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Author (up) Baylis, H.A.; Vazquez-Manrique, R.P. file  url
openurl 
  Title Genetic analysis of IP3 and calcium signalling pathways in C. elegans Type Journal Article
  Year 2012 Publication Biochimica et Biophysica Acta Abbreviated Journal Biochim Biophys Acta  
  Volume 1820 Issue 8 Pages 1253-1268  
  Keywords Animals; Caenorhabditis elegans--genetics, metabolism, physiology; Caenorhabditis elegans Proteins--genetics, metabolism; Calcium Signaling; Inositol 1,4,5-Trisphosphate Receptors--genetics, metabolism; Inositol Phosphates--physiology; Mutagenesis; Phenotype; Protein Interaction Maps; RNA Interference; Reverse Genetics  
  Abstract BACKGROUND: The nematode, Caenorhabditis elegans is an established model system that is particularly well suited to genetic analysis. C. elegans is easily manipulated and we have an in depth knowledge of many aspects of its biology. Thus, it is an attractive system in which to pursue integrated studies of signalling pathways. C. elegans has a complement of calcium signalling molecules similar to that of other animals. SCOPE OF REVIEW: We focus on IP3 signalling. We describe how forward and reverse genetic approaches, including RNAi, have resulted in a tool kit which enables the analysis of IP3/Ca2+ signalling pathways. The importance of cell and tissue specific manipulation of signalling pathways and the use of epistasis analysis are highlighted. We discuss how these tools have increased our understanding of IP3 signalling in specific developmental, physiological and behavioural roles. Approaches to imaging calcium signals in C. elegans are considered. MAJOR CONCLUSIONS: A wide selection of tools is available for the analysis of IP3/Ca2+ signalling in C. elegans. This has resulted in detailed descriptions of the function of IP3/Ca2+ signalling in the animal's biology. Nevertheless many questions about how IP3 signalling regulates specific processes remain. GENERAL SIGNIFICANCE: Many of the approaches described may be applied to other calcium signalling systems. C. elegans offers the opportunity to dissect pathways, perform integrated studies and to test the importance of the properties of calcium signalling molecules to whole animal function, thus illuminating the function of calcium signalling in animals. This article is part of a Special Issue entitled Biochemical, biophysical and genetic approaches to intracellular calcium signalling.  
  Call Number Serial 258  
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Author (up) Cho, J.H.; Bandyopadhyay, J.; Lee, J.; Park, C.S.; Ahnn, J. file  url
openurl 
  Title Two isoforms of sarco/endoplasmic reticulum calcium ATPase (SERCA) are essential in Caenorhabditis elegans Type Journal Article
  Year 2000 Publication Gene Abbreviated Journal Gene  
  Volume 261 Issue 2 Pages 211-219  
  Keywords Alternative Splicing; Amino Acid Sequence; Animals; Caenorhabditis elegans/embryology/enzymology/*genetics; Calcium-Transporting ATPases/*genetics/metabolism; Embryo, Nonmammalian/drug effects/enzymology; Embryonic Development; Gene Expression Regulation, Enzymologic; Green Fluorescent Proteins; Isoenzymes/genetics/metabolism; Luminescent Proteins/genetics/metabolism; Microscopy, Fluorescence; Molecular Sequence Data; Phenotype; Promoter Regions, Genetic/genetics; RNA, Double-Stranded/administration & dosage/genetics; Recombinant Fusion Proteins/genetics/metabolism; Sarcoplasmic Reticulum Calcium-Transporting ATPases; Sequence Homology, Amino Acid; Tissue Distribution  
  Abstract SERCA (Sarco/Endoplasmic Reticulum Calcium ATPase), a membrane bound Ca(2+)- /Mg(2+)- dependent ATPase that sequesters Ca(2+) into the SR/ER lumen, is one of the essential components for the maintenance of intracellular Ca(2+) homeostasis. Here we describe the identification and functional characterization of a C. elegans SERCA gene (ser-1). ser-1 is a single gene alternatively spliced at its carboxyl terminus to form two isoforms (SER-1A and SER-1B) and displays a high homology (70% identity, 80% similarity) with mammalian SERCAs. Green fluorescent protein (GFP) and whole-mount immunostaining analyses reveal that SER-1 expresses in neuronal cells, body-wall muscles, pharyngeal and vulval muscles, excretory cells, and vulva epithelial cells. Furthermore, SER-1::GFP expresses during embryonic stages and the expression is maintained through the adult stages. Double-stranded RNA injection (also known as RNAi) targeted to each SER-1 isoform results in severe phenotypic defects: ser-1A(RNAi) animals show embryonic lethality, whereas ser-1B(RNAi) results in L1 larval arrest phenotype. These findings suggest that both isoforms of C. elegans SERCA, like in mammals, are essential for embryonic development and post-embryonic growth and survival.  
