Article
Biology
Antonino Malacrino, Martin I. Brengdahl, Christopher M. Kimber, Avani Mital, Vinesh N. Shenoi, Claudio Mirabello, Urban Friberg
Summary: A study found that the fruit fly brain transcriptome becomes desexualized with age, in line with the general prediction that individuals in low condition invest less in sexual traits.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Microbiology
Amelia R. Lindsey, Tamanash Bhattacharya, Richard W. Hardy, Irene L. G. Newton
Summary: Wolbachia is a bacterium that can manipulate the biology of arthropods and nematodes in various ways. The strain of Wolbachia in Drosophila melanogaster causes sperm-egg incompatibilities and protects the host against RNA viruses, making it a potential tool for vector control. Research using the Drosophila model has identified metabolic pathways affected by Wolbachia colonization and virus infection, shedding light on the mechanisms of pathogen blocking for effective vector control programs leveraging Wolbachia.
Article
Biology
Tatjana Krama, Diana Bahhir, Liina Ots, Sergejs Popovs, Vadims Bartkevics, Iveta Pugajeva, Ronalds Krams, Enno Merivee, Anne Must, Markus J. J. Rantala, Indrikis Krams, Priit Joers
Summary: Predation can have lethal and non-lethal effects on prey, and non-lethal effects can cause adaptive evolution. Chronic predation stress can lead to metabolic disorders, similar to conditions in humans. This study found that predator stress impairs carbohydrate metabolism in fruit flies, but the flies grown with predators have better survival under direct predation. Treatment with metformin and 5-hydroxytryptophan reversed these effects, suggesting a link between predator stress and metabolic impairment. This research provides an animal model to explore the mechanisms behind prevalent metabolic disorders in humans.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Behavioral Sciences
Julia Ryvkin, Assa Bentzur, Anat Shmueli, Miriam Tannenbaum, Omri Shallom, Shiran Dokarker, Jennifer I. C. Benichou, Mali Levi, Galit Shohat-Ophir
Summary: The study revealed that neurons expressing the NPF receptor exhibit a unique transcriptome enriched with receptors for various neuropeptides and genes known to regulate behavioral processes. Manipulating RNA editing and protein ubiquitination specifically in these neurons is necessary to suppress certain behaviors. These findings highlight the importance of transcriptome and proteome diversity in regulating complex behaviors.
FRONTIERS IN BEHAVIORAL NEUROSCIENCE
(2021)
Article
Microbiology
Xin Liu, Meng Yang, Runzhou Liu, Fan Zhou, Haibing Zhu, Xiaoyun Wang
Summary: This study investigates the impact of Parkinson's disease (PD)-associated gut microbiota on host transcriptome using various PD models with fecal microbiota transplantation in Drosophila. The results reveal that PD-associated gut microbiota can influence host gene expression and regulate diverse metabolic pathways. This study helps to better understand the link between gut microbiota and PD pathogenesis through the gut-brain axis.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Xin Liu, Meng Yang, Runzhou Liu, Fan Zhou, Haibing Zhu, Xiaoyun Wang
Summary: This study reveals the influence of PD-associated gut microbiota on host gene expression, and provides insights into the link between gut microbiota and PD pathogenesis through the gut-brain axis.
MICROBIOLOGY SPECTRUM
(2023)
Article
Ecology
Christina M. May, Erik B. Van den Akker, Bas J. Zwaan
Summary: Developmental diet has significant effects on gene expression in early life of fruit flies, with larval diet being the major contributor to transcriptional variation, particularly in females. Gene expression in young adult female flies is mainly related to reproduction-related processes influenced by larval diet, while in males, nutrient sensing and metabolic functions are associated with both larval and adult diets.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Review
Biology
Milo S. Johnson, Gautam Reddy, Michael M. Desai
Summary: As organisms evolve, the effects of mutations change due to interactions with other accumulated mutations. This leads to adaptability or robustness shifts that shape subsequent evolution. Recent advances in measuring, modeling, and predicting epistasis along evolutionary trajectories are reviewed, focusing on simple patterns of global epistasis that emerge in data. These patterns can be predicted by a small number of variables, offering promise for modeling epistasis and predicting evolution.
