Article
Biochemistry & Molecular Biology
Mitchell J. Syberg-Olsen, Arkadiy Garber, Patrick J. Keeling, John P. McCutcheon, Filip Husnik
Summary: Pseudofinder is an open-source software for detecting and analyzing pseudogenes in bacterial and archaeal genomes. The software's multi-pronged, reference-based approach allows it to detect a wide variety of pseudogenes, including highly degraded ones missed by gene-calling pipelines, as well as newly formed pseudogenes with few inactivating mutations. Additionally, Pseudofinder can identify genes that lack inactivating substitutions but experience relaxed selection. Implementation of Pseudofinder in annotation pipelines enables more precise estimation of the functional potential of sequenced microbes and generates new hypotheses about the evolutionary dynamics of bacterial and archaeal genomes.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemical Research Methods
Bruno Merlin, Jorianne Thyeska Castro Alves, Pablo Henrique Caracciolo Gomes de Sa, Monica Silva de Oliveira, Larissa Maranhao Dias, Gislenne da Silva Moia, Victoria Cardoso dos Santos, Adonney Allan de Oliveira Veras
Summary: Manual curation of genome annotation is time-consuming and requires specialized labor, but is essential for adding complementary information to gene products. The CODON software streamlines this process and provides access to accurate database information and additional gene acronyms, metabolic pathways, and Gene Ontology terms.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Kaihao Tang, Weiquan Wang, Yamin Sun, Yiqing Zhou, Pengxia Wang, Yunxue Guo, Xiaoxue Wang
Summary: Prophage Tracer is a tool designed to identify active prophages in prokaryotic genomes by taking advantage of the lysis-lysogeny switch of temperate phages. It can recognize discriminative reads containing att sites representing prophage excision signals using split-read alignment criteria. The tool showed precision in predicting known and novel prophages, such as identifying two novel prophages with highly divergent major capsid proteins in coral-associated bacteria.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Connor D. Harris, Ellis L. Torrance, Kasie Raymann, Louis-Marie Bobay
Summary: The core genome represents the set of genes shared by all, or nearly all, strains of a given population or species of prokaryotes. CoreCruncher is a robust and fast program that can construct core genomes across hundreds or thousands of genomes. Compared to other tools, CoreCruncher is more conservative and less sensitive to the presence of paralogs and xenologs.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Supriya Khedkar, Georgy Smyshlyaev, Ivica Letunic, Oleksandr M. Maistrenko, Luis Pedro Coelho, Askarbek Orakov, Sofia K. Forslund, Falk Hildebrand, Mechthild Luetge, Thomas S. B. Schmidt, Orsolya Barabas, Peer Bork
Summary: Prokaryotic Mobile Genetic Elements (MGEs) play important roles in evolution and the spread of antibiotic resistance. However, current understanding of their global dispersal is limited. In this study, a computational framework was developed to capture different MGE types and their cargos, allowing for a better understanding of MGE dispersal. The findings were integrated into a resource, providing a valuable tool for future research on the mobile part of genomes and its horizontal dispersal.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Chemistry, Medicinal
Sumera Zaib, Mushtaq A. Saleem, Imtiaz Khan
Summary: CRISPR-Cas9 is a widely used gene editing technology in medical research, which offers a simple, fast, flexible, and reliable method for treating various diseases by editing the genome.
MINI-REVIEWS IN MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Anthony Fullam, Ivica Letunic, Thomas S. B. Schmidt, Quinten R. Ducarmon, Nicolai Karcher, Supriya Khedkar, Michael Kuhn, Martin Larralde, Oleksandr M. Maistrenko, Lukas Malfertheiner, Alessio Milanese, Joao Frederico Matias Rodrigues, Claudia Sanchis-Lopez, Christian Schudoma, Damian Szklarczyk, Shinichi Sunagawa, Georg Zeller, Jaime Huerta-Cepas, Christian von Mering, Peer Bork, Daniel R. Mende
Summary: The interpretation of 'omics data relies on well-annotated genomes. As the number of available microbial genomes increases, quality control and consistent annotation become crucial. proGenomes3 is a database containing 907,388 high-quality genomes with consistent annotation, including functional and taxonomic information.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Askarbek Orakov, Anthony Fullam, Luis Pedro Coelho, Supriya Khedkar, Damian Szklarczyk, Daniel R. Mende, Thomas S. B. Schmidt, Peer Bork
Summary: GUNC is a tool that accurately detects and quantifies genome chimerism based on lineage homogeneity of individual contigs, providing a fast and robust way to improve prokaryotic genome quality. It targets previously underdetected types of contamination and can substantially enhance genome quality.
