Article
Biology
Pan Cheng, Xin Zhao, Lizabeth Katsnelson, Elaine M. Camacho-Hernandez, Angela Mermerian, Joseph C. Mays, Scott M. Lippman, Reyna Edith Rosales-Alvarez, Raquel Moya, Jasmine Shwetar, Dominic Grun, David Fenyo, Teresa Davoli
Summary: This study reveals the regulation of RNA and protein abundance in genes with somatic copy number alterations (SCNAs), providing insights into gene regulation. Protein complex genes are primarily regulated at the protein level, while non-complex genes are primarily regulated at the RNA level. Interestingly, genes in the same pathway show similar levels of RNA and protein regulation, with certain pathways showing stronger regulation at either the protein level or the RNA level.
Article
Infectious Diseases
Ruichao Li, Yongjia Jiang, Kai Peng, Yanhong Wang, Mianzhi Wang, Yuan Liu, Zhiqiang Wang
Summary: This study confirms the high prevalence of tet(X) in R. anatipestifer. Further investigations are needed to assess the transfer risk of tet(X) from R. anatipestifer to other clinical pathogens.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2022)
Article
Plant Sciences
Huaxing Huang, Hongli Ji, Song Ju, Wei Lin, Jing Li, Xuanrui Lv, Lixian Lin, Lijin Guo, Dongliang Qiu, Jianyong Yan, Xiaokai Ma
Summary: This study investigated the genomic information and gene regulation network for color variation of bracts in Bougainvillea plants. It identified differentially expressed genes and co-expressed hub genes that are responsible for the color variations. These findings provide valuable insights into the molecular basis of color variation in key bracts of horticultural Bougainvillea.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Sarah Janati-Idrissi, Mariana Roza de Abreu, Cervin Guyomar, Fernanda de Mello, Thaovi Nguyen, Nazim Mechkouri, Stephanie Gay, Jerome Montfort, Anne Alicia Gonzalez, Marzieh Abbasi, Jerome Bugeon, Violette Thermes, Herve Seitz, Julien Bobe
Summary: This study provides a proof of concept for the successful identification of miRNA phenotypic targets from RNA-seq data. The researchers identified tead3b as a target of miR-202-5p, which is involved in ovarian function and egg production. This study highlights the importance of understanding miRNA functions and their targets in order to better understand biological processes.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Joshua E. Burda, Timothy M. O'Shea, Yan Ao, Keshav B. Suresh, Shinong Wang, Alexander M. Bernstein, Ashu Chandra, Sandeep Deverasetty, Riki Kawaguchi, Jae H. Kim, Sarah McCallum, Alexandra Rogers, Shalaka Wahane, Michael Sofroniew
Summary: This study reveals the regulatory mechanism of genes associated with astrocyte reactivity through biological and informatic analyses. These genes show heterogeneity across different central nervous system disorders and are regulated by transcriptional regulators. By modulating reactivity, these transcriptional regulators can alter the outcome of the disorders and may serve as therapeutic targets.
Article
Biochemistry & Molecular Biology
Di Wu, Yiming Wei, Xiangyu Zhao, Boka Li, Huankai Zhang, Gang Xu, Juntong Lv, Dajian Zhang, Xiansheng Zhang, Min Ni
Summary: Evolution is driven by various mechanisms, and the directional increase in the embryo to endosperm ratio is an evolutionary trend within angiosperms. The duration of endosperm proliferation, controlled by PRC2-mediated epigenetic silencing, contributes to silenced or persistent endosperm proliferation in different species.
