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G3: Genes—Genomes—Genetics

Jasper Braun, Lukas Nabergall, Rafik Neme, Laura F Landweber, Masahico Saito, Nataša Jonoska
Ciliates have two different types of nuclei per cell, with one acting as a somatic, transcriptionally active nucleus (macronucleus; abbr. MAC) and another serving as a germline nucleus (micronucleus; abbr. MIC). Furthermore, Oxytricha trifallax undergoes extensive genome rearrangements during sexual conjugation and post-zygotic development of daughter cells. These rearrangements are necessary because the precursor MIC loci are often both fragmented and scrambled, with respect to the corresponding MAC loci. Such genome architectures are remarkably tolerant of encrypted MIC loci, because RNA-guided processes during MAC development reorganize the gene fragments in the correct order to resemble the parental MAC sequence...
March 15, 2018: G3: Genes—Genomes—Genetics
Kristie Wrasman, Salvatore L Alioto, Yorke Zhang, Kyle Hoban, Marjon Khairy, Bruce L Goode, Beverly Wendland
Endocytosis is a fundamental process for internalizing material from the plasma membrane, including many transmembrane proteins that are selectively internalized depending on environmental conditions. In most cells, the main route of entry is clathrin-mediated endocytosis (CME), a process that involves the coordinated activity of over 60 proteins; however, there are likely as-yet unidentified proteins involved in cargo selection and/or regulation of endocytosis. We performed a mutagenic screen to identify novel endocytic genes in Saccharomyces cerevisiae expressing the methionine permease Mup1 tagged with pHluorin (pHl), a pH-sensitive GFP variant whose fluorescence is quenched upon delivery to the acidic vacuole lumen...
March 14, 2018: G3: Genes—Genomes—Genetics
Shan Wei, Zachary R Weiss, Zev Williams
Real-time sequencing of short DNA reads has a wide variety of clinical and research applications including screening for mutations, target sequences and aneuploidy. We recently demonstrated that MinION, a nanopore-based DNA sequencing device the size of a USB drive, could be used for short-read DNA sequencing. In this study, an ultra-rapid multiplex library preparation and sequencing method for the MinION is presented and applied to accurately test normal diploid and aneuploidy samples' genomic DNA in under three hours, including library preparation and sequencing...
March 14, 2018: G3: Genes—Genomes—Genetics
Cécile Molinier, Céline M O Reisser, Peter Fields, Adeline Ségard, Yan Galimov, Christoph R Haag
Daphnia reproduce by cyclic-parthenogenesis, where phases of asexual reproduction are intermitted by sexual production of diapause stages. This life cycle, together with environmental sex determination, allow the comparison of gene expression between genetically identical males and females. We investigated gene expression differences between males and females in four genotypes of Daphnia magna and compared the results with published data on sex-biased gene expression in two other Daphnia species, each representing one of the major phylogenetic clades within the genus...
March 13, 2018: G3: Genes—Genomes—Genetics
Ilias Kounatidis, Lauren Ames, Rupal Mistry, Hsueh-Lui Ho, Ken Haynes, Petros Ligoxygakis
Candida glabrata ( C. glabrata ) forms part of the normal human gut microbiota but can cause life-threatening invasive infections in immune-compromised individuals. C. glabrata displays high resistance to common azole antifungals, which necessitates new treatments. In this investigation, we identified five C. glabrata deletion mutants ( Δada2 , Δbas1 , Δhir3, Δino2 and Δmet31 ) from a library of 196 transcription factor mutants that were unable to grow and activate an immune response in Drosophila larvae...
March 13, 2018: G3: Genes—Genomes—Genetics
Anthony J Greenberg
Explosive growth in the amount of genomic data is matched by increasing power of consumer grade computers. Even applications that require powerful servers can be quickly tested on desktop or laptop machines if we can generate representative samples from large data sets. I describe a fast and memory efficient implementation of an on-line sampling method developed for tape drives 30 years ago. Focusing on genotype files, I test the performance of this technique on modern solid-state and spinning hard drives, and show that it performs well compared to a simple sampling scheme...
March 12, 2018: G3: Genes—Genomes—Genetics
Alex Bronstein, Shay Bramson, Keren Shemesh, Batia Liefshitz, Martin Kupiec
Proper DNA damage repair is one of the most vital and fundamental functions of every cell. Several different repair mechanisms exist to deal with various types of DNA damage, in various stages of the cell cycle and under different conditions. Homologous recombination is one of the most important repair mechanisms in all organisms. Srs2, a regulator of homologous recombination, is a DNA helicase involved in DNA repair, cell cycle progression and genome integrity. Srs2 can remove Rad51 from ssDNA, and is thought to inhibit unscheduled recombination...
