Article
Biochemistry & Molecular Biology
Murray Stewart
Summary: Although the nuclear envelope separates the nucleus and cytoplasm in eukaryotes, a semipermeable barrier is necessary to allow material exchange between these compartments. This barrier is achieved through nuclear pores, which facilitate the active transport of macromolecules. The diffusion of macromolecules through these pores is impeded by a dense network of unfolded regions of nucleoporins. Additional mechanisms, such as binding to immobile components and active removal, are required to maintain the distinctive compositions of each compartment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Laetitia Van Wonterghem, Matteo De Chiara, Gianni Liti, Jonas Warringer, Anne Farewell, Natalie Verstraeten, Jan Michiels
Summary: This study focused on bacterial host factors that assist in the transfer of conjugative plasmids, observing significant differences in conjugation efficiency among donor Escherichia coli strains. Through genome-wide association studies, candidate genes involved in conjugation were identified, with the roles of some genes confirmed by validating defects in single-gene deletion mutants. The study suggests that factors such as motility, energy supply, intracellular pH or salinity of the donor may affect the efficiency of plasmid transfer.
Article
Biology
Nikhil Kumar Singh, Sabina Moser Tralamazza, Leen Nanchira Abraham, Gaetan Glauser, Daniel Croll
Summary: In this study, the metabolite production of a large population of the fungal pathogen of wheat, Zymoseptoria tritici, was analyzed. Significant variation in metabolite abundance among different isolates was found. By integrating whole-genome sequencing data, metabolite genome-wide association mapping was performed to identify loci underlying variation in metabolite production. The study provides a significant resource for unraveling the genetic basis of metabolome diversity within a species.
Article
Allergy
Michelle Daya, Corey Cox, Nathalie Acevedo, Meher P. Boorgula, Monica Campbell, Sameer Chavan, Michael H. Cho, Gloria L. David, Priyadarshini Kachroo, Jessica Lasky-Su, Xingnan Li, Caitlin P. McHugh, Dandi Qiao, Nicholas Rafaels, Lisa A. Beck, Eugene R. Bleecker, Luis Caraballo, Adrienne L. Cupples, Camila A. Figueiredo, Richard L. Gallo, Jon Hanifin, Nadia N. Hansel, Tissa R. Hata, Craig P. Hersh, Jennifer Knight-Madden, Donald Y. M. Leung, Emma Guttman-Yassky, Deborah A. Meyers, George O'Connor, Carole Ober, Peck Y. Ong, Victor E. Ortega, Amy S. Paller, Nirupama Putcha, Robert M. Reed, Lynda C. Schneider, Edwin K. Silverman, Mark K. Slifka, Jonathan M. Spergel, Ramachandran S. Vasan, Karine A. Viaud-Martinez, Harold Watson, Scott T. Weiss, Ingo Ruczinski, Terri H. Beaty, Rasika A. Mathias, Kathleen C. Barnes
Summary: This study conducted the largest genome-wide association study and HLA association study of tIgE focusing on ancestrally diverse populations and identified several known genetic loci associated with tIgE and allergic diseases.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2021)
Article
Biology
Mengyun Wu, Fan Wang, Yeheng Ge, Shuangge Ma, Yang Li
Summary: Genome-wide association studies have been successful in identifying genotype-phenotype associations for complex human diseases. However, the high dimensionality of single nucleotide polymorphisms (SNPs) poses challenges for analysis. To overcome this, a novel bi-level structured functional analysis method is developed to simultaneously investigate disease-associated genetic variants at the SNP and SNP group levels.
Review
Cell Biology
Joanna Kalita, Larisa E. Kapinos, Roderick Y. H. Lim
Summary: This review examines the role of the nuclear pore complex in nucleocytoplasmic transport and discusses unresolved issues such as the partitioning of importin and exportin in the cytoplasm and nucleus, and the maintenance of the RanGTP-RanGDP gradient across the nuclear envelope.
