Article
Biotechnology & Applied Microbiology
Gagandeep Singh, Vikram Singh, Vikram Singh
Summary: The proposed genome-wide interologous protein-protein interaction network TeaGPIN provides valuable insights into understanding the sub-cellular interactome of tea, identifying key proteins, and exploring potential candidates involved in regulatory processes. The high-confidence TeaGPIN, prioritized interactions, and network centralities evaluation enhance the understanding of growth, development, and defense mechanisms of tea plant. Functional content assessment using KEGG and GO annotations as well as modular architecture exploration further contribute to uncovering novel aspects of tea biology.
Article
Multidisciplinary Sciences
Qingqin S. Li, Randall L. Morrison, Gustavo Turecki, Wayne C. Drevets
Summary: Epigenetic mechanisms play a significant role in the etiology of major depressive disorder (MDD), as indicated by a meta-analysis study. The study identified differentially methylated positions (DMPs) and differentially methylated regions (DMRs) associated with MDD, highlighting the involvement of pathways related to neuronal synaptic plasticity, calcium signaling, and inflammation.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Yasser Al-Sarraj, Eman Al-Dous, Rowaida Z. Taha, Dina Ahram, Fouad Alshaban, Mohammed Tolfat, Hatem El-Shanti, Omar M. E. Albagha
Summary: Autism spectrum disorder (ASD) is a neurodevelopmental disease with genetic factors playing a crucial role. A GWAS in the Middle Eastern population of Qatar identified multiple genetic loci associated with ASD, some near genes implicated in ASD or related neurodevelopmental disorders. Further functional studies and replication are needed to better understand the genetic architecture of ASD.
Review
Pharmacology & Pharmacy
Randi J. Hagerman, Paul J. Hagerman
Summary: Fragile X syndrome is a common form of inherited intellectual disability and autism spectrum disorder, caused by large expansions of noncoding CGG repeats in the FMR1 gene. While there is currently no direct way to reverse the loss of FMRP, there is potential for effective treatments targeting dysregulated pathways in the near future.
ANNUAL REVIEW OF PHARMACOLOGY AND TOXICOLOGY
(2022)
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
Genetics & Heredity
Keegan Flanagan, Alireza Baradaran-Heravi, Qi Yin, Khanh Dao Duc, Allan C. Spradling, Ethan J. Greenblatt
Summary: Mutations in FMR1 are the most common cause of autism spectrum disorder, and FMRP, an RNA-binding protein encoded by this gene, plays an essential role in neuronal and ovarian development. Previous research showed that FMRP activates translation initiation in Drosophila oocytes, and a recent study found that FMRP-dependent translation is also conserved in the mammalian brain. Comparisons of ribosome profiling data from mammalian cortex and Drosophila oocytes revealed similar decreases in the translation of FMRP-bound mRNAs in FMRP-deficient tissues from both species.
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
Cell Biology
Haojie Wang, Meixia Ye, Yaru Fu, Ang Dong, Miaomiao Zhang, Li Feng, Xuli Zhu, Wenhao Bo, Libo Jiang, Christopher H. Griffin, Dan Liang, Rongling Wu
Summary: The study presents a conceptual model integrating evolutionary game theory, developmental modularity theory, and a variable selection method to dissect the genotype-environment interplay. It reconstructs multilayer genetic networks that are sparse, informative, and environmentally-induced, revealing novel molecular mechanisms in trees' response to saline stress. The model serves as a tool to understand genetic architecture of trait variation and evolution within omnigenic networks, tracing information flow from genes to phenotypes.
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
Multidisciplinary Sciences
Xiaoyu Liang, Xuewei Cao, Qiuying Sha, Shuanglin Zhang
Summary: The article introduces a novel multivariate method for phenome-wide association studies (PheWAS) and demonstrates its superiority through extensive simulation studies and real-life application. The proposed method involves hierarchical clustering, clustering linear combination, and false discovery rate control steps.
Article
Multidisciplinary Sciences
Abbas Saad Alatrany, Wasiq Khan, Abir Hussain, Dhiya Al-Jumeily
Summary: The increasing incidence of Alzheimer's disease (AD) poses socioeconomic challenges. In this study, a hybrid feature selection approach and neural network models are used to predict AD. The approach outperformed existing methods with 99% accuracy and f1-score, providing impactful outcomes for other chronic diseases.
