Adapting Drosophila melanogaster Cell Lines to Serum-Free Culture Conditions
Successful Drosophila cell culture relies on media containing xenogenic components such as fetal bovine serum to support continuous cell proliferation. Here, we report a serum-free culture condition that supports the growth and proliferation of Drosophila S2R+ and Kc167 cell lines. Importantly, the gradual adaptation of S2R+ and Kc167 cells to a media lacking serum was supported by supplementing the media with adult Drosophila soluble extract, commonly known as fly extract. The utility of these adapted cells lines is largely unchanged. The adapted cells exhibited robust proliferative capacity and a transfection efficiency ...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Luhur, A., Mariyappa, D., Klueg, K. M., Buddika, K., Tennessen, J. M., Zelhof, A. C. Tags: Investigations Source Type: research
BioLitMine: Advanced Mining of Biomedical and Biological Literature About Human Genes and Genes from Major Model Organisms
The accumulation of biological and biomedical literature outpaces the ability of most researchers and clinicians to stay abreast of their own immediate fields, let alone a broader range of topics. Although available search tools support identification of relevant literature, finding relevant and key publications is not always straightforward. For example, important publications might be missed in searches with an official gene name due to gene synonyms. Moreover, ambiguity of gene names can result in retrieval of a large number of irrelevant publications. To address these issues and help researchers and physicians quickly ...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Hu, Y., Chung, V., Comjean, A., Rodiger, J., Nipun, F., Perrimon, N., Mohr, S. E. Tags: Investigations Source Type: research
Adoption and Optimization of Genomic Selection To Sustain Breeding for Apricot Fruit Quality
Genomic selection (GS) is a breeding approach which exploits genome-wide information and whose unprecedented success has shaped several animal and plant breeding schemes through delivering their genetic progress. This is the first study assessing the potential of GS in apricot (Prunus armeniaca) to enhance postharvest fruit quality attributes. Genomic predictions were based on a F1 pseudo-testcross population, comprising 153 individuals with contrasting fruit quality traits. They were phenotyped for physical and biochemical fruit metrics in contrasting climatic conditions over two years. Prediction accuracy (PA) varied fro...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Nsibi, M., Gouble, B., Bureau, S., Flutre, T., Sauvage, C., Audergon, J.-M., Regnard, J.-L. Tags: Genomic Prediction Source Type: research
Dehydrated Caenorhabditis elegans Stocks Are Resistant to Multiple Freeze-Thaw Cycles
Ultracold preservation is widely used for storage of genetic stocks of Caenorhabditis elegans. Current cryopreservation protocols are vulnerable to refrigeration failures, which can result in the loss of stock viability due to damage during re-freezing. Here we present a method for preserving worms in a dehydrated and frozen form that retains viability after multiple freeze-thaw cycles. After dehydration in the presence of trehalose or glycerol, C. elegans stocks can be frozen and thawed multiple times while maintaining viability. While both dauer and non-dauer larvae survive desiccation and freezing, the dauer defective m...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: McClanahan, P. D., McCloskey, R. J., Ng Tung Hing, M., Raizen, D. M., Fang-Yen, C. Tags: Investigations Source Type: research
Genome-Wide Association Study Reveals the Genetic Architecture of Seed Vigor in Oats
This study presents the first GWA study on oat seed vigor and data of this study can provide guidelines and foundation for further investigations. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Huang, C.-T., Klos, K. E., Huang, Y.-F. Tags: Investigations Source Type: research
Enhanced Efficiency of flySAM by Optimization of sgRNA Parameters in Drosophila