JOURNAL OF CELL SCIENCE
(2021)
Article
Plant Sciences
Nathan Bryant, Jin Zhang, Kai Feng, Mengjun Shu, Raphael Ployet, Jin-Gui Chen, Wellington Muchero, Chang Geun Yoo, Timothy J. Tschaplinski, Yunqiao Pu, Arthur J. Ragauskas
Summary: By characterizing a population of 409 naturally varying Populus trichocarpa genotypes, a genome-wide association study identified 756 genes significantly associated with lignin phenotypes, providing insights into the molecular mechanisms of lignin biosynthesis and new targets for genetic improvement in poplar.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Priyanka Sharma, Ardashir Kharabian Masouleh, Bruce Topp, Agnelo Furtado, Robert J. Henry
Summary: Recent advances in sequencing and assembly of plant genomes have led to increased contiguity and accuracy, allowing for near complete chromosome level assemblies. The use of proximity analysis and highly accurate long reads has greatly improved the quality of genome assemblies, making de novo assembly of plant genomes feasible.
Article
Biochemistry & Molecular Biology
Monika Mokrzycka, Stefan Stojalowski, Miroslaw Tyrka, Przemyslaw Matysik, Barbara Zmijewska, Rafal Marcinkowski, Urszula Wozna-Pawlak, Roza Martofel, Michal Rokicki, Monika Rakoczy-Trojanowska, Pawel Krajewski
Summary: This study identified markers associated with wheat agronomic traits using genome-wide association analysis. The study also investigated the effects of markers on heterosis and their linkage disequilibrium grouping. The results revealed a large number of single nucleotide polymorphisms with significant effects, predominantly influencing protein translation modification. These findings provide valuable insights for developing new wheat varieties with desirable properties.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Orthopedics
Jing Wu, Jiali Su, Yangyang Wang, Jianfeng Chen, Yuanyuan Shang, Jing Li
Summary: This study found a positive association between total bilirubin concentration and bone mineral density levels in adolescents in the United States. Total bilirubin concentration may serve as a protective marker against bone loss in adolescents.
BMC MUSCULOSKELETAL DISORDERS
(2022)
Article
Biochemical Research Methods
Zhiyu Hao, Jin Gao, Yuxin Song, Runqing Yang, Di Liu
Summary: In this study, a hierarchical mixed model (Hi-LMM) was proposed to estimate genomic breeding values and infer the association between genotypes and phenotypes, effectively correcting confounding factors and improving the statistical power of association analysis.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Clinical Neurology
Shogo Dofuku, Kyuto Sonehara, Satoru Miyawaki, Saori Sakaue, Hideaki Imai, Masahiro Shimizu, Hiroki Hongo, Yuki Shinya, Kenta Ohara, Yu Teranishi, Atsushi Okano, Hideaki Ono, Hirofumi Nakatomi, Akira Teraoka, Kenichi Yamamoto, Yuichi Maeda, Takuro Nii, Toshihiro Kishikawa, Ken Suzuki, Jun Hirata, Meiko Takahashi, Koichi Matsuda, Atsushi Kumanogoh, Fumihiko Matsuda, Yukinori Okada, Nobuhito Saito
Summary: This study conducted the first genome-wide association study (GWAS) of intracranial artery stenosis (ICAS) in a Japanese population. They identified a functional variant of RNF2J3, rs112735431, that was significantly associated with ICAS. Furthermore, they found that this variant was also associated with high blood pressure and angina.
TRANSLATIONAL STROKE RESEARCH
(2023)
Article
Endocrinology & Metabolism
Erica T. Warner, Lai Jiang, David Nana Adjei, Constance Turman, William Gordon, Lu Wang, Rulla Tamimi, Peter Kraft, Sara Lindstrom
Summary: This study identified additional loci contributing to childhood adiposity, further elucidating its genetic architecture.
