Article
Oncology
Robin J. N. Coope, Colin Schlosser, Richard D. Corbett, Stephen Pleasance, Basile Tessier-Cloutier, Pawan Pandoh, Heather Kirk, Simon Haile, Yongjun Zhao, Andrew J. Mungall, Marco A. Marra
Summary: Flexible tissue processing strategies are essential for the practical application of genome-scale technologies in precision oncology research. A semi-automated laser microdissection method has been developed to enrich tumor cells and yield sequence data of sufficient quality.
JOURNAL OF PATHOLOGY
(2021)
Review
Immunology
Laurence Don Wai Luu, Vasilli Kasimov, Samuel Phillips, Garry S. A. Myers, Martina Jelocnik
Summary: This review examines the progress made in Chlamydia genomics over the past twenty-five years, focusing on the revolutionary impact of whole genome sequencing in understanding Chlamydia virulence, evolution, and phylogeny. The review also highlights the developments in multi-omics and other approaches that have advanced our knowledge of Chlamydia pathogenesis and future directions for chlamydial genomics.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Zhe Xu, Si Cheng, Xin Qiu, Xiaoqi Wang, Qiuwen Hu, Yanfeng Shi, Yang Liu, Jinxi Lin, Jichao Tian, Yongfei Peng, Yong Jiang, Yadong Yang, Jianwei Ye, Yilong Wang, Xia Meng, Zixiao Li, Hao Li, Yongjun Wang
Summary: This study constructed an optimized pipeline and identified applicable fingerprint panels to address the sample tagging problem in whole genome bisulfite sequencing (WGBS) data. By using autosome-wide A/T polymorphic single nucleotide variants (SNVs), a fingerprint panel was designed and genotypes were called from the WGBS data. The capability to tag WGBS data was validated and the lower boundary for the number of fingerprint genetic variants needed for correct sample tagging was determined.
Article
Biochemistry & Molecular Biology
Ying Ni, Xudong Liu, Zemenu Mengistie Simeneh, Mengsu Yang, Runsheng Li
Summary: This study evaluates the application of the recently released R10.4 flow cell from Oxford Nanopore Technologies in human cancer genomics and epigenomic research. The results show that R10.4 performs better than R9.4.1 in terms of read accuracy, variant detection, methylation calling, and genome recovery rate. In addition, the study proposes a promising method for high-yield single-cell whole-genome amplification sequencing and provides a possible solution for filtering false positive sites using R10.4 data.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Multidisciplinary Sciences
Brigitte Glanzmann, Tracey Jooste, Samira Ghoor, Richard Gordon, Rizwana Mia, Jun Mao, Hao Li, Patrick Charls, Craig Douman, Maritha J. Kotze, Armand V. Peeters, Glaudina Loots, Monika Esser, Caroline T. Tiemessen, Robert J. Wilkinson, Johan Louw, Glenda Gray, Robin M. Warren, Marlo Moeller, Craig Kinnear
Summary: The emergence of next generation sequencing has had a significant impact on genomic research, enabling South African researchers to access high quality data comparable to international standards at the South African Medical Research Council's Genomics Centre. This has enhanced the capacity of African researchers to sequence whole genomes and analyze data locally.
SCIENTIFIC REPORTS
(2021)
Article
Plant Sciences
Hisashi Udagawa, Hiroyuki Ichida, Takanori Takeuchi, Tomoko Abe, Yoshimitsu Takakura
Summary: In this study, a whole-exome sequencing (WES) procedure was developed in tobacco to characterize EMS-induced mutations in a test population, revealing a high number of single nucleotide variants. The amount of mutations detected by WES was 93.5% of those detected by whole-genome sequencing, while requiring significantly less sequencing data, making it a cost-effective tool for high-throughput mutation identification in tobacco.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biology
Michael D. Linderman, Crystal Paudyal, Musab Shakeel, William Kelley, Ali Bashir, Bruce D. Gelb
Summary: The study introduces a new machine-learning based approach, NPSV, for accurately genotyping known structural variants, overcoming limitations and biases present in traditional methods. NPSV demonstrates high accuracy and robustness across different datasets and samples.
