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CORRIGENDUM [Corrigendum]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(Source: Genetics)
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Tags: Corrigendum Source Type: journals

Ectopic Overproduction of a Sporulation-Specific Transcription Factor Induces Assembly of Prespore-Like Membranous Compartments in Vegetative Cells of Fission Yeast [Cellular genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Mei4 is a key sporulation-specific transcription factor in fission yeast. Ectopic expression of Mei4 in vegetative cells caused formation of nucleated membranous compartments, which shared common features with normal forespore membranes, thereby perturbing nuclear division. These results suggest why expression of development-specific transcription factors must be strictly controlled. (Source: Genetics)
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Nakase, Y., Hirata, A., Shimoda, C., Nakamura, T. Tags: Cellular genetics Source Type: journals

Removal of the Bloom Syndrome DNA Helicase Extends the Utility of Imprecise Transposon Excision for Making Null Mutations in Drosophila [Genome integrity and transmission]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Transposable elements are frequently used in Drosophila melanogaster for imprecise excision screens to delete genes of interest. However, these screens are highly variable in the number and size of deletions that are recovered. Here, we show that conducting excision screens in mus309 mutant flies that lack DmBlm, the Drosophila ortholog of the Bloom syndrome protein, increases the percentage and overall size of flanking deletions recovered after excision of either P or Minos elements. (Source: Genetics)
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Witsell, A., Kane, D. P., Rubin, S., McVey, M. Tags: Genome integrity and transmission Source Type: journals

Evolution of Sex-Dependent Gene Expression in Three Recently Diverged Species of Drosophila [Genome and systems biology]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Sexual dimorphism in morphological, physiological, and behavioral traits is pervasive in animals, as is the observation of strong sexual dimorphism in genomewide patterns of gene expression in the few species where this has been studied. Studies of transcriptome divergence show that most interspecific transcriptional divergence is highly sex dependent, an observation consistent with the action of sex-dependent natural selection during species divergence. However, few transcriptome evolution studies have been conducted between recently diverged species (<1 MY). Here, we present analyses of sex-biased transcriptome diverg...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Jiang, Z.-F., Machado, C. A. Tags: Genome and systems biology Source Type: journals

Cross-Species RNAi Rescue Platform in Drosophila melanogaster [Genome and systems biology]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
RNAi-mediated gene knockdown in Drosophila melanogaster is a powerful method to analyze loss-of-function phenotypes both in cell culture and in vivo. However, it has also become clear that false positives caused by off-target effects are prevalent, requiring careful validation of RNAi-induced phenotypes. The most rigorous proof that an RNAi-induced phenotype is due to loss of its intended target is to rescue the phenotype by a transgene impervious to RNAi. For large-scale validations in the mouse and Caenorhabditis elegans, this has been accomplished by using bacterial artificial chromosomes (BACs) of related species. Howe...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Kondo, S., Booker, M., Perrimon, N. Tags: Genome and systems biology Source Type: journals

Identification of a Cis-Acting Regulatory Polymorphism in a Eucalypt COBRA-Like Gene Affecting Cellulose Content [Genetics of complex traits]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study demonstrates the potential to reveal functional polymorphisms underlying quantitative traits in low LD populations. (Source: Genetics)
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Thumma, B. R., Matheson, B. A., Zhang, D., Meeske, C., Meder, R., Downes, G. M., Southerton, S. G. Tags: Genetics of complex traits Source Type: journals

A Combined-Cross Analysis Reveals Genes With Drug-Specific and Background-Dependent Effects on Drug Sensitivity in Saccharomyces cerevisiae [Genetics of complex traits]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Effective pharmacological therapy is often inhibited by variable drug responses and adverse drug reactions. Dissecting the molecular basis of different drug responses is difficult due to complex interactions involving multiple genes, pathways, and cellular processes. We previously found a single nucleotide polymorphism within cystathionine β-synthase (CYS4) that causes multi-drug sensitivity in a vineyard strain of Saccharomyces cerevisiae. However, not all variation was accounted for by CYS4. To identify additional genes influencing drug sensitivity, we used CYS4 as a covariate and conducted both single- and combined...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Kim, H. S., Fay, J. C. Tags: Genetics of complex traits Source Type: journals