Article
Chemistry, Physical
Mokshada Varma, Bhupendra Shravage, Sakharam Tayade, Avinash Kumbhar, Ray Butcher, Vinod Jani, Uddhavesh Sonavane, Rajendra Joshi, Prasad P. Kulkarni
Summary: Alzheimer's disease is a complex brain disorder involving multiple pathophysiological events, and targeting multiple mechanisms is necessary for its treatment. A novel methyl-substituted 3-acetylcoumarin thiosemicarbazone derivative shows potential in protecting against acetylcholinesterase activity, inflammation, and autophagy induction, as demonstrated in various cellular and animal models. The compound's molecular structure allows for better inhibition of AChE activity and peptide aggregation, suggesting promising therapeutic effects for AD.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Biochemical Research Methods
Manuel Rueda, Roberto Ariosa, Mauricio Moldes, Jordi Rambla
Summary: Beacon v2 is an API specification that defines a standard for federated discovery of genomic and phenotypic data. B2RI is a set of open-source software tools that allow quick setup of a local Beacon instance.
Article
Biology
Stefanny Villalobos-Cantor, Ruth M. Barrett, Alec F. Condon, Alicia Arreola-Bustos, Kelsie M. Rodriguez, Michael S. Cohen, Ian Martin
Summary: Controlled protein synthesis is crucial for regulating gene expression in a cell type-specific manner. We developed a new method to specifically label and visualize newly-synthesized proteins in targeted cell populations in the fly brain, allowing for quantitative analysis of protein synthesis states in vivo.
Article
Biochemistry & Molecular Biology
Alexandru Al. Ecovoiu, Attila Cristian Ratiu, Miruna Mihaela Micheu, Mariana Carmen Chifiriuc
Summary: Drosophila melanogaster is a versatile model organism in genetics that has been used to study and simulate human genetic diseases. By transferring human genes into fruit flies and observing the effects, researchers can identify and validate genetic variants associated with human diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Tai-Ting Lee, Po-Lin Chen, Matthew P. Su, Jian-Chiuan Li, Yi-Wen Chang, Rei-Wen Liu, Hsueh-Fen Juan, Jinn-Moon Yang, Shih-Peng Chan, Yu-Chen Tsai, Sophia von Stockum, Elena Ziviani, Azusa Kamikouchi, Horng-Dar Wang, Chun-Hong Chen
Summary: By using the Drosophila melanogaster model, researchers discovered that the mitochondrial outer membrane protein Fis1 plays a crucial role in muscle dysfunction and several age-related conditions, with mutations leading to damaged mitochondria, increased oxidative stress, and decreased muscle function. Mutations in Fis1 also affect mitochondrial proteostasis in fly muscle, reducing flight capabilities and lifespan, indicating the significance of Fis1 in fly mitochondrial dynamics.
Article
Biology
Dagmara Korona, Benedict Dirnberger, Carlo N. G. Giachello, Rayner M. L. Queiroz, Rebeka Popovic, Karin H. Mueller, David-Paul Minde, Michael J. Deery, Glynnis Johnson, Lucy C. Firth, Fergus G. Earley, Steven Russell, Kathryn S. Lilley, Stephan A. Pless
Summary: This study utilized a CRISPR/Cas9 strategy to generate null alleles for all ten nAChR subunit genes in Drosophila, and investigated their interactions with peptide neurotoxins. The findings have important implications for the development of more effective insecticides.
Article
Multidisciplinary Sciences
Christopher M. Ward, Roswitha A. Aumann, Mark A. Whitehead, Katerina Nikolouli, Gary Leveque, Georgia Gouvi, Elisabeth Fung, Sarah J. Reiling, Haig Djambazian, Margaret A. Hughes, Sam Whiteford, Carlos Caceres-Barrios, Thu N. M. Nguyen, Amanda Choo, Peter Crisp, Sheina B. Sim, Scott M. Geib, Frantisek Marec, Irina Haecker, Jiannis Ragoussis, Alistair C. Darby, Kostas Bourtzis, Simon W. Baxter, Marc F. Schetelig
Summary: By using classical and modern genetic approaches, the gene responsible for the white pupae phenotype in multiple fruit fly species has been identified, offering a new method for generating sexing strains.
