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G3: Genes—Genomes—Genetics

Jacob M Riveron, Sulaiman S Ibrahim, Charles Mulamba, Rousseau Djouaka, Helen Irving, Murielle J Wondji, Intan H Ishak, Charles S Wondji
Pyrethroid resistance in malaria vector, An. Funestus is increasingly reported across Africa, threatening the sustainability of pyrethroid-based control interventions including long lasting insecticidal Nets (LLINs). Managing this problem requires understanding of the molecular basis of the resistance from different regions of the continent, to establish whether it is being driven by a single or independent selective events. Here, using a genome-wide transcription profiling of pyrethroid resistant populations from Southern (Malawi), East (Uganda) and West Africa (Benin), we investigated the molecular basis of resistance, revealing strong differences between the different African regions...
April 19, 2017: G3: Genes—Genomes—Genetics
Christine Zimmermann, Ignacio Garcia, Manja Omerzu, Pierre Chymkowitch, Beibei Zhang, Jorrit M Enserink
Cdk1 (Cdc28 in yeast) is a cyclin dependent kinase (CDK) essential for cell cycle progression and cell division in normal cells. However, CDK activity also underpins proliferation of tumor cells, making it a relevant study subject. While numerous targets and processes regulated by Cdc28 have been identified, the exact functions of Cdc28 are only partially understood. To further explore the functions of Cdc28 we systematically overexpressed approximately 4800 genes in wild-type cells and in cells with artificially reduced Cdc28 activity...
April 19, 2017: G3: Genes—Genomes—Genetics
Inge Seim, Penny L Jeffery, Patrick B Thomas, Colleen C Nelson, Lisa K Chopin
The bone metastasis-derived PC3 and the lymph node metastasis-derived LNCaP prostate cancer cell lines are widely studied, having been described in thousands of publications over the last four decades. Here, we report short-read whole-genome sequencing and de novo assembly of PC3 (ATCC CRL-1435) and LNCaP (clone FGC; ATCC CRL-1740) at ~70X coverage. A known homozygous mutation in TP53 and homozygous loss of PTEN were robustly identified in the PC3 cell line, whereas the LNCaP cell line exhibited a larger number of putative inactivating somatic point and indel mutations (and in particular loss of stop codon events)...
April 16, 2017: G3: Genes—Genomes—Genetics
Qun-Jie Zhang, Li-Zhi Gao
The dynamics of LTR retrotransposons and their contribution to genome evolution during plant speciation have remained largely unanswered. Here, we perform a genome-wide comparison of all eight Oryza AA- genome species, and identify 3,911 intact LTR retrotransposons classified into 790 families. The top 44 most abundant LTR retrotransposon families show patterns of rapid and distinct diversification since the species split over the last ~4.8 Myr. Phylogenetic and read depth analyses of 11 representative retrotransposon families further provide a comprehensive evolutionary landscape of these changes...
April 16, 2017: G3: Genes—Genomes—Genetics
J Noelia Dufay, J Pedro Fernández-Murray, Christopher R McMaster
The SLC25 family member SLC25A38 (Hem25 in yeast) was recently identified as a mitochondrial glycine transporter that provides substrate to initiate heme/hemoglobin synthesis. Mutations in the human SLC25A38 gene cause congenital sideroblastic anemia. The full extent to which SLC25 family members co-regulate heme synthesis with other mitochondrial functions is not clear. In this study, we surveyed 29 non-essential SLC25 family members in Saccharomyces cerevisiae for their ability to support growth in the presence and absence of HEM25...
April 12, 2017: G3: Genes—Genomes—Genetics
Anthony D Fouad, Shelly Teng, Shelley H Pu, Julian R Mark, Moyu Fu, Kevin Zhang, Jonathan Huang, David M Raizen, Christopher Fang-Yen
The roundworm Caenorhabditis elegans is widely used as a model for studying conserved pathways for fat storage, aging, and metabolism. The most broadly used methods for imaging fat in C. elegans require fixing and staining the animal. Here, we show that dark field images acquired through an ordinary light microscope can be used to estimate fat levels in worms. We define a metric based on the amount of light scattered per area, and show that this light scattering metric is strongly correlated with worm fat levels as measured by Oil Red O staining across a wide variety of genetic backgrounds and feeding conditions...
April 12, 2017: G3: Genes—Genomes—Genetics
Karin Mittelman, Naama Barkai
Cells grow on a wide range of carbon sources by regulating substrate flow through the metabolic network. Incoming sugar, for example, can be fermented or respired, depending on the carbon identity, cell type, or growth conditions. Despite this genetically-encoded flexibility of carbon metabolism, attempts to exogenously manipulate central carbon flux by rational design have proven difficult, suggesting a robust network structure. To examine this robustness, we characterized the ethanol yield of 411 regulatory and metabolic mutants in budding yeast...