Article
Microbiology
Pranvera Hiseni, Knut Rudi, Robert C. Wilson, Finn Terje Hegge, Lars Snipen
Summary: The study aimed to create a collection of the most prevalent healthy human gut prokaryotic genomes, including both MAGs and RefSeq genomes, to be used as a reference database. By screening over 5,700 healthy human gut metagenomes, a pool of over 381,000 genomes was obtained and clustered to form the HumGut collection, comprising 30,691 cluster representatives, demonstrating superior performance in metagenomic reads classification.
Article
Biochemistry & Molecular Biology
Satoshi Hiraoka, Tomomi Sumida, Miho Hirai, Atsushi Toyoda, Shinsuke Kawagucci, Taichi Yokokawa, Takuro Nunoura
Summary: In this study, culture-independent "metaepigenomic" analysis using single-molecule real-time sequencing was conducted on marine microbial communities, revealing diverse unexplored DNA modifications and novel alternative specificities in MTases. These findings are significant for understanding the co-evolutionary history of methylation systems and genomes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Sara Saheb Kashaf, Alexandre Almeida, Julia A. Segre, Robert D. Finn
Summary: This protocol outlines a seven-stage process for recovering genomes from shotgun metagenomic sequence data, resulting in MAGs that can be used for taxonomic and functional analysis. The protocol takes approximately 1 week to run and requires prior experience with high-performance computing, shell script programming and Python.
Article
Multidisciplinary Sciences
Reem Aldaihani, Lenwood S. Heath
Summary: Prokaryotic genomes evolve through horizontal gene transfer, mutations, and rearrangements. Genomic islands (GIs) play an important role in the horizontal gene transfer process. Previous research in computational biology has focused on developing tools to detect GIs in prokaryotic genomes, but little is known about GI patterns and biological connections across species. In this study, we connected GIs across prokaryotic and phage genomes using patterns of protein families, which led to the discovery of broad HGT connections across the bacterial kingdom and its associated phages.
SCIENTIFIC REPORTS
(2023)
Review
Biotechnology & Applied Microbiology
Jun Ren, Hyang-Mi Lee, JunHao Shen, Dokyun Na
Summary: The prokaryotic restriction-modification (RM) system protects the host by cleaving foreign DNA, making it difficult to introduce engineered plasmid DNAs into newly isolated microorganisms. Methyltransferases can be utilized to methylate engineered plasmid DNAs before transformation, enhancing stability within cells. Study on methyltransferases in newly isolated bacteria is essential for genetic engineering.
BIOTECHNOLOGY LETTERS
(2022)
Article
Ecology
Dan Huang, Mengting Maggie Yuan, Juhong Chen, Xiaoxuan Zheng, Dongsheng Wong, Pedro J. J. Alvarez, Pingfeng Yu
Summary: This study investigates the prokaryotic antiviral systems in the drinking water microbiome and their association with symbiotic phages. Chlorine disinfectant is found to be the main driver influencing the differences in the prokaryotic antiviral systems and prokaryote-phage interactions. Under disinfectant stress, the prokaryotic antiviral systems exhibit higher abundance, broader antiviral spectrum, and lower metabolic burden. Symbiotic phages in the disinfected microbiome carry more auxiliary metabolic genes (AMGs) related to prokaryotic adaptability and antiviral systems, enhancing prokaryote survival in drinking water distribution systems.
ISME COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Zongyi Yi, Xiaoxue Zhang, Wei Tang, Ying Yu, Xiaoxu Wei, Xue Zhang, Wensheng Wei
Summary: In this study, researchers propose mitochondrial DNA base editors (mitoBEs), which combine a transcription activator-like effector (TALE)-fused nickase and a deaminase for precise base editing in mitochondrial DNA. By combining mitochondria-localized, programmable TALE binding proteins with the nickase MutH or Nt.BspD6I(C) and either the single-stranded DNA-specific adenine deaminase TadA8e or the cytosine deaminase ABOBEC1 and UGI, they achieve A-to-G or C-to-T base editing with high efficiency and specificity. Furthermore, they demonstrate the potential of mitoBEs in correcting pathogenic mitochondrial DNA mutations in patient-derived cells by delivering mitoBEs encoded in circular RNAs.
