Article
Biochemistry & Molecular Biology
Xiaoyu Zhuo, Silas Hsu, Deepak Purushotham, Prashant Kumar Kuntala, Jessica K. Harrison, Alan Y. Du, Samuel Chen, Daofeng Li, Ting Wang
Summary: Genome browsers are important tools to visualize and analyze genomic features and data, and there is a growing need for a comparative epigenome browser that can display and compare genomic and epigenomic data sets across different species. The WashU Comparative Epigenome Browser allows users to load functional genomic data sets mapped to different genomes and display them over syntenic regions simultaneously, while also visualizing genetic differences between the genomes. This browser expands on the widely used WashU Epigenome Browser infrastructure and supports multiple species, facilitating comparative genomic/epigenomic research and comparison of different genome assemblies.
Review
Computer Science, Information Systems
Dong Wang, Raula Gaikovina Kula, Takashi Ishio, Kenichi Matsumoto
Summary: Contemporary code review tools are popular for software quality assurance, with the ability to post linkages between patches during discussions. Patch linkage notifications exhibit latency, with patches having Alternative Solution linkages undergoing quicker reviews and fewer revisions. Detection models show promising recall rates for Alternative Solution linkages, but precision can be improved.
INFORMATION AND SOFTWARE TECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Hina Dalal, Malin Dahlgren, Sergii Gladchuk, Christian Brueffer, Sofia K. Gruvberger-Saal, Lao H. Saal
Summary: This study found that estrogen receptor beta (ESR2) is expressed at low levels in breast cancer, but high expression is associated with improved overall survival, particularly in patients receiving endocrine therapy and those with triple-negative breast cancer. In addition, gene modules associated with ESR2-high tumors were consistent with immune response.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
A. J. Harris, Aaron David Goldman
Summary: The study investigates the early evolutionary history of cellularity, focusing on the roles of cell membranes, proteins, and the signal recognition particle (SRP) system in embedding and secreting proteins. The results suggest that the last universal common ancestor (LUCA) had an SRP system and SecY channel similar to present organisms, with a more rudimentary system in an earlier ancestor. The ancestral Ffh/FtsY protein likely emerged around the completion of the genetic code.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Telecommunications
Ke Han, Yunfei Xu, Zhongliang Deng, Jiawei Fu
Summary: A new indoor fingerprint positioning method, called DFF-EDR, is proposed in this study to improve the feature resolution of the system by dynamically fusing features and using an improved edit distance metric. The method effectively reduces noise interference and positioning errors, showing promising performance in indoor localization.
CHINA COMMUNICATIONS
(2021)
Proceedings Paper
Computer Science, Software Engineering
Jianwei Zeng, Tao Zhang, Zhou Xu
Summary: The paper introduces a novel code summarization model named Dynamic Graph attention-based Transformer (DG-Trans), which effectively addresses the limited structural information and Out-Of-Vocabulary problems in existing methods. Extensive experiments demonstrate that DG-Trans outperforms state-of-the-art models, increasing average BLEU scores and ROUGUEL by 8.39% and 8.86%, respectively.
2021 IEEE 21ST INTERNATIONAL CONFERENCE ON SOFTWARE QUALITY, RELIABILITY AND SECURITY (QRS 2021)
(2021)
Proceedings Paper
Computer Science, Information Systems
Liu Kai, Han Yiliang, Wang Jingjing, Guo Kaiyang
Summary: This paper proposes a k-anonymous location privacy protection scheme based on geohash coding and pseudo-random sequence generation technology, which can effectively protect users' location privacy and has higher efficiency.
2022 3RD INFORMATION COMMUNICATION TECHNOLOGIES CONFERENCE (ICTC 2022)
(2022)
Article
Multidisciplinary Sciences
Grant Kemp, Ola B. Nilsson, Pengfei Tian, Robert B. Best, Gunnar von Heijne
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biology
Felix Nicolaus, Ane Metola, Daphne Mermans, Amanda Liljenstrom, Ajda Krc, Salmo Mohammed Abdullahi, Matthew Zimmer, Thomas F. Miller, Gunnar von Heijne
Summary: The study investigates the cotranslational biosynthesis of E. coli inner membrane proteins and reveals the complexities in membrane integration process, including protein folding in the ribosome exit tunnel and interactions between charged residues and the membrane. The results also suggest residue-specific interactions between transmembrane helices during the integration process, supporting the 'sliding' model of translocon-mediated membrane protein integration.
Article
Microbiology
Sneider Alexander Gutierrez Guarnizo, Elena B. Tikhonova, Masoud Zabet-Moghaddam, Kai Zhang, Carlos Muskus, Andrey L. Karamyshev, Zemfira N. Karamysheva
Summary: The study used lipidomic profiles to differentiate between sensitive and resistant Leishmania strains, showing that resistant phenotypes had downregulated phosphatidylcholines, decreased sphingolipids, and increased lysophosphatidylcholines, while sensitive phenotypes had upregulated triglycerides and decreased phosphatidylethanolamine. The changes in lipid composition in antimony-resistant parasites appear to contribute to their physiological response to combat oxidative stress caused by the drug, highlighting several lipids as potential biomarkers for drug resistance.
