Article
Biochemical Research Methods
Angel Galvez-Merchan, Kyung Hoi (Joseph) Min, Lior Pachter, A. Sina Booeshaghi
Summary: Researchers have developed a command-line tool, ffq, for extracting user data and metadata from genomic databases. The modularity and simplicity of this tool make it applicable to any genomic database that allows programmatic access.
Article
Medicine, General & Internal
Jose Camara, Roberto Rezende, Ivan Miguel Pires, Antonio Cunha
Summary: Public databases provide color images of the optic papilla for research in glaucoma. However, the heterogeneous nature of the images and the lack of certain elements pose challenges. This study aims to improve the structure and content of public databases used for automated screening.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Cell Biology
Elma Zaganjor, Haejin Yoon, Jessica B. Spinelli, Elizabeth R. Nunn, Gaelle Laurent, Paulina Keskinidis, Suganja Sivaloganathan, Shakchhi Joshi, Giulia Notarangelo, Stacy Mulei, Mathew T. Chvasta, Sarah A. Tucker, Krystle Kalafut, Robert A. H. van de Ven, Clary B. Clish, Marcia C. Haigis
Summary: This study provides a temporal analysis of adipocyte differentiation, uncovering early metabolic events that stimulate transcriptional reprogramming.
Article
Computer Science, Artificial Intelligence
Yang Liu, Anthony C. Constantinou
Summary: Learning from data with missing values is a common phenomenon in many domains. However, few Bayesian Network structure learning algorithms consider missing data, and those that do often assume missing data are missing at random. This paper proposes three variants of greedy search structure learning that effectively deal with systematically missing data. Empirical investigations demonstrate that the proposed approach outperforms the commonly used Structural EM algorithm in terms of accuracy and efficiency, regardless of whether the data is missing at random or not.
Article
Chemistry, Physical
Simon Stemplinger, Jeremy Causse, Sylvain Prevost, Stephane Pellet-Rostaing, Thomas Zemb, Dominik Horinek
Summary: This study investigates a derivative of the classic surfactant Aerosol OT with a shorter chain length. The short chain derivative exhibits high solubility and progressively weak aggregation. The hydration of head groups hinders the penetration into hydrophobic cores, resulting in well-defined liquid chain nanodomains. The unusual small angle X-ray scattering pattern is attributed to the sulfonate group of the head groups rather than the aggregate-aggregate interaction.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Letter
Biochemistry & Molecular Biology
Sofia N. Barreira, Anh-Dao Nguyen, Mark T. Fredriksen, Tyra G. Wolfsberg, R. Travis Moreland, Andreas D. Baxevanis
Summary: The study developed a pipeline for generating de novo assemblies of proteomes from 100 animal species across 21 phyla, creating the Animal Proteome Database (AniProtDB) to provide open access to this collection. This solution addresses the issue of limited availability of high-quality proteomic data and enables the utilization of data from nontraditional research organisms for biomedical research.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Xing Chang, Nur Izzah Ismail, Attaur Rahman, Dachun Xu, Renee Wan Yi Chan, Sang-Ging Ong, Sang-Bing Ong
Summary: Although COVID-19 has been categorized as an endemic, the long-term effect of the disease in causing multiorgan disorders, including cardiovascular dysfunction, is gaining attention. The role of cardiac mitochondria in mediating cardiac dysfunction post-SARS-CoV-2 infection remains unclear. Further studies are crucial to unravel the association between SARS-CoV-2 infection, mitochondrial dysfunction, and cardiovascular disorders.
ANTIOXIDANTS & REDOX SIGNALING
(2023)
Article
Multidisciplinary Sciences
Jinjun Gao, Xinlei Sheng, Jianfeng Du, Di Zhang, Chang Han, Yue Chen, Chu Wang, Yingming Zhao
Summary: We developed a new database search strategy called CHiMA, which uses 50% matched fragment ions as the key criterion to identify high-confidence PSMs. Compared to conventional methods, CHiMA identified twice as many histone modification sites in benchmark datasets. Reanalysis of previous proteomics data using CHiMA led to the discovery of 113 new histone marks, almost doubling the number of previously reported marks. This tool not only offers a valuable approach for identifying histone modifications but also greatly expands the repertoire of histone marks.
News Item
Multidisciplinary Sciences
Nidhi Subbaraman
Summary: Evaluation of death certificates from national database reveals a grim situation for pregnant women.