NATURE COMMUNICATIONS
(2021)
Article
Ecology
Johannes W. R. Martini, Fernando H. Toledo, Jose Crossa
THEORETICAL POPULATION BIOLOGY
(2020)
Article
Genetics & Heredity
Matias F. Schrauf, Johannes W. R. Martini, Henner Simianer, Gustavo de los Campos, Rodolfo Cantet, Jan Freudenthal, Arthur Korte, Sebastian Munilla
G3-GENES GENOMES GENETICS
(2020)
Article
Genetics & Heredity
Diego Jarquin, Reka Howard, Jose Crossa, Yoseph Beyene, Manje Gowda, Johannes W. R. Martini, Giovanny Covarrubias Pazaran, Juan Burgueno, Angela Pacheco, Martin Grondona, Valentin Wimmer, Boddupalli M. Prasanna
G3-GENES GENOMES GENETICS
(2020)
Article
Plant Sciences
Johannes W. R. Martini, Jose Crossa, Fernando H. Toledo, Jaime Cuevas
Article
Biology
Nidhi Kaihnsa, Yue Ren, Mohab Safey El Din, Johannes W. R. Martini
JOURNAL OF MATHEMATICAL BIOLOGY
(2020)
Article
Genetics & Heredity
Zhengcao Li, Henner Simianer
Article
Genetics & Heredity
Jaime Cuevas, Osval A. Montesinos-Lopez, J. W. R. Martini, Paulino Perez-Rodriguez, Morten Lillemo, Jose Crossa
FRONTIERS IN GENETICS
(2020)
Review
Biotechnology & Applied Microbiology
Osval Antonio Montesinos-Lopez, Abelardo Montesinos-Lopez, Paulino Perez-Rodriguez, Jose Alberto Barron-Lopez, Johannes W. R. Martini, Silvia Berenice Fajardo-Flores, Laura S. Gaytan-Lugo, Pedro C. Santana-Mancilla, Jose Crossa
Summary: Deep learning methods have been widely applied in genomic selection, showing potential to capture nonlinear patterns and improve prediction accuracy. However, their advantages compared to traditional genomic prediction methods are not significantly clear, and the key to utilizing DL lies in having an adequate amount of high-quality training data.
Article
Genetics & Heredity
Bartolo de Jesus Villar-Hernandez, Sergio Perez-Elizalde, Johannes W. R. Martini, Fernando Toledo, P. Perez-Rodriguez, Margaret Krause, Irma Delia Garcia-Calvillo, Giovanny Covarrubias-Pazaran, Jose Crossa
Summary: The decision of which individuals to select and intermate in breeding programs is crucial for improving genetic stocks. With the advancement of computational tools and genomic selection, researchers are focusing on multi-trait selection to consider economic value and net genetic merits. A Bayesian decision theory (BDT) has been proposed to facilitate multi-trait parental selection, summarizing important genetic concepts such as heritability and response to selection. The study applied BDT to provide a treatment for the complexity of multi-trait parental selection using three multivariate loss functions, showing different performance in selecting the best-performing parents for the next breeding cycle.
G3-GENES GENOMES GENETICS
(2021)
Correction
Genetics & Heredity
Bartolo de Jesus Villar-Hernandez, Sergio Perez-Elizalde, Johannes W. R. Martini, Fernando Toledo, P. Perez-Rodriguez, Margaret Krause, Irma Delia Garcia-Calvillo, Giovanny Covarrubias-Pazaran, Jose Crossa
G3-GENES GENOMES GENETICS
(2021)
Article
Agronomy
Elaheh Vojgani, Torsten Pook, Johannes W. R. Martini, Armin C. Holker, Manfred Mayer, Chris-Carolin Schon, Henner Simianer
Summary: By selectively incorporating pairwise SNP interactions with the highest effect variances in a bivariate model using sERRBLUP, predictive ability can be significantly increased compared to univariate models. Bivariate models consistently outperform univariate models in predictive ability.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Plant Sciences
Johannes W. R. Martini, Terence L. Molnar, Jose Crossa, Sarah J. Hearne, Kevin Pixley
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Giovanny Covarrubias-Pazaran, Johannes W. R. Martini, Michael Quinn, Gary Atlin
FRONTIERS IN PLANT SCIENCE
(2021)
Editorial Material
Plant Sciences
Mahmood Gholami, Valentin Wimmer, Carolina Sansaloni, Cesar Petroli, Sarah J. Hearne, Giovanny Covarrubias-Pazaran, Stefan Rensing, Johannes Heise, Paulino Perez-Rodriguez, Susanne Dreisigacker, Jose Crossa, Johannes W. R. Martini
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
Ruifeng Zhang, Yi Zhang, Tongni Liu, Bo Jiang, Zhenyang Li, Youping Qu, Yaosheng Chen, Zhengcao Li
Summary: This study utilized three genome-wide association study methods to identify variants related to growth traits in pigs and performed genomic selection. The results showed that genomic best linear unbiased prediction (GBLUP) models with pre-selected variants significantly improved prediction accuracies compared to using 60K SNP-chip data, with improvements ranging from 4% to 46% for the four traits; and a two-kernel based GBLUP model showed improvements ranging from 5% to 27%.