Adult Movement Defects Associated with a CORL Mutation in Drosophila Display Behavioral Plasticity
The CORL family of CNS-specific proteins share a Smad-binding region with mammalian SnoN and c-Ski protooncogenes. In this family Drosophila CORL has two mouse and two human relatives. Roles for the mouse and human CORL proteins are largely unknown. Based on genome-wide association studies linking the human CORL proteins Fussel15 and Fussel18 with ataxia, we tested the hypothesis that dCORL mutations will cause adult movement disorders. For our initial tests, we conducted side by side studies of adults with the small deletion Df(4)dCORL and eight control strains. We found that deletion mutants exhibit three types of behavi...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Dimitriadou, A., Chatzianastasi, N., Zacharaki, P. I., OConnor, M., Goldsmith, S. L., OConnor, M. B., Consoulas, C., Newfeld, S. J. Tags: Investigations Source Type: research
A Genome-Wide Association Study To Understand the Effect of Fusarium verticillioides Infection on Seedlings of a Maize Diversity Panel
Fusarium verticillioides, which causes ear, kernel and stem rots, has been reported as the most prevalent species on maize worldwide. Kernel infection by F. verticillioides results in reduced seed yield and quality as well as fumonisin contamination, and may affect seedling traits like germination rate, entire plant seedling length and weight. Maize resistance to Fusarium is a quantitative and complex trait controlled by numerous genes with small effects. In the present work, a Genome Wide Association Study (GWAS) of traits related to Fusarium seedling rot was carried out in 230 lines of a maize association population usin...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Stagnati, L., Rahjoo, V., Samayoa, L. F., Holland, J. B., Borrelli, V. M. G., Busconi, M., Lanubile, A., Marocco, A. Tags: Investigations Source Type: research
Genome-Wide Association Study for Maize Leaf Cuticular Conductance Identifies Candidate Genes Involved in the Regulation of Cuticle Development
The cuticle, a hydrophobic layer of cutin and waxes synthesized by plant epidermal cells, is the major barrier to water loss when stomata are closed at night and under water-limited conditions. Elucidating the genetic architecture of natural variation for leaf cuticular conductance (gc) is important for identifying genes relevant to improving crop productivity in drought-prone environments. To this end, we conducted a genome-wide association study of gc of adult leaves in a maize inbred association panel that was evaluated in four environments (Maricopa, AZ, and San Diego, CA, in 2016 and 2017). Five genomic regions signif...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Lin, M., Matschi, S., Vasquez, M., Chamness, J., Kaczmar, N., Baseggio, M., Miller, M., Stewart, E. L., Qiao, P., Scanlon, M. J., Molina, I., Smith, L. G., Gore, M. A. Tags: Investigations Source Type: research
Early Drought-Responsive Genes Are Variable and Relevant to Drought Tolerance
In this study, we generated time-series transcriptomic data from the maize inbred line B73 under well-watered and drought conditions. Comparisons between the two conditions identified 8,626 DRGs and the stages (early, middle, and late drought) at which DRGs occurred. Different functional groups of genes were regulated at the three stages. Specifically, early and middle DRGs display higher copy number variation among diverse Zea mays lines, and they exhibited stronger associations with drought tolerance as compared to late DRGs. In addition, correlation of expression between small RNAs (sRNAs) and DRGs from the same samples...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: He, C., Du, Y., Fu, J., Zeng, E., Park, S., White, F., Zheng, J., Liu, S. Tags: Investigations Source Type: research
Restriction Enzyme Based Enriched L1Hs Sequencing (REBELseq): A Scalable Technique for Detection of Ta Subfamily L1Hs in the Human Genome
Long interspersed element-1 retrotransposons (LINE-1 or L1) are ~6 kb mobile DNA elements implicated in the origins of many Mendelian and complex diseases. The actively retrotransposing L1s are mostly limited to the L1 human specific (L1Hs) transcriptional active (Ta) subfamily. In this manuscript, we present REBELseq as a method for the construction of Ta subfamily L1Hs-enriched next-generation sequencing libraries and bioinformatic identification. REBELseq was performed on DNA isolated from NeuN+ neuronal nuclei from postmortem brain samples of 177 individuals and empirically-driven bioinformatic and experimental cutoffs...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Reiner, B. C., Doyle, G. A., Weller, A. E., Levinson, R. N., Namoglu, E., Pigeon, A., Perea, E. D., Weickert, C. S., Turecki, G., Mash, D. C., Crist, R. C., Berrettini, W. H. Tags: Investigations Source Type: research
