Article
Genetics & Heredity
Mildred K. Cho, Maria Laura Duque Lasio, Ina Amarillo, Kevin Todd Mintz, Robin L. Bennett, Kyle B. Brothers
Summary: Efforts to promote diversity, equity, and inclusion in academia have prompted publishers and journals to reevaluate their use of terminology in scientific research. This is particularly important in the field of human genetics, where differences between individuals and populations are studied. Recent guidelines acknowledge the potential inaccuracy and harm of certain language and concepts related to disability, sex, gender, race, ethnicity, and ancestry. This article summarizes critiques of current terminology and provides recommendations for alternative language to make genetics more inclusive and ethically sound.
GENETICS IN MEDICINE
(2023)
Article
Multidisciplinary Sciences
Claire Chung, Bert M. Verheijen, Xinmin Zhang, Biao Huang, Aeowynn Coakley, Eric McGann, Emily Wade, Olivia Dinep-Schneider, Jessica LaGosh, Maria-Eleni Anagnostou, Stephen Simpson, Kelly Thomas, Mimi Ernst, Allison Rattray, Michael Lynch, Mikhail Kashlev, Berenice A. Benayoun, Zhongwei Li, Jeffrey Strathern, Jean-Francois Gout, Marc Vermulst
Summary: To determine the error rate of transcription in human cells, researchers analyzed the transcriptome of H1 human embryonic stem cells using a high-fidelity circle-sequencing approach. They found approximately 100,000 errors in major RNA species, indicating that different RNA species have different error rates. Cross-referencing the errors with genetic and epigenetic features revealed that the error rate changes along the transcript length and is modified by genetic context, repetitive elements, and epigenetic markers. The study also discovered a novel role of BRCA1 in suppressing transcription errors and found that transcription errors preferentially occur in neurons, suggesting their involvement in neurological disorders.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Fabian Zech, Daniel Schniertshauer, Christoph Jung, Alexandra Herrmann, Arne Cordsmeier, Qinya Xie, Rayhane Nchioua, Caterina Prelli Bozzo, Meta Volcic, Lennart Koepke, Janis A. Mueller, Jana Krueger, Sandra Heller, Steffen Stenger, Markus Hoffmann, Stefan Poehlmann, Alexander Kleger, Timo Jacob, Karl-Klaus Conzelmann, Armin Ensser, Konstantin M. J. Sparrer, Frank Kirchhoff
Summary: By exchanging residue 403 between RaTG13 and SARS-CoV-2 spike proteins, researchers demonstrated the impact on binding to human ACE2 and entry of pseudotyped viruses. This finding suggests the potential of vaccination to protect against future zoonotic diseases.
NATURE COMMUNICATIONS
(2021)
Article
Computer Science, Information Systems
Jihye Kim, Ok-Ran Jeong
Summary: Most embedding models in natural language processing require retraining the entire model to get embedding values for new words, which is inefficient. To address this, a new embedding model MVS is proposed, which can obtain embedding values for new words without retraining the existing model.
Article
Cell Biology
Burcak Otlu, Marcos Diaz-Gay, Ian Vermes, Erik N. Bergstrom, Maria Zhivagui, Mark Barnes, Ludmil B. Alexandrov
Summary: By integrating mutations from 5,120 whole-genome-sequenced tumors from 40 cancer types with 516 topographical features from ENCODE, we evaluated the impact of various topographical features on cancer-specific mutational processes. Most mutational signatures were influenced by topographical features, especially those related to similar etiologies. Certain signatures exhibited periodic behaviors or cancer-type-specific enrichments/depletions near topographical features, providing further insights into the underlying mutational processes. Our findings, disseminated via the COSMIC signatures database, offer a comprehensive online resource for exploring the interactions between mutational signatures and topographical features in human cancer.
Article
Biochemistry & Molecular Biology
Reina Sasaki-Tanaka, Toshikatsu Shibata, Hiroaki Okamoto, Mitsuhiko Moriyama, Tatsuo Kanda
Summary: In this study, several novel therapeutic drugs were investigated through a drug repositioning approach, with favipiravir identified as a potential antiviral against hepatitis A virus (HAV) infection. The study examined the replication of HAV and introduced nucleotide mutations in the HAV genome using different drugs. Favipiravir showed inhibitory effects on HAV replication and introduced more nucleotide mutations compared to ribavirin. Further in vivo experiments are needed to confirm the efficacy of favipiravir in treating severe HAV infection.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Computer Science, Information Systems
Imad-Eddine Benkoudad, Abdelmalek Azizi, Mouhammed El Amrani
Summary: This research project analyzes the formal structure of Arabic rhythms in words and establishes a connection with Fibonacci words, demonstrating a unique approach to using Arabic poems as secret keys in cryptographic systems.
