Article
Biochemistry & Molecular Biology
Jorge Botas, Alvaro Rodriguez del Rio, Joaquin Giner-Lamia, Jaime Huerta-Cepas
Summary: GeCoViz is an online resource that provides fast and interactive visualization of custom genomic regions, allowing for easy investigation of the functional and evolutionary interpretation of prokaryotic genes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
Kimberly A. Luddy, Jamie K. Teer, Audrey Freischel, Cliona O'Farrelly, Robert Gatenby
Summary: In an evolving population, fitness determines proliferation and the dominant population usually has the most well adapted phenotype. Negative selection provides crucial information about genes involved in essential cellular processes. Similar to immunoediting, evolutionary triage eliminates mutations in tumor cells that increase susceptibility to immune response while mutations that shield them from immune attack increase proliferation. This new approach can be used to investigate evolutionary triage in immune-related genes and potentially lead to new treatment options.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Peter Fuchs, Corinne Drexler, Sonia Ratajczyk, Leopold Eckhart
Summary: The evolutionary transition from land to water in cetaceans led to the loss of multiple epithelial keratins, including EPPK1, suggesting a change in the molecular composition and regulation of epithelia.
SCIENTIFIC REPORTS
(2022)
Article
Biology
Zachary T. Wood, Eric P. Palkovacs, Brian J. Olsen, Michael T. Kinnison
Summary: Humans are dominant global drivers of ecological and evolutionary change, affecting the reshaping of ecosystems and natural selection. Human activities play a crucial role in shaping eco-evolutionary potential, influencing the stability and resilience of populations, communities, and ecosystems. Proper management of anthropogenic effects requires a science of human effects on eco-evolutionary potential.
Article
Multidisciplinary Sciences
Jedediah F. Brodie, Sara Williams, Brittany Garner
Summary: Biodiversity is declining globally, primarily driven by habitat loss and harvest activities. Herbivores and frugivores are particularly vulnerable to declines from hunting and habitat loss, with significant implications for plant communities and nutrient cycling. While globally phylogenetically unique species do not have an elevated risk of decline, in certain areas they are more likely to be threatened.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Abdul Jalal, Jinrui Sun, Yeqing Chen, Chunguo Fan, Jinyi Liu, Changquan Wang
Summary: In this study, clock PRRs in roses were identified and their evolutionary profiles and functional roles in controlling flowering were analyzed. The results showed that clock PRRs were significantly expanded in Rosaceae and had a strong association with flowering controlling genes. Functional analysis confirmed their negative regulation of flowering. This study provides insights into the evolutionary profiles and functional roles of clock PRRs in controlling flowering in roses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Xuye Yuan, Yu Zhu, David Ruiz-Carrillo, Tatsuhiko Kadowaki
Summary: Most members of the TMEM16 family act as Ca2+-activated chloride channels or phospholipid scramblases, playing different physiological roles. The family is highly conserved in eukaryotes, but the origin and evolution of its subfamilies in Metazoa are still unclear. Through evolutionary genomics analysis, this study reveals the evolutionary history of the TMEM16 family, identifying vertebrate-specific subfamilies and ancient subfamilies present in many metazoan species. The findings suggest that the TMEM16 family has evolved through gene gain and loss, with purifying selection maintaining protein structures and functions.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
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
Environmental Sciences
James Nicholas Furze, El Hassan Mayad
Summary: The evolution of major life kingdoms over the past 4 billion years on Earth involves a diverse range of study fields and perspectives. This paper focuses on the mathematical unification of the subject area and uses laboratory and field studies to illustrate emergence in evolutionary processes within the terrestrial/soil environment, showcasing different strategic groupings and growth trends in the soil community. Various classification methods and novel algorithms are recommended for the development of constructs covering different categories of life.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Article
Plant Sciences
Carles Quesada-Traver, Alba Lloret, Lorenzo Carretero-Paulet, Maria Luisa Badenes, Gabino Rios
Summary: This study identified and characterized DAM proteins, which are master regulators of bud dormancy in perennials, in the Rosaceae family. The study found that DAM proteins play a role in inflorescence development and growth, independent of dormancy habit.