March 12, 2018: G3: Genes—Genomes—Genetics
Sébastien Bélanger, Suzanne Marchand, Pierre-Étienne Jacques, Blake Meyers, François Belzile
In barley, it is possible to induce embryogenesis in the haploid and uninucleate microspore to obtain a diploid plant that is perfectly homozygous. To change developmental fates in this fashion, microspores need to engage in cellular de-differentiation, interrupting the pollen formation, and restore totipotency prior to engaging in embryogenesis. In this work, we used the barley cultivar Gobernadora to characterize the transcriptome of microspores prior to (day 0) and immediately after (days 2 and 5) the application of a stress pretreatment...
March 12, 2018: G3: Genes—Genomes—Genetics
Roumen Voutev, Richard S Mann
Effective genome engineering should lead to a desired locus change with minimal adverse impact to the genome itself. However, flanking loci with site-directed recombinase recognition sites, such as those of the phage FC31 integrase, allows for creation of platforms for cassette exchange and manipulation of genomic regions in an iterative manner, once specific loci have been targeted. Here we show that a genomic locus engineered with inverted minimal phage FC31 attP/attB sites can undergo efficient recombinase-mediated cassette exchange (RMCE) in the fruit fly Drosophila melanogaster ...
March 9, 2018: G3: Genes—Genomes—Genetics
Michael Babokhov, Mohammad M Mosaheb, Richard W Baker, Stephen M Fuchs
The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (RNAPII) is required to regulate transcription and to integrate it with other essential cellular processes. In the budding yeast Saccharomyces cerevisiae , the CTD of Rpb1p consists of 26 conserved heptad repeats that are post-translationally modified to orchestrate protein factor binding at different stages of the transcription cycle. A long-standing question in the study of the CTD is if there are any functional differences between the 26 repeats...
March 9, 2018: G3: Genes—Genomes—Genetics
Christoph Müller, Milica Krunic, Judith Wendt, Arndt von Haeseler, Ichiro Okamoto
Risk of melanoma is in part determined by genetic factors. Currently the only established high penetrance familial melanoma genes are CDKN2A and CDK4. Recent studies reported germline variants in POT1 in melanoma families. In the present study, we sequenced the entire POT1 gene in 694 patients from the M3-study. Patients with multiple primary melanomas (n=163) or with a positive family history (n=133) were classified as high-risk melanoma patients. Additionally, 200 single primary melanoma patients and 198 non-melanoma controls were sequenced...
March 9, 2018: G3: Genes—Genomes—Genetics
Carson Holt, Michael Campbell, David A Keays, Nathaniel Edelman, Aurélie Kapusta, Emily Maclary, Eric Domyan, Alexander Suh, Wesley C Warren, Mark Yandell, M Thomas P Gilbert, Michael D Shapiro
The domestic rock pigeon ( Columba livia ) is among the most widely distributed and phenotypically diverse avian species. C. livia is broadly studied in ecology, genetics, physiology, behavior, and evolutionary biology, and has recently emerged as a model for understanding the molecular basis of anatomical diversity, the magnetic sense, and other key aspects of avian biology. Here we report an update to the C. livia genome reference assembly and gene annotation dataset. Greatly increased scaffold lengths in the updated reference assembly, along with an updated annotation set, provide improved tools for evolutionary and functional genetic studies of the pigeon, and for comparative avian genomics in general...
March 8, 2018: G3: Genes—Genomes—Genetics
Ata Ghavidel, Kunal Baxi, Martin Prusinkiewicz, Cynthia Swan, Zach R Belak, Christopher H Eskiw, Carlos E Carvalho, Troy A Harkness
The yeast, Saccharomyces cerevisiae , like other higher eukaryotes, undergo a finite number of cell divisions before exiting the cell cycle due to the effects of aging. Here, we show that yeast aging begins with the nuclear exclusion of Hcm1 in young cells, resulting in loss of acidic vacuoles. Autophagy is required for healthy aging in yeast, with proteins targeted for turnover by autophagy directed to the vacuole. Consistent with this, vacuolar acidity is necessary for vacuolar function and yeast longevity...
