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3,447 results on '"Li, Wen-Jun"'

64. LILRB2/PirB mediates macrophage recruitment in fibrogenesis of nonalcoholic steatohepatitis

Author

Li, Dan-Pei, Huang, Li, Kan, Ran-Ran, Meng, Xiao-Yu, Wang, Shu-Yun, Zou, Hua-Jie, Guo, Ya-Ming, Luo, Pei-Qiong, Pan, Li-Meng, Xiang, Yu-Xi, Mao, Bei-Bei, Xie, Yu-Yu, Wang, Zhi-Han, Yang, Min, He, Rui, Yang, Yan, Liu, Zhe-Long, Xie, Jun-Hui, Ma, De-Lin, Zhang, Ben-Ping, Shao, Shi-Ying, Chen, Xi, Xu, Si-Miao, He, Wen-Tao, Li, Wen-Jun, Chen, Yong, and Yu, Xue-Feng

Published
2023
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69. Synthesis and characterization of marine seagrass (Cymodocea serrulata) mediated titanium dioxide nanoparticles for antibacterial, antibiofilm and antioxidant properties

Author

Narayanan, Mohankumar, Srinivasan, Suganthi, Gnanasekaran, Chackaravarthi, Ramachandran, Govindan, Chelliah, Chenthis Kanisha, Rajivgandhi, Govindan, Maruthupandy, Muthuchamy, Quero, Franck, Li, Wen-Jun, Hayder, Gasim, Khaled, Jamal M., Arunachalam, Arulraj, and Manoharan, Natesan

Published
2024
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72. Insight into the function and evolution of the Wood–Ljungdahl pathway in Actinobacteria

Author

Jiao, Jian-Yu, Fu, Li, Hua, Zheng-Shuang, Liu, Lan, Salam, Nimaichand, Liu, Peng-Fei, Lv, Ai-Ping, Wu, Geng, Xian, Wen-Dong, Zhu, Qiyun, Zhou, En-Min, Fang, Bao-Zhu, Oren, Aharon, Hedlund, Brian P, Jiang, Hong-Chen, Knight, Rob, Cheng, Lei, and Li, Wen-Jun

Subjects
Biotechnology, Genetics, Actinobacteria, Aldehyde Oxidoreductases, Carbon Monoxide, Multienzyme Complexes, Environmental Sciences, Biological Sciences, Technology, Microbiology
Abstract

Carbon fixation by chemoautotrophic microbes such as homoacetogens had a major impact on the transition from the inorganic to the organic world. Recent reports have shown the presence of genes for key enzymes associated with the Wood-Ljungdahl pathway (WLP) in the phylum Actinobacteria, which adds to the diversity of potential autotrophs. Here, we compiled 42 actinobacterial metagenome-assembled genomes (MAGs) from new and existing metagenomic datasets and propose three novel classes, Ca. Aquicultoria, Ca. Geothermincolia and Ca. Humimicrobiia. Most members of these classes contain genes coding for acetogenesis through the WLP, as well as a variety of hydrogenases (NiFe groups 1a and 3b-3d; FeFe group C; NiFe group 4-related hydrogenases). We show that the three classes acquired the hydrogenases independently, yet the carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS) was apparently present in their last common ancestor and was inherited vertically. Furthermore, the Actinobacteria likely donated genes for CODH/ACS to multiple lineages within Nitrospirae, Deltaproteobacteria (Desulfobacterota), and Thermodesulfobacteria through multiple horizontal gene transfer events. Finally, we show the apparent growth of Ca. Geothermincolia and H2-dependent acetate production in hot spring enrichment cultures with or without the methanogenesis inhibitor 2-bromoethanesulfonate, which is consistent with the proposed homoacetogenic metabolism.