  Call Number Serial 451  
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Author (up) Coleman, C.; Copetti, D.; Cipriani, G.; Hoffmann, S.; Kozma, P.; Kovacs, L.; Morgante, M.; Testolin, R.; Di Gaspero, G. file  url
doi  openurl
  Title The powdery mildew resistance gene REN1 co-segregates with an NBS-LRR gene cluster in two Central Asian grapevines Type Journal Article
  Year 2009 Publication BMC Genetics Abbreviated Journal BMC Genet  
  Volume 10 Issue Pages 89  
  Keywords *Evolution, Molecular; Genetic Markers; Genome, Plant; Multigene Family; Phenotype; Phylogeny; Plant Diseases/*genetics/microbiology; Plant Proteins/*genetics; Segmental Duplications, Genomic; Vitis/*genetics  
  Abstract BACKGROUND: Grape powdery mildew is caused by the North American native pathogen Erysiphe necator. Eurasian Vitis vinifera varieties were all believed to be susceptible. REN1 is the first resistance gene naturally found in cultivated plants of Vitis vinifera. RESULTS: REN1 is present in 'Kishmish vatkana' and 'Dzhandzhal kara', two grapevines documented in Central Asia since the 1920's. These cultivars have a second-degree relationship (half sibs, grandparent-grandchild, or avuncular), and share by descent the chromosome on which the resistance allele REN1 is located. The REN1 interval was restricted to 1.4 cM using 38 SSR markers distributed across the locus and the segregation of the resistance phenotype in two progenies of collectively 461 offspring, derived from either resistant parent. The boundary markers delimit a 1.4-Mbp sequence in the PN40024 reference genome, which contains 27 genes with known functions, 2 full-length coiled-coil NBS-LRR genes, and 9 NBS-LRR pseudogenes. In the REN1 locus of PN40024, NBS genes have proliferated through a mixture of segmental duplications, tandem gene duplications, and intragenic recombination between paralogues, indicating that the REN1 locus has been inherently prone to producing genetic variation. Three SSR markers co-segregate with REN1, the outer ones confining the 908-kb array of NBS-LRR genes. Kinship and clustering analyses based on genetic distances with susceptible cultivars representative of Central Asian Vitis vinifera indicated that 'Kishmish vatkana' and 'Dzhandzhal kara' fit well into local germplasm. 'Kishmish vatkana' also has a parent-offspring relationship with the seedless table grape 'Sultanina'. In addition, the distant genetic relatedness to rootstocks, some of which are derived from North American species resistant to powdery mildew and have been used worldwide to guard against phylloxera since the late 1800's, argues against REN1 being infused into Vitis vinifera from a recent interspecific hybridisation. CONCLUSION: The REN1 gene resides in an NBS-LRR gene cluster tightly delimited by two flanking SSR markers, which can assist in the selection of this DNA block in breeding between Vitis vinifera cultivars. The REN1 locus has multiple layers of structural complexity compared with its two closely related paralogous NBS clusters, which are located some 5 Mbp upstream and 4 Mbp downstream of the REN1 interval on the same chromosome.  
  Call Number Serial 193  
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Author (up) Cram, E.J.; Shang, H.; Schwarzbauer, J.E. file  url
openurl 
  Title A systematic RNA interference screen reveals a cell migration gene network in C. elegans Type Journal Article
  Year 2006 Publication Journal of Cell Science Abbreviated Journal J Cell Sci  
  Volume 119 Issue Pt 23 Pages 4811-4818  
  Keywords Animals; Animals, Genetically Modified; Caenorhabditis elegans/embryology/*genetics; Cell Movement/*genetics; *Gene Regulatory Networks; Genes, Helminth; Gonads/embryology; Phenotype; *RNA Interference  
  Abstract Cell migration is essential during embryonic development and tissue morphogenesis. During gonadogenesis in the nematode Caenorhabditis elegans, migration of the distal tip cells forms two U-shaped gonad arms. Malformation results if the distal tip cells stop prematurely or follow an aberrant path, and abnormalities are easily visualized in living nematodes. Here we describe the first comprehensive in vivo RNA interference screen for genes required for cell migration. In this non-biased screen, we systematically analyzed 16,758 RNA-interference depletion experiments by light microscopy and identified 99 genes required for distal tip cell migration. Genetic and physical interaction data connect 59 of these genes to form a cell migration gene network that defines distal tip cell migration in vivo.  
