Article
Mathematics
Antonio Aviles, Gonzalo Martinez-Cervantes, Grzegorz Plebanek
Summary: This article introduces Rosenthal's theorem, which states that a compact space is ccc if and only if its every Eberlein continuous image is metrizable. Motivated by this result, the orthogonal C-perpendicular class of a class of compact spaces C is defined as the class of all compact spaces for which every continuous image in C is metrizable. The problems of relating classes where centeredness is scarce with classes where it is abundant and classes where independence is scarce with classes where it is abundant are studied. Special attention is given to zero-dimensional compact spaces, where Boolean algebras are used and the main difficulties in dealing with general settings are shown. Several relevant examples are constructed as the main results.
REVISTA DE LA REAL ACADEMIA DE CIENCIAS EXACTAS FISICAS Y NATURALES SERIE A-MATEMATICAS
(2022)
Article
Engineering, Biomedical
Meryem Altin Karagoz, O. Ufuk Nalbantoglu
Summary: A CNN approach based on k-mer representation was proposed for metagenomic fragment classification, utilizing Relative Abundance Index to represent DNA and deep learning algorithm for classification. The comparison with existing spectral methods showed competitive performance across various metagenomic datasets, indicating the effectiveness of the proposed method.
BIOMEDICAL SIGNAL PROCESSING AND CONTROL
(2021)
Article
Biotechnology & Applied Microbiology
Sebastien Tempel, Justin Bedo, Emmanuel Talla
Summary: This study provides new insights into the functional and evolutionary relationships between insertion sequences (ISs) and neighboring genes through a large-scale comparative genomic analysis. The results indicate that IS families are widely distributed in prokaryotes and are associated with genes involved in transcriptional regulation and transport activities. The occurrence and associations of different IS families vary across different taxonomic lineages. Additionally, the short distance between IS and neighboring genes, along with the presence of predicted regulatory motifs, suggests that ISs may have regulatory roles.
Article
Infectious Diseases
Daniely Martins da Silva, Celio Faria-Junior, Danielly Rocha Nery, Pamela Maria de Oliveira, Lilian de Oliveira Rodrigues Silva, Everton Giovanni Alves, Glaura Regina de Castro e Caldo Lima, Alex Leite Pereira
Summary: This study identified that the insertion mutations disrupting the mgrB gene in carbapenem-resistant Klebsiella pneumoniae mainly involved IS5 sequences, with the first observation of mgrB::ISSen4 (IS3) in CRKp.
JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE
(2021)
Article
Biochemistry & Molecular Biology
Mengyu Li, Hongzhao Wang, Zhenwu Yang, Longgui Zhang, Yushan Zhu
Summary: Thermally stable proteins are important in industrial and pharmaceutical applications, and their prediction is crucial for protein engineering. In this study, a deep learning model called DeepTM was introduced, which accurately predicts the melting temperature of thermophilic proteins using only protein sequences as input. DeepTM demonstrated good performance and outperformed other methods in predicting the thermal stability of proteins.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Eunjung Shin, Qianying Ye, Sung-Jae Lee
Summary: Bacterial genomes contain insertion sequences (ISs) that can influence the responsive capacity of organisms t environmental challenges. This review discusses how certain ISs are transposed to carotenoid biosynthesis genes and the genetic features and stress responses associated with bacterial IS transposition. The redox signaling mechanism is believed to play a crucial role in IS transposition.
Article
Biotechnology & Applied Microbiology
Xiaolong Li, Hong Li, Zhenhua Yang, Yuan Wu, Mengchuan Zhang
Summary: Our study provides objective feature sets in constructing evolution relationships at the genomic level.
Article
Genetics & Heredity
Kevin Heieck, Thomas Brueck
Summary: Insertion sequence elements (ISE) can cause production collapse in synthetically engineered Escherichia coli. By transposing ISE into the synthetic pathway, E. coli cells gain an advantage over cells expressing burdensome production genes. In this study, we identified the exact entry sites of IS families 3 and 5 within plasmids for l-cysteine production in evolved E. coli populations. We also observed an unusual occurrence of an 8-bp direct repeat of IS5, indicating a potential new target site.
Article
Genetics & Heredity
Florian Pichot, Virginie Marchand, Mark Helm, Yuri Motorin
Summary: Deep-sequencing approaches for RNA analysis have widespread applications in modern biology, particularly for mapping and quantifying RNA modifications. The major challenge in tRNA examination lies in duplicated and point-mutated genes encoding those RNA molecules, as well as the complications caused by multiple isoacceptors/isodecoders.
