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https://www.readbyqxmd.com/read/28235888/adaptation-of-candida-albicans-to-reactive-sulfur-species
#1
Yasmin Chebaro, Michael Lorenz, Alice Fa, Rui Zheng, Michael Gustin
Candida albicans is an opportunistic fungal pathogen that is highly resistant to different oxidative stresses. How reactive sulfur species (RSS) such as sulfite regulate gene expression and the role of the transcription factor Zcf2 and the sulfite exporter Ssu1 in such responses is not known. Here, we show that C. albicans specifically adapts to sulfite stress and that Zcf2 is required for that response as well as induction of genes predicted to remove sulfite from cells and to increase the intracellular amount of a subset of nitrogen metabolites...
February 24, 2017: Genetics
https://www.readbyqxmd.com/read/28213477/soft-selective-sweeps-in-evolutionary-rescue
#2
Benjamin A Wilson, Pleuni S Pennings, Dmitri A Petrov
Evolutionary rescue occurs when a population that is declining in size because of an environmental change is rescued from extinction by genetic adaptation. Evolutionary rescue is an important phenomenon at the intersection of ecology and population genetics, and the study of evolutionary rescue is critical to understanding processes ranging from species conservation to the evolution of drug and pesticide resistance. While most population genetic models of evolutionary rescue focus on estimating the probability of rescue, we focus on whether one or more adaptive lineages contribute to evolutionary rescue...
February 17, 2017: Genetics
https://www.readbyqxmd.com/read/28213476/editing-of-mitochondrial-transcripts-nad3-and-cox2-by-dek10-is-essential-for-mitochondrial-function-and-maize-plant-development
#3
Weiwei Qi, Zhongrui Tian, Lei Lu, Xiuzu Chen, Xinze Chen, Wei Zhang, Rentao Song
Respiration, the core of mitochondrial metabolism, depends on the function of five respiratory complexes. Many respiratory chain related proteins are encoded by the mitochondrial genome and their RNAs undergo post-transcriptional modifications by nuclear genome expressed factors, including pentatricopeptide repeat (PPR) proteins. Maize defective kernel 10 (dek10) is a classic mutant with small kernels and delayed development. Through positional cloning we found that Dek10 encodes an E-subgroup PPR protein localized in mitochondria...
February 17, 2017: Genetics
https://www.readbyqxmd.com/read/28213475/wheat-landrace-genome-diversity
#4
Luzie U Wingen, Claire West, Michelle Leverington-Waite, Sarah Collier, Simon Orford, Richard Goram, Cai-Yun Yang, Julie King, Alexandra M Allen, Amanda Burridge, Keith J Edwards, Simon Griffiths
Understanding the genomic complexity of bread wheat (Triticum aestivum L.) is a cornerstone in the quest to unravel the processes of domestication and the following adaptation of domesticated wheat to a wide variety of environments across the globe. Additionally, it is of importance for future improvement of the crop, particularly in the light of climate change. Focussing on the adaptation after domestication, a nested association mapping (NAM) panel of 60 segregating bi-parental populations were developed mainly involving landrace accessions from the core set of the Watkins hexaploid wheat collection optimized for genetic diversity (WINGEN et al...
February 17, 2017: Genetics
https://www.readbyqxmd.com/read/28213474/a-bayesian-approach-for-analysis-of-whole-genome-bisulphite-sequencing-data-identifies-disease-associated-changes-in-dna-methylation
#5
Owen J L Rackham, Sarah R Langley, Thomas Oates, Eleni Vradi, Nathan Harmston, Prashant K Srivastava, Jacques Behmoaras, Petros Dellaportas, Leonardo Bottolo, Enrico Petretto
DNA methylation is a key epigenetic modification involved in gene regulation whose contribution to disease susceptibility remains to be fully understood. Here, we present a novel Bayesian smoothing approach (called ABBA) to detect differentially methylated regions (DMRs) from whole-genome bisulphite sequencing (WGBS). We also show how this approach can be leveraged to identify disease-associated changes in DNA methylation, suggesting mechanisms through which these alterations might affect disease. From a data modeling perspective, ABBA has the distinctive feature of automatically adapting to different correlation structures in CpG methylation levels across the genome whilst taking into account the distance between CpG sites as a covariate...
