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Showing papers by "Stephen J. O'Brien published in 2009"


Journal ArticleDOI
TL;DR: A precipitous drop in costs and increase in sequencing efficiency is anticipated, with concomitant development of improved annotation technology, and it is proposed to create a collection of tissue and DNA specimens for 10,000 vertebrate species specifically designated for whole-genome sequencing in the very near future.
Abstract: American Genetic Association, Gordon and Betty Moore Foundation, NHGRI Intramural Sequencing Center, and UCSC Alumni Association to cost of the Genome 10K workshop; Howard Hughes Medical Institute to D. H.; Gordon and Betty Moore Foundation to S. C. S.; A

545 citations


Journal Article
01 Jan 2009-PLOS ONE
TL;DR: The authors performed a genome-wide association study in a cohort of 2,554 infected Caucasian subjects and found common genetic variants explaining down to 1.3% of the variability in viral load at set point.
Abstract: To extend the understanding of host genetic determinants of HIV-1 control, we performed a genome-wide association study in a cohort of 2,554 infected Caucasian subjects. The study was powered to detect common genetic variants explaining down to 1.3% of the variability in viral load at set point. We provide overwhelming confirmation of three associations previously reported in a genome-wide study and show further independent effects of both common and rare variants in the Major Histocompatibility Complex region (MHC). We also examined the polymorphisms reported in previous candidate gene studies and fail to support a role for any variant outside of the MHC or the chemokine receptor cluster on chromosome 3. In addition, we evaluated functional variants, copy-number polymorphisms, epistatic interactions, and biological pathways. This study thus represents a comprehensive assessment of common human genetic variation in HIV-1 control in Caucasians.

395 citations


Journal ArticleDOI
TL;DR: This study provides overwhelming confirmation of three associations previously reported in a genome-wide study and shows further independent effects of both common and rare variants in the Major Histocompatibility Complex region (MHC).
Abstract: To extend the understanding of host genetic determinants of HIV-1 control, we performed a genome-wide association study in a cohort of 2,554 infected Caucasian subjects. The study was powered to detect common genetic variants explaining down to 1.3% of the variability in viral load at set point. We provide overwhelming confirmation of three associations previously reported in a genome-wide study and show further independent effects of both common and rare variants in the Major Histocompatibility Complex region (MHC). We also examined the polymorphisms reported in previous candidate gene studies and fail to support a role for any variant outside of the MHC or the chemokine receptor cluster on chromosome 3. In addition, we evaluated functional variants, copy-number polymorphisms, epistatic interactions, and biological pathways. This study thus represents a comprehensive assessment of common human genetic variation in HIV-1 control in Caucasians.

388 citations


Journal ArticleDOI
TL;DR: The first domestic cats had limited utility and initiated their domestication among the earliest agricultural Neolithic settlements in the Near East as mentioned in this paper, and their evolution to companion animals was initially a process of natural, rather than artificial, selection over time driven during their sympatry with forbear wildcats.
Abstract: Artificial selection is the selection of advantageous natural variation for human ends and is the mechanism by which most domestic species evolved. Most domesticates have their origin in one of a few historic centers of domestication as farm animals. Two notable exceptions are cats and dogs. Wolf domestication was initiated late in the Mesolithic when humans were nomadic hunter-gatherers. Those wolves less afraid of humans scavenged nomadic hunting camps and over time developed utility, initially as guards warning of approaching animals or other nomadic bands and soon thereafter as hunters, an attribute tuned by artificial selection. The first domestic cats had limited utility and initiated their domestication among the earliest agricultural Neolithic settlements in the Near East. Wildcat domestication occurred through a self-selective process in which behavioral reproductive isolation evolved as a correlated character of assortative mating coupled to habitat choice for urban environments. Eurasian wildcats initiated domestication and their evolution to companion animals was initially a process of natural, rather than artificial, selection over time driven during their sympatry with forbear wildcats.

