Article
Plant Sciences
Lovepreet Singh, Rajat Pruthi, Sandeep Chapagain, Prasanta K. Subudhi
Summary: Alkalinity stress is a major obstacle to rice production, and understanding the mechanisms of alkalinity tolerance is limited. A genome-wide association study was conducted to identify tolerant genotypes and candidate genes for alkalinity tolerance in rice seedlings. Principal component analysis revealed the traits with the highest contributions to tolerance, and clustering analysis grouped the genotypes into different subgroups. Several significant SNPs associated with alkalinity tolerance were identified, as well as novel QTLs and candidate genes. These genomic and genetic resources are valuable for investigating alkalinity tolerance mechanisms and improving tolerance in rice.
Article
Plant Sciences
Lu Yin, Avinash Karn, Lance Cadle-Davidson, Cheng Zou, Jason Londo, Qi Sun, Matthew D. Clark
Summary: This study fine-mapped the foliar resistance QTL in a cold-hardy hybrid grape population, leading to the identification of candidate genes and markers for future marker-assisted breeding.
HORTICULTURE RESEARCH
(2022)
Article
Plant Sciences
Yang Liu, Congyang Yi, Qian Liu, Chunhui Wang, Wenpeng Wang, Fangpu Han, Xiaojun Hu
Summary: This study investigated the mechanisms regulating seed size in peanut by using a multi-omics approach. Two mutants with bigger seed size were isolated and analyzed through whole genome sequencing and RNA-Seq analysis, leading to the identification of candidate genes associated with seed size.
Article
Neurosciences
Simon N. Katner, Alena M. Sentir, Kevin B. Steagall, Zheng-Ming Ding, Leah Wetherill, Frederic W. Hopf, Eric A. Engleman
Summary: Understanding risk factors that increase the development of addiction is crucial, and studying genetically-selected EtOH-preferring rodents can provide insights into mechanisms underlying compulsive drinking and lead to new treatments for AUDs.
Article
Biochemistry & Molecular Biology
Chen Cao, Jianhua Wang, Devin Kwok, Feifei Cui, Zilong Zhang, Da Zhao, Mulin Jun Li, Quan Zou
Summary: webTWAS is a new resource that combines comprehensive disease GWAS datasets with information on potential causal genes, allowing researchers to explore gene-disease associations. With data from 1298 high-quality GWAS summary statistics, a total of 235,064 gene-disease associations can be accessed, and custom TWAS analyses can be run on a user-friendly web server.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Agronomy
Jiaowen Pan, Ximeng Zhou, Naveed Ahmad, Kun Zhang, Ronghua Tang, Huiling Zhao, Jing Jiang, Mengdi Tian, Changsheng Li, Aiqin Li, Xianying Zhang, Liangqiong He, Jing Ma, Xiaojie Li, Ruizheng Tian, Changle Ma, Manish K. Pandey, Rajeev K. Varshney, Xingjun Wang, Chuanzhi Zhao
Summary: The candidate gene AhLBA1, which controls the lateral branch angle of peanut, was fine-mapped to a specific physical region on chromosome 15 using BSA-seq and QTL mapping. Genes related to hormone metabolism and regulation were found in this region, suggesting their potential role in determining the lateral branch angle of peanut.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Plant Sciences
Most. Humaira Sultana, Md. Alamin, Jie Qiu, Longjiang Fan, Chuyu Ye
Summary: This study identified candidate genes responsible for allelopathic interactions between rice and barnyardgrass through transcriptome analysis. The results showed a quick allelopathic response in rice within 3 hours. Comparison of differentially expressed genes (DEGs) between rice and barnyardgrass revealed different mechanisms underlying allelopathic interaction in these two species.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Jae-Ryoung Park, Yoon-Hee Jang, Eun-Gyeong Kim, Sang-Sun Hur, Kyung-Min Kim, Deyong Ren
Summary: In this study, QTLs and candidate genes related to rice plant height regulation were identified, which can provide information and foundation for marker-assisted selection and breeding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Huiqin Bian, Ting Zhu, Yuting Liang, Ruoxuan Hei, Xiaojing Zhang, Xiaochen Li, Jinnan Chen, Yaojuan Lu, Junxia Gu, Longwei Qiao, Qiping Zheng
Summary: This study identified several TFs that play important roles in the expression of the Col10a1 gene and chondrocyte hypertrophy, with Tbx5 being shown as a negative regulator of Col10a1. Overexpression of Tbx5 not only reduced Col10a1 expression but also slightly delayed ossification in cell culture and limb tissue.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Enyu Tang, Yang Zhou, Siyang Liu, Zhiming Zhang, Rixin Zhang, Dejing Huang, Tong Gao, Tianze Zhang, Guangquan Xu
Summary: In this study, differential metabolic patterns in thymic tumors were identified through untargeted metabolomics analysis, and these differential metabolisms were closely associated with clinical outcomes and tumorigenesis. Transcriptomic alterations in differential metabolism-related genes may serve as potential targets for predicting survival outcomes and treating patients with thymic tumors.
