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G3: Genes—Genomes—Genetics

Meredith B Metzger, Jessica L Scales, Mitchell F Dunklebarger, Allan M Weissman
Protein degradation by the ubiquitin-proteasome system is essential to many processes. We sought to assess its involvement in the turnover of mitochondrial proteins in Saccharomyces cerevisiae We find that deletion of a specific ubiquitin ligase (E3), Psh1p, increases the abundance of a temperature-sensitive mitochondrial protein, mia40-4pHA, when it is expressed from a centromeric plasmid. Deletion of Psh1p unexpectedly elevates the levels of other proteins expressed from centromeric plasmids. Loss of Psh1p does not increase the rate of turn-over of mia40-4pHA, affect total protein synthesis, or increase the protein levels of chromosomal genes...
September 19, 2017: G3: Genes—Genomes—Genetics
Daniel Rossbach, D Suzi Bryan, Jay R Hesselberth, Robert Sclafani
DDK, a conserved serine-threonine protein kinase composed of a regulatory subunit, Dbf4, and a catalytic subunit, Cdc7, is essential for DNA replication initiation during S phase of the cell cycle through MCM2-7 helicase phosphorylation. The biological significance of DDK is well characterized, but the full mechanism of how DDK associates with substrates remains unclear. Cdc7 is bound to chromatin in the Saccharomyces cerevisiae genome throughout the cell cycle, but there is little empirical evidence as to specific Cdc7 binding locations...
September 18, 2017: G3: Genes—Genomes—Genetics
Da Huo, Lina Sun, Xiaoni Li, Xiaoshang Ru, Shilin Liu, Libin Zhang, Lili Xing, Hongsheng Yang
Sea cucumber, an important economic species, has encountered high mortality since 2013 in northern China because of seasonal environmental stress such as hypoxia, high temperature, and low salinity. MicroRNAs (miRNAs) are important in regulating gene expression in marine organisms in response to environmental change. In the present study, high-throughput sequencing was used to investigate alterations in miRNA expression in the sea cucumber under different levels of dissolved oxygen (DO). Nine small RNA libraries were constructed from the sea cucumber respiratory trees...
September 15, 2017: G3: Genes—Genomes—Genetics
Pascal Schopp, Dominik Müller, Yvonne C J Wientjes, Albrecht E Melchinger
A major application of genomic prediction (GP) in plant breeding is the identification of superior inbred lines within families derived from biparental crosses. When models for various traits were trained within related or unrelated biparental families (BPFs), experimental studies found substantial variation in prediction accuracy (PA), but little is known about the underlying factors. We used SNP marker genotypes of inbred lines from either elite germplasm or landraces of maize (Zea mays L.) as parents to generate in silico 300 BPFs of doubled-haploid lines...
September 15, 2017: G3: Genes—Genomes—Genetics
Abhishek Dutta, Gen Lin, Ajith V Pankajam, Parijat Chakraborty, Nahush Bhat, Lars M Steinmetz, Koodali T Nishant
Mutation and recombination are the major sources of genetic diversity in all organisms. In the baker's yeast, all mutation rate estimates are in homozygous background. We determined the extent of genetic change through mutation and loss of heterozygosity (LOH) in a heterozygous Saccharomyces cerevisiae genome during successive vegetative and meiotic divisions. We measured genome wide LOH and base mutation rates during vegetative and meiotic divisions in a hybrid (S288c/YJM789) S. cerevisiae strain. The S288c/YJM789 hybrid showed nearly complete reduction in heterozygosity within 31 generations of meioses and improved spore viability...
September 15, 2017: G3: Genes—Genomes—Genetics
Erik Lavington, Andrew D Kern
Chromosomal inversions are an ubiquitous feature of genetic variation. Theoretical models describe several mechanisms by which inversions can drive adaptation and be maintained as polymorphisms. While inversions have been shown previously to be under selection, or contain genetic variation under selection, the specific phenotypic consequences of inversions leading to their maintenance remain unclear. Here we use genomic sequence and expression data from the Drosophila Genetic Reference Panel to explore the effects of two cosmopolitan inversions, In(2L)t and In(3R)Mo, on patterns of transcriptional variation...
September 15, 2017: G3: Genes—Genomes—Genetics
Washington da Silva, Jason Ingram, Christine A Hackett, Joseph J Coombs, David Douches, Glenn Bryan, Walter De Jong, Stewart Gray
Potato tuber necrotic ringspot disease (PTNRD) is a tuber deformity associated with infection by the tuber necrotic strain of Potato virus Y (PVY(NTN)). PTNRD negatively impacts tuber quality and marketability and poses a serious threat to seed and commercial potato production worldwide. PVY(NTN) symptoms differ in the cultivars Waneta and Pike: Waneta expresses severe PTNRD and foliar mosaic with vein and leaf necrosis, whereas Pike does not express PTNRD and mosaic is the only foliar symptom. To map loci that influence tuber and foliar symptoms, 236 F1 progeny of a cross between Waneta and Pike were inoculated with PVY(NTN) isolate NY090029 and genotyped using 12,808 Potato SNPs...