NATURE BIOTECHNOLOGY
(2023)
Article
Nanoscience & Nanotechnology
Timofey E. Karpov, Oleksii O. Peltek, Albert R. Muslimov, Yana V. Tarakanchikova, Tatiana M. Grunina, Maria S. Poponova, Anna S. Karyagina, Roman V. Chernozem, Igor O. Pariy, Yulia R. Mukhortova, Mikhail V. Zhukov, Maria A. Surmeneva, Mikhail V. Zyuzin, Alexander S. Timin, Roman A. Surmenev
ACS APPLIED MATERIALS & INTERFACES
(2020)
Article
Materials Science, Biomaterials
Fedor Senatov, Gulbanu Amanbek, Polina Orlova, Mikhail Bartov, Tatyana Grunina, Evgeniy Kolesnikov, Aleksey Maksimkin, Sergey Kaloshkin, Maria Poponova, Kirill Nikitin, Mikhail Krivozubov, Natalia Strukova, Vasily Manskikh, Natalya Anisimova, Mikhail Kiselevskiy, Ronja Scholz, Marina Knyazeva, Frank Walther, Vladimir Lunin, Alexander Gromov, Anna Karyagina
MATERIALS SCIENCE & ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS
(2020)
Article
Materials Science, Characterization & Testing
Alexander Chubrik, Fedor Senatov, Evgeniy Kolesnikov, Polina Orlova, Maria Poponova, Tatyana Grunina, Mikhail Bartov, Kirill Nikitin, Mikhail Krivozubov, Maria Generalova, Vasily Manskikh, Vladimir Lunin, Alexander Gromov, Anna Karyagina
Correction
Biotechnology & Applied Microbiology
Sofya A. Medvedeva, Alexander Y. Panchin, Andrei V. Alexeevski, Sergey A. Spirin, Yuri V. Panchin
BIOMED RESEARCH INTERNATIONAL
(2020)
Review
Microbiology
Alexander Grishin, Anna S. Karyagina, Daria V. Vasina, Irina V. Vasina, Vladimir A. Gushchin, Vladimir G. Lunin
CRITICAL REVIEWS IN MICROBIOLOGY
(2020)
Article
Polymer Science
Anna Zimina, Fedor Senatov, Rajan Choudhary, Evgeniy Kolesnikov, Natalya Anisimova, Mikhail Kiselevskiy, Polina Orlova, Natalia Strukova, Mariya Generalova, Vasily Manskikh, Alexander Gromov, Anna Karyagina
Article
Infectious Diseases
Alexander Grishin, Svetlana Konstantinova, Irina V. Vasina, Nikita Shestak, Anna S. Karyagina, Vladimir G. Lunin
Article
Engineering, Biomedical
F. Senatov, A. Maksimkin, A. Chubrik, E. Kolesnikov, P. Orlova, M. Krivozubov, K. Nikitin, A. Gromov, A. Karyagina
Summary: In this study, a push-out mechanical test was used to evaluate the effectiveness of implant-skull fusion in a mouse model with critical-size cranial defects. Results showed that loading BMP-2 led to a significant increase in bone tissue and BV/TV values at the implantation site, with high correlation to maximum load and elastic modulus values. The adapted push-out test can be used to assess the quality of osseointegration of implanted materials.