Article
Biology
Jason Cheok Kuan Leong, Masahiro Uesaka, Naoki Irie
Summary: The concept of evolutionary conservation is used to explain ancestral features and traits, but it has been misused to evaluate derivedness. Distinguishing these two concepts can help understand phenotypic and organismal evolution. Conservation focuses on common genes or traits, while derivedness covers novel or lost traits and genes to evaluate changes from a common ancestor. Conservation-oriented methods are effective in identifying ancestral features, but may underestimate overall changes. A new method, the transcriptomic derivedness index, uses whole-embryonic transcriptome as a phenotype to estimate phenotypic derivedness.
Article
Biochemistry & Molecular Biology
Marina L. Garcia-Vaquero, Margarida Gama-Carvalho, Francisco R. Pinto, Javier De Las Rivas
Summary: The centrality measures of individual proteins are insufficient to dissect the functional properties of cells, a more comprehensive, relational and context-specific method is needed. The study reveals tissue-specific functional diversification based on the identification of specific protein units.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Multidisciplinary Sciences
Doron Levin, Neta Raab, Yishay Pinto, Daphna Rothschild, Gal Zanir, Anastasia Godneva, Nadav Mellul, David Futorian, Doran Gal, Sigal Leviatan, David Zeevi, Ido Bachelet, Eran Segal
Summary: Research analyzed the gut microbiota of over 180 species of wild animals, finding associations with animal taxonomy, diet, activity, and other factors. These findings suggest that the gut microbiota of wild animals could be a valuable resource for discovering therapeutics and biotechnology applications in the future.
Article
Biochemistry & Molecular Biology
Frederic B. Bastian, Julien Roux, Anne Niknejad, Aurelie Comte, Sara S. Fonseca Costa, Tarcisio Mendes de Farias, Sebastien Moretti, Gilles Parmentier, Valentine Rech de Laval, Marta Rosikiewicz, Julien Wollbrett, Amina Echchiki, Angelique Escoriza, Walid H. Gharib, Mar Gonzales-Porta, Yohan Jarosz, Balazs Laurenczy, Philippe Moret, Emilie Person, Patrick Roelli, Komal Sanjeev, Mathieu Seppey, Marc Robinson-Rechavi
Summary: Bgee is a database that allows retrieval and comparison of gene expression patterns in multiple animal species using curated healthy wild-type data, enabling the detection of expression conditions for any single gene across different species. It integrates various data types and ensures consistent data annotation and processing for cross-species comparisons.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Luyao Wang, Jin Han, Kening Lu, Menglin Li, Mengtao Gao, Zeyi Cao, Ting Zhao, Xue Chen, Xiaoyuan Tao, Quanjia Chen, Xueying Guan
Summary: An evolutionary model using diploid and allotetraploid cotton species found that 80% of non-coding transcripts in allotetraploid cotton are uniquely activated compared to its diploid ancestors. The function of activated lncRNAs in allotetraploid cotton is largely unknown. Transcriptome analysis revealed that lncRNA expression is preferentially associated with flanking PCGs, and a low-throughput functional screening identified lncRNAs related to plant height and stress tolerance. The study suggests that lncRNAs are more active under abiotic stresses, such as temperature stress, and may play a cis-regulatory role in response to environmental stimuli.
Article
Genetics & Heredity
Longguang Qin, Ang Li, Kaeling Tan, Shuhui Guo, Yingying Chen, Fang Wang, Koon Ho Wong
FUNGAL GENETICS AND BIOLOGY
(2019)
Article
Biotechnology & Applied Microbiology
Dane Vassiliadis, Koon Ho Wong, Alex Andrianopoulos, Brendon J. Monahan
Article
Microbiology
Sang Hu Kim, Kali R. Iyer, Lakhansing Pardeshi, Jose F. Munoz, Nicole Robbins, Christina A. Cuomo, Koon Ho Wong, Leah E. Cowen
Correction
Microbiology
Sang Hu Kim, Kali R. Iyer, Lakhansing Pardeshi, Jose F. Munoz, Nicole Robbins, Christina A. Cuomo, Koon Ho Wong, Leah E. Cowen
Article
Biochemical Research Methods
Gigi C. G. Choi, Peng Zhou, Chaya T. L. Yuen, Becky K. C. Chan, Feng Xu, Siyu Bao, Hoi Yee Chu, Dawn Thean, Kaeling Tan, Koon Ho Wong, Zongli Zheng, Alan S. L. Wong
Article
Mycology
Pooja Sethiya, Maruti Nandan Rai, Rikky Rai, Chirag Parsania, Kaeling Tan, Koon Ho Wong
Article
Genetics & Heredity
Dane Vassiliadis, Koon Ho Wong, Jo Blinco, Geoff Dumsday, Alex Andrianopoulos, Brendon Monahan
G3-GENES GENOMES GENETICS
(2020)
Article
Microbiology
Fang Wang, Pooja Sethiya, Xiaohui Hu, Shuhui Guo, Yingying Chen, Ang Li, Kaeling Tan, Koon Ho Wong
Summary: Transcriptional activity of fungal conidia before dormancy plays a crucial role in conidia maturation, fitness, drug resistance, and virulence post-germination. The environmental-specific transcriptional responses can alter conidial content and gene expression, affecting the capabilities of fungal cells after germination. Fungal conidia prepare for the future by synthesizing and storing transcripts according to environmental conditions present before dormancy.