Article
Multidisciplinary Sciences
Anna Paola Carrieri, Niina Haiminen, Sean Maudsley-Barton, Laura-Jayne Gardiner, Barry Murphy, Andrew E. Mayes, Sarah Paterson, Sally Grimshaw, Martyn Winn, Cameron Shand, Panagiotis Hadjidoukas, Will P. M. Rowe, Stacy Hawkins, Ashley MacGuire-Flanagan, Jane Tazzioli, John G. Kenny, Laxmi Parida, Michael Hoptroff, Edward O. Pyzer-Knapp
Summary: Alterations in the human microbiome have been observed in various conditions, and there is still much to learn about the links between the microbiome and human health. The combination of artificial intelligence and rich microbiome datasets offers a better understanding of the microbiome's role in human health. Using an explainable artificial intelligence approach, predictions of phenotypes can be made from leg skin microbiome samples, providing explanations based on variations in key microbes.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Qing Xiong, Angel Tsz-Yau Wan, Xiaoyu Liu, Cathy Sin-Hang Fung, Xiaojun Xiao, Nat Malainual, Jinpao Hou, Lingyi Wang, Mingqiang Wang, Kevin Yi Yang, Yubao Cui, Elaine Lai-Han Leung, Wenyan Nong, Soo-Kyung Shin, Shannon Wing-Ngor Au, Kyoung Yong Jeong, Fook-Tim Chew, Jerome Ho-Lam Hui, Ting-Fan Leung, Anchalee Tungtrongchitr, Nanshan Zhong, Zhigang Liu, Stephen Kwok-Wing Tsui
Summary: This study examines the evolutionary origin, diverse lifestyles, and quick adaptation of astigmatic mites in human household environments using six high-quality assembled and annotated genomes. The research reveals that astigmatic mites evolved from Prostigmata, notorious plant pests, and rapidly diversified from soil oribatid mites. The study also highlights the rapid expansion of gene families via tandem gene duplications in astigmatic mites, providing genetic resources for adaptation to changing household environments. Additionally, massive horizontal gene transfer events occurred during the evolution of astigmatic mites, enabling detoxification and digestive functions and offering potential drug targets for pest control.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Emmanuel N. Paul, Gregory W. Burns, Tyler J. Carpenter, Joshua A. Grey, Asgerally T. Fazleabas, Jose M. Teixeira
Summary: Transcriptome analysis revealed significant phenotypic and gene expression differences between fibroid-associated myometrium and non-diseased myometrium, particularly in upregulated genes related to extracellular matrix and structure organization. These results suggest that fibroid studies should consider using both matched myometrium and non-diseased myometrium as controls to better understand the pathophysiology of uterine fibroids.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Madeleine Carruthers, Duncan E. Edgley, Andrew D. Saxon, Nestory P. Gabagambi, Asilatu Shechonge, Eric A. Miska, Richard Durbin, Jon R. Bridle, George F. Turner, Martin J. Genner
Summary: In an African crater lake, the cichlid Astatotilapia calliptera has diverged into shallow-littoral and deep-benthic ecomorphs within the last 1,000 years. Through analysis of transcriptome data, this study reveals that regulatory variants play a crucial role in driving ecologically relevant divergence in gene expression during adaptive diversification.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biology
Cecilia Trivellin, Peter Rugbjerg, Lisbeth Olsson
Summary: In order to design strains that can efficiently function in complex industrial environments, it is important to consider their robustness, which is the stability of their performance when faced with disturbances. This study cultivated 24 Saccharomyces cerevisiae strains under conditions simulating perturbations encountered in lignocellulosic bioethanol production, and assessed the performance and robustness of multiple phenotypes simultaneously. The results demonstrated a trade-off between performance and robustness, confirming previous findings that showed a negative correlation between ethanol yield, biomass yield, and cell dry weight. The specific growth rate performance positively correlated with robustness, likely due to evolutionary selection for robust, fast-growing cells. The Ethanol Red strain exhibited both high performance and robustness, making it a good candidate for bioproduction in perturbation-prone environments.
LIFE SCIENCE ALLIANCE
(2023)
Article
Agricultural Engineering
Ming Yin, Gen Pan, Jie Tao, Monika S. Doblin, Wei Zeng, Langlang Pan, Lining Zhao, Zheng Li, Hui Jiang, Li Chang, Yong Deng, Defang Li, Siqi Huang
Summary: Cadmium is an inorganic heavy metal pollutant in China, while industrial hemp is an important fiber crop used for soil remediation. Studies have shown that Cd stress affects the production of secondary metabolites in hemp plants. Through genome analysis, several key genes in the hemp MYB family have been identified, including seven genes that play important roles in response to Cd stress.
INDUSTRIAL CROPS AND PRODUCTS
(2022)
Article
Biology
Victor Boussange, Loic Pellissier
Summary: This study investigates the impact of habitat connectivity and heterogeneity on phenotypic differentiation using a stochastic eco-evolutionary model. The research reveals that both low connectivity and heterogeneity promote neutral differentiation, while habitat assortativity drives differentiation under habitat-dependent selection. The study establishes fundamental links between landscape features and phenotypic differentiation, providing insights into how habitat connectivity and heterogeneity affect differentiation.
COMMUNICATIONS BIOLOGY
(2022)
Article
Microbiology
Alex R. J. Lima, Christiane B. de Araujo, Saloe Bispo, Jose Patane, Ariel M. Silber, M. Carolina Elias, Julia P. C. da Cunha
Summary: This study revealed differences in nucleosome organization at strategic genomic regions among replicative and nonreplicative T. cruzi forms. The nonreplicative forms have less dynamic nucleosomes, while dynamic nucleosomes are enriched at regulatory transcription initiation regions and multigenic family members associated with infective stage and virulence factors. Genes related to DNA replication, cytokinesis, transcription and translation regulation are mainly enriched on dynamic nucleosomes.