Published
2021

75. User-item matching for recommendation fairness

Author

Dong, Qiang, Xie, Shuang-Shuang, and Li, Wen-Jun

Subjects
Computer Science - Information Retrieval, Computer Science - Social and Information Networks
Abstract

As we all know, users and item-providers are two main parties of participants in recommender systems. However, most existing research efforts on recommendation were focused on better serving users and overlooked the purpose of item-providers. This paper is devoted to improve the item exposure fairness for item-providers' objective, and keep the recommendation accuracy not decreased or even improved for users' objective. We propose to set stock volume constraints on items, to be specific, limit the maximally allowable recommended times of an item to be proportional to the frequency of its being interacted in the past, which is validated to achieve superior item exposure fairness to common recommenders and thus mitigates the Matthew Effect on item popularity. With the two constraints of pre-existing recommendation length of users and our stock volumes of items, a heuristic strategy based on normalized scores and a Minimum Cost Maximum Flow (MCMF) based model are proposed to solve the optimal user-item matching problem, whose accuracy performances are even better than that of baseline algorithm in regular recommendation context, and in line with state-of-the-art enhancement of the baseline. What's more, our MCMF based strategy is parameter-free, while those counterpart algorithms have to resort to parameter traversal process to achieve their best performance.

Published
2020
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80. Investigation of a kind of neutrino mass matrix

Author

Huang, Chao-Shang and Li, Wen-Jun

Subjects
High Energy Physics - Phenomenology
Abstract

We carry out diagonalization of a kind of Majorana neutrino mass matrix $M=M_\nu M_\nu^\dagger$ of which Real part and Imaginary part are commutative. For the kind of matrix M, it is shown in a model-independent way that $\delta = \pm\pi/2$ which implies the maximal strength of CP violation in neutrino oscillations and atmospherical mixing angle would be in the ranges, $\pi/4 < \theta_{23} < 3\pi/4$, or $-3\pi/4<\theta_{23} < - \pi/4$. It is shown that the kind of Hermitian Majorana neutrino mass matrix M has only five real parameters and furthermore, only one free real parameter (A or D) if using the measured values of three mixing angles and mass squared differences as inputs., Comment: 14 pages

Published
2019
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82. Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways.

Author

De Anda, Valerie, Chen, Lin-Xing, Dombrowski, Nina, Hua, Zheng-Shuang, Jiang, Hong-Chen, Banfield, Jillian F, Li, Wen-Jun, and Baker, Brett J

Subjects
Archaea, Carbon, Methane, RNA, Ribosomal, 16S, Hot Springs, Phylogeny, Species Specificity, Genome, Archaeal, Geography, Geologic Sediments, China, Metagenome, Carbon Cycle, Hydrothermal Vents, RNA, Ribosomal, 16S, Genome, Archaeal
Abstract

Geothermal environments, such as hot springs and hydrothermal vents, are hotspots for carbon cycling and contain many poorly described microbial taxa. Here, we reconstructed 15 archaeal metagenome-assembled genomes (MAGs) from terrestrial hot spring sediments in China and deep-sea hydrothermal vent sediments in Guaymas Basin, Gulf of California. Phylogenetic analyses of these MAGs indicate that they form a distinct group within the TACK superphylum, and thus we propose their classification as a new phylum, 'Brockarchaeota', named after Thomas Brock for his seminal research in hot springs. Based on the MAG sequence information, we infer that some Brockarchaeota are uniquely capable of mediating non-methanogenic anaerobic methylotrophy, via the tetrahydrofolate methyl branch of the Wood-Ljungdahl pathway and reductive glycine pathway. The hydrothermal vent genotypes appear to be obligate fermenters of plant-derived polysaccharides that rely mostly on substrate-level phosphorylation, as they seem to lack most respiratory complexes. In contrast, hot spring lineages have alternate pathways to increase their ATP yield, including anaerobic methylotrophy of methanol and trimethylamine, and potentially use geothermally derived mercury, arsenic, or hydrogen. Their broad distribution and their apparent anaerobic metabolic versatility indicate that Brockarchaeota may occupy previously overlooked roles in anaerobic carbon cycling.

