Article
Biochemistry & Molecular Biology
Neel Prabh, Christian Roedelsperger
Summary: The birth of new genes is a major driving force behind phenotypic diversity in all life forms. Previous studies have focused on the duplication of existing protein-coding material as the main process of new gene formation, but recent research has found that transcriptionally active sequences can also be a rich source of new genes. However, the high birth rates of these new genes have to be balanced with the loss rates in order to explain the dominance of ancient gene families in individual genomes. In this study, the researchers tested the hypothesis of rapid turnover in the nematode model organism Pristionchus pacificus. By sequencing the genomes of six divergent P. pacificus strains, they studied the evolutionary dynamics of different age classes and categories of origin at a population level. They found that de novo candidates, new genes that are not derived from duplication and divergence of known genes, are typically shorter, show less expression, and are overrepresented on the sex chromosome. In addition, the researchers discovered that de novo candidates have higher attrition rates compared to known genes within the same age class. These findings provide empirical evidence for the rapid turnover hypothesis and emphasize the importance of considering the evolutionary timescale when studying new gene formation.
Article
Biochemistry & Molecular Biology
Marc Tollis, Elliott Ferris, Michael S. Campbell, Valerie K. Harris, Shawn M. Rupp, Tara M. Harrison, Wendy K. Kiso, Dennis L. Schmitt, Michael M. Garner, Christina Athena Aktipis, Carlo C. Maley, Amy M. Boddy, Mark Yandell, Christopher Gregg, Joshua D. Schiffman, Lisa M. Abegglen
Summary: Disease susceptibility and resistance are crucial for the conservation of endangered species like elephants. Research found that Asian elephants are more prone to tumors and malignancies compared to African elephants, and show higher susceptibility to tuberculosis and elephant endotheliotropic herpesvirus. Genetic regulation plays a significant role in the differential inflammatory response between Asian and African elephants, leading to increased susceptibility to infectious diseases and cancer in Asian elephants.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biology
Kaleb Abram, Zulema Udaondo, Carissa Bleker, Visanu Wanchai, Trudy M. Wassenaar, Michael S. Robeson, David W. Ussery
Summary: In this study, over 100,000 publicly available Escherichia coli and Shigella genome sequences were analyzed using Mash-based analysis to identify 14 unique phylogroups. The results revealed that most of the sequenced E. coli genomes belong to four distinct phylogroups.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Dahu Zou, Shilin Tian, Tongzuo Zhang, Nima Zhuoma, Guosheng Wu, Muyang Wang, Lu Dong, Stephen J. Rossiter, Huabin Zhao
Summary: Vultures, with their rare dietary specialization of obligate scavenging, provide essential ecological services but many species are endangered. Research suggests that their unique adaptations may have led to low genetic diversity, making them particularly vulnerable to human activities.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Juan J. Roda-Garcia, Jose M. Haro-Moreno, Francisco Rodriguez-Valera, Salvador Almagro-Moreno, Mario Lopez-Perez
Summary: The SAR86 clade of bacteria shows genome reduction and relies on co-occurring microbes for survival in the marine environment, as evidenced by the streamlined genomes, reduced biosynthesis of essential molecules, and decreased ability to sense and respond to environmental factors.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Plant Sciences
Beibei Liu, Aiko Iwata-Otsubo, Diya Yang, Robert L. Baker, Chun Liang, Scott A. Jackson, Shengyi Liu, Jianxin Ma, Meixia Zhao
Summary: In this study, it was found that the TNP2-like transposase genes of Bot1 transposable elements in Brassica oleracea retain three AT-rich introns, while these introns were lost in the majority of the Bot1 elements in Brassica rapa. Additionally, a recent burst of transposition of Bot1 was observed in B. oleracea, but not in B. rapa. Analysis of small RNAs showed different populations in B. oleracea compared to B. rapa, indicating the differential activity and silencing of the Bot1 family in the two closely related Brassica species.
