohn, Alisa Borman, Alexey Y. Malyshev, Pavel M. Balaban, Leonid L. Moroz
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2020)
Review
Biology
Leonid L. Moroz, Daria Y. Romanova, Andrea B. Kohn
Summary: Transmitter signalling is the universal chemical language of the nervous system, with origins possibly in secretory cells capable of volume chemical transmission and behavior integration. Different neurotransmitters may have been recruited relatively early or late in animal evolution.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Janos Gyori, Andrea B. Kohn, Daria Y. Romanova, Leonid L. Moroz
Summary: ATP and its ionotropic P2X receptors are components of the most ancient signaling system, with little known about their distribution and function in invertebrates. This study focuses on the cloning, expression, and pharmacological characterization of P2X receptors in the sea slug Aplysia californica, revealing unique expression patterns and functions, especially in development and homeostasis. The findings provide novel insights into the evolution of neurotransmitters.
SCIENTIFIC REPORTS
(2021)
Article
Cell Biology
Daria Y. Romanova, Frederique Varoqueaux, Jean Daraspe, Mikhail A. Nikitin, Michael Eitel, Dirk Fasshauer, Leonid L. Moroz
Summary: Placozoans are among the simplest free-living animals, with bodies consisting of three cell layers and roughly seven major cell types. They lack muscle cells and neurons but are able to move using ciliated surfaces and coordinate food intake. Recent research has revealed a higher level of cell-type diversity in placozoans than previously anticipated.
CELL AND TISSUE RESEARCH
(2021)
Article
Anatomy & Morphology
Tigran P. Norekian, Leonid L. Moroz
Summary: Ctenophores are descendants of an early branching basal metazoan lineage that may have evolved neurons and muscles independently. The neuromuscular system development in Mnemiopsis is similar to Pleurobrachia, but faster. Adult Mnemiopsis exhibits distinct neuronal populations in the feeding lobes and auricles, unique to the Lobata clade.
JOURNAL OF MORPHOLOGY
(2021)
Review
Neurosciences
Leonid L. Moroz, Mikhail A. Nikitin, Pavlin G. Policar, Andrea B. Kohn, Daria Y. Romanova
Summary: Glutamate plays a key role as the primary excitatory transmitter in the mammalian brain, with its origin possibly traced back to primordial nitrogen and carbon metabolic pathways. The versatile chemistry of L-Glu places it at the intersection of cellular biochemistry as one of the most abundant metabolites.
Article
Multidisciplinary Sciences
Jennifer M. Polinski, Aleksey V. Zimin, K. Fraser Clark, Andrea B. Kohn, Norah Sadowski, Winston Timp, Andrey Ptitsyn, Prarthana Khanna, Daria Y. Romanova, Peter Williams, Spencer J. Greenwood, Leonid L. Moroz, David R. Walt, Andrea G. Bodnar
Summary: The American lobster plays a crucial role in marine ecosystems and supports commercial fishing. It serves as a valuable model for studying neural networks and olfaction, with complex chemosensory and defense mechanisms contributing to its longevity and ecological success in the marine environment.
Article
Anatomy & Morphology
Naama Stern-Mentch, Gabriela Winter, Michael Belenky, Leonid Moroz, Binyamin Hochner
Summary: The vertical lobe (VL) in the octopus brain plays a crucial role in learning and memory. Recent studies have discovered more heterogeneity in the VL neurons than previously thought, including glutamatergic and cholinergic neurons, as well as inhibitory and neuromodulatory elements. These findings contribute to a deeper understanding of the efficient learning and memory network.
JOURNAL OF MORPHOLOGY
(2022)
Article
Biology
Marie Drabkova, Kevin M. Kocot, Kenneth M. Halanych, Todd H. Oakley, Leonid L. Moroz, Johanna T. Cannon, Armand Kuris, Ana Elisa Garcia-Vedrenne, M. Sabrina Pankey, Emily A. Ellis, Rebecca Varney, Jan Stefka, Jan Zrzavy
Summary: Dicyemids and orthonectids, traditionally classified as Mesozoa, had uncertain positions within Metazoa. This study used multiple phylogenomic approaches and obtained new transcriptomes and genomes to investigate their placement. The results suggest that Mesozoa is monophyletic and closely related to Platyhelminthes or Gnathifera, but caution is needed due to potential long-branch attraction. The classic hypothesis on monophyletic Mesozoa may need further testing.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)