February 17, 2017: Genetics
https://www.readbyqxmd.com/read/28209589/second-generation-drosophila-chemical-tags-sensitivity-versatility-and-speed
#6
Ben Sutcliffe, Julian Ng, Thomas O Auer, Mathias Pasche, Richard Benton, Gregory S X E Jefferis, Sebastian Cachero
Labeling and visualizing cells and subcellular structures within thick tissues, whole organs and even intact animals is key to studying biological processes. This is particularly true for studies of neural circuits where neurons form submicron synapses but have arbors that may span millimeters in length. Traditionally, labeling is achieved by immunofluorescence; however diffusion of antibody molecules (>100 kDa) is slow and often results in uneven labeling with very poor penetration into the centre of thick specimens; these limitations can be partially addressed by extending staining protocols to over a week (Drosophila brain) and months (mice)...
February 16, 2017: Genetics
https://www.readbyqxmd.com/read/28193730/mismatch-repair-incompatibilities-in-diverse-yeast-populations
#7
Duyen T Bui, Anne Friedrich, Najla Al-Sweel, Gianni Liti, Joseph Schacherer, Charles F Aquadro, Eric Alani
An elevated mutation rate can provide cells with a source of mutations to adapt to changing environments. We identified a negative-epistatic interaction involving naturally occurring variants in the MLH1 and PMS1 mismatch repair (MMR) genes of Saccharomyces cerevisiae We hypothesized that this MMR incompatibility, created through mating between divergent S. cerevisiae, yields mutator progeny that can rapidly but transiently adapt to an environmental stress. Here we analyzed the MLH1 and PMS1 genes across 1,010 S...
February 13, 2017: Genetics
https://www.readbyqxmd.com/read/28193729/sequential-divergent-and-cooperative-requirements-of-foxl2a-and-foxl2b-in-ovary-development-and-maintenance-of-zebrafish
#8
Yan-Jing Yang, Yang Wang, Zhi Li, Li Zhou, Jian-Fang Gui
Foxl2 is essential for mammalian ovary maintenance. Although sexually dimorphic expression of foxl2 was observed in many teleost, its role and regulative mechanism in fish remained largely unclear. In this study, we first identified two transcript variants of foxl2a and its homologous gene foxl2b in zebrafish, and revealed their specific expression in follicular layer cells in a sequential and divergent fashion during ovary differentiation, maturation and maintenance. Then, homozygous foxl2a mutants (foxl2a(-/-)) and foxl2b mutants (foxl2b(-/-)) were constructed, and detailed comparisons, such as sex ratio, gonadal histological structure, transcriptome profiling and dynamic expression of gonadal development-related genes, were carried out...
February 13, 2017: Genetics
https://www.readbyqxmd.com/read/28193728/mobile-introns-shape-the-genetic-diversity-of-their-host-genes
#9
Jelena Repar, Tobias Warnecke
Self-splicing introns populate several highly conserved protein-coding genes in fungal and plant mitochondria. In fungi, many of these introns have retained their ability to spread to intron-free target sites, often assisted by intron-encoded endonucleases that initiate the homing process. Here, leveraging population genomic data from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Lachancea kluyveri, we expose non-random patterns of genetic diversity in exons that border self-splicing introns. In particular, we show that, in all three species, the density of single nucleotide polymorphisms increases as one approaches a mobile intron...
February 13, 2017: Genetics
https://www.readbyqxmd.com/read/28193727/inference-of-gene-flow-in-the-process-of-speciation-an-efficient-maximum-likelihood-method-for-the-isolation-with-initial-migration-model
#10
Rui J Costa, Hilde Wilkinson-Herbots
The isolation-with-migration (IM) model is commonly used to make inferences about gene flow during speciation, using polymorphism data. However, Becquet and Przeworski (2009) report that the parameter estimates obtained by fitting the IM model are very sensitive to the model's assumptions, including the assumption of constant gene flow until the present. This paper is concerned with the isolation-with-initial-migration (IIM) model, which drops precisely this assumption. In the IIM model, one ancestral population divides into two descendant subpopulations, between which there is an initial period of gene flow and a subsequent period of isolation...