Article
Multidisciplinary Sciences
Jack W. O'Sullivan, John P. A. Ioannidis
Summary: This study compared SNVs from earlier and later GWAS and found a replication rate of 85.0% in subsequent studies, with a lower replication rate for binary phenotypes compared to quantitative phenotypes. The study also identified a decrease in SNV effect size for binary phenotypes, but an increase for quantitative phenotypes, and developed a model that could predict SNV replication effectively.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Alexander J. Cammack, Arnav Moudgil, Jiayang Chen, Michael J. Vasek, Mark Shabsovich, Katherine McCullough, Allen Yen, Tomas Lagunas, Susan E. Maloney, June He, Xuhua Chen, Misha Hooda, Michael N. Wilkinson, Timothy M. Miller, Robi D. Mitra, Joseph D. Dougherty
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Multidisciplinary Sciences
Nathan Pomper, Yating Liu, Mariah L. Hoye, Joseph D. Dougherty, Timothy M. Miller
SCIENTIFIC REPORTS
(2020)
Article
Behavioral Sciences
Shyam K. Akula, Katherine B. McCullough, Claire Weichselbaum, Joseph D. Dougherty, Susan E. Maloney
BRAIN AND BEHAVIOR
(2020)
Article
Cell & Tissue Engineering
Corina Anastasaki, Michelle L. Wegscheid, Kelly Hartigan, Jason B. Papke, Nathan D. Kopp, Jiayang Chen, Olivia Cobb, Joseph D. Dougherty, David H. Gutmann
Review
Neurosciences
Bernard Mulvey, Tomas Lagunas, Joseph D. Dougherty
Summary: Studies in neuropsychiatric genetics have shown that diseases may be influenced by numerous small-effect noncoding variants and/or rare but significant coding variants. Novel genetic technologies, particularly MPRAs, offer opportunities to experimentally identify these variants on a large scale. Researchers are exploring the use of MPRA to better understand the polygenic nature of psychiatric disorders.
BIOLOGICAL PSYCHIATRY
(2021)
Article
Behavioral Sciences
Kayla R. Nygaard, Raylynn G. Swift, Rebecca M. Glick, Rachael E. Wagner, Susan E. Maloney, Georgianna G. Gould, Joseph D. Dougherty
Summary: Williams Syndrome leads to distinct behavioral phenotypes, such as learning deficits, anxiety, heightened phobias, and hypersociability. While some studies suggest a possible involvement of oxytocin dysregulation, experimental results did not confirm this hypothesis.
GENES BRAIN AND BEHAVIOR
(2022)
Article
Biochemical Research Methods
Yating Liu, Joseph D. Dougherty
Summary: Whole genome sequencing of patient populations is identifying thousands of new variants in untranslated regions (UTRs). While the consequences of UTR mutations are not as easily predicted from primary sequence as coding mutations are, there are known features that modulate their function. The utr.annotation R package can be used to annotate potential deleterious variants in UTR regions, providing detailed information on each variant.
Article
Neurosciences
Rachel M. Rahn, Lindsey M. Brier, Annie R. Bice, Matthew D. Reisman, Joseph D. Dougherty, Joseph P. Culver
Summary: The study used optical fluorescence imaging to track calcium functional connectivity (FC) in the mouse cortex across 5 developmental timepoints, revealing coherent functional maps as early as postnatal day 15. FC varied significantly across development, with specific developmental trajectories in different functional regions. The study identified periods of dynamic changes in FC during development, providing a resource dataset for further examination of disease states.
Article
Psychiatry
Bernard Mulvey, Joseph D. Dougherty
Summary: Family and population studies show that MDD has a genetic component involving SNP alterations in transcriptional regulators. Understanding the functional SNPs and their convergence in causing the disease is crucial in elucidating MDD pathophysiology. Additionally, retinoids can induce MDD and depressive behaviors through a regulatory system involving transcription factors.
TRANSLATIONAL PSYCHIATRY
(2021)
Review
Psychiatry
Jiayang Chen, Allen Yen, Colin P. Florian, Joseph D. Dougherty
Summary: This article provides an overview of published studies on MYT1L gene, including patient cases and experimental research in cells, zebrafish, and mice. These studies contribute to understanding the role of MYT1L in brain development and the relationship between its dysfunction and neurodevelopmental disorders. Additionally, conflicting findings are highlighted, leading to a reevaluation of MYT1L's role as a transcriptional activator and/or repressor.