Article
Biochemistry & Molecular Biology
Zheng-Shan He, Andan Zhu, Jun-Bo Yang, Weishu Fan, De-Zhu Li
Summary: By utilizing different sequencing technologies such as PacBio, Iso-seq, and Illumina, combined with direct evidence, the chloroplast and mitochondrial genomes of N. 'Joey Tomocik' were assembled and analyzed in this study. Multiple intermediates during intron-splicing were observed, along with their interplay with RNA editing. Additionally, similar features were found in RNA editing sites in both organelles, suggesting a common evolutionary origin and shared editing machinery.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Xiaofei Yang, Shenghan Gao, Li Guo, Bo Wang, Yanyan Jia, Jian Zhou, Yizhuo Che, Peng Jia, Jiadong Lin, Tun Xu, Jianyong Sun, Kai Ye
Summary: The authors reported the genome assemblies of three Papaver species and the evolution of benzylisoquinoline alkaloids biosynthetic pathway, demonstrating the importance of gene recruitment and structural rearrangements in evolving metabolic pathways.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Matthew G. Durrant, Ami S. Bhatt
Summary: Research reveals that small open reading frames (smORFs) and their encoded microproteins play central roles in microbes, with a vast unexplored space of smORFs within human-associated microbes. The introduction of SmORFinder combines profile hidden Markov models and deep learning models to predict small protein families enriched for Ribo-seq translation signals. Deep learning models are shown to identify Shine-Dalgarno sequences, deprioritize the wobble position in each codon, and group codon synonyms.
CELL HOST & MICROBE
(2021)
Article
Microbiology
Nomfundo Ntombizinhle Nsele, Tiara Padayachee, David R. Nelson, Khajamohiddin Syed
Summary: This study observed the presence of different cytochrome P450 families in saprophytic and ectomycorrhizal fungi, with only four families being conserved across all species. It was found that the switch from a saprophytic to an ectomycorrhizal lifestyle led to the development of diverse P450 families as well as the loss of certain families, resulting in lower P450 family diversity in ectomycorrhizal fungi.
Article
Biochemistry & Molecular Biology
Lei Xia, Han Wang, Xiaokun Zhao, Hesbon Ochieng Obel, Xiaqing Yu, Qunfeng Lou, Jinfeng Chen, Chunyan Cheng
Summary: This study constructed the first cucumber chloroplast pan-genome based on 121 cucumber germplasms, and investigated genetic variations and gene expression changes in cucumber chloroplast genome. The results revealed more genetic variation in Indian ecotype cucumbers compared to other cultivars, and classified the cucumber germplasms into three types based on phylogenetic analysis. The transcriptomic analysis showed the up-regulation of matK gene and higher editing efficiency of accD gene under temperature stresses, indicating the response and adaptation mechanisms of cucumber chloroplasts to temperature adversity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Krishna Neupane, Meng Zhao, Aaron Lyons, Sneha Munshi, Sandaru M. Ileperuma, Dustin B. Ritchie, Noel Q. Hoffer, Abhishek Narayari, Michael T. Woodside
Summary: The RNA pseudoknot of SARS-CoV-2 that induces programmed ribosomal frameshifting is a potential drug target. Through optical tweezer experiments, researchers identified two pseudoknotted conformers with distinct topologies and revealed the folding mechanism of the frameshift signal, shedding light on its conformational heterogeneity and implications for drug discovery based on structure.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Laura Henao, Ramin Shirali Hossein Zade, Silvia Restrepo, Johana Husserl, Thomas Abeel
Summary: This study investigated the taxonomic classification, pathogenicity, and unique secondary metabolites of four Streptomyces isolates. Two isolates were identified as putative new species, while the other two isolates were non-toxin-producing pathogens. The study also discovered novel secondary metabolites and potential medicinal compounds produced by these isolates.