Quantitative Genetic Bases of Anthocyanin Variation in Grape (Vitis vinifera L. ssp. sativa) Berry: A Quantitative Trait Locus to Quantitative Trait Nucleotide Integrated Study [Genetics of complex traits]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The combination of QTL mapping studies of synthetic lines and association mapping studies of natural diversity represents an opportunity to throw light on the genetically based variation of quantitative traits. With the positional information provided through quantitative trait locus (QTL) mapping, which often leads to wide intervals encompassing numerous genes, it is now feasible to directly target candidate genes that are likely to be responsible for the observed variation in completely sequenced genomes and to test their effects through association genetics. This approach was performed in grape, a newly sequenced genome...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Fournier-Level, A., Le Cunff, L., Gomez, C., Doligez, A., Ageorges, A., Roux, C., Bertrand, Y., Souquet, J.-M., Cheynier, V., This, P. Tags: Genetics of complex traits Source Type: journals

The Accuracy of Genomic Selection in Norwegian Red Cattle Assessed by Cross-Validation [Genetics of complex traits]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Genomic Selection (GS) is a newly developed tool for the estimation of breeding values for quantitative traits through the use of dense markers covering the whole genome. For a successful application of GS, accuracy of the prediction of genomewide breeding value (GW-EBV) is a key issue to consider. Here we investigated the accuracy and possible bias of GW-EBV prediction, using real bovine SNP genotyping (18,991 SNPs) and phenotypic data of 500 Norwegian Red bulls. The study was performed on milk yield, fat yield, protein yield, first lactation mastitis traits, and calving ease. Three methods, best linear unbiased predictio...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Luan, T., Woolliams, J. A., Lien, S., Kent, M., Svendsen, M., Meuwissen, T. H. E. Tags: Genetics of complex traits Source Type: journals

The Sheltered Genetic Load Linked to the S Locus in Plants: New Insights From Theoretical and Empirical Approaches in Sporophytic Self-Incompatibility [Population and evolutionary genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Inbreeding depression and mating systems evolution are closely linked, because the purging of deleterious mutations and the fitness of individuals may depend on outcrossing vs. selfing rates. Further, the accumulation of deleterious mutations may vary among genomic regions, especially for genes closely linked to loci under balancing selection. Sporophytic self-incompatibility (SSI) is a common genetic mechanism in angiosperm that enables hermaphrodite plants to avoid selfing and promote outcrossing. The SSI phenotype is determined by the S locus and may depend on dominance relationships among alleles. Since most individual...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Llaurens, V., Gonthier, L., Billiard, S. Tags: Population and evolutionary genetics Source Type: journals

Closed-Form Two-Locus Sampling Distributions: Accuracy and Universality [Population and evolutionary genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Sampling distributions play an important role in population genetics analyses, but closed-form sampling formulas are generally intractable to obtain. In the presence of recombination, there is no known closed-form sampling formula that holds for an arbitrary recombination rate. However, we recently showed that it is possible to obtain useful closed-form sampling formulas when the population-scaled recombination rate is large. Specifically, in the case of the two-locus infinite-alleles model, we considered an asymptotic expansion of the sampling formula in inverse powers of and obtained closed-form expressions for the first...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Jenkins, P. A., Song, Y. S. Tags: Population and evolutionary genetics Source Type: journals

The Population Genetics of Adaptation: Multiple Substitutions on a Smooth Fitness Landscape [Population and evolutionary genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Much recent work in the theoretical study of adaptation has focused on the so-called strong selection–weak mutation (SSWM) limit, wherein adaptation is due to new mutations of definite selective advantage. This work, in turn, has focused on the first step (substitution) during adaptive evolution. Here we extend this theory to allow multiple steps during adaptation. We find analytic solutions to the probability that adaptation follows a certain path during evolution as well as the probability that adaptation arrives at a given genotype regardless of the path taken. We also consider the probability of parallel adaptati...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Unckless, R. L., Orr, H. A. Tags: Population and evolutionary genetics Source Type: journals

Population Differentiation as an Indicator of Recent Positive Selection in Humans: An Empirical Evaluation [Population and evolutionary genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We have evaluated the extent to which SNPs identified by genomewide surveys as showing unusually high levels of population differentiation in humans have experienced recent positive selection, starting from a set of 32 nonsynonymous SNPs in 27 genes highlighted by the HapMap1 project. These SNPs were genotyped again in the HapMap samples and in the Human Genome Diversity Project–Centre d'Etude du Polymorphisme Humain (HGDP–CEPH) panel of 52 populations representing worldwide diversity; extended haplotype homozygosity was investigated around all of them, and full resequence data were examined for 9 genes (5 from...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Xue, Y., Zhang, X., Huang, N., Daly, A., Gillson, C. J., MacArthur, D. G., Yngvadottir, B., Nica, A. C., Woodwark, C., Chen, Y., Conrad, D. F., Ayub, Q., Mehdi, S. Q., Li, P., Tyler-Smith, C. Tags: Population and evolutionary genetics Source Type: journals