September 13, 2017: G3: Genes—Genomes—Genetics
Misako Okumura, Martin Wilecki, Ralf J Sommer
Feeding behaviors in a wide range of animals are regulated by the neurotransmitter serotonin, although the exact neural circuits and associated mechanism are often unknown. The nematode Pristionchus pacificus can kill other nematodes by opening prey cuticles with movable teeth. Previous studies showed that exogenous serotonin treatment induces a predatory-like tooth movement and slower pharyngeal pumping in the absence of prey, however, physiological functions of serotonin during predation and other behaviors in P...
September 13, 2017: G3: Genes—Genomes—Genetics
Annabel C Beichman, Tanya N Phung, Kirk E Lohmueller
Inference of demographic history from genetic data is a primary goal of population genetics of model and non-model organisms. Whole genome-based approaches such as the Pairwise/Multiple Sequentially Markovian Coalescent (PSMC/MSMC) methods use genomic data from one to four individuals to infer the demographic history of an entire population, while site frequency spectrum (SFS)-based methods use the distribution of allele frequencies in a sample to reconstruct the same historical events. Although both methods are extensively used in empirical studies and perform well on data simulated under simple models, there have been only limited comparisons of them in more complex and realistic settings...
September 11, 2017: G3: Genes—Genomes—Genetics
Harriet Prior, Ali K Jawad, Lauren MacConnachie, Asim A Beg
We describe a rapid and highly efficient method to generate point mutations in C. elegans using direct injection of CRISPR-Cas9 ribonucleoproteins. This versatile method does not require sensitized genetic backgrounds or co-CRISPR selection-based methods, and represents a single strategy that can used for creating genomic point mutations, regardless of location. As proof-of-principle, we show that knock-in mutants more faithfully report variant-associated phenotypes compared to transgenic overexpression. Data for nine knock-in mutants across five genes are presented that demonstrate high editing efficiencies (60%), a reduced screening workload (24 F1 progeny), and a rapid timescale (4-5 days)...
September 11, 2017: G3: Genes—Genomes—Genetics
Balint Z Kacsoh, Casey S Greene, Giovanni Bosco
High throughput experiments are becoming increasingly common, and scientists must balance hypothesis driven experiments with genome wide data acquisition. We sought to predict novel genes involved in Drosophila learning and long-term memory from existing public high-throughput data. We performed an analysis using PILGRM, which analyzes public gene expression compendia using machine learning. We evaluated the top prediction alongside genes involved in learning and memory in IMP, an interface for functional relationship networks...
September 9, 2017: G3: Genes—Genomes—Genetics
Sheina B Sim, Raul Ruiz-Arce, Norman B Barr, Scott M Geib
The Mediterranean fruit fly Ceratitis capitata (Wiedemann) is a destructive agricultural pest and the subject of exclusion efforts in many countries. Suppression and eradication of invasive populations to prevent establishment is facilitated by the release of sterile males using the sterile insect technique (SIT). In active SIT release areas, it is critical to accurately discriminate between released sterile males and wild-caught individuals to be able to detect extremely rare invasive individuals in areas inundated with millions of sterile male flies...
September 9, 2017: G3: Genes—Genomes—Genetics
Irini Topalidou, Dana L Miller
Hydrogen sulfide is common in the environment, and is also endogenously produced by animal cells. Although hydrogen sulfide is often toxic, exposure to low levels of hydrogen sulfide improves outcome in a variety of mammalian models of ischemia-reperfusion injury. In Caenorhabditis elegans, the initial transcriptional response to hydrogen sulfide depends on the hif-1 transcription factor, and hif-1 mutant animals die when exposed to hydrogen sulfide. In this study, we use rescue experiments to identify tissues in which hif-1 is required to survive exposure to hydrogen sulfide...
September 9, 2017: G3: Genes—Genomes—Genetics
Helian Liu, Ya Wu, Aqin Cao, Bigang Mao, Bingran Zhao, Jianbo Wang
The regulation of female fertility is an important field of rice sexual reproduction research. DNA methylation is an essential epigenetic modification that dynamically regulates gene expression during development processes. However, few reports have described the methylation profiles of female sterile rice during ovule development. In this study, ovules were continuously acquired from the beginning of megaspore mother cell meiosis until the mature female gametophyte formation period, and global DNA methylation patterns were compared in the ovules of a high-frequency female-sterile line (fsv1) and a wild-type rice line (Gui99) using whole-genome bisulfite sequencing (WGBS)...