Article
Clinical Neurology
Ryan L. Davis, Kishore R. Kumar, Eloise C. Watson, Carolyn M. Sue
Summary: We strongly agree that alpha-methylacyl-CoA racemase (AMACR) deficiency should be considered in patients with combinations of stroke-like episodes, seizures, encephalopathy, and retinal pigmentary changes. Our study and other case reports highlight the importance of a comprehensive sequencing approach to identify mitochondrial disease phenocopies. Such phenocopies include individuals with causative AMACR variants, as well as those from other studies and projects.
Article
Health Care Sciences & Services
Makenzie Beaman, Kimberley Fisher, Marie McDonald, Queenie K. G. Tan, David Jackson, Benjamin T. Cocanougher, Andrew P. Landstrom, Charlotte A. Hobbs, Michael Cotten, Jennifer L. Cohen
Summary: Rapid genome sequencing is crucial for providing targeted care to critically ill infants. A pilot study involving eight neonates showed a diagnostic rate of 37.5% using rapid whole genome sequencing alone, and 50% for the cohort overall. The diagnoses led to changes in management and identification of affected relatives. Challenges with sample collection were also discussed. The study also established a research protocol pipeline for cases where a diagnosis was not reached by rapid genome sequencing or other clinical testing. The benefits, limitations, challenges, and potential for incorporating rapid whole genome sequencing into routine clinical evaluation in the neonatal period were described.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Article
Immunology
Kamila Romanowski, Benjamin Sobkowiak, Jennifer L. Guthrie, Victoria J. Cook, Jennifer L. Gardy, James C. Johnston
Summary: By combining WGS data with patient-level information, the timing of secondary TB among contacts of active TB patients in British Columbia, Canada can be calculated.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Biotechnology & Applied Microbiology
Chuanxue Liu, Pei Peng, Weiguo Li, Changrong Ye, Shuhua Zhang, Ruiying Wang, Dong Li, Shiwu Guan, Lanmin Zhang, Xiaoqun Huang, Zhenhua Guo, Junxiang Guo, Yu Long, Le Li, Guojun Pan, Bingchuan Tian, Jinhua Xiao
Summary: This study resequenced 239 japonica rice elites to reveal the genetic diversity and relationships among them, constructed a japonica rice pan-genome, predicted numerous novel genes, and detected strong selection signals in genomic regions. The results provide a foundation for future whole genome sequences-enabled breeding in rice and serve as a paradigm for other species.
Article
Microbiology
Hon S. Ip, Sarah Uhm, Mary Lea Killian, Mia K. Torchetti
Summary: As shown by the response to the SARS-CoV-2 pandemic, whole-genome sequencing is crucial for monitoring viral evolution and guiding antiviral treatments. With the rapid spread of highly pathogenic avian influenza virus, there is a need for rapid sequencing to aid in response and mitigation efforts. This study evaluates a portable nanopore sequencing platform for routine use in a diagnostic laboratory, finding that limited amplification and rapid procedures are the most effective approaches.
Article
Biotechnology & Applied Microbiology
Anthony J. Silva, Zhihui Yang, Julia Wolfe, Kirsten A. Hirneisen, Shannon B. Ruelle, Angelica Torres, Donna Williams-Hill, Michael Kulka, Rosalee S. Hellberg
Summary: This study compared the ability of whole-genome sequencing (WGS) and Sanger sequencing to differentiate norovirus strains, showing that WGS enables better genetic differentiation of strains and provides valuable information for outbreak investigation and surveillance efforts.
Article
Oncology
Kris G. Samsom, Luuk J. Schipper, Paul Roepman, Linda J. W. Bosch, Ferry Lalezari, Elisabeth G. Klompenhouwer, Adrianus J. de Langen, Tineke E. Buffart, Immy Riethorst, Lieke Schoenmaker, Daoin Schout, Vincent van der Noort, Jose G. van den Berg, Ewart de Bruijn, Jacobus J. M. van der Hoeven, Hans van Snellenberg, Lizet E. van der Kolk, Edwin Cuppen, Emile E. Voest, Gerrit A. Meijer, Kim Monkhorst
Summary: This study aimed to evaluate the feasibility and efficacy of whole-genome sequencing (WGS) in routine clinical practice. The results showed that WGS can be successfully applied to patients with metastatic cancer, providing comprehensive genomic profiling for the majority of patients and identifying actionable biomarkers and treatment options.