Article
Biochemistry & Molecular Biology
R. Crystal Chaw, Thomas H. Clarke, Peter Arensburger, Nadia A. Ayoub, Cheryl Y. Hayashi
Summary: The molecular studies revealed candidate genes for silk synthesis in spider silk production. The differential gene expression profiles among different silk gland types provided insight into defining silk glands generally and from each other. The analysis showed similarities and differences among major ampullate, minor ampullate, and aggregate silk glands, indicating the evolution of multiple silk gland types within an individual spider.
INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Watchara Phetluan, Samart Wanchana, Wanchana Aesomnuk, Julian Adams, Mutiara K. Pitaloka, Vinitchan Ruanjaichon, Apichart Vanavichit, Theerayut Toojinda, Julie E. Gray, Siwaret Arikit
Summary: Stomatal density in rice varies significantly and is regulated by multiple QTLs and candidate genes, some of which have been previously associated with stomatal traits in Arabidopsis. These findings provide valuable genetic information for future breeding programs aimed at improving photosynthetic capacity, water use efficiency, and drought tolerance in rice.
Article
Medicine, General & Internal
Barbara Biedziak, Ewa Firlej, Justyna Dabrowska, Agnieszka Bogdanowicz, Malgorzata Zadurska, Adrianna Mostowska
Summary: This study identified pathogenic and likely pathogenic variants associated with non-syndromic tooth agenesis (ns-TA) through screening coding sequences of candidate genes. Known candidate genes and newly discovered gene variants may play important roles in the development of ns-TA. Further research is needed to confirm the role of these genes and understand the etiology of ns-TA.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Jiayao Wang, Priyanka R. Ahimaz, Somaye Hashemifar, Julie Khlevner, Joseph A. Picoraro, William Middlesworth, Mahmoud M. Elfiky, Jianwen Que, Yufeng Shen, Wendy K. Chung
Summary: This study identified de novo deleterious variants in EA/TEF patients, especially in genes related to EFTUD2 or SOX2. It is estimated that 33% of patients can be attributed to these variants, and further genomic analysis may uncover previously undescribed genetic causes of EA/TEF.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Horticulture
Yang Li, Youjian Yu, Liai Xu, Erbiao Guo, Yunxiang Zang, Yong He, Zhujun Zhu
Summary: This study identified a total of 184 GSL biosynthetic genes in Brassica nigra, with some key genes showing high expression contributing to sinigrin synthesis, while low expression of certain genes explaining the low content of indolic and aromatic GSLs in B. nigra. The findings provide genetic insights into the unique GSL profile in B. nigra and offer potential for functional analysis and genetic improvement of GSLs in Brassica species.
Article
Gastroenterology & Hepatology
Hani Shamseddeen, Abhishek Madathanapalli, Vijay S. Are, Vijay H. Shah, Arun J. Sanyal, Qing Tang, Tiebing Liang, Kayla Gelow, Teresa A. Zimmers, Naga Chalasani, Archita P. Desai
Summary: This study found that myostatin levels are significantly lower in AH patients compared to heavy drinkers, and are negatively correlated with total bilirubin, WBC, and platelet count. Myostatin levels increased as patients experienced decreases in MELD scores. Future studies are needed to further understand the prognostic role of myostatin in AH.
DIGESTIVE DISEASES AND SCIENCES
(2021)
Article
Gastroenterology & Hepatology
Tae-Hwi Schwantes-An, Rebecca Darlay, Philippe Mathurin, Steven Masson, Suthat Liangpunsakul, Sebastian Mueller, Guruprasad P. Aithal, Florian Eyer, Dermot Gleeson, Andrew Thompson, Beat Muellhaupt, Felix Stickel, Michael Soyka, David Goldman, Tiebing Liang, Lawrence Lumeng, Munir Pirmohamed, Bertrand Nalpas, Jean-Marc Jacquet, Romain Moirand, Pierre Nahon, Sylvie Naveau, Pascal Perney, Greg Botwin, Paul S. Haber, Helmut K. Seitz, Christopher P. Day, Tatiana M. Foroud, Ann K. Daly, Heather J. Cordell, John B. Whitfield, Timothy R. Morgan, Devanshi Seth
Summary: The study identified several genetic variants associated with the risk of alcohol-associated cirrhosis, including PNPLA3, HSD17B13, and FAF2. Through GWAS and meta-analysis, these genetic variants were confirmed to be related to the risk of cirrhosis. For heavy drinkers, the FAF2 gene may be associated with a reduced risk of ALC.