Testing for Spatially Divergent Selection: Comparing QST to FST [Population and evolutionary genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
QST is a standardized measure of the genetic differentiation of a quantitative trait among populations. The distribution of QST's for neutral traits can be predicted from the FST for neutral marker loci. To test for the neutral differentiation of a quantitative trait among populations, it is necessary to ask whether the QST of that trait is in the tail of the probability distribution of neutral traits. This neutral distribution can be estimated using the Lewontin–Krakauer distribution and the FST from a relatively small number of marker loci. We develop a simulation method to test whether the QST of a given trait is ...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Whitlock, M. C., Guillaume, F. Tags: Population and evolutionary genetics Source Type: journals

Adaptive Divergence in Experimental Populations of Pseudomonas fluorescens. IV. Genetic Constraints Guide Evolutionary Trajectories in a Parallel Adaptive Radiation [Population and evolutionary genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The capacity for phenotypic evolution is dependent upon complex webs of functional interactions that connect genotype and phenotype. Wrinkly spreader (WS) genotypes arise repeatedly during the course of a model Pseudomonas adaptive radiation. Previous work showed that the evolution of WS variation was explained in part by spontaneous mutations in wspF, a component of the Wsp-signaling module, but also drew attention to the existence of unknown mutational causes. Here, we identify two new mutational pathways (Aws and Mws) that allow realization of the WS phenotype: in common with the Wsp module these pathways contain a di-g...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: McDonald, M. J., Gehrig, S. M., Meintjes, P. L., Zhang, X.-X., Rainey, P. B. Tags: Population and evolutionary genetics Source Type: journals

stall Encodes an ADAMTS Metalloprotease and Interacts Genetically With Delta in Drosophila Ovarian Follicle Formation [Developmental and behavioral genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Ovarian follicle formation in Drosophila melanogaster requires stall (stl) gene function, both within and outside the ovary, for follicle individualization, stalk cell intercalation, and oocyte localization. We have identified the stl transcript as CG3622 and confirmed the presence of three alternatively spliced isoforms, contrary to current genome annotation. Here we show that the gene is expressed in both ovarian and brain tissues, which is consistent with previous evidence of an ovary nonautonomous function. On the basis of amino acid sequence, stl encodes a metalloprotease similar to the "a disintegrin and metalloprote...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Ozdowski, E. F., Mowery, Y. M., Cronmiller, C. Tags: Developmental and behavioral genetics Source Type: journals

A Gain-of-Function Screen Identifying Genes Required for Growth and Pattern Formation of the Drosophila melanogaster Wing [Developmental and behavioral genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The Drosophila melanogaster wing is a model system for analyzing the genetic control of organ size, shape, and pattern formation. The formation of the wing involves a variety of processes, such as cell growth, proliferation, pattern formation, and differentiation. These developmental processes are under genetic control, and many genes participating in specific aspects of wing development have already being characterized. In this work, we aim to identify novel genes regulating wing growth and patterning. To this end, we have carried out a gain-of-function screen generating novel P-UAS (upstream activating sequences) inserti...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Cruz, C., Glavic, A., Casado, M., de Celis, J. F. Tags: Developmental and behavioral genetics Source Type: journals

A Combinatorial Interplay Among the 1-Aminocyclopropane-1-Carboxylate Isoforms Regulates Ethylene Biosynthesis in Arabidopsis thaliana [Developmental and behavioral genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Ethylene (C2H4) is a unique plant-signaling molecule that regulates numerous developmental processes. The key enzyme in the two-step biosynthetic pathway of ethylene is 1-aminocyclopropane-1-carboxylate synthase (ACS), which catalyzes the conversion of S-adenosylmethionine (AdoMet) to ACC, the precursor of ethylene. To understand the function of this important enzyme, we analyzed the entire family of nine ACS isoforms (ACS1, ACS2, ACS4-9, and ACS11) encoded in the Arabidopsis genome. Our analysis reveals that members of this protein family share an essential function, because individual ACS genes are not essential for Arab...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Tsuchisaka, A., Yu, G., Jin, H., Alonso, J. M., Ecker, J. R., Zhang, X., Gao, S., Theologis, A. Tags: Developmental and behavioral genetics Source Type: journals