The flySAM/CRISPRa system has recently emerged as a powerful tool for gain-of-function studies in Drosophila melanogaster. This system includes Gal4/UAS-driven dCas9 activators and U6 promoter-controlled sgRNA. Having established dCas9 activators superior to other combinations, to further enhance the efficiency of the targeting activators we systematically optimized the parameters of the sgRNA. Interestingly, the most efficient sgRNAs were found to accumulate in the region from -150bp to -450bp upstream of the transcription start site (TSS), and the activation efficiency showed a strong positive correlation with the GC con...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Mao, D., Jia, Y., Peng, P., Shen, D., Ren, X., Zhu, R., Qiu, Y., Han, Y., Yu, J., Che, Q., Li, Y., Lu, X., Liu, L.-P., Wang, Z., Liu, Q., Sun, J., Ni, J.-Q. Tags: Investigations Source Type: research
A Mutation in the Drosophila melanogaster eve Stripe 2 Minimal Enhancer Is Buffered by Flanking Sequences
Enhancers are DNA sequences composed of transcription factor binding sites that drive complex patterns of gene expression in space and time. Until recently, studying enhancers in their genomic context was technically challenging. Therefore, minimal enhancers, the shortest pieces of DNA that can drive an expression pattern that resembles a gene’s endogenous pattern, are often used to study features of enhancer function. However, evidence suggests that some enhancers require sequences outside the minimal enhancer to maintain function under environmental perturbations. We hypothesized that these additional sequences als...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Lopez-Rivera, F., Foster Rhoades, O. K., Vincent, B. J., Pym, E. C. G., Bragdon, M. D. J., Estrada, J., DePace, A. H., Wunderlich, Z. Tags: Investigations Source Type: research
Maintenance of Cell Fate by the Polycomb Group Gene Sex Combs Extra Enables a Partial Epithelial Mesenchymal Transition in Drosophila
Epigenetic silencing by Polycomb group (PcG) complexes can promote epithelial-mesenchymal transition (EMT) and stemness and is associated with malignancy of solid cancers. Here we report a role for Drosophila PcG repression in a partial EMT event that occurs during wing disc eversion, an early event during metamorphosis. In a screen for genes required for eversion we identified the PcG genes Sex combs extra (Sce) and Sex combs midleg (Scm). Depletion of Sce or Scm resulted in internalized wings and thoracic clefts, and loss of Sce inhibited the EMT of the peripodial epithelium and basement membrane breakdown, ex vivo. Targ...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Jefferies, G., Somers, J., Lohrey, I., Chaturvedi, V., Calabria, J., Marshall, O. J., Southall, T. D., Saint, R., Murray, M. J. Tags: Investigations Source Type: research
Programmed Cell Death 2-Like (Pdcd2l) Is Required for Mouse Embryonic Development
In this study, we generated a Pdcd2l knockout mouse to test its role in male fertility. Contrary to the phenotype predicted from its testis-enriched expression pattern, Pdcd2l null mice died during embryogenesis. Specifically, we identified that Pdcd2l is essential for post-implantation embryonic development. Pdcd2l–/– embryos were resorbed at embryonic days 12.5-17.5 and no knockout pups were born, while adult heterozygous Pdcd2l males had comparable fertility to wildtype males. To specifically investigate the role of PDCD2L in germ cells, we employed Drosophila melanogaster as a model system. Consistent with ...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Houston, B. J., Oud, M. S., Aguirre, D. M., Merriner, D. J., OConnor, A. E., Okutman, O., Viville, S., Burke, R., Veltman, J. A., OBryan, M. K. Tags: Investigations Source Type: research
A Multiple-Trait Bayesian Variable Selection Regression Method for Integrating Phenotypic Causal Networks in Genome-Wide Association Studies
Bayesian regression methods that incorporate different mixture priors for marker effects are used in multi-trait genomic prediction. These methods can also be extended to genome-wide association studies (GWAS). In multiple-trait GWAS, incorporating the underlying causal structures among traits is essential for comprehensively understanding the relationship between genotypes and traits of interest. Therefore, we develop a GWAS methodology, SEM-Bayesian alphabet, which, by applying the structural equation model (SEM), can be used to incorporate causal structures into multi-trait Bayesian regression methods. SEM-Bayesian alph...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Wang, Z., Chapman, D., Morota, G., Cheng, H. Tags: Genomic Prediction Source Type: research
Loss of Pseudouridine Synthases in the RluA Family Causes Hypersensitive Nociception in Drosophila
