Article
Agronomy
Yurong He, Wei Liu, Zhihao Huang, Jishuai Huang, Yanghong Xu, Qiannan Zhang, Jun Hu
Summary: This study provides a comprehensive analysis of the GA oxidase gene family in rice. The genes were divided into four subgroups and shared some common features with GAox genes in Arabidopsis. Tissue-specific expression patterns were observed for each GAox gene, and some genes may play a major role in regulating the level of bioactive GA.
Article
Plant Sciences
Sushuang Liu, Yanmin Liu, Chundong Liu, Feixue Zhang, Jiaping Wei, Bingxuan Li
Summary: This study identified and named 9 GmGeBP genes in the soybean genome, and analyzed their functions. The results suggest that these genes may have different functions and characteristics in the soybean life cycle, and that the GeBP4 gene may be involved in trichome development.
Article
Biotechnology & Applied Microbiology
Le Yang, Yao Chen, Xuejiao Liu, Sheng Zhang, Qingquan Han
Summary: The study identifies the crucial role of the XTH family in grafting, with five XTH genes potentially influencing the survival rate of poplar and willow grafted combinations. The research sheds new light on the roles of PcXTH and SrXTH genes in grafting, offering insights into molecular mechanisms for future exploration.
Article
Horticulture
Yu Zong, Lili Gu, Zhuli Shen, Haiting Kang, Yongqiang Li, Fanglei Liao, Lishan Xu, Weidong Guo
Summary: The study conducted a genome-wide investigation on the blueberry ARF genes, identifying 70 genes divided into six subfamilies scattered across 40 chromosomes. These genes encode proteins of varying lengths and exon numbers. The promoter regions of VcARF genes contain functional domains related to plant growth and stress responses. VcARF3, VcARF4, and VcARF14 were found to play crucial roles in fruit development.
Article
Genetics & Heredity
Jeremy Schwartzentruber, Sarah Cooper, Jimmy Z. Liu, Inigo Barrio-Hernandez, Erica Bello, Natsuhiko Kumasaka, Adam M. H. Young, Robin J. M. Franklin, Toby Johnson, Karol Estrada, Daniel J. Gaffney, Pedro Beltrao, Andrew Bassett
Summary: A genome-wide AD meta-analysis identified 37 risk loci, including new associations near CCDC6, TSPAN14, NCK2, and SPRED2. By fine-mapping SNPs and using functional annotation, 21 SNPs with >50% probability of being causally involved in AD risk were identified. Protein interaction networks and tissue-specific expression helped prioritize genes, leading to the discovery of likely causal genes.
Article
Genetics & Heredity
Jing Zhang, Cheungchuk Ng, Yan Jiang, Xianxu Wang, Shaodong Wang, Sui Wang
Summary: In this study, 36 lipoxygenase (LOX) gene family members were identified and annotated in the soybean cultivar Zhonghuang 13. These genes play important roles in plant growth, development, and stress response. The majority of the identified LOX genes belonged to the 13-LOX group, and they were unevenly distributed on different chromosomes. The analysis also revealed the conservation of gene sequences and the presence of cis-elements involved in various physiological processes. The study provides valuable information for further research on the soybean LOX gene family.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Dalu Li, YongJun He, Shaohang Li, Suli Shi, Linzhi Li, Yang Liu, Huoying Chen
Summary: The study comprehensively analyzed the putative AP2/ERF gene family members in eggplant and their response to abiotic stress, as well as their involvement in anthocyanin biosynthesis regulation. The research sheds light on the role of AP2/ERF genes in physiological processes and stress response in eggplant, and provides insights for further functional characterization of these genes.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Biotechnology & Applied Microbiology
Dili Lai, Xin Yao, Jun Yan, Anjing Gao, Hao Yang, Dabing Xiang, Jingjun Ruan, Yu Fan, Jianping Cheng
Summary: In this study, 28 GATA genes were identified and characterized in foxtail millet. Certain genes were found to be induced under stress conditions, providing important insights for future research and breeding of foxtail millet.