Article
Biochemistry & Molecular Biology
Alex Reed, Timothy Ware, Haoxin Li, J. Fernando Bazan, Benjamin F. Cravatt
Summary: Our study reveals that TMEM164 is an enzyme that plays a crucial role in ferroptosis by producing PUFA ether phospholipids (ePLs). Deletion of TMEM164 reduces the levels of C20:4 ePLs, which in turn affects the sensitivity of cancer cells to ferroptosis. These findings provide important insights into the understanding of this form of cell death.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Cell Biology
Leticia Soriano-Baguet, Melanie Grusdat, Henry Kurniawan, Mohaned Benzarti, Carole Binsfeld, Anouk Ewen, Joseph Longworth, Lynn Bonetti, Luana Guerra, Davide G. Franchina, Takumi Kobayashi, Veronika Horkova, Charlene Verschueren, Sergio Helgueta, Deborah Gerard, Tushar H. More, Antonia Henne, Catherine Dostert, Sophie Farinelle, Antoine Lesur, Jean-Jacques Gerardy, Christian Jager, Michel Mittelbronn, Lasse Sinkkonen, Karsten Hiller, Johannes Meiser, Dirk Brenner
Summary: Pyruvate dehydrogenase (PDH) plays a crucial role in the metabolism and function of T helper 17 (Th17) cells. PDH is necessary for the generation of a glucose-derived citrate pool, which is essential for Th17 cell proliferation, survival, and effector function. In the absence of PDH, Th17 cells exhibit increased glutaminolysis, glycolysis, and lipid uptake, but critically low levels of cellular citrate, leading to impaired oxidative phosphorylation, lipid synthesis, and histone acetylation.
Article
Multidisciplinary Sciences
Vinitha N. Ragavan, Pramod C. Nair, Natalia Jarzebska, Ramcharan Singh Angom, Luana Ruta, Elisa Bianconi, Silvia Grottelli, Natalia D. Tararova, Daniel Ryazanskiy, Steven R. Lentz, Sara Tommasi, Jens Martens-Lobenhoffer, Toshiko Suzuki-Yamamoto, Masumi Kimoto, Elena Rubets, Sarah Chau, Yingjie Chen, Xinli Hu, Nadine Bernhardt, Peter M. Spieth, Norbert Weiss, Stefan R. Bornstein, Debabrata Mukhopadhyay, Stefanie M. Bode-Boeger, Renke Maas, Ying Wang, Antonio Macchiarulo, Arduino A. Mangoni, Barbara Cellini, Roman N. Rodionov
Summary: An international consortium of research groups used various methods to investigate whether DDAH2 directly metabolizes ADMA, the risk factor for cardiovascular disease. Their findings unanimously showed that DDAH2 is unable to metabolize ADMA, resolving a 20-year controversy and providing a starting point for exploring alternative functions of DDAH2.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Amit Kumar Singh Gautam, Houqing Yu, Christopher Yellman, Adrian H. Elcock, Andreas Matouschek
Summary: The proteasome is a powerful intracellular protease that can degrade any protein, self or foreign, through ubiquitin tagging. It consists of approximately 33 subunits, and their assembly and activity are regulated by post-translational modifications on long disordered regions of the subunits. Molecular modeling and biochemical experiments have shown that some disordered regions of proteasome subunits access the substrate recognition sites and are constructed from amino acid sequences that escape recognition.
Article
Microbiology
Epshita M. Islam, Jamie C. Fegan, Takele Tefera, David Curran, Regula Waeckerlin, Dixon Ng, Sang Kyun Ahn, Chun Heng Royce Lai, Quynh Huong Nguyen, Megha W. Shah, Liyuwork Tesfaw, Kassaye Adamu, Wubet Medhin, Abinet Legesse, Getaw Deresse, Belayneh Getachew, Neil B. Rawlyk, Brock D. Evans, Andrew F. Potter, Anthony Schryvers, Scott Gray-Owen, Trevor Moraes
Summary: The researchers discovered a predicted lipoprotein called PmSLP that can be used as a new vaccine to prevent hemorrhagic septicemia (HS) and bovine respiratory disease (BRD) in cattle. They found that PmSLP provides immune protection, especially in cattle. This study offers an effective and cost-effective solution for preventing related infections.
Editorial Material
Biology
Samuel Brudner, Thierry Emonet
Summary: A computational model explains the importance of pausing and sniffing the air for animals to track scents when they are far away from the source.
