G3: Genes, Genomes, Genetics current issue
- Tissue-Specific Transcriptomes Reveal Gene Expression Trajectories in Two Maturing Skin Epithelial Layers in Zebrafish EmbryosEpithelial cells are the building blocks of many organs, including skin. The vertebrate skin initially consists of two epithelial layers, the outer periderm and inner basal cell layers, which have distinct properties, functions, and fates. The embryonic periderm ultimately disappears during development, whereas basal cells proliferate to form the mature, stratified epidermis. Although much is known about mechanisms of homeostasis in mature skin,
- Genomic Prediction Including SNP-Specific Variance PredictorsThe increasing amount of available biological information on the markers can be used to inform the models applied for genomic selection to improve predictions. The objective of this study was to propose a general model for genomic selection using a link function approach within the hierarchical generalized linear model framework (hglm) that can include external information on the markers. These models can be fitted using the well-established hglm
- Greenlip Abalone (Haliotis laevigata) Genome and Protein Analysis Provides Insights into Maturation and SpawningWild abalone (Family Haliotidae) populations have been severely affected by commercial fishing, poaching, anthropogenic pollution, environment and climate changes. These issues have stimulated an increase in aquaculture production; however production growth has been slow due to a lack of genetic knowledge and resources. We have sequenced a draft genome for the commercially important temperate Australian ‘greenlip’ abalone (Haliotis laevigata, Don
- IslandCafe: Compositional Anomaly and Feature Enrichment Assessment for Delineation of Genomic IslandsOne of the evolutionary forces driving bacterial genome evolution is the acquisition of clusters of genes through horizontal gene transfer (HGT). These genomic islands may confer adaptive advantages to the recipient bacteria, such as, the ability to thwart antibiotics, become virulent or hypervirulent, or acquire novel metabolic traits. Methods for detecting genomic islands either search for markers or features typical of islands or examine anoma
- De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneriCotton is an agriculturally important crop. Because of its importance, a genome sequence of a diploid cotton species (Gossypium raimondii, D-genome) was first assembled using Sanger sequencing data in 2012. Improvements to DNA sequencing technology have improved accuracy and correctness of assembled genome sequences. Here we report a new de novo genome assembly of G. raimondii and its close relative G. turneri. The two genomes were assembled to a
- A Bayesian Genomic Multi-output Regressor Stacking Model for Predicting Multi-trait Multi-environment Plant Breeding DataIn this paper we propose a Bayesian multi-output regressor stacking (BMORS) model that is a generalization of the multi-trait regressor stacking method. The proposed BMORS model consists of two stages: in the first stage, a univariate genomic best linear unbiased prediction (GBLUP including genotype x environment interaction GE) model is implemented for each of the traits under study; then the predictions of all traits are included as covariates
- An RNAi Screen for Genes Required for Growth of Drosophila Wing TissueCell division and tissue growth must be coordinated with development. Defects in these processes are the basis for a number of diseases, including developmental malformations and cancer. We have conducted an unbiased RNAi screen for genes that are required for growth in the Drosophila wing, using GAL4-inducible short hairpin RNA (shRNA) fly strains made by the Drosophila RNAi Screening Center. shRNA expression down the center of the larval wing d
- Destabilization of the Tumor-Inducing Plasmid from an Octopine-Type Agrobacterium tumefaciens Lineage Drives a Large Deletion in the Co-resident At MegaplasmidBacteria with multi-replicon genome organizations, including members of the family Rhizobiaceae, often carry a variety of niche-associated functions on large plasmids. While evidence exists for cross-replicon interactions and co-evolution between replicons in many of these systems, remarkable strain-to-strain variation is also observed for extrachromosomal elements, suggesting increased genetic plasticity. Here, we show that curing of the tumor-i
- micRocounter: Microsatellite Characterization in Genome AssembliesMicrosatellites are repetitive DNA sequences usually found in non-coding regions of the genome. Their quantification and analysis have applications in fields from population genetics to evolutionary biology. As genome assemblies become commonplace, the need for software that can facilitate analyses has never been greater. In particular, R packages that can analyze genomic data are particularly important since this is one of the most popular softw
- Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov ModelsModern SNP genotyping technologies allow measurement of the relative abundance of different alleles for a given locus and consequently estimation of their allele dosage, opening a new road for genetic studies in autopolyploids. Despite advances in genetic linkage analysis in autotetraploids, there is a lack of statistical models to perform linkage analysis in organisms with higher ploidy levels. In this paper, we present a statistical method to e
- Programmed Chromosome Deletion in the Ciliate Oxytricha trifallaxThe ciliate Oxytricha trifallax contains two nuclei: a germline micronucleus and a somatic macronucleus. These two nuclei diverge significantly in genomic structure. The micronucleus contains approximately 100 chromosomes of megabase scale, while the macronucleus contains 16,000 gene-sized, high ploidy "nanochromosomes." During its sexual cycle, a copy of the zygotic germline micronucleus develops into a somatic macronucleus via DNA excision and
- Exon 3 of the NUMB Gene Emerged in the Chordate Lineage Coopting the NUMB Protein to the Regulation of MDM2MDM2 regulates a variety of cellular processes through its dual protein:protein interaction and ubiquitin ligase activities. One major function of MDM2 is to bind and ubiquitinate P53, thereby regulating its proteasomal degradation. This function is in turn controlled by the cell fate determinant NUMB, which binds to and inhibits MDM2 via a short stretch of 11 amino acids, contained in its phosphotyrosine-binding (PTB) domain, encoded by exon 3 o
- Transformation with Artificial Chromosomes in Oxytricha trifallax and Their ApplicationsOxytricha trifallax, like other ciliates, has separate germline and somatic nuclei. The diploid germline genome in the micronucleus is composed of long conventional chromosomes. The macronucleus contains a somatic genome which is naturally fragmented into thousands of kilobase-sized chromosomes. Here, we develop a method to stably incorporate artificial chromosomes into the macronucleus. We report two cases of successful transformation and demons
- Utilization of Tissue Ploidy Level Variation in de Novo Transcriptome Assembly of Pinus sylvestrisCompared to angiosperms, gymnosperms lag behind in the availability of assembled and annotated genomes. Most genomic analyses in gymnosperms, especially conifer tree species, rely on the use of de novo assembled transcriptomes. However, the level of allelic redundancy and transcript fragmentation in these assembled transcriptomes, and their effect on downstream applications have not been fully investigated. Here, we assessed three assembly strate
- QTG-Finder: A Machine-Learning Based Algorithm To Prioritize Causal Genes of Quantitative Trait Loci in Arabidopsis and RiceLinkage mapping is one of the most commonly used methods to identify genetic loci that determine a trait. However, the loci identified by linkage mapping may contain hundreds of candidate genes and require a time-consuming and labor-intensive fine mapping process to find the causal gene controlling the trait. With the availability of a rich assortment of genomic and functional genomic data, it is possible to develop a computational method to faci
- Genomic Data Reveal Conserved Female Heterogamety in Giant Salamanders with Gigantic Nuclear GenomesSystems of genetic sex determination and the homology of sex chromosomes in different taxa vary greatly across vertebrates. Much progress remains to be made in understanding systems of genetic sex determination in non-model organisms, especially those with homomorphic sex chromosomes and/or large genomes. We used reduced representation genome sequencing to investigate genetic sex determination systems in the salamander family Cryptobranchidae (ge
- Genome-Wide Association and Gene Co-expression Network Analyses Reveal Complex Genetics of Resistance to Gosss Wilt of MaizeGoss’s bacterial wilt and leaf blight is a disease of maize caused by the gram positive bacterium Clavibacter michiganensis subsp. nebraskensis (Cmn). First discovered in Nebraska, Goss’s wilt has now spread to major maize growing states in the United States and three provinces in Canada. Previous studies conducted using elite maize inbred lines and their hybrids have shown that resistance to Goss’s wilt is a quantitative trait. The objective of
- Whole Genome Sequence of the Commercially Relevant Mushroom Strain Agaricus bisporus var. bisporus ARP23Agaricus bisporus is an extensively cultivated edible mushroom. Demand for cultivation is continuously growing and difficulties associated with breeding programs now means strains are effectively considered monoculture. While commercial growing practices are highly efficient and tightly controlled, the over-use of a single strain has led to a variety of disease outbreaks from a range of pathogens including bacteria, fungi and viruses. To address
- Multi-trait Improvement by Predicting Genetic Correlations in Breeding CrossesThe many quantitative traits of interest to plant breeders are often genetically correlated, which can complicate progress from selection. Improving multiple traits may be enhanced by identifying parent combinations – an important breeding step – that will deliver more favorable genetic correlations (rG). Modeling the segregation of genomewide markers with estimated effects may be one method of predicting rG in a cross, but this approach remains
