Biochemistry & Molecular Biology

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Article Biochemistry & Molecular Biology

Multiple early factors anticipate post-acute COVID-19 sequelae

Yapeng Su, Dan Yuan, Daniel G. Chen, Rachel H. Ng, Kai Wang, Jongchan Choi, Sarah Li, Sunga Hong, Rongyu Zhang, Jingyi Xie, Sergey A. Kornilov, Kelsey Scherler, Ana Jimena Pavlovitch-Bedzyk, Shen Dong, Christopher Lausted, Inyoul Lee, Shannon Fallen, Chengzhen L. Dai, Priyanka Baloni, Brett Smith, Venkata R. Duvvuri, Kristin G. Anderson, Jing Li, Fan Yang, Caroline J. Duncombe, Denise J. McCulloch, Clifford Rostomily, Pamela Troisch, Jing Zhou, Sean Mackay, Quinn DeGottardi, Damon H. May, Ruth Taniguchi, Rachel M. Gittelman, Mark Klinger, Thomas M. Snyder, Ryan Roper, Gladys Wojciechowska, Kim Murray, Rick Edmark, Simon Evans, Lesley Jones, Yong Zhou, Lee Rowen, Rachel Liu, William Chour, Heather A. Algren, William R. Berrington, Julie A. Wallick, Rebecca A. Cochran, Mary E. Micikas, Terri Wrin, Christos J. Petropoulos, Hunter R. Cole, Trevan D. Fischer, Wei Wei, Dave S. B. Hoon, Nathan D. Price, Naeha Subramanian, Joshua A. Hill, Jennifer Hadlock, Andrew T. Magis, Antoni Ribas, Lewis L. Lanier, Scott D. Boyd, Jeffrey A. Bluestone, Helen Chu, Leroy Hood, Raphael Gottardo, Philip D. Greenberg, Mark M. Davis, Jason D. Goldman, James R. Heath

Summary: Post-acute sequelae of COVID-19 (PASC) is an emerging global crisis, and the quantifiable risk factors and biological associations are not well understood. In this study, a deep multi-omic investigation was conducted on 309 COVID-19 patients, and four PASC-anticipating risk factors were identified at the time of initial diagnosis. The study also observed changes in immune states during recovery from COVID-19.

CELL (2022)

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Article Biochemistry & Molecular Biology

Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum

Aekkachai Tuekprakhon, Rungtiwa Nutalai, Aiste Dijokaite-Guraliuc, Daming Zhou, Helen M. Ginn, Muneeswaran Selvaraj, Chang Liu, Alexander J. Mentzer, Piyada Supasa, Helen M. E. Duyvesteyn, Raksha Das, Donal Skelly, Thomas G. Ritter, Ali Amini, Sagida Bibi, Sandra Adele, Sile Ann Johnson, Bede Constantinides, Hermione Webster, Nigel Temperton, Paul Klenerman, Eleanor Barnes, Susanna J. Dunachie, Derrick Crook, Andrew J. Pollard, Teresa Lambe, Philip Goulder, Neil G. Paterson, Mark A. Williams, David R. Hall, Elizabeth E. Fry, Jiandong Huo, Juthathip Mongkolsapaya, Jingshan Ren, David Stuart, Gavin R. Screaton

Summary: The Omicron variant of SARS-CoV-2 has rapidly spread globally and has evolved into different sublineages, with BA.4 and BA.5 dominating in South Africa. These sublineages show reduced neutralization by vaccine and naturally immune serum, indicating the possibility of repeat Omicron infections.

CELL (2022)

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Article Biochemistry & Molecular Biology

Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa

Houriiyah Tegally, Monika Moir, Josie Everatt, Marta Giovanetti, Cathrine Scheepers, Eduan Wilkinson, Kathleen Subramoney, Zinhle Makatini, Sikhulile Moyo, Daniel G. Amoako, Cheryl Baxter, Christian L. Althaus, Ugochukwu J. Anyaneji, Dikeledi Kekana, Raquel Viana, Jennifer Giandhari, Richard J. Lessells, Tongai Maponga, Dorcas Maruapula, Wonderful Choga, Mogomotsi Matshaba, Mpaphi B. Mbulawa, Nokukhanya Msomi, Yeshnee Naidoo, Sureshnee Pillay, Tomasz Janusz Sanko, James E. San, Lesley Scott, Lavanya Singh, Nonkululeko A. Magini, Pamela Smith-Lawrence, Wendy Stevens, Graeme Dor, Derek Tshiabuila, Nicole Wolter, Wolfgang Preiser, Florette K. Treurnicht, Marietjie Venter, Georginah Chiloane, Caitlyn McIntyre, Aine O'Toole, Christopher Ruis, Thomas P. Peacock, Cornelius Roemer, Sergei L. Kosakovsky Pond, Carolyn Williamson, Oliver G. Pybus, Jinal N. Bhiman, Allison Glass, Darren P. Martin, Ben Jackson, Andrew Rambaut, Oluwakemi Laguda-Akingba, Simani Gaseitsiwe, Anne von Gottberg, Tulio de Oliveira, Armand Phillip Bester, Mathilda Claassen, Deelan Doolabh, Innocent Mudau, Nokuzola Mbhele, Susan Engelbrecht, Dominique Goedhals, Diana Hardie, Nei-Yuan Hsiao, Arash Iranzadeh, Arshad Ismail, Rageema Joseph, Arisha Maharaj, Boitshoko Mahlangu, Kamela Mahlakwane, Ashlyn Davis, Gert Marais, Koleka Mlisana, Anele Mnguni, Thabo Mohale, Gerald Motsatsi, Peter Mwangi, Noxolo Ntuli, Martin Nyaga, Luicer Olubayo, Botshelo Radibe, Yajna Ramphal, Upasana Ramphal, Wilhelmina Strasheim, Naume Tebeila, Stephanie van Wyk, Shannon Wilson, Alexander G. Lucaci, Steven Weaver, Akhil Maharaj, Yusasha Pillay, Michaela Davids, Adriano Mendes, Simnikiwe Mayaphi

Summary: The genomic characterization of the SARS-CoV-2 Omicron lineages BA.4 and BA.5, responsible for the fifth wave of the COVID-19 pandemic in South Africa, reveals their continued viral diversification and sheds light on the potential mechanisms that allow these new lineages to outcompete their predecessors. These new lineages, BA.4 and BA.5, share identical spike proteins with BA.2 but have certain differences such as the presence of the 69-70 deletion, L452R, F486V, and the wild-type amino acid at Q493. They can be identified by the S-gene target failure, a proxy marker associated with the 69-70 deletion. BA.4 and BA.5 have rapidly replaced BA.2 and have become the dominant lineages in South Africa.

NATURE MEDICINE (2022)

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Article Biochemistry & Molecular Biology

The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest

Damian Szklarczyk, Rebecca Kirsch, Mikaela Koutrouli, Katerina Nastou, Farrokh Mehryary, Radja Hachilif, Annika L. Gable, Tao Fang, Nadezhda T. Doncheva, Sampo Pyysalo, Peer Bork, Lars J. Jensen, Christian von Mering

Summary: The STRING database systematically collects and integrates protein-protein interaction information, providing researchers with valuable insights into the functional and regulatory interactions within cells. It offers various data access and analysis tools.

NUCLEIC ACIDS RESEARCH (2023)

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Article Biochemistry & Molecular Biology

Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus

Joana Isidro, Vitor Borges, Miguel Pinto, Daniel Sobral, Joao Dourado Santos, Alexandra Nunes, Veronica Mixao, Rita Ferreira, Daniela Santos, Silvia Duarte, Luis Vieira, Maria Jose Borrego, Sofia Nuncio, Isabel Lopes de Carvalho, Ana Pelerito, Rita Cordeiro, Joao Paulo Gomes

Summary: In this study, shotgun metagenomics were used to rapidly reconstruct and characterize the genome sequences of the largest monkeypox virus outbreak in non-endemic countries so far. The findings indicate that the outbreak most likely has a single origin and that the virus belongs to clade 3. Furthermore, the study suggests the involvement of host APOBEC3 in viral evolution and reveals signs of ongoing microevolution in the virus.

NATURE MEDICINE (2022)

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Article Biochemistry & Molecular Biology

Effectiveness of mRNA-1273 against SARS-CoV-2 Omicron and Delta variants

Hung Fu Tseng, Bradley K. Ackerson, Yi Luo, Lina S. Sy, Carla A. Talarico, Yun Tian, Katia J. Bruxvoort, Julia E. Tubert, Ana Florea, Jennifer H. Ku, Gina S. Lee, Soon Kyu Choi, Harpreet S. Takhar, Michael Aragones, Lei Qian

Summary: A test-negative case-control analysis using data from a diverse population in California, USA, demonstrates that vaccine efficacy of a three-dose regimen of the mRNA-1273 COVID-19 vaccine is reduced against infection with the Omicron SARS-CoV-2 variant in comparison to Delta, but that efficacy against hospitalization remained high for both variants.

