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Chiao-Ming Lin, Jiajun Xu, Wen-Ting Yang, Chao Wang, Yu-Chiao Li, Lien-Chieh Cheng, Lei Zhang, Jui-Chou Hsu
Drosophila dorsal closure is a morphogenetic movement that involves flanking epidermal cells, assembling actomyosin cables and migrating dorsally over the underlying amnioserosa to seal at the dorsal midline. Echinoid (Ed), a cell adhesion molecule of adherens junctions (AJs), participates in several developmental processes. The disappearance of Ed from the amnioserosa is required to define the epidermal leading edge for actomyosin cable assembly and coordinated cell migration. However, the mechanism by which Ed is cleared from amnioserosa is unknown...
April 19, 2017: Genetics
Tetsunari Fukushige, Harold E Smith, Johji Miwa, Michael W Krause, John A Hanover
Oxidative damage contributes to human diseases of aging including diabetes, cancer, and cardiovascular disorders. Reactive oxygen species resulting from xenobiotic and endogenous metabolites are sensed by a poorly understood process, triggering a cascade of regulatory factors and leading to the activation of the transcription factor Nrf2 (SKN-1 in Caenorhabditis elegans). Nrf2/SKN-1 activation promotes the induction of the Phase II detoxification system that serves to limit oxidative stress. We have extended a previous C...
April 19, 2017: Genetics
Rupal Mistry, Ilias Kounatidis, Petros Ligoxygakis
Resident gut bacteria are constantly influencing the immune system. Yet the role of the immune system in shaping microbiota composition during an organism's lifespan has remained unclear. Experiments in mice have been inconclusive due to differences in husbandry schemes that led to conflicting results. We used Drosophila as a genetically tractable system with simpler gut bacterial population structure and streamlined genetic backgrounds and established cross schemes to address this issue. We found that depending on their genetic background, young flies had microbiota of different diversities that converged with age to the same Acetobacteraceae-dominated pattern in healthy flies...
April 16, 2017: Genetics
Yu-Yang Jiang, Wolfgang Maier, Ralf Baumeister, Gregory Minevich, Ewa Joachimiak, Zheng Ruan, Natarajan Kannan, Diamond Clarke, Joseph Frankel, Jacek Gaertig
The mechanisms that govern pattern formation within the cell are poorly understood. Ciliates carry on their surface an elaborate pattern of cortical organelles that are arranged along the anteroposterior and circumferential axes by largely unknown mechanisms. Ciliates divide by tandem duplication: the cortex of the pre-division cell is remodeled into two similarly-sized and complete daughters. In the conditional cdaI-1 mutant of Tetrahymena thermophile, the division plane migrates from its initially correct equatorial position toward the cell's anterior, resulting in unequal cell division, and defects in nuclear divisions and cytokinesis...
April 16, 2017: Genetics
Aaron P Ragsdale, Ryan N Gutenkunst
Population demographic history may be learned from contemporary genetic variation data. Methods based on aggregating the statistics of many single loci into an allele frequency spectrum (AFS) have proven powerful, but such methods ignore potentially informative patterns of linkage disequilibrium (LD) between neighboring loci. To leverage such patterns, we developed a composite-likelihood framework for inferring demographic history from aggregated statistics of pairs of loci. Using this framework, we show that two-locus statistics are more sensitive to demographic history than single-locus statistics such as the AFS...
April 16, 2017: Genetics
Sandra G Zimmerman, Gennifer E Merrihew, Michael J MacCoss, Celeste A Berg
Elevated levels of human chitinase-like proteins (CLPs) are associated with numerous chronic inflammatory diseases and several cancers, often correlating with poor prognosis. Nevertheless, there is scant knowledge of their function. The CLPs normally mediate immune responses and wound healing, and when upregulated, they can promote disease progression by remodeling tissue, activating signaling cascades, stimulating proliferation and migration, and by regulating adhesion. We identified Imaginal disc growth factors (Idgfs), orthologs of human CLPs CHI3L1, CHI3L2, and OVGP1, in a proteomics analysis designed to discover factors that regulate tube morphogenesis in a Drosophila melanogaster model of tube formation...