  Call Number Serial 1705  
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Author (up) Dawson, G.; Webb, S.; Schellenberg, G.D.; Dager, S.; Friedman, S.; Aylward, E.; Richards, T. file  url
openurl 
  Title Defining the broader phenotype of autism: genetic, brain, and behavioral perspectives Type Journal Article
  Year 2002 Publication Development and Psychopathology Abbreviated Journal Dev Psychopathol  
  Volume 14 Issue 3 Pages 581-611  
  Keywords Autistic Disorder/*complications/*genetics; Brain/*abnormalities; Child; Child Behavior Disorders/*etiology; Evoked Potentials/physiology; Humans; Language Disorders/etiology; Magnetic Resonance Imaging; Perceptual Disorders/etiology; Phenotype; Phonetics; Speech Perception; Temporal Lobe/abnormalities; Twin Studies as Topic  
  Abstract Achieving progress in understanding the cause, nature, and treatment of autism requires an integration of concepts, approaches, and empirical findings from genetic, cognitive neuroscience, animal, and clinical studies. The need for such integration has been a fundamental tenet of the discipline of developmental psychopathology from its inception. It is likely that the discovery of autism susceptibility genes will depend on the development of dimensional measures of broader phenotype autism traits. It is argued that knowledge of the cognitive neuroscience of social and language behavior will provide a useful framework for defining such measures. In this article, the current state of knowledge of the cognitive neuroscience of social and language impairments in autism is reviewed. Following from this, six candidate broader phenotype autism traits are proposed: (a) face processing, including structural encoding of facial features and face movements, such as eye gaze; (b) social affiliation or sensitivity to social reward, pertaining to the social motivational impairments found in autism; (c) motor imitation ability, particularly imitation of body actions; (d) memory, specifically those aspects of memory mediated by the medial temporal lobe-prefrontal circuits; (e) executive function, especially planning and flexibility; and (f) Language ability, particularly those aspects of language that overlap with specific language impairment, namely, phonological processing.  
  Call Number Serial 1118  
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Author (up) Domingue, B.W.; Fletcher, J.; Conley, D.; Boardman, J.D. file  url
doi  openurl
  Title Genetic and educational assortative mating among US adults Type Journal Article
  Year 2014 Publication Proceedings of the National Academy of Sciences of the United States of America Abbreviated Journal Proc Natl Acad Sci U S A  
  Volume 111 Issue 22 Pages 7996-8000  
  Keywords Continental Population Groups/genetics; Databases, Genetic; Educational Status; Ethnic Groups/genetics; Female; Genome-Wide Association Study; Genotype; Humans; Male; *Marriage; Metagenomics/*methods; Phenotype; *Sexual Behavior; *Spouses; United States; genetic homogamy; homophily; random mating  
  Abstract Understanding the social and biological mechanisms that lead to homogamy (similar individuals marrying one another) has been a long-standing issue across many fields of scientific inquiry. Using a nationally representative sample of non-Hispanic white US adults from the Health and Retirement Study and information from 1.7 million single-nucleotide polymorphisms, we compare genetic similarity among married couples to noncoupled pairs in the population. We provide evidence for genetic assortative mating in this population but the strength of this association is substantially smaller than the strength of educational assortative mating in the same sample. Furthermore, genetic similarity explains at most 10% of the assortative mating by education levels. Results are replicated using comparable data from the Framingham Heart Study.  
  Call Number Serial 1127  
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Author (up) Ellis, H.M.; Horvitz, H.R. file  url
openurl 
  Title Genetic control of programmed cell death in the nematode C. elegans Type Journal Article
  Year 1986 Publication Cell Abbreviated Journal Cell  
  Volume 44 Issue 6 Pages 817-829  
  Keywords Alleles; Animals; Caenorhabditis/*cytology/genetics; Cell Differentiation; Cell Division; *Cell Survival; Male; *Mutation; Phenotype; Receptors, Dopamine/analysis; Receptors, Serotonin/analysis  
  Abstract The wild-type functions of the genes ced-3 and ced-4 are required for the initiation of programmed cell deaths in the nematode Caenorhabditis elegans. The reduction or loss of ced-3 or ced-4 function results in a transformation in the fates of cells that normally die; in ced-3 or ced-4 mutants, such cells instead survive and differentiate, adopting fates that in the wild type and associated with other cells. ced-3 and ced-4 mutants appear grossly normal in morphology and behavior, indicating that programmed cell death is not an essential aspect of nematode development. The genes ced-3 and ced-4 define the first known step of a developmental pathway for programmed cell death, suggesting that these genes may be involved in determining which cells die during C. elegans development.  