JOURNAL OF KING SAUD UNIVERSITY-COMPUTER AND INFORMATION SCIENCES
(2021)
Article
Food Science & Technology
Irene De Guidi, Jean-Luc Legras, Virginie Galeote, Delphine Sicard
Summary: Starting from the concept of domestication itself, this paper presents examples of advanced research on the domestication of yeasts in fermented foods and beverages, focusing on both the well-known model species, Saccharomyces cerevisiae, and other species encountered in fermented products. Different fermented food or beverage environments are discussed, highlighting how humans have shaped yeast evolution, from fermentation practices to targeted strain improvement. The paper also emphasizes the negative effects of domestication and the need to consider yeast diversity and evolution for sustainable food chains.
CURRENT OPINION IN FOOD SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Pavlina Nekvasilova, Michaela Hovorkova, Zuzana Meszaros, Lucie Petraskova, Helena Pelantova, Vladimir Kren, Kristyna Slamova, Pavla Bojarova
Summary: Enzymatic synthesis is a biocompatible method for the synthesis of complex compounds, including human milk oligosaccharides. Previous studies have been limited to analytical reactions, but this study demonstrates the successful synthesis of three tetrasaccharides derived from lacto-N-tetraose using engineered glycosidases. The reaction products were isolated and characterized.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Engineering, Electrical & Electronic
Chao Wu, Yaqian Li, Yaru Zhang, Bin Liu
Summary: The DC-BoW method improves recognition accuracy by effectively utilizing spatial distribution information between features and introducing double constraints.
SIGNAL PROCESSING-IMAGE COMMUNICATION
(2021)
Article
Biochemistry & Molecular Biology
Yuru Wang, Christopher D. Katanski, Christopher Watkins, Jessica N. Pan, Qing Dai, Zhuoxun Jiang, Tao Pan
Summary: A high-throughput screening method was introduced to evaluate AlkB variants for demethylation activity on RNA and DNA substrates, leading to the identification of variants with improved activity. This method provides a tool for in vitro evolution of any demethylase enzyme.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biology
Hidehiko Kawai, Ren Iwata, Shungo Ebi, Ryusei Sugihara, Shogo Masuda, Chiho Fujiwara, Shingo Kimura, Hiroyuki Kamiya
Summary: This study presents an advanced method for mutation analysis using the supF gene. The method is simple, versatile, and cost-effective, and provides valuable insights into mutation frequencies and spectra. The results reveal previously undetected mutations and offer a novel perspective on the mechanisms of mutagenesis.
Article
History & Philosophy Of Science
Kate Hazel Stanton
Summary: Recent work in supersemantics and the semantic interpretation of prosody has shown that non-words can contribute to truth conditions. This paper explores the case of a prosodic contour that functions as an intensifier and argues that its integration into sentence meaning challenges foundational assumptions about semantics, revealing a novel form of layering in semantic interpretation.
Article
Computer Science, Artificial Intelligence
Leyuan Qu, Cornelius Weber, Stefan Wermter
Summary: Due to the dynamic nature of human language, automatic speech recognition (ASR) systems need to continuously acquire new vocabulary. Out-Of-Vocabulary (OOV) words pose problems to modern ASR systems. We propose to generate OOV words using text-to-speech systems and to rescale losses to encourage neural networks to pay more attention to OOV words. Our proposed combined loss rescaling and weight consolidation methods can support continual learning of an ASR system.
Article
Microbiology
Jyotsna Chawla, Ilana Goldowitz, Jenna Oberstaller, Min Zhang, Camilla Valente Pires, Francesca Navarro, Lauriane Sollelis, Chengqi C. Q. Wang, Andreas Seyfang, Jeffrey Dvorin, Thomas D. D. Otto, Julian C. C. Rayner, Matthias Marti, John H. H. Adams
Summary: This article reports a study to identify genes associated with gametocyte development in the deadly malaria parasite Plasmodium falciparum. The study found a new set of genes that have not been implicated in gametocytogenesis before and demonstrated the potential of forward genetic screens in isolating genes impacting parasite sexual biology, which could lead to the discovery of new antimalarials.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
I. S. Rusinov, A. S. Ershova, A. S. Karyagina, S. A. Spirin, A. V. Alexeevski
BIOCHEMISTRY-MOSCOW
(2018)
Article
Biochemical Research Methods
Dmitry Penzar, Mikhail Krivozubov, Sergey Spirin
BMC BIOINFORMATICS
(2018)
Article
Biology
A. Y. Panchin, V. V. Aleoshin, Y. V. Panchin
Article
Biochemistry & Molecular Biology
Kirill V. Mikhailov, Boris D. Efeykin, Alexander Y. Panchin, Dmitry A. Knorre, Maria D. Logacheva, Aleksey A. Penin, Maria S. Muntyan, Mikhail A. Nikitin, Olga V. Popova, Olga N. Zanegina, Mikhail Y. Vyssokikh, Sergei E. Spiridonov, Vladimir V. Aleoshin, Yuri V. Panchin
NUCLEIC ACIDS RESEARCH
(2019)
Correction
Biotechnology & Applied Microbiology
Sofya A. Medvedeva, Alexander Y. Panchin, Andrei V. Alexeevski, Sergey A. Spirin, Yuri V. Panchin
BIOMED RESEARCH INTERNATIONAL
(2020)
Article
Genetics & Heredity
Alexey Meshkov, Alexandra Ershova, Anna Kiseleva, Evgenia Zotova, Evgeniia Sotnikova, Anna Petukhova, Anastasia Zharikova, Pavel Malyshev, Tatyana Rozhkova, Anastasia Blokhina, Alena Limonova, Vasily Ramensky, Mikhail Divashuk, Zukhra Khasanova, Anna Bukaeva, Olga Kurilova, Olga Skirko, Maria Pokrovskaya, Valeriya Mikova, Ekaterina Snigir, Alexsandra Akinshina, Sergey Mitrofanov, Daria Kashtanova, Valentin Makarov, Valeriy Kukharchuk, Sergey Boytsov, Sergey Yudin, Oxana Drapkina
Summary: This study examined LDLR, APOB, and PCSK9 gene variants in 595 index Russian patients with FH, identifying 224 variants, 36.1% of which were specific to the Russian population. The findings significantly expand knowledge of FH genetics in Russia and may enhance genetic diagnostics for FH patients in the country.