JOURNAL OF PATHOLOGY
(2022)
Article
Virology
Florence Nicot, Pauline Tremeaux, Justine Latour, Romain Carcenac, Sofia Demmou, Nicolas Jeanne, Noemie Ranger, Clementine De Smet, Stephanie Raymond, Chloe Dimeglio, Jacques Izopet
Summary: This study evaluated a target capture SMRT sequencing protocol for SARS-CoV-2 Omicron variants and compared it to an amplicon SMRT sequencing protocol optimized for Omicron variants. The target capture protocol had a lower failure rate and higher genome coverage compared to the amplicon protocol, making it an efficient method for whole genome sequencing, genotyping, and mutation detection of SARS-CoV-2 Omicron variants.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Virology
Dmitriy A. Shirokov, Valentin A. Manuvera, Olga A. Miroshina, Alexandr S. Dubovoi, Galina N. Samuseva, Margarita E. Dmitrieva, Vassili N. Lazarev
ARCHIVES OF VIROLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Vladislav V. Babenko, Oleg Podgorny, Valentin A. Manuvera, Artem S. Kasianov, Alexander Manolov, Ekaterina N. Grafskaia, Dmitriy A. Shirokov, Alexey S. Kurdyumov, Dmitriy V. Vinogradov, Anastasia S. Nikitina, Sergey Kovalchuk, Nickolay A. Anikanov, Ivan O. Butenko, Olga Pobeguts, Daria S. Matyushkina, Daria Rakitina, Elena S. Kostryukova, Victor G. Zgoda, Isolda P. Baskova, Vladimir M. Trukhan, Mikhail S. Gelfand, Vadim M. Govorun, Helgi B. Schioth, Vassili N. Lazarev
Article
Biochemistry & Molecular Biology
Andrey Letarov, Vladislav V. Babenko, Eugene E. Kulikov
Summary: The imbalance of the renin-angiotensin system is considered to be a potentially important factor in the pathogenesis of COVID-19. The shedding of SARS-CoV-2 S protein's soluble S1 subunits may bind to ACE2 and downregulate its cell surface expression, leading to increased angiotensin II effects and promoting thrombosis, inflammation, and lung damage. The less pronounced shedding of S1 particles reported for the S protein carrying the D614G mutation may be associated with the lack of increased severity of COVID-19 infection caused by the mutant SARS-CoV-2 strain.
BIOCHEMISTRY-MOSCOW
(2021)
Article
Biochemistry & Molecular Biology
Irina Lyapina, Anna Filippova, Sergey Kovalchuk, Rustam Ziganshin, Anna Mamaeva, Vassili Lazarev, Ivan Latsis, Elena Mikhalchik, Oleg Panasenko, Oleg Ivanov, Vadim Ivanov, Igor Fesenko
Summary: Research has shown that bryophytes share common predicted small secreted peptides with vascular plants, with mosses having a higher number of SSPs in their genomes compared to liverworts and hornworts. This indicates the possibility of moss receptors recognizing peptide ligands from angiosperms, suggesting a potential evolutionary link between bryophytes and vascular plants in immune signaling.
PLANT MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Vladimir Tsvetkov, Anna Varizhuk, Liubov Kozlovskaya, Anna Shtro, Olga Lebedeva, Andrey Komissarov, Tatjana Vedekhina, Valentin Manuvera, Olga Zubkova, Artem Eremeev, Elena Shustova, Galina Pozmogova, Dmitry Lioznov, Aydar Ishmukhametov, Vassili Lazarev, Maria Lagarkova
Summary: EGCG, a component of green tea, shows significant antiviral activity against the native virus from COVID-19 patients, especially when using the preincubation scheme. Molecular modeling experiments reveal its interactions with viral protein subunits, providing insight into its mechanism of action.