Article
Microbiology
Gaurav Agarwal, Divya Choudhary, Shaun P. Stice, Brendon K. Myers, Ronald D. Gitaitis, Stephanus N. Venter, Brian H. Kvitko, Bhabesh Dutta
Summary: The study identified chromosomal and plasmid gene clusters as well as novel genes associated with pathogenicity in Pantoea ananatis through a comprehensive pan-genome wide association study. These genes play a role in the development of center rot disease in onions.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Plant Sciences
Mariana de Lima Santos, Mario Lucio Vilela de Resende, Gabriel Sergio Costa Alves, Jose Carlos Huguet-Tapia, Marcio Fernando Ribeiro de Resende Junior, Jeremy Todd Brawner
Summary: This study conducted a genome-wide analysis of NLR loci in coffee species and found a rich set of NLR genes. These genes are mainly clustered on chromosomes and shared some orthologous genes with other plants like tomato and potato. The NLR family in coffee is divided into TIR-NLR and non-TIR-NLR, with the non-TIR-NLRs playing an important role in disease resistance. These findings will contribute to functional studies and breeding of disease-resistant coffee cultivars.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Can Wang, Jing Han, Ting Wang, Chunhua Chen, Junyi Liu, Zhixuan Xu, Qingxia Zhang, Lina Wang, Zhonghai Ren
Summary: In this study, 55 CsDREBs were identified from the cucumber pan-genomes of 13 accessions, with most of them showing variations in sequence length and/or amino acids. Expression pattern analysis revealed specific high expression of different CsDREBs in various cucumber tissues, suggesting their importance in morphogenesis and development. Additionally, different CsDREBs showed differential expression in response to different stresses, with one CsDREB gene responding to all tested stresses. These results provide a basis for further research on the function and mechanism of DREB genes in cucumber resistance breeding.
Article
Veterinary Sciences
Bingzhi Li, Jianfang Wang, Sayed Haidar Abbas Raza, Sihu Wang, Chengcheng Liang, Wenzheng Zhang, Shengchen Yu, Mujahid Ali Shah, Waleed Al Abdulmonem, Yousef Mesfer Alharbi, Abdullah S. M. Aljohani, Sameer D. Pant, Linsen Zan
Summary: In this study, 13 MAPK genes were identified in cattle and their protein properties were characterized. These genes were divided into three subfamilies and showed tissue-specific expression. BtMAPK6 and BtMAPK12 were highly expressed in muscle tissues and had different effects on muscle cell differentiation. These findings provide new insights into the specific mechanisms of MAPK genes in myogenesis.
RESEARCH IN VETERINARY SCIENCE
(2023)
Article
Genetics & Heredity
Jianfang Qiu, Lei Ni, Xue Xia, Shihao Chen, Yan Zhang, Min Lang, Mengyu Li, Binman Liu, Yu Pan, Jinhua Li, Xingguo Zhang
Summary: This study conducted a comprehensive investigation of the SlPP2C gene family in tomato and found that these genes play important roles in tomato development, stress response, and phytohormone signaling. The study also revealed that gene duplication was a major factor in the expansion of SlPP2Cs, and confirmed their diverse expression patterns in different tomato tissues.
Article
Plant Sciences
Zibo Zhao, Daowu Hu, Muhammad Tehseen Azhar, Hongge Li, Chenhui Ma, Shoupu He, Xiaoyang Wang, Gaofei Sun, Tahir Mahmood, Washu Dev, Xiongming Du
Summary: This study identified significant loci and candidate genes related to root color in Gossypium arboreum through GWAS and RNAseq analysis, providing a theoretical basis for cotton breeders to utilize elite genes and SNPs associated with root color and economically important traits.