April 12, 2017: Genetics
Shinya Matsuoka, Alissa Armstrong, Leesa L Sampson, Kaitlin M Laws, Daniela Drummond-Barbosa
Nutrients affect adult stem cells through complex mechanisms involving multiple organs. Adipocytes are highly sensitive to diet and have key metabolic roles, and obesity increases the risk for many cancers. How diet-regulated adipocyte metabolic pathways influence normal stem cell lineages, however, remains unclear. Drosophila melanogaster has highly conserved adipocyte metabolism and a well-characterized female germline stem cell (GSC) lineage response to diet. Here, we conducted an isobaric tags for relative and absolute quantification (iTRAQ) proteomic analysis to identify diet-regulated adipocyte metabolic pathways that control the female GSC lineage...
April 10, 2017: Genetics
Debdeep Dutta, Maimuna Sali Paul, Ankita Singh, Mousumi Mutsuddi, Ashim Mukherjee
Notch signaling is an evolutionarily conserved pathway that is found to be involved in a number of cellular events throughout development. The deployment of Notch signaling pathway in numerous cellular contexts is possible due to its regulation at multiple levels. In an effort to identify the novel components integrated into the molecular circuitry affecting Notch signaling, we carried out a protein-protein interaction screen based on the identification of cellular protein complexes using co-immunoprecipitation followed by mass-spectrometry...
April 10, 2017: Genetics
Arya Iranmehr, Ali Akbari, Christian Schlötterer, Vineet Bafna
The advent of next generation sequencing technologies has made whole-genome and whole-population sampling possible, even for eukaryotes with large genomes. With this development, experimental evolution studies can be designed to observe molecular evolution "in-action" via Evolve-and-Resequence (E&R) experiments. Among other applications, E&R studies can be used to locate the genes and variants responsible for genetic adaptation. Most of existing literature on time-series data analysis often assumes large population size, accurate allele frequency estimates, or wide time spans...
April 10, 2017: Genetics
Joanna Ilska, Marie J Haskell, Sarah C Blott, Enrique Sánchez-Molano, Zita Polgar, Sarah E Lofgren, Dylan N Clements, Pam Wiener
The genetic architecture of behavioural traits in dogs is of great interest to owners, breeders and professionals involved in animal welfare, as well as to scientists studying the genetics of animal (including human) behaviour. The genetic component of dog behaviour is supported by between-breed differences and some evidence of within-breed variation. However, it is a challenge to gather sufficiently large datasets to dissect the genetic basis of complex traits such as behaviour, which are both time-consuming and logistically difficult to measure, and known to be influenced by non-genetic factors...
April 10, 2017: Genetics
Christoph Theunert, Fernando Racimo, Montgomery Slatkin
We develop and test a method to address whether DNA samples sequenced from a group of fossil hominin bone or teeth fragments originate from the same individual or from closely related individuals. Our method assumes low amounts of retrievable DNA, significant levels of sequencing error and contamination from one or more present-day humans. We develop and implement a maximum likelihood method that estimates levels of contamination, sequencing error rates and pairwise relatedness coefficients in a set of individuals...
April 10, 2017: Genetics
Shintaro Yamada, Mika Okamura, Arisa Oda, Hiroshi Murakami, Kunihiro Ohta, Takatomi Yamada
Meiotic homologous recombination, a critical event for ensuring faithful chromosome segregation and creating genetic diversity, is initiated by programed DNA double strand breaks (DSBs) formed at recombination hotspots. Meiotic DSB formation is likely to be influenced by other DNA-templated processes including transcription, but how DSB formation and transcription interact with each other has not been understood well. In this study, we used fission yeast to investigate a possible interplay of these two events...
April 10, 2017: Genetics
Herman De Beukelaer, Yvonne Badke, Veerle Fack, Geert De Meyer
Long-term genomic selection (GS) requires strategies that balance genetic gain with population diversity, to sustain progress for traits under selection and to keep diversity for future breeding. In a simulation model for a recurrent selection scheme we provide the first head-to-head comparison of two such existing strategies: genomic optimal contributions selection (GOCS) that limits realized genomic relationship among selection candidates, and weighted genomic selection (WGS) that upscales rare allele effects in GS...