Article
Urology & Nephrology
Cassianne Robinson-Cohen, Jefferson L. Triozzi, Bryce Rowan, Jing He, Hua C. Chen, Neil S. Zheng, Wei-Qi Wei, Otis D. Wilson, Jacklyn N. Hellwege, Philip S. Tsao, J. Michael Gaziano, Alexander Bick, Michael E. Matheny, Cecilia P. Chung, Loren Lipworth, Edward D. Siew, T. Alp Ikizler, Ran Tao, Adriana M. Hung
Summary: By conducting a meta-analysis of genome-wide association studies, three genetic loci associated with longitudinal eGFR change have been identified, shedding light on the molecular mechanisms of eGFR decline and potentially contributing to the development of new therapeutic approaches for progressive CKD.
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2023)
Article
Urology & Nephrology
Cassianne Robinson-Cohen, Jefferson L. Triozzi, Bryce Rowan, Jing He, Hua C. Chen, Neil S. Zheng, Wei-Qi Wei, Otis D. Wilson, Jacklyn N. Hellwege, Philip S. Tsao, J. Michael Gaziano, Alexander Bick, Michael E. Matheny, Cecilia P. Chung, Loren Lipworth, Edward D. Siew, T. Alp Ikizler, Ran Tao, Adriana M. Hung
Summary: The study identified three significant loci associated with longitudinal decline in eGFR, providing insights into the molecular mechanisms of eGFR decline and potential therapeutic approaches for progressive CKD.
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2023)
Article
Endocrinology & Metabolism
Pankaj Kumar, Michael Traurig, Leslie J. Baier
INTERNATIONAL JOURNAL OF OBESITY
(2020)
Article
Gastroenterology & Hepatology
Ankita Chatterjee, Analabha Basu, Kausik Das, Pankaj Singh, Dipankar Mondal, Biswanath Bhattacharya, Shweta Roychoudhury, Partha P. Majumder, Abhijit Chowdhury, Priyadarshi Basu
ANNALS OF HEPATOLOGY
(2020)
Article
Endocrinology & Metabolism
Paolo Piaggi, Cigdem Koroglu, Anup K. Nair, Jeff Sutherland, Yunhua L. Muller, Pankaj Kumar, Wen-Chi Hsueh, Sayuko Kobes, Alan R. Shuldiner, Hye In Kim, Nehal Gosalia, Cristopher V. Van Hout, Marcus Jones, William C. Knowler, Jonathan Krakoff, Robert L. Hanson, Clifton Bogardus, Leslie J. Baier
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2020)
Article
Biochemistry & Molecular Biology
Abhinav Jain, Rahul C. Bhoyar, Kavita Pandhare, Anushree Mishra, Disha Sharma, Mohamed Imran, Vigneshwar Senthivel, Mohit Kumar Divakar, Mercy Rophina, Bani Jolly, Arushi Batra, Sumit Sharma, Sanjay Siwach, Arun G. Jadhao, Nikhil Palande, Ganga Nath Jha, Nishat Ashrafi, Prashant Kumar Mishra, A. K. Vidhya, Suman Jain, Debasis Dash, Nachimuthu Senthil Kumar, Andrew Vanlallawma, Ranjan Jyoti Sarma, Lalchhandama Chhakchhuak, Shantaraman Kalyanaraman, Radha Mahadevan, Sunitha Kandasamy, B. M. Pabitha, Raskin Erusan Rajagopal, Ezhil J. Ramya, Nirmala P. Devi, Anjali Bajaj, Vishu Gupta, Samatha Mathew, Sangam Goswami, Mohit Mangla, Savinitha Prakash, Kandarp Joshi, S. Sreedevi, Devarshi Gajjar, Ronibala Soraisham, Rohit Yadav, Yumnam Silla Devi, Aayush Gupta, Mitali Mukerji, Sivaprakash Ramalingam, B. K. Binukumar, Vinod Scaria, Sridhar Sivasubbu
Summary: With the advent of next-generation sequencing, a pilot phase of the 'IndiGen' program performed whole genome sequencing of 1029 healthy Indian individuals to create the IndiGenomes database, which is now freely accessible. This comprehensive genetic variant resource for the Indian population has been extensively accessed by the worldwide community.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Ankita Chatterjee, Analabha Basu, Kausik Das, Abhijit Chowdhury, Priyadarshi Basu
Summary: Non-alcoholic fatty liver disease (NAFLD) is a global epidemic that often leads to serious liver conditions. A study on Indian populations identified genetic determinants of hepatic fat content (HFC) using an exome-wide approach, with 4 SNPs significantly associated with HFC. One SNP, rs4788084, regulates the expression of IL-27, an immune regulatory gene, and affects NAFLD pathogenesis. Adiposity was shown to impact HFC regardless of genetic predisposition.