Published
2021

83. Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan

Author

Thomas, Scott C, Payne, Devon, Tamadonfar, Kevin O, Seymour, Cale O, Jiao, Jian-Yu, Murugapiran, Senthil K, Lai, Dengxun, Lau, Rebecca, Bowen, Benjamin P, Silva, Leslie P, Louie, Katherine B, Huntemann, Marcel, Clum, Alicia, Spunde, Alex, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Chen, I-Min, Stamatis, Dimitrios, Reddy, TBK, O’Malley, Ronan, Daum, Chris, Shapiro, Nicole, Ivanova, Natalia, Kyrpides, Nikos C, Woyke, Tanja, Eloe-Fadrosh, Emiley, Hamilton, Trinity L, Dijkstra, Paul, Dodsworth, Jeremy A, Northen, Trent R, Li, Wen-Jun, and Hedlund, Brian P

Subjects
Biological Sciences, Genetics, Biotechnology, Human Genome, exometabolomics, thermophile, genomics, Chloroflexi, Thermoflexus, Thermoflexus hugenholtzii, metagenome-assembled genomes, Environmental Science and Management, Soil Sciences, Microbiology, Medical microbiology
Abstract

Thermoflexus hugenholtzii JAD2T, the only cultured representative of the Chloroflexota order Thermoflexales, is abundant in Great Boiling Spring (GBS), NV, United States, and close relatives inhabit geothermal systems globally. However, no defined medium exists for T. hugenholtzii JAD2T and no single carbon source is known to support its growth, leaving key knowledge gaps in its metabolism and nutritional needs. Here, we report comparative genomic analysis of the draft genome of T. hugenholtzii JAD2T and eight closely related metagenome-assembled genomes (MAGs) from geothermal sites in China, Japan, and the United States, representing "Candidatus Thermoflexus japonica," "Candidatus Thermoflexus tengchongensis," and "Candidatus Thermoflexus sinensis." Genomics was integrated with targeted exometabolomics and 13C metabolic probing of T. hugenholtzii. The Thermoflexus genomes each code for complete central carbon metabolic pathways and an unusually high abundance and diversity of peptidases, particularly Metallo- and Serine peptidase families, along with ABC transporters for peptides and some amino acids. The T. hugenholtzii JAD2T exometabolome provided evidence of extracellular proteolytic activity based on the accumulation of free amino acids. However, several neutral and polar amino acids appear not to be utilized, based on their accumulation in the medium and the lack of annotated transporters. Adenine and adenosine were scavenged, and thymine and nicotinic acid were released, suggesting interdependency with other organisms in situ. Metabolic probing of T. hugenholtzii JAD2T using 13C-labeled compounds provided evidence of oxidation of glucose, pyruvate, cysteine, and citrate, and functioning glycolytic, tricarboxylic acid (TCA), and oxidative pentose-phosphate pathways (PPPs). However, differential use of position-specific 13C-labeled compounds showed that glycolysis and the TCA cycle were uncoupled. Thus, despite the high abundance of Thermoflexus in sediments of some geothermal systems, they appear to be highly focused on chemoorganotrophy, particularly protein degradation, and may interact extensively with other microorganisms in situ.

Published
2021

91. Roadmap for naming uncultivated Archaea and Bacteria

Author

Murray, Alison E, Freudenstein, John, Gribaldo, Simonetta, Hatzenpichler, Roland, Hugenholtz, Philip, Kämpfer, Peter, Konstantinidis, Konstantinos T, Lane, Christopher E, Papke, R Thane, Parks, Donovan H, Rossello-Mora, Ramon, Stott, Matthew B, Sutcliffe, Iain C, Thrash, J Cameron, Venter, Stephanus N, Whitman, William B, Acinas, Silvia G, Amann, Rudolf I, Anantharaman, Karthik, Armengaud, Jean, Baker, Brett J, Barco, Roman A, Bode, Helge B, Boyd, Eric S, Brady, Carrie L, Carini, Paul, Chain, Patrick SG, Colman, Daniel R, DeAngelis, Kristen M, de los Rios, Maria Asuncion, Estrada-de los Santos, Paulina, Dunlap, Christopher A, Eisen, Jonathan A, Emerson, David, Ettema, Thijs JG, Eveillard, Damien, Girguis, Peter R, Hentschel, Ute, Hollibaugh, James T, Hug, Laura A, Inskeep, William P, Ivanova, Elena P, Klenk, Hans-Peter, Li, Wen-Jun, Lloyd, Karen G, Löffler, Frank E, Makhalanyane, Thulani P, Moser, Duane P, Nunoura, Takuro, Palmer, Marike, Parro, Victor, Pedrós-Alió, Carlos, Probst, Alexander J, Smits, Theo HM, Steen, Andrew D, Steenkamp, Emma T, Spang, Anja, Stewart, Frank J, Tiedje, James M, Vandamme, Peter, Wagner, Michael, Wang, Feng-Ping, Yarza, Pablo, Hedlund, Brian P, and Reysenbach, Anna-Louise