NATURE MEDICINE (2022)

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Article Biochemistry & Molecular Biology

InterPro in 2022

Typhaine Paysan-Lafosse, Matthias Blum, Sara Chuguransky, Tiago Grego, Beatriz Lazaro Pinto, Gustavo A. Salazar, Maxwell L. Bileschi, Peer Bork, Alan Bridge, Lucy Colwell, Julian Gough, Daniel H. Haft, Ivica Letunic, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Christine A. Orengo, Arun P. Pandurangan, Catherine Rivoire, Christian J. A. Sigrist, Ian Sillitoe, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Alex Bateman

Summary: The InterPro database has been updated with new data content and website features, providing a more user-friendly access to protein sequence classification and functional domain identification. It has also integrated features from the retiring Pfam website and developed a card game to engage the non-scientific community. Furthermore, the database explores the benefits and challenges of using artificial intelligence for protein structure prediction.

NUCLEIC ACIDS RESEARCH (2023)

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Review Biochemistry & Molecular Biology

Microbiota in health and diseases

Kaijian Hou, Zhuo-Xun Wu, Xuan-Yu Chen, Jing-Quan Wang, Dongya Zhang, Chuanxing Xiao, Dan Zhu, Jagadish B. Koya, Liuya Wei, Jilin Li, Zhe-Sheng Chen

Summary: The role of microbiota in health and disease is significant, contributing to homeostasis and immune regulation. Dysbiosis of microbiota can lead to disease progression, associated with dysregulation of community composition, modulation of host immune response, and induction of chronic inflammation. Clinical approaches utilizing microbiota, such as microbiota modulation and fecal microbial transplantation, can be effective for disease treatment.

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2022)

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Article Biochemistry & Molecular Biology

Long COVID after breakthrough SARS-CoV-2 infection

Ziyad Al-Aly, Benjamin Bowe, Yan Xie

Summary: This study analyzed the US Department of Veterans Affairs national healthcare databases to investigate the occurrence of Long COVID and death risk after breakthrough SARS-CoV-2 infection. The findings showed that vaccination significantly reduced the risk of death and post-acute sequelae but did not eliminate them completely. These results underscore the importance of further research on prevention and post-acute care for breakthrough infections.

NATURE MEDICINE (2022)

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Article Biochemistry & Molecular Biology

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

Donovan H. Parks, Maria Chuvochina, Christian Rinke, Aaron J. Mussig, Pierre-Alain Chaumeil, Philip Hugenholtz

Summary: The Genome Taxonomy Database (GTDB) provides a phylogenetically consistent taxonomy for prokaryotic genomes sourced from the NCBI database. It includes a large number of bacterial and archaeal genomes, highlights the importance of metagenome-assembled genomes, and discusses improvements to the GTDB website and the procedure for updating species clusters.

NUCLEIC ACIDS RESEARCH (2022)

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Article Biochemistry & Molecular Biology

Risks of myocarditis, pericarditis, and cardiac arrhythmias associated with COVID-19 vaccination or SARS-CoV-2 infection

Martina Patone, Xue W. Mei, Lahiru Handunnetthi, Sharon Dixon, Francesco Zaccardi, Manu Shankar-Hari, Peter Watkinson, Kamlesh Khunti, Anthony Harnden, Carol A. C. Coupland, Keith M. Channon, Nicholas L. Mills, Aziz Sheikh, Julia Hippisley-Cox

Summary: The study found that there is an increased risk of myocarditis associated with the first dose of ChAdOx1 and BNT162b2 vaccines, as well as the first and second doses of the mRNA-1273 vaccine in the 1-28 days post-vaccination period. Additionally, individuals with SARS-CoV-2 infection also face a greater risk of myocarditis, pericarditis, and cardiac arrhythmia.

NATURE MEDICINE (2022)

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Review Biochemistry & Molecular Biology

Combination strategies with PD-1/PD-L1 blockade: current advances and future directions

Ming Yi, Xiaoli Zheng, Mengke Niu, Shuangli Zhu, Hong Ge, Kongming Wu

Summary: Antibodies targeting PD-1/PD-L1 revive immune response against cancer cells, but the low response rate calls for combination therapies. Combining with chemotherapy, radiotherapy, and other treatments can achieve better outcomes, and individualized combination selection is needed to overcome treatment resistance.

MOLECULAR CANCER (2022)

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Article Biochemistry & Molecular Biology

The SGLT2 inhibitor empagliflozin in patients hospitalized for acute heart failure: a multinational randomized trial

Adriaan A. Voors, Christiane E. Angermann, John R. Teerlink, Sean P. Collins, Mikhail Kosiborod, Jan Biegus, Joao Pedro Ferreira, Michael E. Nassif, Mitchell A. Psotka, Jasper Tromp, C. Jan Willem Borleffs, Changsheng Ma, Joseph Comin-Colet, Michael Fu, Stefan P. Janssens, Robert G. Kiss, Robert J. Mentz, Yasushi Sakata, Henrik Schirmer, Morten Schou, P. Christian Schulze, Lenka Spinarova, Maurizio Volterrani, Jerzy K. Wranicz, Uwe Zeymer, Shelley Zieroth, Martina Brueckmann, Jonathan P. Blatchford, Afshin Salsali, Piotr Ponikowski

Summary: The sodium-glucose cotransporter 2 inhibitor empagliflozin improves clinical outcomes in patients hospitalized for acute heart failure, regardless of ejection fraction or the presence of diabetes.