April 12, 2017: G3: Genes—Genomes—Genetics
Tanel Pärnamaa, Leopold Parts
High throughput microscopy of many single cells generates high-dimensional data that are far from straightforward to analyze. One important problem is automatically detecting the cellular compartment where a fluorescently tagged protein resides, a task relatively simple for an experienced human, but difficult to automate on a computer. Here, we train an 11-layer neural network on data from mapping thousands of yeast proteins, achieving per cell localization classification accuracy of 91%, and per protein accuracy of 99% on held out images...
April 8, 2017: G3: Genes—Genomes—Genetics
Adriana L Somavilla, Luciana C A Regitano, Guilherme J M Rosa, Fabiana B Mokry, Mauricio A Mudadu, Polyana C Tizioto, Priscila S N Oliveira, Marcela M Souza, Luiz L Coutinho, Danísio P Munari
Nelore is the most economically important cattle breed in Brazil, and the use of genetically improved animals has contributed to increase beef production efficiency. The Brazilian beef feedlot industry has grown considerably in the last decade, so the selection of animals with higher growth rates on feedlot has become quite important. Genomic selection could be used to reduce generation intervals and improve the rate of genetic gains. The aim of this study was to evaluate the prediction of genomic estimated breeding values for average daily gain in 718 feedlot-finished Nelore steers...
April 8, 2017: G3: Genes—Genomes—Genetics
Osval A Montesinos-López, Abelardo Montesinos-López, José Crossa, José Cricelio Montesinos-López, Francisco Javier Luna-Vázquez, Josaphat Salinas, José Herrera-Morales, Raymundo Buenrostro-Mariscal
There are Bayesian and non-Bayesian genomic models that take into account G×E interaction. However, the computational cost of implementing the Bayesian models is high and becomes almost impossible when the number of genotypes, environments and traits is very large, while in the non-Bayesian models, many times there are important and often unsolved convergence problems. The variational Bayes method is popular in machine learning and, by approximating the probability distributions through optimization, it tends to be faster than the Markov Chain Monte Carlo methods...
April 8, 2017: G3: Genes—Genomes—Genetics
Saasha Le, Zachary C Martin, David J Samuelson
Human breast and rat mammary cancer susceptibility are complex phenotypes where complete sets of risk associated loci remain to be identified for both species. We tested multiple congenic rat strains to physically confirm and positionally map rat Mammary carcinoma susceptibility 3 (Mcs3), a mammary cancer resistance allele previously predicted at Rattus norvegicus chromosome 1 (RNO1). The mammary cancer susceptible Wistar Furth (WF) strain was the recipient, and the mammary cancer resistant Copenhagen (Cop) strain was the RNO1-segment donor for congenics...
April 8, 2017: G3: Genes—Genomes—Genetics
Daniel Cook, Bruno G G Donzelli, Rebecca Creamer, Deana L Baucom, Dale R Gardner, Juan Pan, Neil Moore, Jerzy W Jaromczyk, Christopher L Schardl
Swainsonine, a cytotoxic fungal alkaloid and a potential cancer therapy drug, is produced by the insect pathogen and plant symbiont, Metarhizium robertsii, the clover pathogen Slafractonia leguminicola, locoweed symbionts belonging to Alternaria sect. Undifilum, and a recently discovered morning glory symbiont belonging to order Chaetothyriales. Genome sequence analyses revealed that these fungi shared orthologous gene clusters, designated "SWN," which included a multifunctional swnK gene comprising predicted adenylylation and acyltransferase domains with their associated thiolation domains, a β-ketoacyl synthase domain, and two reductase domains...
April 4, 2017: G3: Genes—Genomes—Genetics
Kai Zhang, Guangyu Fan, Xinxin Zhang, Fang Zhao, Wei Wei, Guohua Du, Xiaolei Feng, Xiaoming Wang, Feng Wang, Guoliang Song, Hongfeng Zou, Xiaolei Zhang, Shuangdong Li, Xuemei Ni, Gengyun Zhang, Zhaihai Zhao
Foxtail millet (Setaria italic) is an important crop possessing C4 photosynthesis capability. The S. italic genome was de novo sequenced in 2012, but the sequence lacked high-density genetic maps with agronomic and yield traits linkages. In the present study, we resequenced a foxtail millet population of 439 recombinant inbred lines (RILs), developed high resolution bin map and high density SNP markers, of which could provide an effective approach for gene identification. A total of 59 QTLs for 14 agronomic traits in plants grown under long day and short day photoperiods were identified...