MAP Kinase Signaling Antagonizes PAR-1 Function During Polarization of the Early Caenorhabditis elegans Embryo [Developmental and behavioral genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PAR proteins (partitioning defective) are major regulators of cell polarity and asymmetric cell division. One of the par genes, par-1, encodes a Ser/Thr kinase that is conserved from yeast to mammals. In Caenorhabditis elegans, par-1 governs asymmetric cell division by ensuring the polar distribution of cell fate determinants. However the precise mechanisms by which PAR-1 regulates asymmetric cell division in C. elegans remain to be elucidated. We performed a genomewide RNAi screen and identified six genes that specifically suppress the embryonic lethal phenotype associated with mutations in par-1. One of these suppressors...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Spilker, A. C., Rabilotta, A., Zbinden, C., Labbe, J.-C., Gotta, M. Tags: Developmental and behavioral genetics Source Type: journals

Dissection of Genetic Factors Modulating Fetal Growth in Cattle Indicates a Substantial Role of the Non-SMC Condensin I Complex, Subunit G (NCAPG) Gene [Developmental and behavioral genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The increasing evidence of fetal developmental effects on postnatal life, the still unknown fetal growth mechanisms impairing offspring generated by somatic nuclear transfer techniques, and the impact on stillbirth and dystocia in conventional reproduction have generated increasing attention toward mammalian fetal growth. We identified a highly significant quantitative trait locus (QTL) affecting fetal growth on bovine chromosome 6 in a specific resource population, which was set up by consistent use of embryo transfer and foster mothers and, thus, enabled dissection of fetal-specific genetic components of fetal growth. Me...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Eberlein, A., Takasuga, A., Setoguchi, K., Pfuhl, R., Flisikowski, K., Fries, R., Klopp, N., Furbass, R., Weikard, R., Kuhn, C. Tags: Developmental and behavioral genetics Source Type: journals

The Roles of Multiple UNC-40 (DCC) Receptor-Mediated Signals in Determining Neuronal Asymmetry Induced by the UNC-6 (Netrin) Ligand [Developmental and behavioral genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The polarization of post-mitotic neurons is poorly understood. Preexisting spatially asymmetric cues, distributed within the neuron or as extracellular gradients, could be required for neurons to polarize. Alternatively, neurons might have the intrinsic ability to polarize without any preestablished asymmetric cues. In Caenorhabditis elegans, the UNC-40 (DCC) receptor mediates responses to the extracellular UNC-6 (netrin) guidance cue. For the HSN neuron, an UNC-6 ventral-dorsal gradient asymmetrically localizes UNC-40 to the ventral HSN surface. There an axon forms, which is ventrally directed by UNC-6. In the absence of ...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Xu, Z., Li, H., Wadsworth, W. G. Tags: Developmental and behavioral genetics Source Type: journals

A Promiscuous Prion: Efficient Induction of [URE3] Prion Formation by Heterologous Prion Domains [Cellular genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The [URE3] and [PSI+] prions are the infections amyloid forms of the Saccharomyces cerevisiae proteins Ure2p and Sup35p, respectively. Randomizing the order of the amino acids in the Ure2 and Sup35 prion domains while retaining amino acid composition does not block prion formation, indicating that amino acid composition, not primary sequence, is the predominant feature driving [URE3] and [PSI+] formation. Here we show that Ure2p promiscuously interacts with various compositionally similar proteins to influence [URE3] levels. Overexpression of scrambled Ure2p prion domains efficiently increases de novo formation of wild-typ...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Ross, C. D., McCarty, B. R., Hamilton, M., Ben-Hur, A., Ross, E. D. Tags: Cellular genetics Source Type: journals

The Small, Secreted Immunoglobulin Protein ZIG-3 Maintains Axon Position in Caenorhabditis elegans [Cellular genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Vertebrate and invertebrate genomes contain scores of small secreted or transmembrane proteins with two immunoglobulin (Ig) domains. Many of them are expressed in the nervous system, yet their function is not well understood. We analyze here knockout alleles of all eight members of a family of small secreted or transmembrane Ig domain proteins, encoded by the Caenorhabditis elegans zig ("zwei Ig Domänen") genes. Most of these family members display the unusual feature of being coexpressed in a single neuron, PVT, whose axon is located along the ventral midline of C. elegans. One of these genes, zig-4, has previously b...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Benard, C., Tjoe, N., Boulin, T., Recio, J., Hobert, O. Tags: Cellular genetics Source Type: journals