Article
Microbiology
Sina M. Adl, David Bass, Christopher E. Lane, Julius Lukes, Conrad L. Schoch, Alexey Smirnov, Sabine Agatha, Cedric Berney, Matthew W. Brown, Fabien Burki, Paco Cardenas, Ivan Cepicka, Lyudmila Chistyakova, Javier del Campo, Micah Dunthorn, Bente Edvardsen, Yana Eglit, Laure Guillou, Vladimir Hampl, Aaron A. Heiss, Mona Hoppenrath, Timothy Y. James, Anna Karnkowska, Sergey Karpov, Eunsoo Kim, Martin Kolisko, Alexander Kudryavtsev, Daniel J. G. Lahr, Enrique Lara, Line Le Gall, Denis H. Lynn, David G. Mann, Ramon Massana, Edward A. D. Mitchell, Christine Morrow, Jong Soo Park, Jan W. Pawlowski, Martha J. Powell, Daniel J. Richter, Sonja Rueckert, Lora Shadwick, Satoshi Shimano, Frederick W. Spiegel, Guifre Torruella, Noha Youssef, Vasily Zlatogursky, Qianqian Zhang
JOURNAL OF EUKARYOTIC MICROBIOLOGY
(2019)
Article
Ecology
Yuichiro Kashiyama, Akiko Yokoyama, Takashi Shiratori, Sebastian Hess, Fabrice Not, Charles Bachy, Andres Gutierrez-Rodriguez, Jun Kawahara, Toshinobu Suzaki, Masami Nakazawa, Takahiro Ishikawa, Moe Maruyama, Mengyun Wang, Man Chen, Yingchun Gong, Kensuke Seto, Maiko Kagami, Yoko Hamamoto, Daiske Honda, Takahiro Umetani, Akira Shihongi, Motoki Kayama, Toshiki Matsuda, Junya Taira, Akinori Yabuki, Masashi Tsuchiya, Yoshihisa Hirakawa, Akane Kawaguchi, Mami Nomura, Atsushi Nakamura, Noriaki Namba, Mitsufumi Matsumoto, Tsuyoshi Tanaka, Tomoko Yoshino, Rina Higuchi, Akihiro Yamamoto, Tadanobu Maruyama, Aika Yamaguchi, Akihiro Uzuka, Shinya Miyagishima, Goro Tanifuji, Masanobu Kawachi, Yusuke Kinoshita, Hitoshi Tamiaki
Article
Microbiology
Galina Prokopchuk, Daria Tashyreva, Akinori Yabuki, Ales Horak, Petra Masarova, Julius Lukes
Article
Ecology
Sandra Jeudy, Lionel Bertaux, Jean-Marie Alempic, Audrey Lartigue, Matthieu Legendre, Lucid Belmudes, Sebastien Santini, Nadege Philippe, Laure Beucher, Emanuele G. Biondi, Sissel Juul, Daniel J. Turner, Yohann Coute, Jean-Michel Claverie, Chantal Abergel
Article
Virology
Eugene Christo-Foroux, Jean-Marie Alempic, Audrey Lartigue, Sebastien Santini, Karine Labadie, Matthieu Legendre, Chantal Abergel, Jean-Michel Claverie
JOURNAL OF VIROLOGY
(2020)
Article
Multidisciplinary Sciences
Tristan Cordier, Ines Barrenechea Angeles, Nicolas Henry, Franck Lejzerowicz, Cedric Berney, Raphael Morard, Angelika Brandt, Marie-Anne Cambon-Bonavita, Lionel Guidi, Fabien Lombard, Pedro Martinez Arbizu, Ramon Massana, Covadonga Orejas, Julie Poulain, Craig R. Smith, Patrick Wincker, Sophie Arnaud-Haond, Andrew J. Gooday, Colomban de Vargas, Jan Pawlowski
Summary: Remote deep-ocean sediment ecosystems have high biodiversity, with benthic communities being three times more diverse than pelagic realms. These communities are influenced by ocean basins and particulate organic carbon flux from the upper ocean. The presence of plankton DNA in the DOS predicts variations in surface POC export and reveals previously overlooked taxa that may play a role in the biological carbon pump.
Article
Biochemistry & Molecular Biology
Ruben Gonzalez-Miguens, Carmen Soler-Zamora, Fernando Useros, Sandra Nogal-Prata, Cedric Berney, Andres Blanco-Rotea, Maria Isabel Carrasco-Braganza, David De Salvador-Velasco, Antonio Guillen-Oterino, Daniel Tenorio-Rodriguez, David Velazquez, Thierry J. Heger, Isabel Sanmartin, Enrique Lara
Summary: The study shows that crossing the salinity barrier allows organisms to access new ecosystems and experience significant shifts in diversification rates while adapting to changes in selective pressures. Analysis suggests that freshwater environments have triggered four independent transitions since the mid-Miocene, with ancestral euryhaline species adapting to fluctuating salinity levels.
Article
Biochemistry & Molecular Biology
Euki Yazaki, Akinori Yabuki, Ayaka Imaizumi, Keitaro Kume, Tetsuo Hashimoto, Yuji Inagaki
Summary: By clarifying the phylogenetic positions of 'orphan' protists, this study reveals the novel affiliation between major lineages in eukaryotes. The analysis of a 319-gene alignment demonstrates that M. maris represents a basal lineage of Cryptista and proposes a new clade name 'Pancryptista'. Additionally, M. maris is found to be a key taxon for recovering the monophyly of Archaeplastida and the sister relationship between Archaeplastida and Pancryptista.