Article
Biochemistry & Molecular Biology
Alexander Tyshkovskiy, Alexander Y. Panchin
Summary: The study highlights the incorrectness of the laboratory origin hypothesis for SARS-CoV-2, stating that it does not align with existing genetic and experimental data, while the hypothesis of a natural origin is more consistent with all available data.
Article
Genetics & Heredity
Roman P. Myasnikov, Olga Kulikova, Alexey N. Meshkov, Anna A. Bukaeva, Anna Kiseleva, Alexandra Ershova, Anna Petukhova, Mikhail G. Divashuk, Evgenia D. Zotova, Evgeniia A. Sotnikova, Alexandra A. Abisheva, Alisa Muraveva, Sergey N. Koretskiy, Sergey Popov, Marina Utkina, Ekaterina A. Snigir, Sergey Mitrofanov, Ksenia D. Konureeva, Elena A. Mershina, Valentin E. Sinitsyn, Sergey M. Yudin, Oxana M. Drapkina
Summary: This article explores the relationship between variants of the MYH7 gene and left ventricular noncompaction cardiomyopathy (LVNC). It suggests that not all predicted truncating variants of MYH7 act through haploinsufficiency, highlighting the importance of a precise assessment of MYH7 splicing variants and their participation in LVNC development.
Article
Cell Biology
Abusaid M. Shaymardanov, Olga A. Antonova, Anastasia D. Sokol, Kseniia A. Deinichenko, Polina G. Kazakova, Mikhail M. Milovanov, Alexander Zakubansky, Alexandra Akinshina, Anastasia Tsypkina, Svetlana Romanova, Vladimir E. Muhin, Sergey Mitrofanov, Vladimir S. Yudin, Sergey M. Yudin, Antonida Makhotenko, Anton A. Keskinov, Sergey A. Kraevoy, Ekaterina A. Snigir, Dmitry Svetlichnyy, Veronika Skvortsova
Summary: By performing single-cell transcriptome profiling, this study uncovers immune factors and molecular characteristics associated with different COVID-19 severity and virus lineages. The specific gene expression signatures found in monocytes of the Delta lineage contribute to the understanding of COVID-19 pathogenesis and provide potential immune components for targeted therapy.
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.
Article
Biochemistry & Molecular Biology
Y. N. Akhmerova, T. A. Shpakova, K. S. Grammatikati, S. I. Mitrofanov, P. G. Kazakova, A. A. Mkrtchian, P. U. Zemsky, M. N. Pilipenko, N. V. Feliz, L. V. Frolova, A. A. Frolovskaya, V. S. Yudin, A. A. Keskinov, S. A. Kraevoy, S. M. Yudin, V. I. Skvortsova
Summary: Bronchial asthma lacks a comprehensive treatment protocol, and the medical community is examining the genetic factors associated with the disease. A study conducted by the Federal Medical Biological Agency of Russia analyzed scientific literature and identified 167 genes associated with bronchial asthma. A group of participants with a history of asthma and apparently healthy individuals were divided into cohorts to search for genetic polymorphisms.
Meeting Abstract
Respiratory System
Alexey Kononikhin, Kristina Fedorchenko, Mia Kushaeva, Eldar Anaev, Sergey Mitrofanov, Anna Ryabokon, Igor Popov, Vitaliy Barmin, Maria Indeykina, Oleg Pikin, Evgeny Nikolaev, Sergey Varfolomeev, Alexander Chuchalin
EUROPEAN RESPIRATORY JOURNAL
(2019)
Article
Medicine, General & Internal
Alexander Y. Panchin, Nikita N. Khromov-Borisov, Evgenia V. Dueva
BMJ EVIDENCE-BASED MEDICINE
(2019)