Article
Biology
Marleen Klann, Magdalena Ines Schacht, Matthew Alan Benton, Angelika Stollewerk
Summary: Insects and other arthropods use external sensory structures for mechanosensory, olfactory, and gustatory reception, with sense organs having characteristic shapes related to their functions. While Drosophila melanogaster regulates sense organ identity through specific combinations of transcription factors, other arthropods do not link sense organ subtypes to the same gene expression code. Sense organ diversity may have evolved differently across insect species, with recruitment of sensory genes to distinct sensory organ specification mechanisms playing a role.
Article
Biochemistry & Molecular Biology
Yanfa Sun, Dan Zhou, Md Rezanur Rahman, Jingjing Zhu, Dalia Ghoneim, Nancy J. Cox, Thomas G. Beach, Chong Wu, Eric R. Gamazon, Lang Wu
Summary: This study identifies 15 genes as potential biomarkers in blood for Alzheimer's disease risk through transcriptome-wide association study.
HUMAN MOLECULAR GENETICS
(2022)
Article
Oncology
Duo Liu, Jingjing Zhu, Dan Zhou, Emily G. Nikas, Nikos T. Mitanis, Yanfa Sun, Chong Wu, Nicholas Mancuso, Nancy J. Cox, Liang Wang, Stephen J. Freedland, Christopher A. Haiman, Eric R. Gamazon, Jason B. Nikas, Lang Wu
Summary: The study combines transcriptome-wide association study and validation to identify candidate genes potentially involved in prostate cancer development. Analysis revealed 573 genes associated with prostate cancer risk, including 451 novel genes and 122 previously reported genes.
INTERNATIONAL JOURNAL OF CANCER
(2022)
Article
Biochemistry & Molecular Biology
Hung-Hsin Chen, Lauren E. Petty, Kari E. North, Joseph B. McCormick, Susan P. Fisher-Hoch, Eric R. Gamazon, Jennifer E. Below
Summary: This study employed an innovative and systematic approach to identify and validate key gene expression changes associated with the transition status of type 2 diabetes, demonstrating their translational relevance in a large clinical resource.
HUMAN MOLECULAR GENETICS
(2022)
Article
Neurosciences
Zachary F. Gerring, Jackson G. Thorp, Eric R. Gamazon, Eske M. Derks
Summary: This study uses global genetic correlation analysis to reveal local bivariate genetic correlations between psychiatric and substance use disorders, and identifies shared credible causal genes through fine-mapping.
BIOLOGICAL PSYCHIATRY
(2022)
Article
Biochemistry & Molecular Biology
Zachary F. Gerring, Jackson G. Thorp, Eric R. Gamazon, Eske M. Derks
Summary: Transcriptome-wide association study revealed the functional gene mechanisms underlying psychiatric disorders and substance use phenotypes using gene expression data.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Vasiliki Thomeas-McEwing, Mitchell A. Psotka, Eric R. Gamazon, Paula Friedman, Anuar Konkashbaev, Michiaki Kubo, Yusuke Nakamura, Mark J. Ratain, Raymond L. Benza, Nancy J. Cox, Mardi Gomberg-Maitland, Michael L. Maitland
Summary: The study aimed to identify new biologically-based predictors of prostacyclin treatment response heterogeneity for patients with pulmonary arterial hypertension. Genome-wide association study and in vitro assays were conducted to identify candidate genes and their effects on prostacyclin-induced vasodilation. The findings suggest that specific genetic variants may affect treatment response and right ventricular function in patients with pulmonary arterial hypertension.
PHARMACOGENETICS AND GENOMICS
(2022)
Article
Biotechnology & Applied Microbiology
Jibril B. Hirbo, Francesca Pasutto, Eric R. Gamazon, Patrick Evans, Priyanka Pawar, Daniel Berner, Julia Sealock, Ran Tao, Peter S. Straub, Anuar I. Konkashbaev, Max A. Breyer, Ursula Schloetzer-Schrehardt, Andre Reis, Milam A. Brantley Jr, Chiea C. Khor, Karen M. Joos, Nancy J. Cox
Summary: Exfoliation syndrome (XFS) is an age-related disorder that causes the accumulation of abnormal extracellular material in the body, leading to ocular manifestations and secondary glaucoma. A global meta-analysis identified seven loci near LOXL1 that are strongly associated with XFS. The study conducted transcriptomic wide association studies and experimental analysis to reveal the role of connective tissues and inflammation pathways in the development of XFS.