TRANSLATIONAL PSYCHIATRY
(2022)
Article
Neurosciences
Rachel M. Rahn, Allen Yen, Siyu Chen, Seana H. Gaines, Annie R. Bice, Lindsey M. Brier, Raylynn G. Swift, LeiLani Lee, Susan E. Maloney, Joseph P. Culver, Joseph D. Dougherty
Summary: In this study, widefield optical fluorescence imaging was used to evaluate calcium functional connectivity (FC) in the brain of the Mecp2 mutant mouse model. Results showed disrupted FC between cortical regions in Mecp2 mutant males during both juvenile development and early adulthood. Female Mecp2 mice exhibited increased contralateral FC in the motor cortex at P35, while more posterior parietal regions were implicated in adulthood. The amplitude of connection strength was increased in the male cortex, with more positive correlations and negative anticorrelations. Restoring MeCP2 protein in GABAergic neurons did not rescue these functional deficits or increase male lifespan.
Article
Neurosciences
Michael J. Vasek, Shayna M. Mueller, Stuart B. Fass, Jelani D. Deajon-Jackson, Yating Liu, Haley W. Crosby, Sarah K. Koester, Jiwon Yi, Qingyun Li, Joseph D. Dougherty
Summary: Vasek et al. demonstrate that distal processes of microglia locally translate specific mRNAs related to immunity and phagocytosis. They show that local protein synthesis is necessary for microglial process-initiated phagocytosis. Neurons, astrocytes and oligodendrocytes also regulate protein translation within distal processes. Using a live slice preparation, they further show that acute translation blockade impairs the formation of peripheral microglial process (PeMP) phagocytic cups, lysosomal protein localization, and phagocytosis. These data suggest the importance of regulated local translation in PeMPs for dynamic microglial functions.
NATURE NEUROSCIENCE
(2023)
Article
Neurosciences
Bernard Mulvey, Hannah E. Frye, Tania Lintz, Stuart Fass, Eric Tycksen, Elliot C. Nelson, Jose A. Moron, Joseph D. Dougherty
Summary: In females, the hippocampus shows altered physiology and behavioral output across the estrous or menstrual cycle. However, the underlying molecular effectors and cell types have only been partially characterized. The study found that mice lacking the AMPA receptor trafficking gene Cnih3 displayed estrous-dependent phenotypes in the dorsal hippocampus. Transcriptomic analysis revealed extensive differences in gene expression between estrous cycle stages and males, highlighting potential cell types and molecular systems impacted by estrous-specific gene expression patterns.
Article
Behavioral Sciences
Kayla R. Nygaard, Susan E. Maloney, Raylynn G. Swift, Katherine B. McCullough, Rachael E. Wagner, Stuart B. Fass, Krassimira Garbett, Karoly Mirnics, Jeremy Veenstra-VanderWeele, Joseph D. Dougherty
Summary: Williams syndrome is a rare neurodevelopmental disorder that affects cognitive and behavioral functions. It is caused by a microdeletion on chromosome 7, which includes the GTF2IRD1 gene. The syndrome is associated with increased social motivation, anxiety, and specific phobias. Duplications of this gene region can lead to autism and language delay. This study investigates the role of Gtf2ird1 in social motivation and behavior using a mouse model.
GENES BRAIN AND BEHAVIOR
(2023)
Article
Biochemical Research Methods
Susan E. Maloney, Simona Sarafinovska, Claire Weichselbaum, Katherine B. McCullough, Raylynn G. Swift, Yating Liu, Joseph D. Dougherty
Summary: Social motivation plays a critical role in the development of typical social functioning. A social operant conditioning task was developed to measure effort to access a social partner and concurrent social orienting in mice, and its reliability and validity were established. The method was then used to study social phenotypes in rodent models of autism, revealing reduced social orienting in Shank3B mutants and decreased social motivation with oxytocin receptor antagonism. This method provides a valuable tool for understanding social motivation neural circuits in autism.
CELL REPORTS METHODS
(2023)