  Call Number Serial 1021  
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Author (up) Ensminger, A.L.; Fernandez-Juricic, E. file  url
openurl 
  Title Individual variation in cone photoreceptor density in house sparrows: implications for between-individual differences in visual resolution and chromatic contrast Type Journal Article
  Year 2014 Publication PloS one Abbreviated Journal PLoS One  
  Volume 9 Issue 11 Pages e111854  
  Keywords Animals; Cell Count; Female; Male; *Phenotype; *Retinal Cone Photoreceptor Cells; *Sparrows; Vision, Ocular  
  Abstract Between-individual variation has been documented in a wide variety of taxa, especially for behavioral characteristics; however, intra-population variation in sensory systems has not received similar attention in wild animals. We measured a key trait of the visual system, the density of retinal cone photoreceptors, in a wild population of house sparrows (Passer domesticus). We tested whether individuals differed from each other in cone densities given within-individual variation across the retina and across eyes. We further tested whether the existing variation could lead to individual differences in two aspects of perception: visual resolution and chromatic contrast. We found consistent between-individual variation in the densities of all five types of avian cones, involved in chromatic and achromatic vision. Using perceptual modeling, we found that this degree of variation translated into significant between-individual differences in visual resolution and the chromatic contrast of a plumage signal that has been associated with mate choice and agonistic interactions. However, there was no evidence for a relationship between individual visual resolution and chromatic contrast. The implication is that some birds may have the sensory potential to perform “better” in certain visual tasks, but not necessarily in both resolution and contrast simultaneously. Overall, our findings (a) highlight the need to consider multiple individuals when characterizing sensory traits of a species, and (b) provide some mechanistic basis for between-individual variation in different behaviors (i.e., animal personalities) and for testing the predictions of several widely accepted hypotheses (e.g., honest signaling).  
  Call Number Serial 2064  
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Author (up) Finkel, S.E. file  url
openurl 
  Title Long-term survival during stationary phase: evolution and the GASP phenotype Type Journal Article
  Year 2006 Publication Nature Reviews. Microbiology Abbreviated Journal Nat Rev Microbiol  
  Volume 4 Issue 2 Pages 113-120  
  Keywords Bacteria/*genetics/*growth & development; *Evolution, Molecular; Genetic Variation; Mutation; Phenotype; SOS Response (Genetics); Selection, Genetic  
  Abstract The traditional view of the stationary phase of the bacterial life cycle, obtained using standard laboratory culture practices, although useful, might not always provide us with the complete picture. Here, the traditional three phases of the bacterial life cycle are expanded to include two additional phases: death phase and long-term stationary phase. In many natural environments, bacteria probably exist in conditions more akin to those of long-term stationary-phase cultures, in which the expression of a wide variety of stress-response genes and alternative metabolic pathways is essential for survival. Furthermore, stressful environments can result in selection for mutants that express the growth advantage in stationary phase (GASP) phenotype.  
  Call Number Serial 1555  
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Author (up) Finkel, S.E. file  url
openurl 
  Title Long-term survival during stationary phase: evolution and the GASP phenotype Type Journal Article
  Year 2006 Publication Nature Reviews. Microbiology Abbreviated Journal Nat Rev Microbiol  
  Volume 4 Issue 2 Pages 113-120  
  Keywords Bacteria/*genetics/*growth & development; *Evolution, Molecular; Genetic Variation; Mutation; Phenotype; SOS Response (Genetics); Selection, Genetic  
  Abstract The traditional view of the stationary phase of the bacterial life cycle, obtained using standard laboratory culture practices, although useful, might not always provide us with the complete picture. Here, the traditional three phases of the bacterial life cycle are expanded to include two additional phases: death phase and long-term stationary phase. In many natural environments, bacteria probably exist in conditions more akin to those of long-term stationary-phase cultures, in which the expression of a wide variety of stress-response genes and alternative metabolic pathways is essential for survival. Furthermore, stressful environments can result in selection for mutants that express the growth advantage in stationary phase (GASP) phenotype.  
  Call Number Serial 1581  
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