Review
Biochemistry & Molecular Biology
Morgana K. Kellogg, Sarah C. Miller, Elena B. Tikhonova, Andrey L. Karamyshev
Summary: Signal recognition particle (SRP) is an RNA and protein complex found across all domains of life, with varying compositions and functions in different organisms. Its main function involves targeting proteins to the endoplasmic reticulum and protecting the mRNA of secretory proteins from degradation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Editorial Material
Multidisciplinary Sciences
Gunnar von Heijne
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Zemfira N. Karamysheva, Samrat Moitra, Andrea Perez, Sumit Mukherjee, Elena B. Tikhonova, Andrey L. Karamyshev, Kai Zhang
Summary: Leishmania parasites, which cause leishmaniasis, do not synthesize cholesterol, but instead make ergostane-based sterols. Inactivation of the key enzyme C-14-demethylase in sterol biosynthesis leads to various defects, including impaired RNA stability and translation. Therefore, sterol biosynthesis in Leishmania unexpectedly plays a crucial role in global gene regulation.
Article
Biochemistry & Molecular Biology
Felix Nicolaus, Fatima Ibrahimi, Anne den Besten, Gunnar von Heijne
Summary: During the cotranslational insertion of membrane proteins mediated by SecYEG, both electrostatic and hydrophobic interactions involving sequence elements can impact the behavior of transmembrane helices, leading to delayed contact with the membrane.
Article
Biotechnology & Applied Microbiology
Felix Teufel, Jose Juan Almagro Armenteros, Alexander Rosenberg Johansen, Magnus Halldor Gislason, Silas Irby Pihl, Konstantinos D. Tsirigos, Ole Winther, Soren Brunak, Gunnar von Heijne, Henrik Nielsen
Summary: Signal peptides are short amino acid sequences that regulate protein secretion and translocation. SignalP 6.0, a machine learning model, is introduced to detect all types of signal peptides, including those applicable to metagenomic data.
NATURE BIOTECHNOLOGY
(2022)
Article
Cell Biology
Sarah M. Hernandez, Elena B. Tikhonova, Kristen R. Baca, Fanpeng Zhao, Xiongwei Zhu, Andrey L. Karamyshev
Summary: The study found that SRP and AGO2 proteins are involved in the control of alpha Syn expression in PD, with reduced expression of AGO2 in PD. SRP was shown for the first time to be involved in mRNA protection of alpha Syn, revealing the potential roles of these factors in the pathogenesis of PD.
Editorial Material
Genetics & Heredity
Morgana K. Kellogg, Elena B. Tikhonova, Andrey L. Karamyshev
Summary: The signal recognition particle (SRP) is an essential ribonucleoprotein complex involved in protein synthesis and its dysfunction can lead to various diseases.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Elena B. Tikhonova, Sneider Alexander Gutierrez Guarnizo, Morgana K. Kellogg, Alexander Karamyshev, Igor M. Dozmorov, Zemfira N. Karamysheva, Andrey L. Karamyshev
Summary: Regulation of Aberrant Protein Production (RAPP) is a protein quality control mechanism in mammalian cells. It degrades the mRNA of nascent proteins that cannot associate with their natural interacting partners. Depletion of human SRP54, an SRP subunit, triggers RAPP and leads to decreased expression of mRNAs encoding secretory and membrane proteins. The loss of SRP54 also results in the upregulation of a specific network of HSP70/40/90 chaperones, increased ribosome-associated ubiquitination, and changes in the expression of RPS27 and RPS27L, indicating ribosome rearrangement.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Daphne Mermans, Felix Nicolaus, Klara Fleisch, Gunnar von Heijne
Summary: In recent years, it has been discovered that many cytoplasmic proteins can dimerize while being translated. However, it was unclear whether this phenomenon also applies to integral membrane proteins. This study demonstrates that the inner membrane protein EmrE in Escherichia coli can indeed undergo cotranslational interactions, suggesting that membrane proteins can start to fold and dimerize during the membrane insertion process.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Daphne Mermans, Felix Nicolaus, Aysel Baygin, Gunnar von Heijne
Summary: Human growth hormone (hGH) is a protein with four helix bundles and has pharmacological interest. This study investigates the folding of hGH during expression in Escherichia coli, both in vitro translation with or without the chaperone trigger factor (TF) and in E. coli. The findings suggest that hGH begins folding before it is fully released from the ribosome and may interact with TF and other chaperones.
Review
Biochemistry & Molecular Biology
Sarah C. Miller, Clinton C. MacDonald, Morgana K. Kellogg, Zemfira N. Karamysheva, Andrey L. Karamyshev
Summary: Ribosomal heterogeneity exists within and between cells, and exhibits specific changes in response to developmental stages and environmental stimuli. These changes regulate the translation of specific groups of genes by altering ribosomal affinity for certain mRNAs or the folding of nascent polypeptides. The identification of specialized ribosomes relies on evidence such as different ribosomal protein composition or modifications to RNA and/or protein, resulting in physiologically relevant changes in translation. In this review, we summarize ribosomal heterogeneity and specialization in mammals and discuss their implications in several human diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Sneider Alexander Gutierrez Guarnizo, Elena B. Tikhonova, Andrey L. Karamyshev, Carlos E. Muskus, Zemfira N. Karamysheva
Summary: Leishmania is a unicellular protozoan with limited transcriptional control. Translational control is identified as a major mechanism of antimony drug resistance in Leishmania, leading to significant differences in mRNA translation between drug-resistant and sensitive strains.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)