Article
Virology
Jian Yu, Shanshan Sun, Qianqian Tang, Chengzhuo Wang, Liangchen Yu, Lulu Ren, Jun Li, Zhenhua Zhang
Summary: COVID-19 is caused by the highly infectious SARS-CoV-2, with mutations affecting vaccine efficacy. Analysis of different clades of SARS-CoV-2 revealed low mutation rates and distinctive characterizing mutations, aiding in the design of targeted antiviral strategies based on geographic distribution.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Robotics
Kento Tariki, Takuya Kiyokawa, Tomoki Nagatani, Jun Takamatsu, Tsukasa Ogasawara
Summary: The researchers proposed an automated sequence planning method to reduce human intervention in teaching industrial robots assembly sequences, using only 3D CAD model. The method employs a genetic algorithm to generate assembly sequences for multiple parts and calculates an insertion matrix to satisfy preferred insertion conditions. Experimental results demonstrate the method's effectiveness in generating assembly sequences for products composed of 32 parts.
Review
Genetics & Heredity
Alessandro Varani, Susu He, Patricia Siguier, Karen Ross, Michael Chandler
Summary: The IS6 family of insertion sequences plays a crucial role in the rearrangement and spread of antibiotic resistance, with particular attention given to IS26 and IS257 for their clinical impact. While limited biochemical data is available on the transposition mechanism of these elements, genetic studies suggest that they may use unexpected mechanisms. This review provides an overview of the family, distribution and impact on host genomes, as well as an analysis of potential transposition pathways.
Article
Multidisciplinary Sciences
Ana Moya-Beltran, Martin Gajdosik, Camila Rojas-Villalobos, Simon Beard, Martin Mandl, Danitza Silva-Garcia, D. Barrie Johnson, Pablo Ramirez, Raquel Quatrini, Jiri Kucera
Summary: The study revealed the existence of two subspecies-level taxa within Acidithiobacillus ferrooxidans and identified their distinct genomic characteristics. The differences in genomic relatedness, gene content, and mobile genetic elements support this differentiation. The presence and conservation of integrated and episomal mobile genetic elements play a significant role in the short- and long-term adaptation of A. ferrooxidans strains to changing growth conditions.
SCIENTIFIC REPORTS
(2023)
Article
Biotechnology & Applied Microbiology
Michael C. U. Hammond-Kosack, Robert King, Kostya Kanyuka, Kim E. Hammond-Kosack
Summary: The study found that most gene promoters are highly conserved, with multiple haplotypes and some being identical to a reference variety. These data are valuable for gene function studies and wheat breeding.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Multidisciplinary Sciences
Javier Alegria Zufia, Catherine Legrand, Hanna Farnelid
Summary: This study monitored the abundance and community composition of picocyanobacteria in the Baltic Sea and found that their abundance was correlated with environmental parameters. Different functional groups and clades showed varying responses, underscoring the need for further studies to understand their role in the ecosystem.
SCIENTIFIC REPORTS
(2022)
Article
Environmental Sciences
Emily B. Graham, Alex R. Crump, David W. Kennedy, Evan Arntzen, Sarah Fansler, Samuel O. Purvine, Carrie D. Nicora, William Nelson, Malak M. Tfaily, James C. Stege
SCIENCE OF THE TOTAL ENVIRONMENT
(2018)
Correction
Multidisciplinary Sciences
James C. Stegen, Tim Johnson, James K. Fredrickson, Michael J. Wilkins, Allan E. Konopka, William C. Nelson, Evan V. Arntzen, William B. Chrisler, Rosalie K. Chu, Sarah J. Fansler, Emily B. Graham, David W. Kennedy, Charles T. Resch, Malak Tfaily, John Zachara
NATURE COMMUNICATIONS
(2018)
Correction
Microbiology
David G. Christensen, Jesse G. Meyer, Jackson T. Baumgartner, Alexandria K. D'Souza, William C. Nelson, Samuel H. Payne, Misty L. Kuhn, Birgit Schilling, Alan J. Wolfe
Article
Microbiology