Genetic Adaptations of an Island Pit-Viper to a Unique Sedentary Life with Extreme Seasonal Food Availability
The Shedao pit-viper (Gloydius shedaoensis) exhibits an extreme sedentary lifestyle. The island species exclusively feeds on migratory birds during migratory seasons and experiences prolonged hibernation and aestivation period each year (up to eight months). The sedentary strategy reduces energy expenditure, but may trigger a series of adverse effects and the snakes have likely evolved genetic modifications to alleviate these effects. To investigate the genetic adaptations, we sequenced and compared the transcriptomes of the Shedao pit-viper and its closest mainland relative, the black eyebrow pit-viper (G. intermedius). T...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Lu, B., Wang, X., Fu, J., Shi, J., Wu, Y., Qi, Y. Tags: Investigations Source Type: research
Extending the Genotype in Brachypodium by Including DNA Methylation Reveals a Joint Contribution with Genetics on Adaptive Traits
Epigenomic changes have been considered a potential missing link underlying phenotypic variation in quantitative traits but is potentially confounded with the underlying DNA sequence variation. Although the concept of epigenetic inheritance has been discussed in depth, there have been few studies attempting to directly dissect the amount of epigenomic variation within inbred natural populations while also accounting for genetic diversity. By using known genetic relationships between Brachypodium lines, multiple sets of nearly identical accession families were selected for phenotypic studies and DNA methylome profiling to i...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Eichten, S. R., Srivastava, A., Reddiex, A. J., Ganguly, D. R., Heussler, A., Streich, J. C., Wilson, P. B., Borevitz, J. O. Tags: Investigations Source Type: research
A Caenorhabditis elegans Model for Integrating the Functions of Neuropsychiatric Risk Genes Identifies Components Required for Normal Dendritic Morphology
Analysis of patient-derived DNA samples has identified hundreds of variants that are likely involved in neuropsychiatric diseases such as autism spectrum disorder (ASD) and schizophrenia (SCZ). While these studies couple behavioral phenotypes to individual genotypes, the number and diversity of candidate genes implicated in these disorders highlights the fact that the mechanistic underpinnings of these disorders are largely unknown. Here, we describe a RNAi-based screening platform that uses C. elegans to screen candidate neuropsychiatric risk genes (NRGs) for roles in controlling dendritic arborization. To benchmark this ...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Aguirre-Chen, C., Stec, N., Ramos, O. M., Kim, N., Kramer, M., McCarthy, S., Gillis, J., McCombie, W. R., Hammell, C. M. Tags: Investigations Source Type: research
Tools for the Genetic Manipulation of Herpetomonas muscarum
Trypanosomatid parasites are causative agents of important human and animal diseases such as sleeping sickness and leishmaniasis. Most trypanosomatids are transmitted to their mammalian hosts by insects, often belonging to Diptera (or true flies). With resistance to both vector-targeted pesticides and trypanocidal drugs being reported, there is a need for novel transmission blocking strategies to be developed. Studies using the blood-feeding vectors themselves are not broadly accessible, as such, new model systems are being developed to unpick insect-trypanosmatids interactions. One such case is the interactions between th...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Sloan, M. A., Ligoxygakis, P. Tags: Investigations Source Type: research
Sirt4 Modulates Oxidative Metabolism and Sensitivity to Rapamycin Through Species-Dependent Phenotypes in Drosophila mtDNA Haplotypes
The endosymbiotic theory proposes that eukaryotes evolved from the symbiotic relationship between anaerobic (host) and aerobic prokaryotes. Through iterative genetic transfers, the mitochondrial and nuclear genomes coevolved, establishing the mitochondria as the hub of oxidative metabolism. To study this coevolution, we disrupt mitochondrial-nuclear epistatic interactions by using strains that have mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) from evolutionarily divergent species. We undertake a multifaceted approach generating introgressed Drosophila strains containing D. simulans mtDNA and D. melanogaster nDNA with S...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Sejour, R., Sanguino, R. A., Mikolajczak, M., Ahmadi, W., Villa-Cuesta, E. Tags: Investigations Source Type: research