Article
Chemistry, Multidisciplinary
Guoping Li, Aidan C. Manning, Alex Bagi, Xinyu Yang, Priyanka Gokulnath, Michail Spanos, Jonathan Howard, Patricia P. Chan, Thadryan Sweeney, Robert Kitchen, Haobo Li, Brice D. Laurent, Sary F. Aranki, Maria Kontaridis, Louise C. Laurent, Kendall Van Keuren-Jensen, Jochen Muehlschlegel, Todd M. Lowe, Saumya Das
Summary: The study highlights the crucial role of transfer RNA-derived small RNAs in different stress responses and introduces a new sequencing technique for generating a comprehensive abundance landscape of cellular and extracellular tDRs. It also reveals that extracellular tDRs have distinct fragmentation signatures which are better indicators of different stress responses than miRNAs.
Article
Biochemistry & Molecular Biology
Bin Zheng, Sarah Gold, Marta Iwanaszko, Benjamin Charles Howard, Lu Wang, Ali Shilatifard
Summary: Bromodomains of BRD4 are not necessary for Pol II pause release, instead, a C-terminal motif that interacts with PTEFb is both necessary and sufficient for this function.
Article
Multidisciplinary Sciences
Chak Kwong Cheng, Xiao Lin, Yujie Pu, Joyce Ka Yu Tse, Yu Wang, Cheng-Lin Zhang, Xiaoyun Cao, Chi Wai Lau, Juan Huang, Lei He, Jiang-Yun Luo, Yu-Tsung Shih, Song Wan, Chi Fai Ng, Li Wang, Ronald Ching Wan, Jeng-Jiann Chiu, Ting Fung Chan, Xiao Yu Tian, Yu Huang
Summary: This study utilized single-cell RNA sequencing to explore the transcriptional landscape and heterogeneity of dysfunctional endothelial cells in atherosclerotic aortae. SOX4 was identified as a novel marker for atherosclerosis and was shown to promote atherogenesis and endothelial-to-mesenchymal transition. Hyperlipidemia-associated cytokines and oscillatory blood flow were found to upregulate SOX4 expression, while the anti-diabetic drug metformin suppressed SOX4 levels in endothelial cells.
JOURNAL OF ADVANCED RESEARCH
(2023)
Article
Genetics & Heredity
Xiaolong Li, Deyuan Yang, Jian-Wen Qiu, Penglong Liu, Dehao Meng, Hongmei Zhu, Limei Guo, Site Luo, Zhi Wang, Caihuan Ke
Summary: The complete mitochondrial genome of Leocrates chinensis, the type species of the genus, was reported in this study. It is 15061 bp in length and contains 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and 1 putative control region. Phylogenetic analysis showed that L. chinensis is closely related to Sirsoe methanicola within the same family Hesionidae.
MITOCHONDRIAL DNA PART B-RESOURCES
(2023)
Article
Endocrinology & Metabolism
Claudia H. T. Tam, Cadmon K. P. Lim, Andrea O. Y. Luk, Mai Shi, Hoi Man Cheung, Alex C. W. Ng, Heung-man Lee, Eric S. H. Lau, Baoqi Fan, Guozhi Jiang, Alice P. S. Kong, Risa Ozaki, Elaine Y. K. Chow, Ka Fai Lee, Shing Chung Siu, Grace Hui, Chiu Chi Tsang, Kam Piu Lau, Jenny Y. Y. Leung, Elaine Y. N. Cheung, Man Wo Tsang, Grace Kam, Ip Tim Lau, June K. Y. Li, Vincent T. F. Yeung, Emmy Lau, Stanley Lo, Samuel Fung, Yuk Lun Cheng, Chun Chung Chow, Xiaodan Fan, Ting Fung Chan, Kevin Y. L. Yip, Si Lok, Weichuan Yu, Stephen K. W. Tsui, Hui-Yao Lan, Cheuk Chun Szeto, Nelson L. S. Tang, Brian Tomlinson, Yu Huang, Alicia J. Jenkins, Anthony Keech, Wing-Yee So, Juliana C. N. Chan, Ronald C. W. Ma
Summary: The objective of this study was to uncover genetic determinants of coronary heart disease (CHD) in type 2 diabetes (T2D) and explore their applications. The study identified a novel variant associated with CHD and blood pressure (BP) in Chinese T2D patients, and found that this variant interacts with BP goal attainment to have divergent effects on CHD risk.