388 citations


Journal ArticleDOI
TL;DR: In vitro analysis of active phosphate transport in ileum segments isolated from wild-type or Npt2b(-/-) mice demonstrated that NPT2b contributes to >90% of total active phosphate absorption, confirming a major role of this transporter in phosphate regulation.
Abstract: Intestinal phosphate absorption occurs through both a paracellular mechanism involving tight junctions and an active transcellular mechanism involving the type II sodium-dependent phosphate cotransporter NPT2b (SLC34a2). To define the contribution of NPT2b to total intestinal phosphate absorption, we generated an inducible conditional knockout mouse, Npt2b(-/-) (Npt2b(fl/fl):Cre(+/-)). Npt2b(-/-) animals had increased fecal phosphate excretion and hypophosphaturia, but serum phosphate remained unchanged. Decreased urinary phosphate excretion correlated with reduced serum levels of the phosphaturic hormone FGF23 and increased protein expression of the renal phosphate transporter Npt2a. These results demonstrate that the absence of Npt2b triggers compensatory renal mechanisms to maintain phosphate homeostasis. In animals fed a low phosphate diet followed by acute administration of a phosphate bolus, Npt2b(-/-) animals absorbed approximately 50% less phosphate than wild-type animals, confirming a major role of this transporter in phosphate regulation. In vitro analysis of active phosphate transport in ileum segments isolated from wild-type or Npt2b(-/-) mice demonstrated that Npt2b contributes to >90% of total active phosphate absorption. In summary, Npt2b is largely responsible for intestinal phosphate absorption and contributes to the maintenance of systemic phosphate homeostasis.

299 citations


Journal ArticleDOI
TL;DR: Guidelines for Naming Nonprimate APOBEC3 Genes and Proteins Rebecca S. LaRue, Valgerdur Andresdottir, Yannick Blanchard, Silvestro G. Conticello, and Simon Wain-Hobson are presented.
Abstract: Guidelines for Naming Nonprimate APOBEC3 Genes and Proteins Rebecca S. LaRue, Valgerdur Andresdottir, Yannick Blanchard, Silvestro G. Conticello, David Derse, Michael Emerman, Warner C. Greene, Stefan R. Jonsson, Nathaniel R. Landau, Martin Lochelt, Harmit S. Malik, Michael H. Malim, Carsten Munk, Stephen J. O’Brien, Vinay K. Pathak, Klaus Strebel, Simon Wain-Hobson, Xiao-Fang Yu, Naoya Yuhki, and Reuben S. Harris*

223 citations


Journal ArticleDOI
TL;DR: This work has shown that high-resolution physical maps of vertebrate species’ chromosomes empower comparative genomics discovery and are indispensable for sequence assembly precision.
Abstract: High-resolution physical maps of vertebrate species’ chromosomes empower comparative genomics discovery and are indispensable for sequence assembly precision. Beginning in 2003, the NIH–NHGRI launched an initiative that designated 24 species of mammals for low-coverage whole-genome sequencing in order to provide evolutionary context to human genome annotation (Green 2007) (http://www.genome.gov/25521745). Four principal goals were anticipated for the bold sequencing initiative: (1) to discover evolutionarily conserved sequence motifs, particularly outside of protein-coding genes, which are responsible for regulatory and other critical genomic functions; (2) to provide a framework for reconstruction of genome organization, content, and dynamics that have occurred during the mammalian radiations; (3) to empower new models of human disease and heritable phenotypes; and (4) to provide a starting point for assessment of the expansion, contraction, and adaptation of gene families in different evolutionary lineages.