Interlock Formation and Coiling of Meiotic Chromosome Axes During Synapsis [Cellular genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The meiotic prophase chromosome has a unique architecture. At the onset of leptotene, the replicated sister chromatids are organized along an axial element. During zygotene, as homologous chromosomes pair and synapse, a synaptonemal complex forms via the assembly of a transverse element between the two axial elements. However, due to the limitations of light and electron microscopy, little is known about chromatin organization with respect to the chromosome axes and about the spatial progression of synapsis in three dimensions. Three-dimensional structured illumination microscopy (3D-SIM) is a new method of superresolution...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Wang, C.-J. R., Carlton, P. M., Golubovskaya, I. N., Cande, W. Z. Tags: Cellular genetics Source Type: journals

Epithelial Polarity: Interactions Between Junctions and Apical-Basal Machinery [Cellular genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Epithelial polarity is established and maintained by competition between determinants that define the apical and basolateral domains. Cell–cell adhesion complexes, or adherens junctions, form at the interface of these regions. Mutations in adhesion components as well as apical determinants normally lead to an expansion of the basolateral domain. Here we investigate the genetic relationship between the polarity determinants and adhesion and show that the levels of the adhesion protein Armadillo affect competition. We find that in arm mutants, even a modest reduction in the basolateral component lgl leads to a full api...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Kaplan, N. A., Liu, X., Tolwinski, N. S. Tags: Cellular genetics Source Type: journals

Retrograde Intraflagellar Transport Mutants Identify Complex A Proteins With Multiple Genetic Interactions in Chlamydomonas reinhardtii [Cellular genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The intraflagellar transport machinery is required for the assembly of cilia. It has been investigated by biochemical, genetic, and computational methods that have identified at least 21 proteins that assemble into two subcomplexes. It has been hypothesized that complex A is required for retrograde transport. Temperature-sensitive mutations in FLA15 and FLA17 show defects in retrograde intraflagellar transport (IFT) in Chlamydomonas. We show that IFT144 and IFT139, two complex A proteins, are encoded by FLA15 and FLA17, respectively. The fla15 allele is a missense mutation in a conserved cysteine and the fla17 allele is an...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Iomini, C., Li, L., Esparza, J. M., Dutcher, S. K. Tags: Cellular genetics Source Type: journals

MNR2 Regulates Intracellular Magnesium Storage in Saccharomyces cerevisiae [Cellular genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We describe a fifth yeast CorA homolog (Mnr2) required for Mg homeostasis. MNR2 gene inactivation was associated with an increase in both the Mg requirement and the Mg content of yeast cells. In Mg-replete conditions, wild-type cells accumulated an intracellular store of Mg that supported growth under deficient conditions. An mnr2 mutant was unable to access this store, suggesting that Mg was trapped in an intracellular compartment. Mnr2 was localized to the vacuole membrane, implicating this organelle in Mg storage. The mnr2 mutant growth and Mg-content phenotypes were dependent on vacuolar proton-ATPase activity, but wer...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Pisat, N. P., Pandey, A., MacDiarmid, C. W. Tags: Cellular genetics Source Type: journals

Suppression of Mitochondrial DNA Instability of Autosomal Dominant Forms of Progressive External Ophthalmoplegia-Associated ANT1 Mutations in Podospora anserina [Cellular genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Maintenance and expression of mitochondrial DNA (mtDNA) are essential for the cell and the organism. In humans, several mutations in the adenine nucleotide translocase gene ANT1 are associated with multiple mtDNA deletions and autosomal dominant forms of progressive external ophthalmoplegia (adPEO). The mechanisms underlying the mtDNA instability are still obscure. A current hypothesis proposes that these pathogenic mutations primarily uncouple the mitochondrial inner membrane, which secondarily causes mtDNA instability. Here we show that the three adPEO-associated mutations equivalent to A114P, L98P, and V289M introduced ...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: El-Khoury, R., Sainsard-Chanet, A. Tags: Cellular genetics Source Type: journals

In Planta Mutagenesis Determines the Functional Regions of the Wheat Puroindoline Proteins [Gene expression]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study demonstrates the feasibility of in planta functional analysis of wheat proteins and that the Tryptophan-rich region is the most important region of both PINA and PINB. (Source: Genetics)
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Feiz, L., Beecher, B. S., Martin, J. M., Giroux, M. J. Tags: Gene expression Source Type: journals