NATURE MICROBIOLOGY
(2021)
Article
Microbiology
Yingying Chen, Liguo Dong, Md Ashiqul Alam, Lakhansing Pardeshi, Zhengqiang Miao, Fang Wang, Kaeling Tan, Michael J. Hynes, Joan M. Kelly, Koon Ho Wong
Summary: This study investigated the regulatory role of the carbon catabolite repression (CCR) transcription factor CreA in Aspergillus nidulans, uncovering its functions in diverse physiological processes beyond carbon metabolism. The research provided mechanistic insights into CreA regulation and highlighted its role as a master regulator controlling multiple transcription factors in different regulatory networks. The discoveries have important implications for understanding CCR in related pathogenic and industrial species.
Article
Biology
Ang Li, Chirag Parsania, Kaeling Tan, Richard B. Todd, Koon Ho Wong
Summary: The study revealed the dual functions of the PnmB protein in Aspergillus nidulans as a moonlighting protein, serving both as an extracellular protease for nutrient degradation and an intracellular protease for controlling the turnover of the co-repressor NmrA, accelerating transcriptional activation under nitrogen starvation conditions.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yimin Zheng, Yitian Chen, Xianting Ding, Koon Ho Wong, Edwin Cheung
Summary: Spatial omics is an approach that integrates spatial knowledge with transcript or protein expression information to explore tissue microenvironment and cellular networks. However, there is a lack of databases for users to access and analyze spatial omics data. To address this limitation, Aquila, a comprehensive platform for managing and analyzing spatial omics data, has been developed. Aquila contains 107 datasets from 30 diseases, covering studies using different technologies.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Betim Karahoda, Lakhansing Pardeshi, Mevlut Ulas, Zhiqiang Dong, Niranjan Shirgaonkar, Shuhui Guo, Fang Wang, Kaeling Tan, Ozlem Sarikaya-Bayram, Ingo Bauer, Paul Dowling, Alastair B. Fleming, Brandon T. Pfannenstiel, Dianiris Luciano-Rosario, Harald Berger, Stefan Graessle, Mohamed M. Alhussain, Joseph Strauss, Nancy P. Keller, Koon Ho Wong, Ozgur Bayram
Summary: This study describes a chromatin binding complex KERS in the fungus Aspergillus nidulans, consisting of H3K4 histone demethylase KdmB, cohesin acetyltransferase EcoA, histone deacetylase RpdA, and histone reader/E3 ligase protein SntB. The KERS complex exerts promoter-specific transcriptional effects at active core promoters.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Chirag Parsania, Ruiwen Chen, Pooja Sethiya, Zhengqiang Miao, Liguo Dong, Koon Ho Wong
Summary: This study presents an intuitive user-friendly platform called FungiExpresZ for gene expression data analysis and visualization, aiming to help wet-lab scientists without computer programming skills to become independent in bioinformatics analysis. The platform includes commonly used data analysis tools and pre-processed RNA-seq datasets of various fungal species, including human, plant, and insect pathogens. FungiExpresZ enables users to analyze their own data alone or in combination with public RNA-seq data for integrated analysis, overcoming limitations in genomics data analysis.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Microbiology
Longguang Qin, Shuhui Guo, Ang Li, Lu Fan, Kaeling Tan, Koon Ho Wong
Summary: Transcription factors (TFs) play a crucial role in regulating gene expression in living organisms. Identifying autogenous regulation events of TFs has been a tedious task. In this study, a straightforward approach is presented that provides a reliable means to identify TF autogenous regulation events, offering valuable insights into TF function.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biology
Natalia Petrenko, Yi Jin, Liguo Dong, Koon Ho Wong, Kevin Struhl