157 citations


Journal ArticleDOI
TL;DR: A case‐control study in Guangxi Province of Southern China in 2004–2005 assessed the contribution of EBV/IgA/VCA antibody serostatus to NPC risk—32.2% of NPC can be explained by IgA+ status, however, family history and environmental risk factors cumulatively explained only 2.7% of NPCs development in NPC high risk population.
Abstract: To understand the role of environmental and genetic influences on nasopharyngeal carcinoma (NPC) in populations at high risk of NPC, we have performed a case-control study in Guangxi Province of Southern China in 2004-2005. NPC cases (n = 1,049) were compared with 785 NPC-free matched controls who were seropositive for IgA antibodies (IgA) to Epstein-Barr virus (EBV) capsid antigen (VCA)-a predictive marker for NPC in Chinese populations. A questionnaire was used to capture exposure and NPC family history data. Risk factors associated with NPC in a multivariant analysis model were the following: (i) a first, second or third degree relative with NPC [attributable risk (AR)= 6%, odds ratio (OR) = 3.1, 95% confidence interval (CI) = 2.0-4.9, p 0.05). We also assessed the contribution of EBV/IgA/VCA antibody serostatus to NPC risk-32.2% of NPC can be explained by IgA+ status. However, family history and environmental risk factors cumulatively explained only 2.7% of NPC development in NPC high risk population. These findings should have important public health implications for NPC risk reduction in endemic regions.

144 citations


Journal ArticleDOI
TL;DR: Findings suggest that cat domestication began in the Fertile Crescent, perhaps around 10,000 years ago, when agriculture was getting under way and cats started making themselves at home around people to take advantage of the mice and food scraps found in their settlements.
Abstract: Unlike other domesticated creatures, the house cat contributes little to human survival. Researchers have therefore wondered how and why cats came to live among people. Experts traditionally thought that the Egyptians were the first to domesticate the cat, some 3,600 years ago. But recent genetic and archaeological discoveries indicate that cat domestication began in the Fertile Crescent, perhaps around 10,000 years ago, when agriculture was getting under way. The findings suggest that cats started making themselves at home around people to take advantage of the mice and food scraps found in their settlements.

117 citations


Journal ArticleDOI
TL;DR: Coronavirus sequence analyses demonstrate distinctive circulating strains in natural populations that are distinct from other coronavirus strains found in the wild.
Abstract: Feline coronavirus (FCoV) is endemic in feral cat populations and cat colonies, frequently preceding outbreaks of fatal feline infectious peritonitis (FIP). FCoV exhibits 2 biotypes: the pathogenic disease and a benign infection with feline enteric coronavirus (FECV). Uncertainty remains regarding whether genetically distinctive avirulent and virulent forms coexist or whether an avirulent form mutates in vivo, causing FIP. To resolve these alternative hypotheses, we isolated viral sequences from FCoV-infected clinically healthy and sick cats (8 FIP cases and 48 FECV-asymptomatic animals); 735 sequences from 4 gene segments were generated and subjected to phylogenetic analyses. Viral sequences from healthy cats were distinct from sick cats on the basis of genetic distances observed in the membrane and nonstructural protein 7b genes. These data demonstrate distinctive circulating virulent and avirulent strains in natural populations. In addition, 5 membrane protein amino acid residues with functional potential differentiated healthy cats from cats with FIP. These findings may have potential as diagnostic markers for virulent FIP-associated FCoV.

109 citations


Journal ArticleDOI
TL;DR: Gene Dosage Note: Letter / Comment in: Nat Med. 2009 Oct;15(10):1112-5 andNat Med. 2008 Apr;14(4):413-20 Reference EPFL-ARTICLE-165167.
Abstract: Keywords: Gene Dosage Note: Letter / Comment in: Nat Med. 2009 Oct;15(10):1112-5 and Nat Med. 2009 Oct;15(10):1127-9 and Nat Med. 2009 Oct;15(10):1117-20 / Comment on: Nat Med. 2008 Apr;14(4):413-20 Reference EPFL-ARTICLE-165167doi:10.1038/nm1009-1110 Record created on 2011-04-19, modified on 2016-08-09