The Developmentally Active and Stress-Inducible Noncoding hsr{omega} Gene Is a Novel Regulator of Apoptosis in Drosophila [Gene expression]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The large nucleus limited noncoding hsr-n RNA of Drosophila melanogaster is known to associate with a variety of heterogeneous nuclear RNA-binding proteins (hnRNPs) and certain other RNA-binding proteins to assemble the nucleoplasmic omega speckles. In this article, we show that RNAi-mediated depletion of this noncoding RNA dominantly suppresses apoptosis, in eye and other imaginal discs, triggered by induced expression of Rpr, Grim, or caspases (initiator as well as effector), all of which are key regulators/effectors of the canonical caspase-mediated cell death pathway. We also show, for the first time, a genetic interac...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Mallik, M., Lakhotia, S. C. Tags: Gene expression Source Type: journals

Two Distinct Roles for EGL-9 in the Regulation of HIF-1-Mediated Gene Expression in Caenorhabditis elegans [Gene expression]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Oxygen is critically important to metazoan life, and the EGL-9/PHD enzymes are key regulators of hypoxia (low oxygen) response. When oxygen levels are high, the EGL-9/PHD proteins hydroxylate hypoxia-inducible factor (HIF) transcription factors. Once hydroxylated, HIF subunits bind to von Hippel-Lindau (VHL) E3 ligases and are degraded. Prior genetic analyses in Caenorhabditis elegans had shown that EGL-9 also acted through a vhl-1-independent pathway to inhibit HIF-1 transcriptional activity. Here, we characterize this novel EGL-9 function. We employ an array of complementary methods to inhibit EGL-9 hydroxylase activity ...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Shao, Z., Zhang, Y., Powell-Coffman, J. A. Tags: Gene expression Source Type: journals

Imprinting of the Y Chromosome Influences Dosage Compensation in roX1 roX2 Drosophila melanogaster [Gene expression]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Drosophila melanogaster males have a well-characterized regulatory system that increases X-linked gene expression. This essential process restores the balance between X-linked and autosomal gene products in males. A complex composed of the male-specific lethal (MSL) proteins and RNA is recruited to the body of transcribed X-linked genes where it modifies chromatin to increase expression. The RNA components of this complex, roX1 and roX2 (RNA on the X1, RNA on the X2), are functionally redundant. Males mutated for both roX genes have dramatically reduced survival. We show that reversal of sex chromosome inheritance suppress...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Menon, D. U., Meller, V. H. Tags: Gene expression Source Type: journals

TEN1 Is Essential for CDC13-Mediated Telomere Capping [Genome integrity and transmission]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Telomere binding proteins protect chromosome ends from degradation and mask chromosome termini from checkpoint surveillance. In Saccharomyces cerevisiae, Cdc13 binds single-stranded G-rich telomere repeats, maintaining telomere integrity and length. Two additional proteins, Ten1 and Stn1, interact with Cdc13 but their contributions to telomere integrity are not well defined. Ten1 is known to prevent accumulation of aberrant single-stranded telomere DNA; whether this results from defective end protection or defective telomere replication is unclear. Here we report our analysis of a new group of ten1 temperature-sensitive (t...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Xu, L., Petreaca, R. C., Gasparyan, H. J., Vu, S., Nugent, C. I. Tags: Genome integrity and transmission Source Type: journals

Telomerase Is Essential to Alleviate Pif1-Induced Replication Stress at Telomeres [Genome integrity and transmission]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Pif1, an evolutionarily conserved helicase, negatively regulates telomere length by removing telomerase from chromosome ends. Pif1 has also been implicated in DNA replication processes such as Okazaki fragment maturation and replication fork pausing. We find that overexpression of Saccharomyces cervisiae PIF1 results in dose-dependent growth inhibition. Strong overexpression causes relocalization of the DNA damage response factors Rfa1 and Mre11 into nuclear foci and activation of the Rad53 DNA damage checkpoint kinase, indicating that the toxicity is caused by accumulation of DNA damage. We screened the complete set of ~4...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Chang, M., Luke, B., Kraft, C., Li, Z., Peter, M., Lingner, J., Rothstein, R. Tags: Genome integrity and transmission Source Type: journals