September 6, 2017: G3: Genes—Genomes—Genetics
Fabien Cottier, Alrina Shin Min Tan, Marina Yurieva, Webber Liao, Josephine Lum, Michael Poidinger, Francesca Zolezzi, Norman Pavelka
Candida albicans is a resident fungus of the human intestinal microflora. Commonly isolated at low abundance in healthy people, C. albicans outcompetes local microbiota during candidiasis episodes. Under normal conditions, members of the human gastrointestinal microbiota were shown to keep C. albicans colonization under control. By releasing weak organic acids (WOAs), bacteria are able to moderate yeast growth. This mechanism displayed a synergistic effect in vitro with the absence of glucose in medium of culture, which underline the complex interaction that C...
September 6, 2017: G3: Genes—Genomes—Genetics
Quanwei Lu, Yuzhen Shi, Xianghui Xiao, Pengtao Li, Juwu Gong, Wankui Gong, Aiying Liu, Haihong Shang, Junwen Li, Qun Ge, Weiwu Song, Shaoqi Li, Zhen Zhang, Harun O Rashid, Renhai Peng, Youlu Yuan, Jinling Huang
As high-strength cotton fibers are critical components of high quality cotton, developing cotton cultivars with high strength fibers as well as high yield is a top priority for cotton development. Recently, chromosome segment substitution lines (CSSLs) have been developed from high-yield Upland cotton (Gossypium hirsutum) crossed with high-quality Sea Island cotton (G. barbadense). Here, we constructed a CSSL population by crossing CCRI45, a high-yield Upland cotton cultivar, with Hai1, a Sea Island cotton cultivar with superior fiber quality...
September 5, 2017: G3: Genes—Genomes—Genetics
Dominik R Laetsch, Mark L Blaxter
The field of comparative genomics is concerned with the study of similarities and differences between the information encoded in the genomes of organisms. A common approach is to define gene families by clustering protein sequences based on sequence similarity, and analyse protein cluster presence and absence in different species groups as a guide to biology. Due to the high dimensionality of these data, downstream analysis of protein clusters inferred from large numbers of species, or species with many genes, is non-trivial, and few solutions exist for transparent, reproducible and customisable analyses...
September 2, 2017: G3: Genes—Genomes—Genetics
Prasanna Katti, Divesh Thimmaya, Aditi Madan, Upendra Nongthomba
miRNAs are small non-coding endogenous RNAs, typically 21-23 nucleotides long, that regulate gene expression, usually post-transcriptionally by binding to the 3'-UTR of target mRNA, thus blocking translation. The expression of several miRNAs is significantly altered during cardiac hypertrophy, myocardial ischemia, fibrosis, heart failure and other cardiac myopathies. Recent studies have implicated miR-9 in myocardial hypertrophy. However a detailed mechanism remains obscure. In this study, we have addressed the roles of miR-9 in muscle development and function using the genetically tractable model system, the indirect flight muscles (IFMs) of Drosophila melanogaster Bioinformatics analysis identified 135 potential miR-9a targets, of which 27 genes were associated with Drosophila muscle development...
September 2, 2017: G3: Genes—Genomes—Genetics
Haipeng Yu, Matthew L Spangler, Ronald M Lewis, Gota Morota
Genetic connectedness refers to a measure of genetic relatedness across management units (e.g., herds and flocks). With the presence of high genetic connectedness in management units, best linear unbiased prediction (BLUP) is known to provide reliable comparisons between genetic values. Genetic connectedness has been studied for pedigree-based BLUP; however, relatively little attention has been paid to using genomic information to measure connectedness. In this study, we assessed genome-based connectedness across management units by applying prediction error variance of difference (PEVD), coefficient of determination (CD), and prediction error correlation (r) to a combination of computer simulation and real data (mice and cattle)...
August 31, 2017: G3: Genes—Genomes—Genetics
Ana Subotić, Erwin Swinnen, Liesbeth Demuyser, Herlinde De Keersmaecker, Hideaki Mizuno, Hélène Tournu, Patrick Van Dijck
Investigation of protein-protein interactions (PPI) in Candida albicans is essential for understanding the regulation of the signal transduction network that triggers its pathogenic lifestyle. Unique features of C. albicans, such as the alternative codon usage and incomplete meiosis, have enforced the optimization of standard genetic methods as well as development of novel approaches. Since the existing methods for detection of PPI are limited for direct visualization of the interacting complex in vivo, we have established a bimolecular fluorescence complementation (BiFC) in C...
August 31, 2017: G3: Genes—Genomes—Genetics
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