- Comparative Transcriptomic Analysis Reveals Molecular Profiles of Central Nervous System in Maternal Diapause Induction of Locusta migratoriaEgg diapause in Locusta migratoria L. (Orthoptera: Acridoidea) is believed to be influenced by maternal photoperiod. However, the molecular mechanism regulating the phenomenon of maternal diapause induction is unclear. Here we performed transcriptomic analyses from the central nervous system (CNS) of migratory locusts under long and short photoperiods to identify differentially expressed genes (DEGs) related to diapause induction. There were tota
- Genome Size Evolution Differs Between Drosophila Subgenera with Striking Differences in Male and Female Genome Size in SophophoraGenome size varies across the tree of life, with no clear correlation to organismal complexity or coding sequence, but with differences in non-coding regions. Phylogenetic methods have recently been incorporated to further disentangle this enigma, yet most of these studies have focused on widely diverged species. Few have compared patterns of genome size change in closely related species with known structural differences in the genome. As a conse
- Disease Resistance Genetics and Genomics in Octoploid StrawberryOctoploid strawberry (Fragaria xananassa) is a valuable specialty crop, but profitable production and availability are threatened by many pathogens. Efforts to identify and introgress useful disease resistance genes (R-genes) in breeding programs are complicated by strawberry’s complex octoploid genome. Recently-developed resources in strawberry, including a complete octoploid reference genome and high-resolution octoploid genotyping, enable new
- Elucidating Drought Stress Tolerance in European Oaks Through Cross-Species TranscriptomicsThe impact of climate change that comes with a dramatic increase of long periods of extreme summer drought associated with heat is a fundamental challenge for European forests. As a result, forests are expected to shift their distribution patterns toward north-east, which may lead to a dramatic loss in value of European forest land. Consequently, unraveling key processes that underlie drought stress tolerance is not only of great scientific but a
- Alternative Lengthening of Telomeres in the Budding Yeast Naumovozyma castelliiThe enzyme telomerase ensures the integrity of linear chromosomes by maintaining telomere length. As a hallmark of cancer, cell immortalization and unlimited proliferation is gained by reactivation of telomerase. However, a significant fraction of cancer cells instead uses alternative telomere lengthening mechanisms to ensure telomere function, collectively known as Alternative Lengthening of Telomeres (ALT). Although the budding yeast Naumovozym
- Positive Selection and Functional Divergence at Meiosis Genes That Mediate Crossing Over Across the Drosophila PhylogenyMeiotic crossing over ensures proper segregation of homologous chromosomes and generates genotypic diversity. Despite these functions, little is known about the genetic factors and population genetic forces involved in the evolution of recombination rate differences among species. The dicistronic meiosis gene, mei-217/mei-218, mediates most of the species differences in crossover rate and patterning during female meiosis between the closely relat
- Predicting Longitudinal Traits Derived from High-Throughput Phenomics in Contrasting Environments Using Genomic Legendre Polynomials and B-SplinesRecent advancements in phenomics coupled with increased output from sequencing technologies can create the platform needed to rapidly increase abiotic stress tolerance of crops, which increasingly face productivity challenges due to climate change. In particular, high-throughput phenotyping (HTP) enables researchers to generate large-scale data with temporal resolution. Recently, a random regression model (RRM) was used to model a longitudinal ri
- Fine Mapping Using Whole-Genome Sequencing Confirms Anti-Müllerian Hormone as a Major Gene for Sex Determination in Farmed Nile Tilapia (Oreochromis niloticus L.)Nile tilapia (Oreochromis niloticus) is one of the most cultivated and economically important species in world aquaculture. Intensive production promotes the use of monosex animals, due to an important dimorphism that favors male growth. Currently, the main mechanism to obtain all-male populations is the use of hormones in feeding during larval and fry phases. Identifying genomic regions associated with sex determination in Nile tilapia is a rese
- Evolutionary Dynamics in Structured Populations Under Strong Population Genetic ForcesIn the long-term neutral equilibrium, high rates of migration between subpopulations result in little population differentiation. However, in the short-term, even very abundant migration may not be enough for subpopulations to equilibrate immediately. In this study, we investigate dynamical patterns of short-term population differentiation in adapting populations via stochastic and analytical modeling through time. We characterize a regime in whi