March 31, 2017: G3: Genes—Genomes—Genetics
Akram Abolbaghaei, Jordan R Silke, Xuhua Xia
The 3' end of the small ribosomal RNAs (ssu rRNA) in bacteria is directly involved in the selection and binding of mRNA transcripts during translation initiation via well-documented interactions between a Shine-Dalgarno (SD) sequence located upstream of the initiation codon and an anti-SD (aSD) sequence at the 3' end of the ssu rRNA. Consequently, the 3' end of ssu rRNA (3'TAIL) is strongly conserved among bacterial species because a change in the region may impact the translation of many protein-coding genes...
March 31, 2017: G3: Genes—Genomes—Genetics
Osval A Montesinos-López, Abelardo Montesinos-López, José Crossa, Fernando H Toledo, José C Montesinos-López, Pawan Singh, Philomin Juliana, Josefhat Salinas-Ruiz
When a plant scientist wishes to make genomic-enabled predictions of multiple traits measured in multiple individuals in multiple environments, the most common strategy for performing the analysis is to use a single trait at a time taking into account genotype x environment interaction (GxE), because there is a lack of comprehensive models that simultaneously take into account the correlated counting traits and G×E. For this reason, in this study we propose a multiple-trait and multiple-environment model for count data...
March 31, 2017: G3: Genes—Genomes—Genetics
Erena A Edae, Pablo D Olivera, Yue Jin, Matthew N Rouse
High-density genetic maps are useful to precisely localize QTL or genes that might be used to improve traits of nutritional and/or economical importance in crops. However, high-density genetic maps are lacking for most wild relatives of crop species including wheat. Aegilops umbelluata is a wild relative of wheat known for its potential as a source of biotic and abiotic stress resistance genes. In this work, we have developed a framework consensus genetic map using two bi-parental populations derived from accessions PI 298905, PI 542369, PI 5422375 and PI 554395...
March 31, 2017: G3: Genes—Genomes—Genetics
Lan-Hua Qian, Guang-Can Zhou, Xiao-Qin Sun, Zhao Lei, Yan-Mei Zhang, Jia-Yu Xue, Yue-Yu Hang
Plant resistance conferred by nucleotide binding site (NBS)-encoding resistance genes plays a key role in the defense against various pathogens throughout the entire plant life cycle. However, comparative analyses for the systematic evaluation and determination of the evolutionary modes of NBS-encoding genes among Solanaceae species are rare. In this study, 447, 255 and 306 NBS-encoding genes were identified from the genomes of potato, tomato and pepper, respectively. These genes usually clustered as tandem arrays on chromosomes; few existed as singletons...
March 31, 2017: G3: Genes—Genomes—Genetics
Marc W Crepeau, Charles H Langley, Kristian Stevens
We investigate the utility and scalability of new read cloud technologies to improve the draft genome assemblies of the colossal and largely repetitive genomes of conifers. Synthetic long read technologies existed in various forms as a means of reducing complexity and resolving repeats since the outset of genome assembly. Recently, technologies that combine sub-haploid pools of high molecular weight DNA with barcoding on a massive scale have brought new efficiencies to sample preparation and data generation...
March 24, 2017: G3: Genes—Genomes—Genetics
Benjamin C Haller, Philipp W Messer
The McDonald-Kreitman (MK) test is a widely used method for quantifying the role of positive selection in molecular evolution. One key shortcoming of this test lies in its sensitivity to the presence of slightly deleterious mutations, which can severely bias its estimates. An asymptotic version of the MK test was recently introduced that addresses this problem by evaluating polymorphism levels for different mutation frequencies separately, and then extrapolating a function fitted to that data. Here we present asymptoticMK, a web-based implementation of this asymptotic McDonald-Kreitman test...
March 24, 2017: G3: Genes—Genomes—Genetics
Damarius S Fleming, Steffen Weigend, Henner Simianer, Annett Weigend, Max Rothschild, Carl Schmidt, Christopher Ashwell, Mike Persia, James Reecy, Susan J Lamont
Global climate change is increasing the magnitude of environmental stressors, such as temperature, pathogens, and drought that limit survivability and sustainability of livestock production. Poultry production and its expansion are dependent upon robust animals that are able to cope with stressors in multiple environments. Understanding the genetic strategies that indigenous, non-commercial breeds have evolved to survive in their environment could help to elucidate molecular mechanisms underlying biological traits of environmental adaptation...
March 24, 2017: G3: Genes—Genomes—Genetics
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