Article
Gastroenterology & Hepatology
Zhewen Xiong, Stephen Lam Chan, Jingying Zhou, Joaquim S. L. Vong, Tsz Tung Kwong, Xuezhen Zeng, Haoran Wu, Jianquan Cao, Yalin Tu, Yu Feng, Weiqin Yang, Patrick Pak-Chun Wong, Willis Wai-Yiu Si-Tou, Xiaoyu Liu, Jing Wang, Wenshu Tang, Zhixian Liang, Jiahuan Lu, Ka Man Li, Jie-Ting Low, Michael Wing-Yan Chan, Howard H. W. Leung, Anthony W. H. Chan, Ka-Fai To, Kevin Yuk-Lap Yip, Yuk Ming Dennis Lo, Joseph Jao-Yiu Sung, Alfred Sze-Lok Cheng
Summary: This study investigates the mechanisms by which tumor cells evade immune-checkpoint targeting through the activation of the PPAR gamma/VEGF-A signaling pathway, providing a strategy to counteract immunotherapeutic resistance in hepatocellular carcinoma (HCC).
Article
Multidisciplinary Sciences
Kelly Yichen Li, Claudia Ha Ting Tam, Hongbo Liu, Samantha Day, Cadmon King Poo Lim, Wing Yee So, Chuiguo Huang, Guozhi Jiang, Mai Shi, Heung Man Lee, Hui-yao Lan, Cheuk-Chun L. Szeto, Robert L. G. Hanson, Robert G. Nelson, Katalin Susztak, Juliana C. N. Y. Chan, Kevin Y. Yip, Ronald C. W. Ma
Summary: In this study, the authors identified CpG sites associated with kidney function and subsequent decline, highlighting the potential of methylation markers in risk stratification of kidney disease in individuals with type 2 diabetes. The use of both single-site and multisite analysis proved to have functional significance in the kidney.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Jennifer L. Hope, Dennis C. Otero, Eun-Ah Bae, Christopher J. Stairiker, Ashley B. Palete, Hannah A. Faso, Michelle Lin, Monique L. Henriquez, Sreeja Roy, Hyungseok Seo, Xue Lei, Eric S. Wang, Savio Chow, Roberto Tinoco, Gregory A. Daniels, Kevin Yip, Alexandre Rosa Campos, Jun Yin, Peter D. Adams, Anjana Rao, Linda M. Bradley
Summary: PSGL-1 is a T cell-intrinsic checkpoint regulator that acts upstream of PD-1 and requires co-ligation with the TCR to attenuate T cell activation and drive terminal T cell exhaustion. PSGL-1 directly restrains TCR signaling via Zap70 and maintains expression of the Zap70 inhibitor Sts-1. Deficiency of PSGL-1 empowers CD8+ T cells to respond to low-affinity TCR ligands and inhibit the growth of PD-1-blockade-resistant melanoma.
Article
Engineering, Environmental
Tsz Chun Ho, Hin Ting Wan, Wang Ka Lee, Thomas Ka Yam Lam, Xiao Lin, Ting Fung Chan, Keng Po Lai, Chris Kong Chu Wong
Summary: Prenatal exposure to PFOS increases the metabolic risk of fetuses and alters lipid and glucose metabolism in fetal livers. PFOS activates AMPK signaling and modulates the expression of PPARα and PPARγ downstream target genes, promoting fatty acid oxidation and lipogenesis, thus affecting the postnatal susceptibility of fetuses to metabolic challenges.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Plant Sciences
Vanika Garg, Aamir W. Khan, Kevin Fengler, Victor Llaca, Yuxuan Yuan, Tri D. Vuong, Charlotte Harris, Ting-Fung Chan, Hon Ming Lam, Rajeev K. Varshney, Henry T. Nguyen
Summary: Highly contiguous genome assemblies were generated for two economically important soybean cultivars, Williams 82 and Lee, using complementary genomics technologies and assembly algorithms. Centromeric and telomeric repeats were clearly annotated on all chromosomes of both cultivars. The complete reconstructions of several chromosomes without any gaps and the identification of protein-coding genes will greatly contribute to soybean research and improvement.