- Phylogenetic Reclassification of Vertebrate Melatonin Receptors To Include Mel1dThe circadian and seasonal actions of melatonin are mediated by high affinity G-protein coupled receptors (melatonin receptors, MTRs), classified into phylogenetically distinct subtypes based on sequence divergence and pharmacological characteristics. Three vertebrate MTR subtypes are currently described: MT1 (MTNR1A), MT2 (MTNR1B), and Mel1c (MTNR1C / GPR50), which exhibit distinct affinities, tissue distributions and signaling properties. We pr
- Environmental Association Identifies Candidates for Tolerance to Low Temperature and DroughtBarley (Hordeum vulgare ssp. vulgare) is cultivated from the equator to the Arctic Circle. The wild progenitor species, Hordeum vulgare ssp. spontaneum, occupies a relatively narrow latitudinal range (~30 - 40° N) primarily at low elevation (< 1,500 m). Adaptation to the range of cultivation has occurred over ~8,000 years. The genetic basis of adaptation is amenable to study through environmental association. An advantage of environmental associa
- Exclusion and Genomic Relatedness Methods for Assignment of Parentage Using Genotyping-by-Sequencing DataGenotypes are often used to assign parentage in agricultural and ecological settings. Sequencing can be used to obtain genotypes but does not provide unambiguous genotype calls, especially when sequencing depth is low in order to reduce costs. In that case, standard parentage analysis methods no longer apply. A strategy for using low-depth sequencing data for parentage assignment is developed here. It entails the use of relatedness estimates alon
- Involvement of a G Protein Regulatory Circuit in Alternative Oxidase Production in Neurospora crassaThe Neurospora crassa nuclear aod-1 gene encodes an alternative oxidase that functions in mitochondria. The enzyme provides a branch from the standard electron transport chain by transferring electrons directly from ubiquinol to oxygen. In standard laboratory strains, aod-1 is transcribed at very low levels under normal growth conditions. However, if the standard electron transport chain is disrupted, aod-1 mRNA expression is induced and the AOD1
- In Silico Karyotyping of Chromosomally Polymorphic Malaria Mosquitoes in the Anopheles gambiae ComplexChromosomal inversion polymorphisms play an important role in adaptation to environmental heterogeneities. For mosquito species in the Anopheles gambiae complex that are significant vectors of human malaria, paracentric inversion polymorphisms are abundant and are associated with ecologically and epidemiologically important phenotypes. Improved understanding of these traits relies on determining mosquito karyotype, which currently depends upon la
- Population Selection and Sequencing of Caenorhabditis elegans Wild Isolates Identifies a Region on Chromosome III Affecting Starvation ResistanceTo understand the genetic basis of complex traits, it is important to be able to efficiently phenotype many genetically distinct individuals. In the nematode Caenorhabditis elegans, individuals have been isolated from diverse populations around the globe and whole-genome sequenced. As a result, hundreds of wild strains with known genome sequences can be used for genome-wide association studies (GWAS). However, phenotypic analysis of these strains
- De Novo Genome Assembly and Comparative Genomics of the Barley Leaf Rust Pathogen Puccinia hordei Identifies Candidates for Three Avirulence GenesPuccinia hordei (Ph) is a damaging pathogen of barley throughout the world. Despite its importance, almost nothing is known about the genomics of this pathogen, and a reference genome is lacking. In this study, the first reference genome was assembled for an Australian isolate of Ph ("Ph560") using long-read SMRT sequencing. A total of 838 contigs were assembled, with a total size of 207 Mbp. This included both haplotype collapsed and separated r
- Overexpression of BnaAOX1b Confers Tolerance to Osmotic and Salt Stress in RapeseedAlternative oxidases (AOXs) are the terminal oxidase in the cyanide-resistant respiration pathway in plant mitochondria, which play an important role in abiotic stress and are proposed as a functional marker for high tolerant breeding. In this study, ten AOX genes (BnaAOXs) were identified, and CysI and CysII of AOX isoforms were highly conserved in rapeseed. Among them, Bna.AOX1b was mainly expressed in the ovule and displayed varying expression
Clinical Oral Implants Research
Medicine by Alexandros G. Sfakianakis,Anapafseos 5 Agios Nikolaos 72100 Crete Greece,00302841026182,00306932607174,alsfakia@gmail.com,
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Τρίτη 8 Οκτωβρίου 2019
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Medicine by Alexandros G. Sfakianakis,Anapafseos 5 Agios Nikolaos 72100 Crete Greece,00302841026182,00306932607174,alsfakia@gmail.com,
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00302841026182,
00306932607174,
alsfakia@gmail.com,
Anapafseos 5 Agios Nikolaos 72100 Crete Greece,
Medicine by Alexandros G. Sfakianakis
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