Article
Biology
Daniel J. Richter, Romain Watteaux, Thomas Vannier, Jade Leconte, Paul Fremont, Gabriel Reygondeau, Nicolas Maillet, Nicolas Henry, Gaetan Benoit, Ophelie Da Silva, Tom O. Delmont, Antonio Fernandez-Guerra, Samir Suweis, Romain Narci, Cedric Berney, Damien Eveillard, Frederick Gavory, Lionel Guidi, Karine Labadie, Eric Mahieu, Julie Poulain, Sarah Romac, Simon Roux, Celine Dimier, Stefanie Kandels, Marc Picheral, Sarah Searson, Tara Oceans Coordinators, Stephane Pesant, Jean-Marc Aury, Jennifer R. Brum, Claire Lemaitre, Eric Pelletier, Peer Bork, Shinichi Sunagawa, Fabien Lombard, Lee Karp-Boss, Chris Bowler, Matthew B. Sullivan, Eric Karsenti, Mahendra Mariadassou, Ian Probert, Pierre Peterlongo, Patrick Wincker, Colomban de Vargas, Maurizio Ribera D'Alcala, Daniele Iudicone, Olivier Jaillon
Summary: This study assesses the global structure of plankton geography by analyzing metagenomes of plankton communities sampled from oceans worldwide. The findings demonstrate the influence of ocean currents on plankton biogeography and reveal characteristic timescales of community dynamics.
Article
Microbiology
Akinori Yabuki, Akihiro Tame, Keiko Mizuno
Summary: Apusomonadida is a group of heterotrophic biflagellates that feed on bacteria and small protists. In this study, a new species called Podomonas kaiyoae was discovered from deep-sea sediment and can be maintained in pure culture.
JOURNAL OF EUKARYOTIC MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Sofia Rigou, Sebastien Santini, Chantal Abergel, Jean-Michel Claverie, Matthieu Legendre
Summary: This study reveals the abundance and diversity of giant viruses in soil through permafrost metagenomics, showing a unique diversity pattern and a high proportion of sequence coverage. Additionally, gene transfers between different viral families were also discovered.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Sebastien Santini, Quentin Schenkelaars, Cyril Jourda, Marc Duchesne, Hassiba Belahbib, Caroline Rocher, Marjorie Selva, Ana Riesgo, Michel Vervoort, Sally P. Leys, Laurent Kodjabachian, Andre Le Bivic, Carole Borchiellini, Jean-Michel Claverie, Emmanuelle Renard
Summary: This study analyzed the genome of the glass sponge Oopsacas minuta and found that its genome is small and lacks several key genes for metazoan development. The study also provided the complete genome of a new archaea species in the sponge's symbiotic microbial community.
Article
Virology
Jean-Marie Alempic, Audrey Lartigue, Artemiy E. E. Goncharov, Guido Grosse, Jens Strauss, Alexey N. N. Tikhonov, Alexander N. N. Fedorov, Olivier Poirot, Matthieu Legendre, Sebastien Santini, Chantal Abergel, Jean-Michel Claverie
Summary: A quarter of the Northern hemisphere is covered by permafrost, releasing organic matter and reviving ancient viruses and microbial cells as it thaws due to climate warming, contributing to greenhouse gas emissions. While previous studies mainly focused on bacteria in permafrost, this study reports the preliminary characterization of 13 new viruses isolated from ancient Siberian permafrost samples, suggesting that zombie viruses are not as rare as previously believed. This highlights the potential public health threat of these revived viruses.
Article
Multidisciplinary Sciences
Masaru Kawato, Takao Yoshida, Masaki Miya, Shinji Tsuchida, Yuriko Nagano, Michiyasu Nomura, Akinori Yabuki, Yoshihiro Fujiwara, Katsunori Fujikura
Summary: The study presents a modified eDNA extraction protocol that significantly increases the amount of eDNA extracted from pumped deep-sea water. The use of Platinum SuperFi II DNA polymerase in PCR amplification improved the efficiency of amplifying trace amounts of MiFish targets in eDNA extracted from deep-sea water while effectively suppressing nonspecific amplifications. This improved procedure resulted in the acquisition of abundant sequence reads of deep-sea fish through next generation sequencing.
Article
Chemistry, Analytical
Tomo Kitahashi, Ryota Nakajima, Hidetaka Nomaki, Masashi Tsuchiya, Akinori Yabuki, Sojiro Yamaguchi, Chunmao Zhu, Yugo Kanaya, Dhugal J. Lindsay, Sanae Chiba, Katsunori Fujikura
Summary: The study found that smaller plastic particles have lower reflectance and weaker peak intensities under wet conditions compared to larger particles. Robust classification models constructed using hyperspectral data can accurately identify polymer types regardless of particle size or filter wetness.
ANALYTICAL METHODS
(2021)