Loss of N-Glycanase 1 Alters Transcriptional and Translational Regulation in K562 Cell Lines
N-Glycanase 1 (NGLY1) deficiency is an ultra-rare, complex and devastating neuromuscular disease. Patients display multi-organ symptoms including developmental delays, movement disorders, seizures, constipation and lack of tear production. NGLY1 is a deglycosylating protein involved in the degradation of misfolded proteins retrotranslocated from the endoplasmic reticulum (ER). NGLY1-deficient cells have been reported to exhibit decreased deglycosylation activity and an increased sensitivity to proteasome inhibitors. We show that the loss of NGLY1 causes substantial changes in the RNA and protein landscape of K562 cells and...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Mueller, W. F., Jakob, P., Sun, H., Clauder-Münster, S., Ghidelli-Disse, S., Ordonez, D., Boesche, M., Bantscheff, M., Collier, P., Haase, B., Benes, V., Paulsen, M., Sehr, P., Lewis, J., Drewes, G., Steinmetz, L. M. Tags: Investigations Source Type: research
Tunable Transcriptional Interference at the Endogenous Alcohol Dehydrogenase Gene Locus in Drosophila melanogaster
Neighboring sequences of a gene can influence its expression. In the phenomenon known as transcriptional interference, transcription at one region in the genome can repress transcription at a nearby region in cis. Transcriptional interference occurs at a number of eukaryotic loci, including the alcohol dehydrogenase (Adh) gene in Drosophila melanogaster. Adh is regulated by two promoters, which are distinct in their developmental timing of activation. It has been shown using transgene insertion that when the promoter distal from the Adh start codon is deleted, transcription from the proximal promoter becomes de-regulated. ...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Jorgensen, V., Chen, J., Vander Wende, H., Harris, D. E., McCarthy, A., Breznak, S., Wong-Deyrup, S. W., Chen, Y., Rangan, P., Brar, G. A., Sawyer, E. M., Chan, L. Y., Ünal, E. Tags: Investigations Source Type: research
Mutations in a Novel Cadherin Gene Associated with Bt Resistance in Helicoverpa zea
Transgenic corn and cotton produce crystalline (Cry) proteins derived from the soil bacterium Bacillus thuringiensis (Bt) that are toxic to lepidopteran larvae. Helicoverpa zea, a key pest of corn and cotton in the U.S., has evolved widespread resistance to these proteins produced in Bt corn and cotton. While the genomic targets of Cry selection and the mutations that produce resistant phenotypes are known in other lepidopteran species, little is known about how selection by Cry proteins shape the genome of H. zea. We scanned the genomes of Cry1Ac-selected and unselected H. zea lines, and identified twelve genes on five sc...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Fritz, M. L., Nunziata, S. O., Guo, R., Tabashnik, B. E., Carriere, Y. Tags: Investigations Source Type: research
Network Analysis of Linkage Disequilibrium Reveals Genome Architecture in Chum Salmon
We examined patterns of LD using network analysis to identify an overlapping chromosome inversion and sex-determining region in chum salmon. The signal of the inversion was strong enough to show up as false population substructure when the entire dataset was analyzed, while the effect of the sex-determining region on population structure was only obvious after restricting analysis to the sex chromosome. Understanding the extent and geographic distribution of inversions is now a critically important part of genetic analyses of natural populations. Our results highlight the importance of analyzing and understanding patterns ...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: McKinney, G., McPhee, M. V., Pascal, C., Seeb, J. E., Seeb, L. W. Tags: Investigations Source Type: research
Sexual Selection Does Not Increase the Rate of Compensatory Adaptation to a Mutation Influencing a Secondary Sexual Trait in Drosophila melanogaster
Theoretical work predicts that sexual selection can enhance natural selection, increasing the rate of adaptation to new environments and helping purge harmful mutations. While some experiments support these predictions, remarkably little work has addressed the role of sexual selection on compensatory adaptation—populations’ ability to compensate for the costs of deleterious alleles that are already present. We tested whether sexual selection, as well as the degree of standing genetic variation, affect the rate of compensatory evolution via phenotypic suppression in experimental populations of Drosophila melanog...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Chandler, C. H., Mammel, A., Dworkin, I. Tags: Investigations Source Type: research