Article
Plant Sciences
Jianlong Liu, Chenxiao Zhang, Jingyue Han, Xiaoyun Fang, Hongpeng Xu, Chenglin Liang, Dingli Li, Yingjie Yang, Zhenhua Cui, Ran Wang, Jiankun Song
Summary: KNOTTED1-like homeobox (KNOX) transcription factors (TFs) in pear play crucial roles in plant growth, development, and stress responses. The study identified 19 PbKNOXs TFs in pear, revealing their importance in various biological processes. This research sheds new light on the function of KNOX TFs in pear and provides a foundation for future studies on dwarf fruit trees.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Xiaoyi Li, Yuri Pritykin, Carla P. Concepcion, Yuheng Lu, Gaspare La Rocca, Minsi Zhang, Bryan King, Peter J. Cook, Yu Wah Au, Olesja Popow, Joao A. Paulo, Hannah G. Otis, Chiara Mastroleo, Paul Ogrodowski, Ryan Schreiner, Kevin M. Haigis, Doron Betel, Christina S. Leslie, Andrea Ventura
Article
Biochemistry & Molecular Biology
Shilpa Nadimpalli Kobren, Bernard Chazelle, Mona Singh
Article
Biochemistry & Molecular Biology
Borislav H. Hristov, Bernard Chazelle, Mona Singh
Article
Cell Biology
Robert A. Marmion, Liu Yang, Yogesh Goyal, Granton A. Jindal, Joshua L. Wetzel, Mona Singh, Trudi Schupbach, Stanislav Y. Shvartsman
Summary: Terminal patterning in Drosophila embryos is regulated by ERK signaling, with recent studies focusing on gain-of-function variants of human MEK1, revealing both signal-independent kinase activity and signal-dependent activation mechanisms.
MOLECULAR BIOLOGY OF THE CELL
(2021)
Article
Multidisciplinary Sciences
Clarissa Campbell, Francois Marchildon, Anthony J. Michaels, Naofumi Takemoto, Joris van der Veeken, Michail Schizas, Yuri Pritykin, Christina S. Leslie, Andrew M. Intlekofer, Paul Cohen, Alexander Y. Rudensky
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Yuri Pritykin, Joris van der Veeken, Allison R. Pine, Yi Zhong, Merve Sahin, Linas Mazutis, Dana Pe'er, Alexander Y. Rudensky, Christina S. Leslie
Summary: CD8 T cells are crucial in defending against viral and bacterial infections as well as tumor immunity, but their loss of functionality is complex due to the heterogeneity of states described in experimental and clinical settings. By analyzing a unified dataset of over 300 experiments, a shared trajectory of differentiation towards dysfunction was defined, revealing an early bifurcation of functional and dysfunctional T cell states across models. Experimental dissection of acute and chronic viral infections identified state-specific drivers and progenitor-like populations at an early branch point, aiding in mechanistic studies and translational efforts.
Article
Biochemistry & Molecular Biology
Anat Etzion-Fuchs, David A. Todd, Mona Singh
Summary: A novel machine learning method dSPRINT has been introduced to predict whether a protein domain binds DNA, RNA, small molecules, ions or peptides, and the positions within it that participate in these interactions. Through stringent cross-validation testing, it has shown excellent performance in uncovering ligand-binding positions and domains.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Chaitanya Aluru, Mona Singh
Summary: The study introduces a reconciliation-based framework that considers the relative positions of protein domains within extant sequences to uncover tandem domain duplications accurately. By developing an integer linear programming approach and a heuristic algorithm, the researchers are able to identify single and tandem domain duplication events with high accuracy. Through extensive simulation studies and testing on an orthogroup with complex domain duplication patterns, the effectiveness of the approach is demonstrated.
Article
Cell Biology
Minggang Zhang, Zeguo Zhao, Yuri Pritykin, Margaret Hannum, Andrew C. Scott, Fengshen Kuo, Viraj Sanghvi, Timothy A. Chan, Venkatraman Seshan, Hans-Guido Wendel, Andrea Schietinger, Michel Sadelain, Morgan Huse
Summary: The study showed that ectopic expression of miR-200c enhanced the antitumor activity of CD8(+) cytotoxic T lymphocytes during adoptive T cell therapy (ACT) in mouse models, leading to reduced apoptosis, increased in vivo persistence, and up-regulation of certain genes. These genetic perturbations resulted in phenotypically distinct T cells with advantageous therapeutic properties, highlighting the potential of the miR-200c-EpCAM axis in improving ACT outcomes.