NATURE MEDICINE (2022)

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Review Biochemistry & Molecular Biology

AI in health and medicine

Pranav Rajpurkar, Emma Chen, Oishi Banerjee, Eric J. Topol

Summary: This Review discusses the potential of AI to reshape medicine and make healthcare more accurate, efficient, and accessible. It covers recent progress in medical AI, including advances in medical image analysis, non-image data sources, and human-AI collaboration. The article also addresses technical and ethical challenges, such as data scarcity and racial bias.

NATURE MEDICINE (2022)

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Review Biochemistry & Molecular Biology

Therapeutic peptides: current applications and future directions

Lei Wang, Nanxi Wang, Wenping Zhang, Xurui Cheng, Zhibin Yan, Gang Shao, Xi Wang, Rui Wang, Caiyun Fu

Summary: Peptide drug development has achieved significant progress in the past decade, thanks to new production, modification, and analytic technologies. These advancements have addressed the inherent limitations of peptides and have resulted in achievements in various therapeutic areas.

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2022)

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Article Biochemistry & Molecular Biology

KEGG mapping tools for uncovering hidden features in biological data

Minoru Kanehisa, Yoko Sato, Masayuki Kawashima

Summary: KEGG relies on human intelligence to develop biological system models through manually creating pathway maps. These models can be used in biological big data analysis to uncover systemic functions in an organism's genome.

PROTEIN SCIENCE (2022)

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Article Biochemistry & Molecular Biology

Neutralizing antibodies against the SARS-CoV-2 Omicron variant BA.1 following homologous and heterologous CoronaVac or BNT162b2 vaccination

Samuel M. S. Cheng, Chris Ka Pun Mok, Yonna W. Y. Leung, Susanna S. Ng, Karl C. K. Chan, Fanny W. Ko, Chunke Chen, Karen Yiu, Bosco H. S. Lam, Eric H. Y. Lau, Ken K. P. Chan, Leo L. H. Luk, John K. C. Li, Leo C. H. Tsang, Leo L. M. Poon, David S. C. Hui, Malik Peiris

Summary: Specific antibody levels against the SARS-CoV-2 Omicron variant decrease significantly after two doses of BNT162b2 or CoronaVac vaccines, but can be markedly increased with a booster dose of BNT162b2. Individuals who previously received two doses of BNT162b2 or CoronaVac showed reduced serum antibody titers against Omicron, while a BNT162b2 booster dose increased the antibody levels in the majority of individuals. This suggests mRNA vaccine boosters may be necessary in countries primarily using CoronaVac vaccines to combat the spread of Omicron.

NATURE MEDICINE (2022)

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Article Biochemistry & Molecular Biology

mRNA booster immunization elicits potent neutralizing serum activity against the SARS-CoV-2 Omicron variant

Henning Gruell, Kanika Vanshylla, Pinkus Tober-Lau, David Hillus, Philipp Schommers, Clara Lehmann, Florian Kurth, Leif E. Sander, Florian Klein

Summary: This study demonstrates that neutralization of the SARS-CoV-2 Omicron variant is greatly reduced in individuals who received two doses of the COVID-19 vaccine or have recovered from the disease, but is significantly increased after a booster vaccine dose.

NATURE MEDICINE (2022)

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Article Biochemistry & Molecular Biology

The IPD-IMGT/HLA Database

Dominic J. Barker, Giuseppe Maccari, Xenia Georgiou, Michael A. Cooper, Paul Flicek, James Robinson, Steven G. E. Marsh

Summary: The IPD-IMGT/HLA Database is a searchable repository of highly curated HLA sequences for the HLA community. With the adoption of Next Generation Sequencing technology, the database has grown in size, prompting the development of tools for enhanced user experience and programmatic access.

NUCLEIC ACIDS RESEARCH (2023)

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Article Biochemistry & Molecular Biology

PubChem 2023 update

Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A. Shoemaker, Paul A. Thiessen, Bo Yu, Leonid Zaslavsky, Jian Zhang, Evan E. Bolton

Summary: PubChem, a popular chemical information resource, has undergone several changes and improvements. It has added data from over 120 sources and introduced new functionalities, including the integration of Google Patents data, creation of Cell Line and Taxonomy data collections, and updates to the bioassay data model.

NUCLEIC ACIDS RESEARCH (2023)

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