Article
Cell Biology
Timothy C. Kenny, Artem Khan, Yeeun Son, Lishu Yue, Soren Heissel, Anurag Sharma, H. Amalia Pasolli, Yuyang Liu, Eric R. Gamazon, Hanan Alwaseem, Richard K. Hite, Kivanc Birsoy
Summary: A genetic analysis linking serum metabolites to membrane transporters revealed a connection between FLVCR1 and phosphocholine. FLVCR1 loss impairs choline metabolism and leads to mitochondrial defects and upregulation of the integrated stress response. The findings suggest FLVCR1 as a major choline transporter in mammals and provide a platform to discover substrates for unknown metabolite transporters.
Article
Ecology
Colin M. Brand, Laura L. Colbran, John A. Capra
Summary: Alternative splicing plays a crucial role in adaptation and divergence. By utilizing the SpliceAI algorithm, researchers have identified thousands of splice-altering variants in archaic hominins. These archaic-specific variants are more commonly found in the genomes of Neanderthals and Denisovans and may contribute to phenotypic differences among hominins.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Psychiatry
Damian J. Woodward, Jackson G. Thorp, Wole Akosile, Jue-Sheng Ong, Eric R. Gamazon, Eske M. Derks, Zachary F. Gerring
Summary: Anxiety disorders are prevalent and heritable neuropsychiatric diseases. By integrating genome-wide association study (GWAS) and functional genomic data, researchers identified genes associated with anxiety and discovered potential drug targets for anxiety treatment through drug repurposing.
PSYCHIATRY RESEARCH
(2023)
Article
Multidisciplinary Sciences
Sylvia Hartmann, Summaira Yasmeen, Benjamin M. Jacobs, Spiros Denaxas, Munir Pirmohamed, Eric R. Gamazon, Mark J. Caulfield, Harry Hemingway, Maik Pietzner, Claudia Langenberg
Summary: The study identified three novel genomic regions related to Raynaud's phenomenon risk, prioritized candidate causal genes, and revealed a likely detrimental effect of low fasting glucose levels on RP risk. The research also highlighted opportunities for drug repurposing and provided robust evidence for a strong genetic contribution to RP.
NATURE COMMUNICATIONS
(2023)
Article
Computer Science, Artificial Intelligence
Ramon Vinas, Chaitanya K. Joshi, Dobrik Georgiev, Phillip Lin, Bianca Dumitrascu, Eric R. Gamazon, Pietro Lio
Summary: Vinas et al. propose a neural network for multi-tissue imputation of gene expression, leveraging the shared regulatory architecture of tissues. This method enhances our understanding of coordinated biological mechanisms involved in disease and homeostasis.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Biochemistry & Molecular Biology
Bo Wang, Shahab Razavi, Eric R. Gamazon
Summary: Deep Mutational Scanning (DMS) allows for the measurement of mutational effects on protein properties with high resolution. In this study, deep learning is applied to model the mutational effects of the Alzheimer's Disease associated peptide A beta 42 on aggregation-related biochemical traits. Neural network architectures such as Convolutional Neural Networks and Recurrent Neural Networks are found to be effective models, even with limited data. The study demonstrates the potential of neural network derived sequence-phenotype mapping in protein engineering and therapeutic design.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Cell Biology
Ying Wang, Shinichi Namba, Esteban Lopera, Sini Kerminen, Kristin Tsuo, Kristi Lall, Masahiro Kanai, Wei Zhou, Kuan-Han Wu, Marie-Julie Fave, Laxmi Bhatta, Philip Awadalla, Ben Brumpton, Patrick Deelen, Kristian Hveem, Valeria Lo Faro, Reedik Magi, Yoshinori Murakami, Serena Sanna, Jordan W. Smoller, Jasmina Uzunovic, Cristen Willer, Eric R. Gamazon, Nancy J. Cox, Ida Surakka, Yukinori Okada, Alicia R. Martin, Jibril Hirbo
Summary: This study utilized data from GBMI to explore methodological considerations and performance of PRS for 14 disease endpoints across global populations. The study provides lessons for PRS construction, evaluation, and interpretation and highlights the importance of PRS in the biobank-scale genomics era.
Article
Biochemical Research Methods
Wanying Zhu, Hung-Hsin Chen, Alexander S. Petty, Lauren E. Petty, Hannah G. Polikowsky, Eric R. Gamazon, Jennifer E. Below, Heather M. Highland
Summary: Combining and handling imputation quality and missing variants in multiple large VCF files in genomic data is challenging. To address this, we developed IMMerge, a Python-based tool that utilizes multiprocessing to reduce running time, and correctly combines imputation quality scores with Fisher's z transformation.
