Browsing Genetics (Scholarly Publications) by Sponsor "Science Foundation Ireland"
Now showing items 1-20 of 40
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AAV-PHP.eB transduces both the inner and outer retina with high efficacy in mice
(2022)Recombinant adeno-associated virus (AAV) vectors are one of the main gene delivery vehicles used in retinal gene therapy ap proaches; however, there is a need to further improve the effi cacy, tropism, and safety of these ... -
Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome.
(PLoS, 2009)Comparative genomics can be used to infer the history of genomic rearrangements that occurred during the evolution of a species. We used the principle of parsimony, applied to aligned synteny blocks from 11 yeast species, ... -
Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser.
(BioMed Central, 2010)Background: Candida species are the most common cause of opportunistic fungal infection worldwide. Recent sequencing efforts have provided a wealth of Candida genomic data. We have developed the Candida Gene Order Browser ... -
Changes in alternative splicing of human and mouse genes are accompanied by faster evolution of constitutive exons
(Oxford University Press, 2005)Alternative splicing is known to be an important source of protein sequence variation, but its evolutionary impact has not been explored in detail. Studying alternative splicing requires extensive sampling of the transcriptome, ... -
Chromosomal G + C content evolution in yeasts: systematic interspecies differences, and GC-poor troughs at centromeres.
(2010)The G + C content at synonymous codon positions (GC3s) in genes varies along chromosomes in most eukaryotes. In Saccharomyces cerevisiae, regions of high GC3s are correlated with recombination hot spots, probably due to ... -
Clusters of co-expressed genes in mammalian genomes are conserved by natural selection
(Oxford University Press, 2005)Genes that belong to the same functional pathways are often packaged into operons in prokaryotes. However, aside from examples in nematode genomes, this form of transcriptional regulation appears to be absent in eukaryotes. ... -
Complete DNA sequences of the mitochondrial genomes of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis: Insight into the evolution of linear DNA genomes from mitochondrial telomere mutants.
(Oxford University Press, 2006)We determined complete mitochondrial DNA sequences of the two yeast species, Candida orthopsilosis and Candida metapsilosis, and compared them with the linear mitochondrial genome of their close relative, C.parapsilosis. ... -
Detailed analysis of an enriched deep intronic ABCA4 variant in Irish Stargardt disease patients
(2023)Over 15% of probands in a large cohort of more than 1500 inherited retinal degeneration patients present with a clinical diagnosis of Stargardt disease (STGD1), a recessive form of macular dystrophy caused by biallelic ... -
Elusive origins of the extra genes in Aspergillus oryzae
(PLoS, 2008)The genome sequence of Aspergillus oryzae revealed unexpectedly that this species has approximately 20% more genes than its congeneric species A. nidulans and A. fumigatus. Where did these extra genes come from? Here, we ... -
Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi
(BioMed Central, 2008)Background Filamentous fungi synthesize many secondary metabolites and are rich in genes encoding proteins involved in their biosynthesis. Genes from the same pathway are often clustered and co-expressed in particular ... -
Evidence from comparative genomics for a complete sexual cycle in the "asexual" pathogenic yeast Candida glabrata
(BioMed Central, 2003)BACKGROUND: Candida glabrata is a pathogenic yeast of increasing medical concern. It has been regarded as asexual since it was first described in 1917, yet phylogenetic analyses have revealed that it is more closely related ... -
Evolutionary erosion of yeast sex chromosomes by mating-type switching accidents
(National Academy of Sciences, 2011)We investigate yeast sex chromosome evolution by comparing genome sequences from 16 species in the family Saccharomycetaceae, including data from genera Tetrapisispora, Kazachstania, Naumovozyma, and Torulaspora. We show ... -
A Family of Vertebrate-Specific Polycombs Encoded by the LCOR/LCORL Genes Balance PRC2 Subtype Activities
(2018)The polycomb repressive complex 2 (PRC2) consists of core subunits SUZ12, EED, RBBP4/7, and EZH1/2 and is responsible for mono-, di-, and tri-methylation of lysine 27 on histone H3. Whereas two distinct forms exist, PRC2.1 ... -
Fourfold faster rate of genome rearrangement in nematodes than in Drosophila
(2002)We compared the genome of the nematode Caenorhabditis elegans to 13% of that of Caenorhabditis briggsae, identifying 252 conserved segments along their chromosomes. We detected 517 chromosomal rearrangements, with the ratio ... -
Functional Partitioning of Yeast Co-Expression Networks after Genome Duplication
(Public Library of Science, 2006)Several species of yeast, including the baker?s yeast Saccharomyces cerevisiae, underwent a genome duplication roughly 100 million years ago. We analyze genetic networks whose members were involved in this duplication. ... -
Genome survey sequencing of the wine spoilage yeast Dekkera (Brettanomyces) bruxellensis.
(American Society for Microbiology, 2007)The hemiascomycete yeast Dekkera bruxellensis, also known as Brettanomyces bruxellensis, is a major cause of wine spoilage worldwide. Wines infected with D. bruxellensis develop distinctive, unpleasant aromas due to volatile ... -
IL-33 deficiency causes persistent inflammation and severe neurodegeneration in retinal detachment
(2019)Background: Interleukin-33 (IL-33) belongs to the IL-1 cytokine family and resides in the nuclei of various cell types. In the neural retina, IL-33 is predominately expressed in Müller cells although its role in health ... -
Increased glycolytic flux as an outcome of whole-genome duplication in yeast
(BioMed Central, 2007)After whole-genome duplication (WGD), deletions return most loci to single copy. However, duplicate loci may survive through selection for increased dosage. Here, we show how the WGD increased copy number of some glycolytic ...