JOURNAL OF THE MECHANICAL BEHAVIOR OF BIOMEDICAL MATERIALS
(2021)
Article
Biochemistry & Molecular Biology
Anna S. Karyagina, Alexander V. Gromov, Tatyana M. Grunina, Alexander M. Lyaschuk, Alexander V. Grishin, Natalia V. Strukova, Maria S. Generalova, Zoya M. Galushkina, Lyubov' A. Soboleva, Olga Yu. Dobrinina, Tatyana N. Bolshakova, Marina E. Subbotina, Ekaterina A. Romanovskaya-Romanko, Igor V. Krasilnikov, Nikita B. Polyakov, Andrey I. Solovyev, Daniil A. Grumov, Vladimir G. Zhukhovitsky, Ekaterina I. Ryabova, Vladimir V. Prokofiev, Vladimir G. Lunin
Summary: A new platform for creating anti-coronavirus epitope vaccines has been developed, where specific loop-like epitopes were selected and hybrid proteins were constructed using protein scaffolds. These proteins demonstrated high immunogenicity and showed interaction with inactivated SARS-CoV-2 virus and Spike protein receptor-binding domain at high titers after immunization in mice.
BIOCHEMISTRY-MOSCOW
(2021)
Article
Materials Science, Biomaterials
Fedor Senatov, Anna Zimina, Alexander Chubrik, Evgeniy Kolesnikov, Elizaveta Permyakova, Andrei Voronin, Maria Poponova, Polina Orlova, Tatyana Grunina, Kirill Nikitin, Mikhail Krivozubov, Natalia Strukova, Maria Generalova, Anna Ryazanova, Vasily Manskikh, Vladimir Lunin, Alexander Gromov, Anna Karyagina
Summary: PLA/PCL/HA and PHB/HA osteoplastic materials and highly porous scaffolds were obtained using solvent casting with thermopressing and salt leaching. These biomimetic scaffolds, with a structure similar to trabecular bones and increased hydrophilicity, have potential applications in regenerative medicine for bone defect reconstruction. Additionally, the materials exhibit high biocompatibility and can be used in conjunction with recombinant proteins BMP-2 and EPO.
BIOMATERIALS ADVANCES
(2022)
Article
Biochemistry & Molecular Biology
Anna S. Karyagina, Alexander Gromov, Tatyana M. Grunina, Alexander M. Lyaschuk, Maria S. Poponova, Denis A. Kleymenov, Natalia Strukova, Maria S. Generalova, Anna Ryazanova, Zoya M. Galushkina, Olga Yu Dobrynina, Tatyana N. Bolshakova, Maria Sergeeva, Ekaterina A. Romanovskaya-Romanko, Igor Krasilnikov, Marina E. Subbotina, Vladimir G. Lunin
Summary: In this study, hybrid recombinant proteins containing short conformational epitopes of SARS-CoV-2 Spike protein were synthesized and used as potential components of epitope vaccines. The immunogenicity of the proteins and their ability to interact with the virus were examined. The results showed that the recombinant proteins had high immunogenicity, with the protein containing epitope 414-425 showing the highest binding assay titer. Additionally, certain proteins were found to activate cell-mediated immunity and exhibit virus-neutralizing activity.
BIOCHEMISTRY-MOSCOW
(2022)
Article
Biotechnology & Applied Microbiology
Svetlana Konstantinova, Alexander Grishin, Alexander Lyashchuk, Irina Vasina, Anna Karyagina, Vladimir Lunin
Summary: Peptidoglycan-degrading enzymes are intensively studied as potential antibacterials, and their modular organization has been used to generate new enzymes through domain exchange. However, the contribution of different domains to bacteriolytic activity is still unclear. This study investigates the influence of ionic strength and pH on the catalytic efficiency and cell binding of lysostaphin, and finds that the combination of domains within lysostaphin leads to increased bacteriolytic activity with increasing NaCl concentration, despite inhibition of catalysis and cell binding by NaCl. This effect is likely mediated by changes in the conformation of bacterial cell wall peptidoglycan.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Biology
Vera V. Panova, Nina G. Dolinnaya, Kirill A. Novoselov, Viktoriia Yu. Savitskaya, Ivan S. Chernykh, Elena A. Kubareva, Andrei V. Alexeevski, Maria I. Zvereva
Summary: This study identified G4 motifs in the TERT promoter regions of 141 mammalian species using bioinformatics approaches, and found that these G4 structures are evolutionarily conserved across mammals, potentially affecting DNA repair pathways and biological evolution.
Review
Biochemistry & Molecular Biology
A. V. Gromov, M. S. Poponova, A. S. Karyagina
MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY
(2020)
Review
Biochemistry & Molecular Biology
A. V. Gromov, M. S. Poponova, A. S. Karyagina
MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY
(2020)