SCIENCE TRANSLATIONAL MEDICINE
(2021)
Article
Immunology
Yi Zhong, Sarah K. Walker, Yuri Pritykin, Christina S. Leslie, Alexander Y. Rudensky, Joris van der Veeken
Summary: Zhong et al. studied the transcriptional regulation of T cell gene expression upon viral challenge using B6/Cast F1 hybrid mice. They found that members of Ets, Runx, and TCF/Lef transcription factor families play key roles in maintaining or increasing chromatin accessibility during T cell activation. Some highly induced immune response genes exhibit a noncanonical TF recruitment pattern.
Article
Biochemical Research Methods
Li Chen, Wenyun Lu, Lin Wang, Xi Xing, Ziyang Chen, Xin Teng, Xianfeng Zeng, Antonio D. Muscarella, Yihui Shen, Alexis Cowan, Melanie R. McReynolds, Brandon J. Kennedy, Ashley M. Lato, Shawn R. Campagna, Mona Singh, Joshua D. Rabinowitz
Summary: NetID is a novel global network optimization approach for annotating untargeted LC-MS metabolomics data. By combining known biochemical and metabolomic principles, it significantly enhances annotation coverage and accuracy, facilitating the discovery of metabolites.
Article
Multidisciplinary Sciences
Prakriti Paul Chacha, Ryoko Horie, Takehiro G. Kusakabe, Yasunori Sasakura, Mona Singh, Takeo Horie, Michael Levine
Summary: The study found that the lateral regions of the neural plate in the protovertebrate Ciona intestinalis type A exhibit characteristics of vertebrate placodes and neural crest, and can generate sensory cell types. Misexpression of the POU IV gene was found to cause epidermal cells to transform into hybrid sensory cell types, which exhibit properties of both palp sensory cells (PSCs) and bipolar tail neurons (BTNs).
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Sean B. King, Mona Singh
Summary: The study suggests that rodents and primates may have had ancient exposures to viruses similar to SARS-CoV-2 and HCoV-229E, respectively, leading to adaptive amino acid substitutions in the ACE2 receptor. This indicates that some rodent species may have acquired tolerance or resistance to SARS-like coronaviruses, while non-adapted mammals and primates may be more susceptible to symptomatic disease.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Immunology
Joris van der Veeken, Clarissa Campbell, Yuri Pritykin, Michail Schizas, Jacob Verter, Wei Hu, Zhong-Min Wang, Fanny Matheis, Daniel Mucida, Louis-Marie Charbonnier, Talal A. Chatila, Alexander Y. Rudensky
Summary: The role of Foxp3 in peripheral pTreg cells and the mechanisms supporting their differentiation remain poorly understood. This study used genetic tracing to identify microbiota-induced pTreg cells and found that many of their distinguishing features were Foxp3 independent. While Foxp3 was critical for the suppression of certain diseases, pTreg cells could suppress colonic effector T cell expansion in a Foxp3-independent manner. Thus, Foxp3 and the tolerogenic signals preceding and promoting its expression confer distinct facets of pTreg functionality.
Article
Biochemical Research Methods
Sean B. B. King, Mona Singh
Summary: This study constructed a structural database of protein-ligand interactions in 18 primate species and found that ligand-binding sites are more conserved than other sites, particularly those binding with DNA and RNA. The study also revealed that variable ligand-binding sites are enriched in gene regulatory pathways, and identified amino acid variations in several transcription factors specific to humans. These findings suggest that ligand-binding sites in primates have undergone selective pressure and may play a significant role in phenotypic variation through pleiotropic effects on gene regulation.
PLOS COMPUTATIONAL BIOLOGY
(2023)