Nociceptive neurons of Drosophila melanogaster larvae are characterized by highly branched dendritic processes whose proper morphogenesis relies on a large number of RNA-binding proteins. Post-transcriptional regulation of RNA in these dendrites has been found to play an important role in their function. Here, we investigate the neuronal functions of two putative RNA modification genes, RluA-1 and RluA-2, which are predicted to encode pseudouridine synthases. RluA-1 is specifically expressed in larval sensory neurons while RluA-2 expression is ubiquitous. Nociceptor-specific RNAi knockdown of RluA-1 caused hypersensitive n...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Song, W., Ressl, S., Tracey, W. D. Tags: Investigations Source Type: research
Genetic Analysis of Walnut (Juglans regia L.) Pellicle Pigment Variation Through a Novel, High-Throughput Phenotyping Platform
Walnut pellicle color is a key quality attribute that drives consumer preference and walnut sales. For the first time a high-throughput, computer vision-based phenotyping platform using a custom algorithm to quantitatively score each walnut pellicle in L* a* b* color space was deployed at large-scale. This was compared to traditional qualitative scoring by eye and was used to dissect the genetics of pellicle pigmentation. Progeny from both a bi-parental population of 168 trees (‘Chandler’ x ‘Idaho’) and a genome-wide association (GWAS) with 528 trees of the UC Davis Walnut Improvement Program were a...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Sideli, G. M., McAtee, P., Marrano, A., Allen, B. J., Brown, P. J., Butterfield, T. S., Dandekar, A. M., Leslie, C. A., Neale, D. B. Tags: Investigations Source Type: research
Meep, a Novel Regulator of Insulin Signaling, Supports Development and Insulin Sensitivity via Maintenance of Protein Homeostasis in Drosophila melanogaster
Insulin signaling is critical for developmental growth and adult homeostasis, yet the downstream regulators of this signaling pathway are not completely understood. Using the model organism Drosophila melanogaster, we took a genomic approach to identify novel mediators of insulin signaling. These studies led to the identification of Meep, encoded by the gene CG32335. Expression of this gene is both insulin receptor- and diet-dependent. We found that Meep was specifically required in the developing fat body to tolerate a high-sugar diet (HSD). Meep is not essential on a control diet, but when reared on an HSD, knockdown of ...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Pereira, M. T., Brock, K., Musselman, L. P. Tags: Investigations Source Type: research
Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae
Both polyploidization and transposable element (TE) activity are known to be major drivers of plant genome evolution. Here, we utilize the Zea-Tripsacum clade to investigate TE activity and accumulation after a shared polyploidization event. Comparisons of TE evolutionary dynamics in various Zea and Tripsacum species, in addition to two closely related diploid species, Urelytrum digitatum and Sorghum bicolor, revealed variation in repeat content among all taxa included in the study. The repeat composition of Urelytrum is more similar to that of Zea and Tripsacum compared to Sorghum, despite the similarity in genome size wi...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Ramachandran, D., McKain, M. R., Kellogg, E. A., Hawkins, J. S. Tags: Investigations Source Type: research
Preventing Photomorbidity in Long-Term Multi-color Fluorescence Imaging of Saccharomyces cerevisiae and S. pombe
Time-lapse imaging of live cells using multiple fluorescent reporters is an essential tool to study molecular processes in single cells. However, exposure to even moderate doses of visible excitation light can disturb cellular physiology and alter the quantitative behavior of the cells under study. Here, we set out to develop guidelines to avoid the confounding effects of excitation light in multi-color long-term imaging. We use widefield fluorescence microscopy to measure the effect of the administered excitation light on growth rate (here called photomorbidity) in yeast. We find that photomorbidity is determined by the c...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Schmidt, G. W., Cuny, A. P., Rudolf, F. Tags: Investigations Source Type: research