Article
Physiology
Atish Gheware, Lipsa Panda, Kritika Khanna, Naveen Kumar Bhatraju, Vaibhav Jain, Shakti Sagar, Manish Kumar, Vijay Pal Singh, Sadasivam Kannan, Venkatesan Subramanian, Mitali Mukerji, Anurag Agrawal, Bhavana Prasher
Summary: This study demonstrates the therapeutic effects of Adhatoda vasica (AV) aqueous extract on mouse models of acute allergic and severe asthma, showing potential for treating severe steroid-resistant asthma by alleviating inflammation and enhancing respiratory function. AV inhibits HIF-1 alpha levels and reverses cellular hypoxic-induced mitochondrial dysfunction, providing new insights into the molecular mechanisms behind its beneficial effects. Through in silico docking, AV constituents show high binding affinity for key players involved in hypoxia inflammation, further supporting its potential as a treatment for respiratory ailments.
AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY
(2021)
Article
Multidisciplinary Sciences
Shashank Gupta, Malini Shariff, Gaura Chaturvedi, Agrima Sharma, Nitin Goel, Monika Yadav, Martin S. Mortensen, Soren J. Sorensen, Mitali Mukerji, Nar Singh Chauhan
Summary: The study reveals that different respiratory illnesses have unique microbial features that can be used as diagnostic markers to differentiate among various respiratory illnesses. The lung microbiome of patients with stable COPD is more diverse compared to those with exacerbated COPD and ILD patients.
SCIENTIFIC REPORTS
(2021)
Article
Cell Biology
Sumita Chakraborty, Sunanda Singhmar, Dayanidhi Singh, Mahua Maulik, Rutuja Patil, Satyam Kumar Agrawal, Anushree Mishra, Madeeha Ghazi, Archana Vats, Vivek T. Natarajan, Sanjay Juvekar, Bhavana Prasher, Mitali Mukerji
Summary: This study investigates the variability in cell proliferation and response to UV stress among healthy individuals with different constitution types, using a lymphoblastoid cell line model. The findings suggest that baseline differences in cell proliferation could be crucial for understanding cell survivability under stress conditions. These results may have implications for individualized therapy in precision medicine.
Article
Endocrinology & Metabolism
Surbhi Dogra, Debajyoti Das, Sujay K. Maity, Avishek Paul, Priya Rawat, P. Vineeth Daniel, Kausik Das, Souveek Mitra, Partha Chakrabarti, Prosenjit Mondal
Summary: Nonalcoholic fatty liver disease (NAFLD) is associated with insulin resistance and type 2 diabetes mellitus (T2DM). This study found that S100A6 protein inhibits insulin secretion from pancreatic β cells by activating RAGE and reducing mitochondrial respiration. Elevated levels of S100A6 were observed in both NAFLD patients and a high-fat diet-induced mouse model. Depletion of S100A6 improved insulin secretion and blood glucose levels in mice. Hepatic S100A6 expression is regulated by ChREBP, which suppresses insulin secretion in a S100A6-sensitive manner. Elevated serum levels of S100A6 may serve as a biomarker for identifying NAFLD patients at risk of b-cell dysfunction.
Article
Gastroenterology & Hepatology
Prasenjit Halder, Susree Roy, Soma Banerjee, Syamsundar Mandat, Kausik Das, Abhijit Chowdhury, Sk Mahiuddin Ahammed
Summary: The aim of this study was to investigate the clinical profile of acute on chronic liver failure (ACLF) and establish Cell-free DNA (Cf DNA) as a predictor of ACLF outcome. The results showed that alcohol and sepsis were the most common causes of acute insult. Cf DNA was found to be a better predictor of 28-day mortality, while CLIF-C ACLF was more accurate in predicting 90-day mortality.