April 4, 2017: Genetics
Luke R Lloyd-Jones, Matthew R Robinson, Gerhard Moser, Jian Zeng, Sandra Beleza, Hua Tang, Gregory S Barsh, Peter M Visscher
Genetic association studies in admixed populations are under-represented in the genomics literature, with a key concern for researchers being the adequate control of spurious associations due to population structure. Linear mixed models (LMMs) are well suited for genome-wide association studies (GWAS) because they account for both population stratification and cryptic relatedness and achieve increased statistical power by jointly modelling all genotyped markers. Additionally, Bayesian LMMs allow for more flexible assumptions about the underlying distribution of genetic effects, and can concurrently estimate the proportion of phenotypic variance explained by genetic markers...
April 4, 2017: Genetics
Ying Zhao, Margaret Dominska, Aleksandra Petrova, Halle Bagshaw, Robert J Kokoska, Thomas D Petes
In the yeast Saccharomyces cerevisiae, the genes encoding the metallothionein protein Cup1 are located in a tandem array on chromosome VIII. Using a diploid strain that is heterozygous for an insertion of a selectable marker (URA3) within this tandem array, and heterozygous for markers flanking the array, we measured inter-homolog recombination and intra-/sister-chromatid exchange in the CUP1 locus. The rate of intra-/sister chromatid recombination exceeded the rate of inter-homolog recombination by more than ten-fold...
April 4, 2017: Genetics
Jan Engelstädter
Many parthenogenetically reproducing animals produce offspring not clonally but through different mechanisms collectively referred to as automixis. Here, meiosis proceeds normally but is followed by a fusion of meiotic products that restores diploidy. This mechanism typically leads to a reduction in heterozygosity among the offspring compared to the mother. Following a derivation of the rate at which heterozygosity is lost at one and two loci, depending on the number of crossovers between loci and centromere, a number of models are developed to gain a better understanding of basic evolutionary processes in automictic populations...
April 4, 2017: Genetics
Alencar Xavier, Benjamin Hall, Anthony A Hearst, Keith A Cherkauer, Katy M Rainey
Digital imagery can help to quantify seasonal changes in desirable crop phenotypes that can be treated as quantitative traits. Because limitations in precise and functional phenotyping restrain genetic improvement in the post-genomic era, imagery-based phenomics could become the next breakthrough to accelerate genetic gains in field crops. Whereas many phenomic studies focus on exploratory analysis of spectral data without obvious interpretative value, we used field images to directly measure soybean canopy development from phenological stage V2 to R5...
March 31, 2017: Genetics
Michael-John Dolan, Haojiang Luan, William C Shropshire, Ben Sutcliffe, Benjamin Cocanougher, Robert L Scott, Shahar Frechter, Marta Zlatic, Gregory S X E Jefferis, Benjamin H White
Efforts to map neural circuits have been galvanized by the development of genetic technologies that permit the manipulation of targeted sets of neurons in the brains of freely behaving animals. The success of these efforts relies on the experimenter's ability to target arbitrarily small subsets of neurons for manipulation, but such specificity of targeting cannot routinely be achieved using existing methods. In Drosophila melanogaster, a widely used technique for refined cell-type specific manipulation is the Split GAL4 system, which augments the targeting specificity of the binary GAL4-UAS system by making GAL4 transcriptional activity contingent upon two enhancers, rather than one...
March 31, 2017: Genetics
Shamoon Naseem, Kyunghun Min, Daniel Spitzer, Justin Gardin, James B Konopka
The amino sugar N-acetylglucosamine (GlcNAc) is increasingly recognized as an important signaling molecule in addition to its well-known structural roles at the cell surface. In the human fungal pathogen Candida albicans, GlcNAc stimulates several responses including the induction of the genes needed for its catabolism and a switch from budding to filamentous hyphal growth. We identified two genes needed for growth on GlcNAc (RON1 and NGS1) and found that mutants lacking these genes fail to induce the genes needed for GlcNAc catabolism...
March 27, 2017: Genetics
Stephen M Blazie, Heather C Geissel, Henry Wilky, Rajan Joshi, Jason Newbern, Marco Mangone
mRNA expression dynamics promotes and maintains the identity of somatic tissues in living organisms, however, its impact in post-transcriptional gene regulation in these processes is not fully understood. Here, we have applied the PAT-Seq approach to systematically isolate, sequence, and map tissue specific mRNA from five highly studied Caenorhabditis elegans somatic tissues: GABAergic and NMDA neurons, arcade and intestinal valve cells, seam cells and hypodermal tissues, and studied their mRNA expression dynamics...
March 27, 2017: Genetics
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