Hyun-Seob Song, Joon-Yong Lee, Shin Haruta, William C. Nelson, Dong-Yup Lee, Stephen R. Lindemann, Jim K. Fredrickson, Hans C. Bernstein
FRONTIERS IN MICROBIOLOGY
(2019)
Article
Biotechnology & Applied Microbiology
Pavlo Bohutskyi, Ryan S. McClure, Eric A. Hill, William C. Nelson, William B. Chrisler, Jamie R. Nunez, Ryan S. Renslow, Moiz A. Charania, Stephen R. Lindemann, Alexander S. Beliaev
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2019)
Article
Multidisciplinary Sciences
William C. Nelson, Emily B. Graham, Alex R. Crump, Sarah J. Fansler, Evan Arntzen, David W. Kennedy, James C. Stegen
Article
Microbiology
Dan Naylor, Sarah Fansler, Colin Brislawn, William C. Nelson, Kirsten S. Hofmockel, Janet K. Jansson, Ryan McClure
Article
Microbiology
Hyun-Seob Song, James C. Stegen, Emily B. Graham, Joon-Yong Lee, Vanessa A. Garayburu-Caruso, William C. Nelson, Xingyuan Chen, J. David Moulton, Timothy D. Scheibe
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Nutrition & Dietetics
David L. Suskind, Dale Lee, Young-Mo Kim, Ghassan Wahbeh, Namita Singh, Kimberly Braly, Mason Nuding, Carrie D. Nicora, Samuel O. Purvine, Mary S. Lipton, Janet K. Jansson, William C. Nelson
Article
Microbiology
Ruonan Wu, Michelle R. Davison, William C. Nelson, Emily B. Graham, Sarah J. Fansler, Yuliya Farris, Sheryl L. Bell, Iobani Godinez, Jason E. Mcdermott, Kirsten S. Hofmockel, Janet K. Jansson
Summary: Soil viruses were compared in grassland soils with different historical precipitation levels, revealing higher viral diversity and abundance in areas with lower precipitation. The drier region also exhibited more lysogenic markers and putative auxiliary metabolic genes, indicating a potential impact of historical precipitation on soil viral communities and their functional potential.
Article
Microbiology
Daniel Zamith-Miranda, Heino M. Heyman, Meagan C. Burnet, Sneha P. Couvillion, Xueyun Zheng, Nathalie Munoz, William C. Nelson, Jennifer E. Kyle, Erika M. Zink, Karl K. Weitz, Kent J. Bloodsworth, Geremy Clair, Jeremy D. Zucker, Jeremy R. Teuton, Samuel H. Payne, Young-Mo Kim, Morayma Reyes Gil, Erin S. Baker, Erin L. Bredeweg, Joshua D. Nosanchuk, Ernesto S. Nakayasu
Summary: This study built a comprehensive map of the Histoplasma capsulatum lipid metabolic pathway by incorporating proteomic and lipidomic analyses. The map identified fatty acid desaturation and sphingolipid biosynthesis pathways as targets for drug development. Experimental results showed inhibitors of these pathways effectively inhibited H. capsulatum growth.
Article
Microbiology
Ryan McClure, Yuliya Farris, Robert Danczak, William Nelson, Hyun-Seob Song, Aimee Kessell, Joon-Yong Lee, Sneha Couvillion, Christopher Henry, Janet K. Jansson, Kirsten S. Hofmockel
Summary: This study investigates microbial interactions during chitin decomposition in a model soil consortium. The findings reveal emergent properties of species and the community, highlighting the importance of community context in species phenotypes. These conclusions provide critical insights into soil microbial interaction networks and central soil microbiome functions.
Article
Microbiology
Arunima Bhattacharjee, Lindsey N. Anderson, Trinidad Alfaro, Andrea Porras-Alfaro, Ari Jumpponen, Kirsten S. Hofmockel, Janet K. Jansson, Christopher R. Anderton, William C. Nelson
Summary: The novel fungal strain Fusarium sp. strain DS 682 was isolated from the rhizosphere of Bouteloua gracilis at the Konza Prairie Biological Station in Kansas. This strain is commonly found in North American grasslands and shows resilience to environmental fluctuations, with an estimated draft genome completeness of 97.2%.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Multidisciplinary Sciences
William C. Nelson, Benjamin J. Tully, Jennifer M. Mobberley
Article
Microbiology
William C. Nelson, Lindsey N. Anderson, Ruonan Wu, Jason E. McDermott, Sheryl L. Bell, Ari Jumpponen, Sarah J. Fansler, Kimberly J. Tyrrell, Yuliya Farris, Kirsten S. Hofmockel, Janet K. Jansson
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2020)