Journal ArticleDOI
14 Jan 2009-PLOS ONE
TL;DR: Phylogeographic analysis with extant tiger subspecies suggests that less than 10,000 years ago the Caspian/Amur tiger ancestor colonized Central Asia via the Gansu Corridor from eastern China then subsequently traversed Siberia eastward to establish the Amur tiger in the Russian Far East.
Abstract: The Caspian tiger (Panthera tigris virgata) flourished in Central Asian riverine forest systems in a range disjunct from that of other tigers, but was driven to extinction in 1970 prior to a modern molecular evaluation. For over a century naturalists puzzled over the taxonomic validity, placement, and biogeographic origin of this enigmatic animal. Using ancient-DNA (aDNA) methodology, we generated composite mtDNA haplotypes from twenty wild Caspian tigers from throughout their historic range sampled from museum collections. We found that Caspian tigers carry a major mtDNA haplotype differing by only a single nucleotide from the monomorphic haplotype found across all contemporary Amur tigers (P. t. altaica). Phylogeographic analysis with extant tiger subspecies suggests that less than 10,000 years ago the Caspian/Amur tiger ancestor colonized Central Asia via the Gansu Corridor (Silk Road) from eastern China then subsequently traversed Siberia eastward to establish the Amur tiger in the Russian Far East. The conservation implications of these findings are far reaching, as the observed genetic depletion characteristic of modern Amur tigers likely reflects these founder migrations and therefore predates human influence. Also, due to their evolutionary propinquity, living Amur tigers offer an appropriate genetic source should reintroductions to the former range of the Caspian tiger be implemented.

Journal ArticleDOI
TL;DR: This study identified the presence of Cronobacter in dried milk and related products sourced from the Nile-Delta region of Egypt and found resistance was observed in three isolates, highlighting the risks associated with Cronobacteria contamination in foods.
Abstract: Background Cronobacter is a recently proposed genus consisting of six genomospecies that encompass the organisms previously identified as Enterobacter sakazakii. Cronobacter are opportunistic pathogens and are known to cause serious infections in infants, particularly neonates. High case fatality rates have been associated with infections and acute sequelae can occur in survivors with severe ramifications on neurological development. Infant formula has been identified as one route of transmission for infection in infants. However, the primary reservoirs for subsequent contamination of foods with Cronobacter remain undefined due to the ubiquitous nature of these organisms. More recently, infections in adults have been reported, especially amongst the elderly and patients who are immunocompromised. To help prevent the transmission of infection, it is important to identify the main food sources for Cronobacter. The aim of this study was to identify and characterize Cronobacter isolated from dried-milk and related products available in an Egyptian food market.

Journal ArticleDOI
TL;DR: The association between mitochondrial haplogroup and severity of lipoatrophy in HIV-infected European American patients on HAART in the Multicenter AIDS cohort Study found that mitochondrialhaplogroup H was strongly associated with increased atrophy.
Abstract: Although highly active antiretroviral therapy (HAART) has been extremely effective in lowering AIDS incidence among patients infected with HIV, certain drugs included in HAART can cause serious mitochondrial toxicities. One of the most frequent adverse events is lipoatrophy, which is the loss of subcutaneous fat in the face, arms, buttocks, and/or legs as an adverse reaction to nucleoside reverse transcriptase inhibitors. The clinical symptoms of lipoatrophy resemble those of inherited mitochondrial diseases, which suggest that host mitochondrial genotype may play a role in susceptibility. We analyzed the association between mitochondrial haplogroup and severity of lipoatrophy in HIV-infected European American patients on HAART in the Multicenter AIDS cohort Study and found that mitochondrial haplogroup H was strongly associated with increased atrophy [arms: P = 0.007, odds ratio (OR) = 1.77, 95% confidence interval (CI) = 1.17 to 2.69; legs: P = 0.037, OR = 1.54, 95% CI = 1.03 to 2.31; and buttocks: P = 0.10, OR = 1.41 95% CI = 0.94 to 2.12]. We also saw borderline significance for haplogroup T as protective against lipoatrophy (P = 0.05, OR = 0.52, 95% CI = 0.20 to 1.00). These data suggest that mitochondrial DNA haplogroup may influence the propensity for lipoatrophy in patients receiving nucleoside reverse transcriptase inhibitors.