Article
Gastroenterology & Hepatology
Eduardo Vilar-Gomez, Pirola Carlos Jose, Silvia Sookoian, Laura A. Wilson, Patricia Belt, Tiebing Liang, Wanqing Liu, Naga Chalasani
Summary: This study suggests that the PNPLA3 rs738409 G-allele may modulate the effect of specific dietary nutrients on the risk of fibrosis in patients with NAFLD. Associations between certain dietary factors and significant fibrosis were stronger among rs738409 G-allele carriers.
AMERICAN JOURNAL OF GASTROENTEROLOGY
(2021)
Article
Pharmacology & Pharmacy
Eduardo Vilar-Gomez, Samer Gawrieh, Tiebing Liang, Adam D. McIntyre, Robert A. Hegele, Naga Chalasani
Summary: Mutations in the APOB gene are common among NAFLD patients with very low LDL-C, and may be associated with increased aminotransferase levels and steatosis severity.
JOURNAL OF CLINICAL LIPIDOLOGY
(2021)
Article
Psychiatry
J. L. Meyers, D. B. Chorlian, T. B. Bigdeli, E. C. Johnson, F. Aliev, A. Agrawal, L. Almasy, A. Anokhin, H. J. Edenberg, T. Foroud, A. Goate, C. Kamarajan, S. Kinreich, J. Nurnberger, A. K. Pandey, G. Pandey, M. H. Plawecki, J. E. Salvatore, J. Zhang, A. Fanous, B. Porjesz
Summary: The study found that polygenic risk for schizophrenia is significantly associated with increased functional neural connectivity in young adults without a schizophrenia diagnosis, with differences observed based on sex and age. Similar associations were also seen in genetically related neuropsychiatric polygenic risk scores, suggesting a link between genetic risk and neural connectivity patterns in unaffected individuals.
TRANSLATIONAL PSYCHIATRY
(2021)
Article
Substance Abuse
James J. Beaudoin, Tiebing Liang, Qing Tang, Bubu A. Banini, Vijay H. Shah, Arun J. Sanyal, Naga P. Chalasani, Samer Gawrieh
Summary: In this study, genetic variants in PNPLA3 and HP were found to be associated with an increased risk of alcoholic hepatitis and severity. These variants were also linked to elevated total bilirubin and MELD score, markers of disease severity.
ALCOHOL-CLINICAL AND EXPERIMENTAL RESEARCH
(2021)
Article
Gastroenterology & Hepatology
John B. Whitfield, Tae-Hwi Schwantes-An, Rebecca Darlay, Guruprasad P. Aithal, Stephen R. Atkinson, Ramon Bataller, Greg Botwin, Naga P. Chalasani, Heather J. Cordell, Ann K. Daly, Christopher P. Day, Florian Eyer, Tatiana Foroud, Dermot Gleeson, David Goldman, Paul S. Haber, Jean-Marc Jacquet, Tiebing Liang, Suthat Liangpunsakul, Steven Masson, Philippe Mathurin, Romain Moirand, Andrew McQuillin, Christophe Moreno, Marsha Y. Morgan, Sebastian Mueller, Beat Muellhaupt, Laura E. Nagy, Pierre Nahon, Bertrand Nalpas, Sylvie Naveau, Pascal Perney, Munir Pirmohamed, Helmut K. Seitz, Michael Soyka, Felix Stickel, Andrew Thompson, Mark R. Thursz, Eric Trepo, Timothy R. Morgan, Devanshi Seth
Summary: This study developed a genetic risk score that can identify individuals at high risk of developing cirrhosis. It was found that the risk of cirrhosis is increased over 10-fold in patients with diabetes and a high genetic risk score. This risk assessment could lead to early and personalized management of the disease in high-risk patients.
JOURNAL OF HEPATOLOGY
(2022)
Article
Neurosciences
Alexander S. Hatoum, Emma C. Johnson, Sarah M. C. Colbert, Renato Polimanti, Hang Zhou, Raymond K. Walters, Joel Gelernter, Howard J. Edenberg, Ryan Bogdan, Arpana Agrawal
Summary: Shared genetic liability partly explains susceptibility to alcohol, tobacco, cannabis, and opioid use disorders. The Addiction-Risk-Factor is associated with risk-taking, neuroticism, executive function, and non-substance psychopathology, retaining specific variance even after accounting for the genetics of substance use.
NEUROPSYCHOPHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Bin Qiu, Zhaohui Zhong, Shawn Righter, Yuxue Xu, Jun Wang, Ran Deng, Chao Wang, Kent E. Williams, Yao-ying Ma, Gavriil Tsechpenakis, Tiebing Liang, Weidong Yong
Summary: The FK506-binding protein 51 (FKBP51) has been linked to stress-related mental illness. In this study, the researchers investigated the effects of deleting the Fkbp51 gene on brain morphology. They found that male Fkbp51 knock-out mice had elongated dentate gyrus but shorter hippocampal height compared to wild-type mice. Further experiments showed that Fkbp51 is involved in the regulation of microtubule-associated protein expression and negatively regulates Parkin protein in a dose-dependent and ubiquitin-mediated manner.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Gastroenterology & Hepatology
Eduardo Vilar-Gomez, Carlos J. Pirola, Silvia Sookoian, Laura A. Wilson, Tiebing Liang, Naga Chalasani
Summary: The rs738409 missense variant in the patatin-like phospholipase domain-containing 3 gene may promote fibrosis development in NAFLD by activating specific fibrogenic pathways. The indirect effect of rs738409 on fibrosis severity is primarily mediated through portal inflammation.
Correction
Gastroenterology & Hepatology
John B. Whitfield, Tae-Hwi Schwantes-An, Rebecca Darlay, Guruprasad P. Aithal, Stephen R. Atkinson, Ramon Bataller, Greg Botwin, Naga P. Chalasani, Heather J. Cordell, Ann K. Daly, Christopher P. Day, Florian Eyer, Tatiana Foroud, Dermot Gleeson, David Goldman, Paul S. Haber, Jean-Marc Jacquet, Tiebing Liang, Suthat Liangpunsakul, Steven Masson, Philippe Mathurin, Romain Moirand, Andrew McQuillin, Christophe Moreno, Marsha Y. Morgan, Sebastian Mueller, Beat Muellhaupt, Laura E. Nagy, Pierre Nahon, Bertrand Nalpas, Sylvie Naveau, Pascal Perney, Munir Pirmohamed, Helmut K. Seitz, Michael Soyka, Felix Stickel, Andrew Thompson, Mark R. Thursz, Eric Trepo, Timothy R. Morgan, Devanshi Seth
JOURNAL OF HEPATOLOGY
(2022)
Article
Psychology, Clinical
Jinni Su, Sally I-Chun Kuo, Angel Trevino, Peter B. Barr, Fazil Aliev, Kathleen Bucholz, Grace Chan, Howard J. Edenberg, Samuel Kuperman, Dongbing Lai, Jacquelyn L. Meyers, Gayathri Pandey, Bernice Porjesz, Danielle M. Dick
Summary: Higher parental educational attainment is associated with higher offspring educational attainment. This study examined the genetic and socioenvironmental pathways underlying this association using data from individuals of European ancestry. The results showed that the genetic scores of paternal and maternal educational attainment were associated with offspring educational attainment, and parental educational attainment, income, and parenting behaviors mediated this effect.
JOURNAL OF FAMILY PSYCHOLOGY
(2022)
Article
Substance Abuse
John B. Whitfield, Devanshi Seth, Timothy R. Morgan
Summary: High alcohol intake is associated with increased mortality. Excessive drinkers have higher mortality rates, and liver abnormalities and alcohol dependence are associated with poorer prognosis.
ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH
(2022)
Article
Multidisciplinary Sciences
Nicholas R. R. Powell, Tiebing Liang, Joseph Ipe, Sha Cao, Todd C. C. Skaar, Zeruesenay Desta, Hui-Rong Qian, Philip J. J. Ebert, Yu Chen, Melissa K. K. Thomas, Naga Chalasani
Summary: This study characterizes the expression of pharmacogenes in different histological severity stages of NAFLD, and shows the downregulation of CYP2C19 in NAFLD, supporting personalized medicine approaches for drugs metabolized by this enzyme. Previous reports suggest that NAFLD is associated with altered drug disposition, and this study aims to determine if patients with NAFLD are at risk for altered drug response by analyzing changes in hepatic mRNA expression of pharmacogenes.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Tiebing Liang, Janaiah Kota, Kent E. Williams, Romil Saxena, Samer Gawrieh, Xiaoling Zhong, Teresa A. Zimmers, Naga Chalasani
Summary: MicroRNA-29a (miR-29a) is a fibro-inflammatory molecule that is associated with liver pathological conditions. The effects of a high-fat diet (HFD) combined with different levels of ethanol (EtOH) consumption on miR-29a expression and liver pathobiology were investigated. The study found that miR-29a was up-regulated with increasing levels of EtOH consumption and was associated with less severe liver injury. A high-fat diet and increasing concentrations of EtOH had progressive adverse effects on the liver, without any beneficial effects of low-dose EtOH consumption.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