March 8, 2018: G3: Genes—Genomes—Genetics
Palle Duun Rohde, Solveig Østergaard, Torsten Nygaard Kristensen, Peter Sørensen, Volker Loeschcke, Trudy F C Mackay, Pernille Sarup
Understanding the genetic underpinnings of complex traits requires knowledge of the genetic variants that contribute to phenotypic variability. Reliable statistical approaches are needed to obtain such knowledge. In genome-wide association studies, variants are tested for association with trait variability to pinpoint loci that contribute to the quantitative trait. Because stringent genome-wide significance thresholds are applied to control the false positive rate, many true causal variants can remain undetected...
March 8, 2018: G3: Genes—Genomes—Genetics
Alexandra Katigbak, Francis Robert, Marilène Paquet, Jerry Pelletier
Genetically engineered mouse models (GEMMs) are powerful tools by which to probe gene function in vivo , obtain insight into disease etiology, and identify modifiers of drug response. Increased sophistication of GEMMs has led to the design of tissue-specific and inducible models in which genes of interest are expressed or ablated in defined tissues or cellular subtypes. Here we describe the generation of a transgenic mouse harboring a doxycycline-regulated Cas9 allele for inducible genome engineering. This model provides a flexible platform for genome engineering since editing is achieved by exogenous delivery of sgRNAs and should allow for the modelling of a range of biological and pathological processes...
March 8, 2018: G3: Genes—Genomes—Genetics
Arunika Das, Jeffry Cesario, Anna Maria Hinman, Janet K Jang, Kim S McKim
Bipolar spindle assembly occurs in the absence of centrosomes in the oocytes of most organisms. In the absence of centrosomes in Drosophila oocytes, we have proposed that the kinesin 6 Subito, a MKLP-2 homolog, is required for establishing spindle bipolarity and chromosome biorientation by assembling a robust central spindle during prometaphase I. Although the functions of the conserved motor domains of kinesins is well studied, less is known about the contribution of the poorly conserved N- and C- terminal domains to motor function...
March 7, 2018: G3: Genes—Genomes—Genetics
Lien D Bertier, Mily Ron, Heiqiang Huo, Kent J Bradford, Richard W Michelmore
CRISPR/Cas9 is a transformative tool for making targeted genetic alterations. In plants, high mutation efficiencies have been reported in primary transformants. However, many of the mutations analyzed were somatic and therefore not heritable. To provide more insights into the efficiency of creating stable homozygous mutants using CRISPR/Cas9, we targeted LsNCED4 ( 9-cis-epoxycarotenoid dioxygenase4) , a gene conditioning thermoinhibition of seed germination in lettuce. Three constructs, each capable of expressing Cas9 and a single gRNA targeting different sites in LsNCED4 , were stably transformed into lettuce (Lactuca sativa) cvs...
March 6, 2018: G3: Genes—Genomes—Genetics
James L Lissemore, Elyse Connors, Ying Liu, Li Qiao, Bing Yang, Mark L Edgley, Stephane Flibotte, Jon Taylor, Vinci Au, Donald G Moerman, Eleanor M Maine
In a genetic screen to identify genes that promote GLP-1/Notch signaling in Caenorhabditis elegans germline stem cells, we found a single mutation, om40 , defining a gene called ego-3. ego-3(om40) causes several defects in the soma and the germline, including paralysis during larval development, sterility, delayed proliferation of germline stem cells, and ectopic germline stem cell proliferation. Whole genome sequencing identified om40 as an allele of hsp-90 , previously known as daf-21 , which encodes the C...
March 5, 2018: G3: Genes—Genomes—Genetics
Megan M Chang, Danielle Allery Nail, Toni Kazic, Susan J Simmons, Ann E Stapleton
Crop improvement must accelerate to feed an increasing human population in the face of environmental changes. Including anticipated climatic changes with genetic architecture in breeding programs could better optimize improvement strategies. Combinations of drought and nitrogen limitation already occur world-wide. We therefore analyzed the genetic architecture underlying the response of Zea mays to combinations of water and nitrogen stresses. Recombinant inbreds were subjected to nine combinations of the two stresses using an optimized response surface design, and their growth was measured...
March 1, 2018: G3: Genes—Genomes—Genetics
Rebecca King, Ying Li, Jiaxing Wang, Felix L Struebing, Eldon E Geisert
Intraocular pressure (IOP) is the primary risk factor for developing glaucoma, yet little is known about the contribution of genomic background to IOP regulation. The present study leverages an array of systems genetics tools to study genomic factors modulating normal IOP in the mouse. The BXD recombinant inbred (RI) strain set was used to identify genomic loci modulating IOP. We measured the IOP in a total of 506 eyes from 38 different strains. Strain averages were subjected to conventional quantitative trait analysis by means of composite interval mapping...
March 1, 2018: G3: Genes—Genomes—Genetics
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