Charles Darwin: Genius or Plodder? [Perspectives]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
There is no doubt about the magnitude of Charles Darwin's contributions to science. There has, however, been a long-running debate about how brilliant he was. His kind of intelligence was clearly different from that of the great physicists who are deemed geniuses. Here, the nature of Darwin's intelligence is examined in the light of Darwin's actual style of working. Surprisingly, the world of literature and the field of neurobiology might supply more clues to resolving the puzzle than conventional scientific history. Those clues suggest that the apparent discrepancy between Darwin's achievements and his seemingly pedestria...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Wilkins, A. S. Tags: Perspectives Source Type: journals

Darwin and Darwinism: The (Alleged) Social Implications of The Origin of Species [Perspectives]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Most scientific theories, even revolutionary ones, change the practice of a particular science but have few consequences for culture or society at large. But Darwinism, it has often been said, is different in this respect. Since the publication of The Origin of Species, many have claimed that Darwinism has a number of profound social implications. Here, I briefly consider three of these: the economic, the political, and the religious. I suggest that, for the most part, these supposed implications have been misconstrued or exaggerated. Indeed, it is reasonably clear that the chain of implication sometimes primarily ran in t...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Orr, H. A. Tags: Perspectives Source Type: journals

Darwin and Genetics [Perspectives]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Darwin's theory of natural selection lacked an adequate account of inheritance, making it logically incomplete. We review the interaction between evolution and genetics, showing how, unlike Mendel, Darwin's lack of a model of the mechanism of inheritance left him unable to interpret his own data that showed Mendelian ratios, even though he shared with Mendel a more mathematical and probabilistic outlook than most biologists of his time. Darwin's own "pangenesis" model provided a mechanism for generating ample variability on which selection could act. It involved, however, the inheritance of characters acquired during an or...
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Authors: Charlesworth, B., Charlesworth, D. Tags: Perspectives Source Type: journals

Celebrating The Origin of Species [Introduction]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(Source: Genetics)
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Tags: Introduction Source Type: journals

ISSUE HIGHLIGHTS [Issue Highlights]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(Source: Genetics)
Source: Genetics - November 18, 2009 Category: Genetics & Stem Cells Tags: Issue Highlights Source Type: journals

CORRIGENDA [Corrigenda]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(Source: Genetics)
Source: Genetics - October 28, 2009 Category: Genetics & Stem Cells Tags: Corrigenda Source Type: journals

Evidence for Gene Length As a Determinant of Gene Coexpression in Protein Complexes [Gene expression]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Variation of gene length imposes a challenge on genes requiring coexpression. Using a large human protein complex data set, we show that genes encoding subunits of the same protein complex tend to have similar length. The length uniformity is greater for complexes with stronger coexpression. We also show that the rate of gene length evolution is associated with gene coexpression level within a complex. These results suggest a new angle in understanding the evolution of protein complexes as well as the regulation of gene coexpression. (Source: Genetics)
Source: Genetics - October 28, 2009 Category: Genetics & Stem Cells Authors: Chen, X., Shi, S., He, X. Tags: Gene expression Source Type: journals

Point Mutation Rate of Bacteriophage {Phi}X174 [Genome integrity and transmission]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The point mutation rate of phage X174 was determined using the fluctuation test. After identifying the genetic changes associated with the selected phenotype, we obtained an estimate of 1.0 x 10–6 substitutions per base per round of copying, which is consistent with Drake's rule (0.003 mutations per genome per round of copying in DNA-based microorganisms). (Source: Genetics)
Source: Genetics - October 28, 2009 Category: Genetics & Stem Cells Authors: Cuevas, J. M., Duffy, S., Sanjuan, R. Tags: Genome integrity and transmission Source Type: journals

Alcohol Sensitivity in Drosophila: Translational Potential of Systems Genetics [Genome and systems biology]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Identification of risk alleles for human behavioral disorders through genomewide association studies (GWAS) has been hampered by a daunting multiple testing problem. This problem can be circumvented for some phenotypes by combining genomewide studies in model organisms with subsequent candidate gene association analyses in human populations. Here, we characterized genetic networks that underlie the response to ethanol exposure in Drosophila melanogaster by measuring ethanol knockdown time in 40 wild-derived inbred Drosophila lines. We associated phenotypic variation in ethanol responses with genomewide variation in gene ex...
Source: Genetics - October 28, 2009 Category: Genetics & Stem Cells Authors: Morozova, T. V., Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. A., Lyman, R. F., Stone, E. A., Govindaraju, D. R., Ellison, R. C., Mackay, T. F. C., Anholt, R. R. H. Tags: Genome and systems biology Source Type: journals