Journal ArticleDOI
20 Jul 2009-Virology
TL;DR: It is concluded that over time FIVple infections in free-ranging lions can lead to adverse clinical, immunological, and pathological outcomes in some individuals that parallel sequelae caused by lentivirus infection in humans (HIV), Asian macaques (SIV) and domestic cats (FIVfca).


Journal ArticleDOI
TL;DR: An ethical quandary is emerging over custodianship of and access to DNA specimens and attached data, clinical and genetic, held in large disease cohort collections in order to realize the promise of gene association studies of complex human disease.
Abstract: An ethical quandary is emerging over custodianship of and access to DNA specimens and attached data, clinical and genetic, held in large disease cohort collections. The balance of patients' rights and science/society's quest for broad open access must be resolved in order to realize the promise of gene association studies of complex human disease. A way forward may be to convene a colloquium of international medical and science organizations charged with developing global consensus guidance and ethical principles for access to and use of genomic biobanks.

Journal Article
TL;DR: Genetic and archaeological findings hint that wildcats became house cats earlier than previously thought as discussed by the authors, and in a different place than previously believed in the wildcat gene pool, where wildcat became house cat earlier.
Abstract: Genetic and archaeological findings hint that wildcats became house cats earlier—and in a different place—than previously thought

Journal ArticleDOI
01 Apr 2009-Genomics
TL;DR: The present version of an autosomal genetic linkage map of the domestic cat represents a marked improvement over previous cat linkage maps as it nearly doubles the number of markers that were present in the second-generation linkage map in the cat, and provides a linkage map generated in a domestic cat pedigree which will more accurately reflect recombination distances.

Journal ArticleDOI
TL;DR: A haplotype trend regression confirmed that individuals carrying the low-producing ATA-inclusive haplotypes in European Americans progress to AIDS faster, and most likely explain the role of IL10.
Abstract: Interleukin-10 (IL-10) is a pleiotropic cytokine with both immunosuppressive and immunostimulatory functions. Its roles in infections and autoimmunity may have resulted in selective pressures on polymorphisms within the gene, leading to genomic coexistence of several semi-conserved haplotypes involved with diverse pathogen interactions during genomic evolution. Previous studies focused either exclusively on promoter haplotypes or on individual SNPs. We genotyped 21 single nucleotide polymorphisms in the human IL10 gene and examined this variation compared to other mammalian species sequences. Haplotype heterogeneity in human populations is centered around ‘classic’ ‘proximal’ promoter polymorphisms: −592, −819 and −1082. High-producing GCC haplotypes are by far the most numerous and diverse group, the intermediate IL-10 producing ACC-inclusive haplotypes seem to be related most closely to the ancestral haplotype, and the ATA-inclusive haplotypes cluster a separate branch with strong bootstrap support. We looked at associations of corresponding haplotypes with HIV progression. A haplotype trend regression confirmed that individuals carrying the low-producing ATA-inclusive haplotypes in European Americans progress to AIDS faster, and most likely explain the role of IL10. Our findings are consistent with the hypothesis that existing polymorphisms in this gene may reflect a balance of historic adaptive responses to autoimmune, infectious and other disease agents.

Journal ArticleDOI
01 Apr 2009-Genetics
TL;DR: Haplotype analysis revealed potential recombination events that could reduce the size of the candidate region to 3.5 Mb and suggested multiple origins for the orange phenotype in the domestic cat, and epistasis of orange over nonagouti was demonstrated at the genetic level.
Abstract: A comprehensive genetic linkage map of the domestic cat X chromosome was generated with the goal of localizing the genomic position of the classic X-linked orange ( O ) locus. Microsatellite markers with an average spacing of 3 Mb were selected from sequence traces of the cat 1.9× whole genome sequence (WGS), including the pseudoautosomal region 1 (PAR1). Extreme variation in recombination rates (centimorgans per megabase) was observed along the X chromosome, ranging from a virtual absence of recombination events in a region estimated to be >30 Mb to recombination frequencies of 15.7 cM/Mb in a segment estimated to be orange gene, placing this locus on the q arm of the X chromosome, as opposed to a previously reported location on the p arm. Fine mapping placed the locus between markers at positions 106 and 116.8 Mb in the current 1.9×-coverage sequence assembly of the cat genome. Haplotype analysis revealed potential recombination events that could reduce the size of the candidate region to 3.5 Mb and suggested multiple origins for the orange phenotype in the domestic cat. Furthermore, epistasis of orange over nonagouti was demonstrated at the genetic level.