February 13, 2017: Genetics
https://www.readbyqxmd.com/read/28193726/genetic-basis-of-melanin-pigmentation-in-butterfly-wings
#11
Linlin Zhang, Arnaud Martin, Michael W Perry, Karin R L van der Burg, Yuji Matsuoka, Antónia Monteiro, Robert D Reed
Despite the variety, prominence, and adaptive significance of butterfly wing patterns surprisingly little known about the genetic basis of wing color diversity. Even though there is intense interest in wing pattern evolution and development, the technical challenge of genetically manipulating butterflies has slowed efforts to functionally characterize color pattern development genes. To identify candidate wing pigmentation genes we used RNA-seq to characterize transcription across multiple stages of butterfly wing development, and between different color pattern elements, in the painted lady butterfly Vanessa cardui This allowed us to pinpoint genes specifically associated with red and black pigment patterns...
February 13, 2017: Genetics
https://www.readbyqxmd.com/read/28188144/elevated-rate-of-genome-rearrangements-in-radiation-resistant-bacteria
#12
Jelena Repar, Fran Supek, Tin Klanjscek, Tobias Warnecke, Ksenija Zahradka, Davor Zahradka
A number of bacterial, archaeal, and eukaryotic species are known for their resistance to ionizing radiation. One of the challenges these species face is a potent environmental source of DNA double-strand breaks, potential drivers of genome structure evolution. Efficient and accurate DNA double-strand break repair systems have been demonstrated in several unrelated radiation-resistant species and are putative adaptations to the DNA damaging environment. Such adaptations are expected to compensate for the genome-destabilizing effect of environmental DNA damage and may be expected to result in a more conserved gene order in radiation-resistant species...
February 10, 2017: Genetics
https://www.readbyqxmd.com/read/28179368/a-common-group-of-eggshell-proteins-ensure-the-transfer-of-both-dorsoventral-and-terminal-information-from-ovary-to-embryo-in-drosophila
#13
Alessandro Mineo, Marc Furriols, Jordi Casanova
The Drosophila eggshell is an extracellular matrix that confers protection to the egg and also plays a role in transferring positional information from the ovary to pattern the embryo. Among the constituents of the Drosophila eggshell, Nasrat, Polehole and Closca form a group of proteins related by sequence, secreted by the oocyte and mutually required for their incorporation into the eggshell. Besides their role in eggshell integrity, Nasrat, Polehole and Closca are also required for embryonic terminal patterning by anchoring or stabilizing Torso-like at the eggshell...
February 7, 2017: Genetics
https://www.readbyqxmd.com/read/28179367/genomic-rearrangements-in-arabidopsis-considered-as-quantitative-traits
#14
Martha Imprialou, André Kahles, Joshua G Steffen, Edward J Osborne, Xiangchao Gan, Janne Lempe, Amarjit Bhomra, Eric Belfield, Anne Visscher, Robert Greenhalgh, Nicholas P Harberd, Richard Goram, Jotun Hein, Alexandre Robert-Seilaniantz, Jonathan Jones, Oliver Stegle, Paula Kover, Miltos Tsiantis, Magnus Nordborg, Gunnar Rätsch, Richard M Clark, Richard Mott
To understand the population genetics of structural variants and their effects on phenotypes, we developed an approach to mapping structural variants that segregate in a population sequenced at low coverage. We avoid calling structural variants directly. Instead, the evidence for a potential structural variant at a locus is indicated by variation in the counts of short-reads that map anomalously to that locus. These structural variant traits are treated as quantitative traits and mapped genetically, analogously to a gene expression study...
February 7, 2017: Genetics
https://www.readbyqxmd.com/read/28159756/structure-and-origin-of-the-white-cap-locus-and-its-role-in-evolution-of-grain-color-in-maize
#15
Bao-Cai Tan, Jiahn-Chou Guan, Shou Ding, Shan Wu, Jonathan W Saunders, Karen E Koch, Donald R McCarty
Selection for yellow and white grain types has been central to post-domestication improvement of maize. While genetic control of carotenoid biosynthesis in endosperm is attributed primarily to the Yellow1 (Y1) phytoene synthase gene, less is known about the role of the dominant white endosperm factor White Cap (Wc). We show that the Wc locus contains multiple, tandem copies of a Carotenoid cleavage dioxygenase 1 (Ccd1) gene that encodes a carotenoid-degrading enzyme. A survey of 111 maize inbreds and landraces, together with 22 teosinte accessions, reveals that Wc is exclusive to maize, where it is prevalent in white-grain (y1) varieties...