Cis-regulatory Changes at FLOWERING LOCUS T Mediate Natural Variation in Flowering Responses of Arabidopsis thaliana [Genetics of complex traits]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Flowering time, a critical adaptive trait, is modulated by several environmental cues. These external signals converge on a small set of genes that in turn mediate the flowering response. Mutant analysis and subsequent molecular studies have revealed that one of these integrator genes, FLOWERING LOCUS T (FT), responds to photoperiod and temperature cues, two environmental parameters that greatly influence flowering time. As the central player in the transition to flowering, the protein coding sequence of FT and its function are highly conserved across species. Using QTL mapping with a new advanced intercross-recombinant in...
Source: Genetics - October 28, 2009 Category: Genetics & Stem Cells Authors: Schwartz, C., Balasubramanian, S., Warthmann, N., Michael, T. P., Lempe, J., Sureshkumar, S., Kobayashi, Y., Maloof, J. N., Borevitz, J. O., Chory, J., Weigel, D. Tags: Genetics of complex traits Source Type: journals

Bayesian Quantitative Trait Locus Mapping Based on Reconstruction of Recent Genetic Histories [Genetics of complex traits]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We assume that quantitative measurements on a considered trait and unphased genotype data at certain marker loci are available on a sample of individuals from a background population. Our goal is to map quantitative trait loci by using a Bayesian model that performs, and makes use of, probabilistic reconstructions of the recent unobserved genealogical history (a pedigree and a gene flow at the marker loci) of the sampled individuals. This work extends variance component-based linkage analysis to settings where the unobserved pedigrees are considered as latent variables. In addition to the measured trait values and unphased...
Source: Genetics - October 28, 2009 Category: Genetics & Stem Cells Authors: Gasbarra, D., Pirinen, M., Sillanpaa, M. J., Arjas, E. Tags: Genetics of complex traits Source Type: journals

The Genetic Basis of Transgressive Ovary Size in Honeybee Workers [Genetics of complex traits]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Ovarioles are the functional unit of the female insect reproductive organs and the number of ovarioles per ovary strongly influences egg-laying rate and fecundity. Social evolution in the honeybee (Apis mellifera) has resulted in queens with 200–360 total ovarioles and workers with usually 20 or less. In addition, variation in ovariole number among workers relates to worker sensory tuning, foraging behavior, and the ability to lay unfertilized male-destined eggs. To study the genetic architecture of worker ovariole number, we performed a series of crosses between Africanized and European bees that differ in worker ov...
Source: Genetics - October 28, 2009 Category: Genetics & Stem Cells Authors: Linksvayer, T. A., Rueppell, O., Siegel, A., Kaftanoglu, O., Page, R. E., Amdam, G. V. Tags: Genetics of complex traits Source Type: journals

Comparing Mutational and Standing Genetic Variability for Fitness and Size in Caenorhabditis briggsae and C. elegans [Population and evolutionary genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The genetic variation present in a species depends on the interplay between mutation, population size, and natural selection. At mutation-(purifying) selection balance (MSB) in a large population, the standing genetic variance for a trait (VG) is predicted to be proportional to the mutational variance for the trait (VM); VM is proportional to the mutation rate for the trait. The ratio VM/VG predicts the average strength of selection (S) against a new mutation. Here we compare VM and VG for lifetime reproductive success ( fitness) and body volume in two species of self-fertilizing rhabditid nematodes, Caenorhabditis briggsa...
Source: Genetics - October 28, 2009 Category: Genetics & Stem Cells Authors: Salomon, M. P., Ostrow, D., Phillips, N., Blanton, D., Bour, W., Keller, T. E., Levy, L., Sylvestre, T., Upadhyay, A., Baer, C. F. Tags: Population and evolutionary genetics Source Type: journals

Effects of Recombination on Complex Regulatory Circuits [Population and evolutionary genetics]Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Mutation and recombination are the two main forces generating genetic variation. Most of this variation may be deleterious. Because recombination can reorganize entire genes and genetic circuits, it may have much greater consequences than point mutations. We here explore the effects of recombination on models of transcriptional regulation circuits that play important roles in embryonic development. We show that recombination has weaker deleterious effects on the expression phenotypes of these circuits than mutations. In addition, if a population of such circuits evolves under the influence of mutation and recombination, we...
Source: Genetics - October 28, 2009 Category: Genetics & Stem Cells Authors: Martin, O. C., Wagner, A. Tags: Population and evolutionary genetics Source Type: journals