Article
Biochemistry & Molecular Biology
Igor Fesenko, Svetlana A. Shabalina, Anna Mamaeva, Andrey Knyazev, Anna Glushkevich, Irina Lyapina, Rustam Ziganshin, Sergey Kovalchuk, Daria Kharlampieva, Vassili Lazarev, Michael Taliansky, Eugene Koonin
Summary: Pervasive transcription of eukaryotic genomes results in the expression of long non-coding RNAs (lncRNAs), with many potentially encoding small open reading frames (smORFs) that can be translated into peptides or microproteins. A comprehensive analysis of lncRNAs-smORFs from a moss species across 479 plant transcriptomes revealed that while many smORFs are subject to purifying selection, they represent a pool for functional innovation. Proteomic analysis confirmed translation of novel species-specific smORFs and indicated that microproteins encoded by smORFs are a functionally diverse component of the plant proteome.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Materials Science, Multidisciplinary
Anna Panyushkina, Natalya Fomchenko, Vladislav Babenko, Maxim Muravyov
Summary: Bioleaching of bulk copper-nickel sulfide concentrate was proposed to remove nickel and obtain a copper concentrate containing chalcopyrite. The study showed that microbial communities cultured at 40 degrees Celsius were the most diverse and had the highest effectiveness in nickel leaching. The bioleaching process at 40 degrees Celsius resulted in a high-grade copper concentrate with low nickel content, indicating the promising potential of biobeneficiation in biohydrometallurgy.
Article
Multidisciplinary Sciences
Julia Galeeva, Vladislav Babenko, Ramiz Bakhtyev, Vladimir Baklaushev, Larisa Balykova, Pavel Bashkirov, Julia Bespyatykh, Anna Blagonravova, Daria Boldyreva, Dmitry Fedorov, Ilshat Gafurov, Raushaniya Gaifullina, Elena Galova, Alina Gospodaryk, Elena Ilina, Konstantin Ivanov, Daria Kharlampieva, Polina Khromova, Ksenia Klimina, Konstantin Kolontarev, Nadezhda Kolyshkina, Andrey Koritsky, Vyacheslav Kuropatkin, Vasily Lazarev, Alexander Manolov, Valentin Manuvera, Daria Matyushkina, Maxim Morozov, Ekaterina Moskaleva, Varvara Musarova, Oleg Ogarkov, Elizaveta Orlova, Alexander Pavlenko, Alla Petrova, Natalia Pozhenko, Dmitry Pushkar, Alexander Rumyantsev, Sergey Rumyantsev, Vladimir Rumyantsev, Lyubov Rychkova, Alexander Samoilov, Irina Shirokova, Vyacheslav Sinkov, Svetlana Solovieva, Elizaveta Starikova, Polina Tikhonova, Galina Trifonova, Alexander Troitsky, Alexander Tulichev, Yuri Udalov, Anna Varizhuk, Alexander Vasiliev, Vladimir Veselovsky, Rinat Vereshchagin, Alexey Volnukhin, Gaukhar Yusubalieva, Vadim Govorun
Summary: This article presents a dataset of the respiratory microbiome from SARS-CoV-2 positive patients in Russia, providing information on the microbial community profile and clinical characteristics of the patients. This study is important for understanding the factors that may protect patients from severe forms of the disease.
Article
Polymer Science
Viacheslav Severov, Vladimir Tsvetkov, Nikolay Barinov, Vladislav Babenko, Dmitry Klinov, Galina Pozmogova
Summary: This study reports the spontaneous formation of DNA-DNA junctions in solution without the involvement of proteins, visualized using atomic force microscopy. The positions of synapsis match with potential G-quadruplex (G4) sites, and these conjugates exhibit an affinity for G4 antibodies. Molecular modeling was employed to elucidate the possible structures of G4/IM-synaptic complexes, indicating a novel role of intermolecular noncanonical structures in chromatin architecture and genomic rearrangement.