Article
Biotechnology & Applied Microbiology
Jacob Schreiber, Carles Boix, Jin Wook Lee, Hongyang Li, Yuanfang Guan, Chun-Chieh Chang, Jen-Chien Chang, Alex Hawkins-Hooker, Bernhard Scholkopf, Gabriele Schweikert, Mateo Rojas Carulla, Arif Canakoglu, Francesco Guzzo, Luca Nanni, Marco Masseroli, Mark James Carman, Pietro Pinoli, Chenyang Hong, Kevin Y. Yip, Jeffrey P. Spence, Sanjit Singh Batra, Yun S. Song, Shaun Mahony, Zheng Zhang, Wuwei Tan, Yang Shen, Yuanfei Sun, Minyi Shi, Jessika Adrian, Richard Sandstrom, Nina Farrell, Jessica Halow, Kristen Lee, Lixia Jiang, Xinqiong Yang, Charles Epstein, J. Seth Strattan, Bradley Bernstein, Michael Snyder, Manolis Kellis, William Stafford, Anshul Kundaje
Summary: A promising alternative to conducting comprehensive genomics experiments is to perform a subset of experiments and use computational methods to impute the remaining data. However, determining the best imputation methods and meaningful performance evaluation measures remains an open question. In this study, we address these questions by comprehensively analyzing 23 methods from the ENCODE Imputation Challenge. Our findings indicate that imputation evaluations are challenging due to distributional shifts caused by differences in data collection and processing, the amount of available data, and redundancy among performance measures. Our analyses provide insights into overcoming these challenges and offer promising directions for more robust research.
Article
Biochemistry & Molecular Biology
Jiamin Chen, Daniel Rebibo, Jianquan Cao, Simon Yat-Man Mok, Neel Patel, Po-Cheng Tseng, Zhenghao Zhang, Kevin Y. Yip
Summary: Immune checkpoint inhibitors (ICIs) have shown durable responses in cancer patients, but their efficacy varies across cancer types and individuals. To address this, a knowledgebase and web-based portal (https://iciefficacy.org/) have been developed, providing access to the latest information on ICI efficacy, including biomarkers, computational models, and evaluation results.
Letter
Plant Sciences
Wai-Shing Yung, Ting-Fung Chan, Fanjiang Kong, Hon-Ming Lam
Article
Plant Sciences
Tri D. Vuong, Liliana Florez-Palacios, Leandro Mozzoni, Michael Clubb, Chuck Quigley, Qijian Song, Shaila Kadam, Yuxuan Yuan, Ting Fung Chan, Mohamed Abdur Rouf Mian, Henry T. Nguyen
Summary: This study identified a new major QTL for seed protein and oil on chromosome 20 using Infinium BARCSoySNP6K BeadChips, which explained high phenotypic variation for these traits across multiple field environments.
Article
Biochemical Research Methods
Chen Li, Ting-Fung Chan, Can Yang, Zhixiang Lin
Summary: The study introduces a method called stVAE, based on the variational autoencoder framework, to deconvolve the cell-type composition of cellular resolution spatial transcriptomic datasets. It accurately identifies spatial patterns of cell types and their relative proportions across spots.
Article
Environmental Sciences
Zulvikar Syambani Ulhaq, Delbert Almerick T. Boncan, Ting Fung Chan, William Ka Fai Tse
Summary: This study investigated the toxicity of PFHxS using a zebrafish model. One experiment demonstrated that PFHxS might affect glucose and fatty acid metabolism, leading to oxidative stress, developmental defects, and cell cycle arrest. Another experiment showed that exposure to PFHxS changed the concentrations of various metabolites.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)