Journal ArticleDOI
TL;DR: The results suggest that one or more loci on the Y chromosome found on haplogroup Y-I have an effect on AIDS progression and treatment responses in European Americans.
Abstract: The host genetic basis of differential outcomes in HIV infection, progression, viral load set point and highly active retroviral therapy (HAART) responses was examined for the common Y haplogroups in European Americans and African Americans. Accelerated progression to acquired immune deficiency syndrome (AIDS) and related death in European Americans among Y chromosome haplogroup I (Y-I) subjects was discovered. Additionally, Y-I haplogroup subjects on HAART took a longer time to HIV-1 viral suppression and were more likely to fail HAART. Both the accelerated progression and longer time to viral suppression results observed in haplogroup Y-I were significant after false-discovery-rate corrections. A higher frequency of AIDS-defining illnesses was also observed in haplogroup Y-I. These effects were independent of the previously identified autosomal AIDS restriction genes. When the Y-I haplogroup subjects were further subdivided into six I subhaplogroups, no one subhaplogroup accounted for the effects on HIV progression, viral load or HAART response. Adjustment of the analyses for population stratification found significant and concordant haplogroup Y-I results. The Y chromosome haplogroup analyses of HIV infection and progression in African Americans were not significant. Our results suggest that one or more loci on the Y chromosome found on haplogroup Y-I have an effect on AIDS progression and treatment responses in European Americans.

Journal ArticleDOI
TL;DR: To determine the prevalence of Cronobacter spp.
Abstract: Aims: To determine the prevalence of Cronobacter spp. (Enterobacter sakazakii) in follow-on formula powders commercially available in European countries. Methods and Results: A total of 470 samples comprising 31 different products from 18 brand names belonging to seven companies were tested for the presence of Cronobacter species. No milk- or soy-based infant formula powders were found to contain Cronobacter species. However, two cereal-based infant drinks were positive for Cronobacter sakazakii. A review of the published cases spanning the past 48 years did not reveal any fatalities attributable to Cronobacter spp. in children over 3 months. Conclusions: The low incidence of Cronobacter in infant powdered drinks, the lack of fatal Cronobacter infections in infants greater than 3 months and the low incidence of Cronobacter-related reported illness in this age group indicated that ingestion of these products presents a low risk for the intended consumers. Significance and Impact of the Study: The risk posed to neonates from the consumption of infant formula contaminated with Cronobacter is clear. Risks associated with powdered follow-on formulae intended for consumption by older infants is now under consideration by the World Health Organization. Our data contributes to the body of knowledge available for the assessment of the risk to consumers from these food products.

Journal ArticleDOI
TL;DR: The observation that the lesser panda highly preferred aspartame could be an example of evolutionary convergence in the identification of sweet stimuli, and the relationship between the structure of the sweet receptors and preference for sugars and artificial sweeteners is studied.
Abstract: The extent to which taste receptor specificity correlates with, or even predicts, diet choice is not known. We recently reported that the insensitivity to sweeteners shown by species of Felidae can be explained by their lacking of a functional Tas1r2 gene. To broaden our understanding of the relationship between the structure of the sweet receptors and preference for sugars and artificial sweeteners, we measured responses to 12 sweeteners in 6 species of Carnivora and sequenced the coding regions of Tas1r2 in these same or closely related species. The lion showed no preference for any of the 12 sweet compounds tested, and it possesses the pseudogenized Tas1r2. All other species preferred some of the natural sugars, and their Tas1r2 sequences, having complete open reading frames, predict functional sweet receptors. In addition to preferring natural sugars, the lesser panda also preferred 3 (neotame, sucralose, and aspartame) of the 6 artificial sweeteners. Heretofore, it had been reported that among vertebrates, only Old World simians could taste aspartame. The observation that the lesser panda highly preferred aspartame could be an example of evolutionary convergence in the identification of sweet stimuli.