JOURNAL OF CLINICAL AND EXPERIMENTAL HEPATOLOGY
(2023)
Article
Health Care Sciences & Services
Partha Sarathi Mukherjee, Sujoy Ghosh, Pradip Mukhopadhyay, Dipesh Kumar Das, Pabak Sarkar, Saibal Majumdar, Kajal Chatterjee, Abhijit Chowdhury, Kausik Das
Summary: This study aimed to assess the prevalence of metabolically unhealthy subjects and their risk of significant NAFLD in a resource-poor community. The results showed that at least one risk factor was present in 51.4% of the subjects, and 63% of the subjects with metabolic abnormality had MU state, with 53% of MU subjects having the risk of significant NAFLD.
LANCET REGIONAL HEALTH - SOUTHEAST ASIA
(2023)
Article
Genetics & Heredity
P. Prakrithi, Khushboo Singhal, Disha Sharma, Abhinav Jain, Rahul C. Bhoyar, Mohamed Imran, Vigneshwar Senthilvel, Mohit Kumar Divakar, Anushree Mishra, Vinod Scaria, Sridhar Sivasubbu, Mitali Mukerji
Summary: This study reports the genomic landscape of Alu InDels in Indian populations, revealing a high frequency of polymorphic Alu insertions that are preferentially located in genic regions and associated with cell morphogenesis and neurogenesis processes. Some insertions correspond to genes present in the OMIM database. Additionally, a subset of these insertions can be used as ancestry informative markers for segregating global populations.
NAR GENOMICS AND BIOINFORMATICS
(2022)
Article
Pediatrics
Aditi Joshi, Aditi Sinha, Aakanksha Sharma, Uzma Shamim, Bharathram Uppilli, Pooja Sharma, Sana Zahra, Shaista Parveen, Aradhana Mathur, Monica Chandan, Prachi Tewari, Priyanka Khandelwal, Pankaj Hari, Mitali Mukerji, Mohammed Faruq, Arvind Bagga
Summary: This study aimed to determine the genetic basis of congenital nephrotic syndrome in Indian patients, finding that variants in the NPHS1 gene are most common in this population. Genetic analysis identified a genetic cause in 82.4% of patients, suggesting the presence of founder mutations.
Article
Respiratory System
Atish Gheware, Dhwani Dholakia, Sadasivam Kannan, Lipsa Panda, Ritu Rani, Bijay Ranjan Pattnaik, Vaibhav Jain, Yash Parekh, M. Ghalib Enayathullah, Kiran Kumar Bokara, Venkatesan Subramanian, Mitali Mukerji, Anurag Agrawal, Bhavana Prasher
Summary: The whole aqueous extract of Adhatoda Vasica showed promising effects in attenuating airway inflammation, reducing levels of TGF-beta 1, IL-6, and HIF-1 alpha, improving survival rates in pulmonary fibrosis and sepsis murine models, and rescuing inflammation and blood coagulation phenotypes induced by siRNA. It also downregulated hypoxia-related genes and upregulated genes related to adaptive immunity in lung transcriptome, while reducing viral load in SARS-CoV2 infected cells, suggesting potential for repurposing in COVID-19-like conditions.
RESPIRATORY RESEARCH
(2021)
Article
Evolutionary Biology
Aniket Bhattacharya, Vineet Jha, Khushboo Singhal, Mahar Fatima, Dayanidhi Singh, Gaura Chaturvedi, Dhwani Dholakia, Rintu Kutum, Rajesh Pandey, Trygve E. Bakken, Pankaj Seth, Beena Pillai, Mitali Mukerji
Summary: Alu repeats play a role in phylogenetic novelties in conserved regulatory networks in primates. An exonized Alu transcript isoform, CYP20A1_Alu-LT, with 23 Alus in its 3'UTR has been characterized. This transcript is widely expressed and potentially acts as a multi-miRNA sponge with cytosolic localization.
GENOME BIOLOGY AND EVOLUTION
(2021)