Subjects
Microbiology, Biological Sciences, Ecology, Archaea, Bacteria, DNA, Bacterial, Metagenome, Phylogeny, Prokaryotic Cells, Sequence Analysis, DNA, Terminology as Topic, Medical Microbiology
Abstract

The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.

Published
2020

92. Clades of huge phages from across Earth’s ecosystems

Author

Al-Shayeb, Basem, Sachdeva, Rohan, Chen, Lin-Xing, Ward, Fred, Munk, Patrick, Devoto, Audra, Castelle, Cindy J, Olm, Matthew R, Bouma-Gregson, Keith, Amano, Yuki, He, Christine, Méheust, Raphaël, Brooks, Brandon, Thomas, Alex, Lavy, Adi, Matheus-Carnevali, Paula, Sun, Christine, Goltsman, Daniela SA, Borton, Mikayla A, Sharrar, Allison, Jaffe, Alexander L, Nelson, Tara C, Kantor, Rose, Keren, Ray, Lane, Katherine R, Farag, Ibrahim F, Lei, Shufei, Finstad, Kari, Amundson, Ronald, Anantharaman, Karthik, Zhou, Jinglie, Probst, Alexander J, Power, Mary E, Tringe, Susannah G, Li, Wen-Jun, Wrighton, Kelly, Harrison, Sue, Morowitz, Michael, Relman, David A, Doudna, Jennifer A, Lehours, Anne-Catherine, Warren, Lesley, Cate, Jamie HD, Santini, Joanne M, and Banfield, Jillian F

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, 2.2 Factors relating to the physical environment, Generic health relevance, Amino Acyl-tRNA Synthetases, Animals, Bacteria, Bacteriophages, Biodiversity, CRISPR-Cas Systems, Earth, Planet, Ecosystem, Evolution, Molecular, Gene Expression Regulation, Bacterial, Gene Expression Regulation, Viral, Genome, Viral, Host Specificity, Humans, Lakes, Molecular Sequence Annotation, Oceans and Seas, Phylogeny, Prophages, Protein Biosynthesis, RNA, Transfer, Ribosomal Proteins, Seawater, Soil Microbiology, Transcription, Genetic, General Science & Technology
Abstract

Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.

Published
2020

93. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.

Author

Zhu, Qiyun, Mai, Uyen, Pfeiffer, Wayne, Janssen, Stefan, Asnicar, Francesco, Sanders, Jon G, Belda-Ferre, Pedro, Al-Ghalith, Gabriel A, Kopylova, Evguenia, McDonald, Daniel, Kosciolek, Tomasz, Yin, John B, Huang, Shi, Salam, Nimaichand, Jiao, Jian-Yu, Wu, Zijun, Xu, Zhenjiang Z, Cantrell, Kalen, Yang, Yimeng, Sayyari, Erfan, Rabiee, Maryam, Morton, James T, Podell, Sheila, Knights, Dan, Li, Wen-Jun, Huttenhower, Curtis, Segata, Nicola, Smarr, Larry, Mirarab, Siavash, and Knight, Rob

Subjects
Bacteria, Archaea, Evolution, Molecular, Phylogeny, Genome, Bacterial, Genome, Archaeal
Abstract

Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer "core" genes, such as the ribosomal proteins. The robustness of the results was tested with respect to several variables, including taxon and site sampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, and the impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide an updated view of domain-level relationships.

Published
2019

100. Vitamins and SARS-CoV-2

Author

Hussain, Firasat, primary, Rahim, Kashif, additional, Siddique, Ateeqah, additional, Ur Rehman, Shafeeq, additional, Shafqat, Furqan, additional, Shuaib, Muhammad, additional, Kalim, Muhammad, additional, and Li, Wen-Jun, additional

Published
2023
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