February 3, 2017: Genetics
https://www.readbyqxmd.com/read/28159755/role-of-ectopic-gene-conversion-in-the-evolution-of-a-candida-krusei-pleiotropic-drug-resistance-transporter-family
#16
Erwin Lamping, Jing-Yi Zhu, Masakazu Niimi, Richard David Cannon
Gene duplications enable the evolution of novel gene function, but strong positive selection is required to preserve advantageous mutations in a population. This is because frequent ectopic gene conversions (EGCs) between highly similar, tandem-duplicated, sequences, can rapidly remove fate determining mutations by replacing them with the neighbouring parent gene sequences. Unfortunately, the high sequence similarities between tandem-duplicated genes severely hamper empirical studies of this important evolutionary process because deciphering their correct sequences is challenging...
February 3, 2017: Genetics
https://www.readbyqxmd.com/read/28159754/reliance-of-wolbachia-on-high-rates-of-host-proteolysis-revealed-by-a-genome-wide-rnai-screen-of-drosophila-cells
#17
Pamela M White, Laura R Serbus, Alain Debec, Adan Codina, Walter Bray, Antoine Guichet, R Scott Lokey, William Sullivan
Wolbachia are gram-negative, obligate, intracellular bacteria carried by a majority of insect species worldwide. Here we use a Wolbachia-infected Drosophila cell line and genome-wide RNAi screening to identify host factors that influence Wolbachia titer. By screening an RNAi library targeting 15,699 transcribed host genes, we identified 36 candidate genes that dramatically reduced Wolbachia titer and 41 that increased Wolbachia titer. Host gene knockdowns that reduced Wolbachia titer spanned a broad array of biological pathways including genes that influenced mitochondrial function and lipid metabolism...
February 3, 2017: Genetics
https://www.readbyqxmd.com/read/28159753/requirements-for-driving-anti-pathogen-effector-genes-into-populations-of-disease-vectors-by-homing
#18
Andrea Beaghton, Andrew Hammond, Tony Nolan, Andrea Crisanti, H Charles J Godfray, Austin Burt
There is a need for new interventions against the on-going burden of vector-borne diseases such as malaria and dengue. One suggestion has been to develop genes encoding effector molecules that block parasite development within the vector, and then use the nuclease-based homing reaction as a form of gene drive to spread those genes through target populations. If the effector gene reduces the fitness of the mosquito and does not contribute to the drive, then loss-of-function mutations in the effector will eventually replace functional copies, but protection may nonetheless persist sufficiently long to provide a public health benefit...
February 3, 2017: Genetics
https://www.readbyqxmd.com/read/28159752/studies-of-an-androgen-binding-protein-knockout-corroborate-a-role-for-salivary-abp-in-mouse-communication
#19
Amanda G Chung, Phillip M Belone, Barbora Vošlajerová Bímová, Robert M Karn, Christina M Laukaitis
The house mouse Androgen-binding protein (Abp) gene family is comprised of 64 paralogs, 30 Abpa and 34 Abpbg, encoding the alpha (ABPA) and betagamma (ABPBG) protein subunits that are disulfide-bridged to form dimers in secretions. Only 14 Abp genes are expressed in distinct patterns in the lacrimal (11) and submandibular glands (3). We created a knockout mouse line lacking two of the three genes expressed in submandibular glands, Abpa27 and Abpbg27, by replacing them with the neomycin resistance gene. The knockout genotype (-/-) showed no Abpa27 or Abpbg27 transcripts in submandibular gland cDNA libraries and there was a concomitant lack of protein expression of ABPA27 and ABPBG27 in the -/- genotype saliva, shown by elimination of these two proteins from the saliva proteome and the loss of cross-reactive material in the acinar cells of the submandibular glands...
February 3, 2017: Genetics
https://www.readbyqxmd.com/read/28159751/x-chromosome-control-of-genome-scale-recombination-rates-in-house-mice
#20
Beth L Dumont
Sex differences in recombination are widespread in mammals, but the causes of this pattern are poorly understood. Previously, males from two interfertile subspecies of house mice, Mus musculus musculus and M. m. castaneus, were shown to exhibit a ~30% difference in their global crossover frequencies. Much of this crossover rate divergence is explained by six autosomal loci and a large-effect locus on the X chromosome. Intriguingly, the allelic effects at this X-linked locus are transgressive, with the allele conferring increased crossover rate transmitted by the low crossover rate M...
February 3, 2017: Genetics
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