Article
Chemistry, Organic
Tatyana N. Makarieva, Lyudmila A. Romanenko, Konstantin S. Mineev, Larisa K. Shubina, Elena B. Guglya, Natalia I. Kalinovskaya, Natalia V. Ivanchina, Alla G. Guzii, Olga A. Belozerova, Sergey I. Kovalchuk, Roman S. Popov, Vladimir A. Denisenko, Valery V. Mikhailov, Vladislav V. Babenko, Elena N. Ilina, Maja V. Malakhova, Stanislav S. Terekhov, Arsen M. Kudzhaev, Pavel S. Dmitrenok, Ilia V. Yampolsky, Valentin A. Stonik
Summary: This article describes a new structural class of highly chlorinated antibiotics, streptocinnamides A and B, produced by the bacterium Streptomyces sp. KMM 9044 isolated from a sample of marine sediment collected in the northwestern part of the Sea of Japan. The structures of streptocinnamides A and B were determined using nuclear magnetic resonance and mass spectrometry studies and their inhibitory activity against various bacteria was demonstrated.
Article
Virology
Natalya Besarab, Andrey Letarov, Eugene E. Kulikov, Vladislav V. Babenko, Ilya S. Belalov, Alexander L. Lagonenko, Alla K. Golomidova, Anatoly N. Evtushenkov
Summary: The complete genomes of the new Erwinia amylovora bacteriophages Loshitsa2 and Micant have been sequenced, and comparative analysis suggests that they are related to LIMElight bacteriophage and could be members of a novel subfamily.
ARCHIVES OF VIROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Iuliia Pavlova, Nikolay Barinov, Roman Novikov, Vjacheslav Severov, Mikhail Iudin, Tatiana Vedekhina, Andrey Larin, Vladislav Babenko, Andrey Aralov, Evgeny Gnuchikh, Makar Sardushkin, Dmitry Klinov, Vladimir Tsvetkov, Anna Varizhuk
Summary: G-quadruplexes (G4s) are potential regulators of chromatin packaging, and a new in vitro model was designed to study their impact on nucleosome occupancy. Stable G4 structures were found to decrease nucleosome formation, supporting the negative correlation between stable G4s and nucleosome density. This study emphasizes the importance of considering chromatin context when targeting genomic G4s.
Article
Biochemistry & Molecular Biology
Dmitry N. Konanov, Danil Krivonos, Elena N. Ilina, Vladislav V. Babenko
Summary: This study developed a tool called BioCAT for finding biosynthetic gene clusters that may produce nonribosomal peptides. By implementing a position-specific score matrix, the method increased alignment sensitivity and was validated on a curated database and other examples.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Margarita N. Baranova, Arsen M. Kudzhaev, Yuliana A. Mokrushina, Vladislav V. Babenko, Maria A. Kornienko, Maja V. Malakhova, Victor G. Yudin, Maria P. Rubtsova, Arthur Zalevsky, Olga A. Belozerova, Sergey Kovalchuk, Yuriy N. Zhuravlev, Elena N. Ilina, Alexander G. Gabibov, Ivan V. Smirnov, Stanislav S. Terekhov
Summary: The biodiversity of microorganisms is maintained by interactions between species, and the functionality of human microbiomes is influenced by aseptic conditions and antibiotic use. Wild animal microbiomes have a protective shield against pathogen invasion. Using ultrahigh-throughput microfluidic technologies, the researchers identified Bacillus pumilus strains in the microbiomes of wild animals that produce antibacterial metabolites, including amicoumacin A, which can inhibit the growth of both Gram-positive and Gram-negative bacteria. The discovery of these strains opens up new opportunities for pathogen control and microbiome remodeling in various industries.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Pavel Bobrovsky, Valentin Manuvera, Izolda Baskova, Svetlana Nemirova, Alexandr Medvedev, Vassili Lazarev
Summary: In this study, the feasibility and effectiveness of using destabilase in relation to blood clots formed during real pathological processes were evaluated. The researchers found that destabilase can be considered as a potential drug for the treatment of aged clots, which are difficult to treat with known thrombolytics. Destabilase is able to destroy isopeptide bonds in both aged and fresh blood clots, and its effect coincides with the morphological characteristics of the clots.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2021)