Journal ArticleDOI
TL;DR: To extend the understanding of the genetic relationship between Cronobacter sakazakii BAA-894 and the other species of this genus, microarray-based comparative genomic indexing was undertaken to determine the presence/absence of genes identified in the former sequenced genome and to compare 276 selected open reading frames within the different Cronobacteria strains.

Journal ArticleDOI
TL;DR: It is shown that even younger THA patients at long-term follow-up do not regain normal age-matched walking characteristics, and most of the temporospatial parameters between the age groups were no difference.
Abstract: While short-term outcome studies of patients following total hip arthroplasty (THA) have shown compromised walking ability, it is often assumed that temporospatial parameters will return to normal levels at long-term follow-up, especially for younger patients. Temporospatial parameters were determined for 149 THA patients selected arbitrarily from routine ten-year post-operative review clinics. Patients were divided into five age groups: 54–64, 65–69, 70–74, 75–79 and over 80 years. The parameters of speed, step length, stride length and cadence were measured. All age groups displayed significantly reduced velocity, step length and stride length compared to an age-matched normal group. There was no difference in most of the temporospatial parameters between the age groups. This study shows that even younger THA patients at long-term follow-up do not regain normal age-matched walking characteristics.

Journal ArticleDOI
TL;DR: Staphylococcus aureus was isolated from bovine, ovine and caprine milk and milk filters from 78 dairy production holdings supplying the farmhouse cheese sector in Ireland, using standard culture methods to study the distribution of genes encoding staphylitiscal enterotoxins and toxic shock syndrome toxin.
Abstract: Enterotoxigenic Staphylococcus aureus frequently contaminate milk and milk products causing food poisoning. Staphylococcus aureus were isolated from bovine, ovine and caprine milk and milk filters from 78 dairy production holdings supplying the farmhouse cheese sector in Ireland, using standard culture methods. Molecular methods were applied to study the distribution of genes encoding staphylococcal enterotoxins and toxic shock syndrome toxin in the collection. Multilocus variable number tandem repeat analysis was used to subtype the collection. One hundred and two Staphylococcus aureus (54 milk filters and 48 bulk milk) were recovered from apparently healthy animals; half of the isolates were toxigenic. Our findings are discussed in light of the risks posed to public health.

Journal ArticleDOI
TL;DR: A new one-step enrichment protocol, consisting of a combined preenrichment and enrichment broth (Cronobacter Enrichment Broth [CEB] used in conjunction with selective-differential agar ChromID Sakazakii, to facilitate a shortened 2-day cultural method for detection of Cronobacter spp.

Journal ArticleDOI
TL;DR: In this article, the authors evaluated the hereditary retinal degeneration in the Abyssinian cat (rdAc) in a recently established closed colony segregating for the rdAc mutation, and evaluated possible differences in the age of onset and progression of disease phenotype.
Abstract: Objective To characterize hereditary retinal degeneration in the Abyssinian cat (rdAc) in a recently established closed colony segregating for the rdAc mutation, and evaluate possible differences in the age of onset and progression of disease phenotype since the initial description of rdAc 25 years ago. The sample size of an earlier study was increased in order to determine the allele frequency in Abyssinian and Somali cats on a worldwide basis. Animals studied Twenty rdAc affected cats from the closed animal facility, 87 Abyssinian and Somali cats for study of genotype–phenotype concordance, and DNA from 131 Abyssinian and Somali cats from Scandinavia, the UK and Australia for evaluation of the rdAc allele frequency. Procedures DNA was extracted from blood and buccal swabs using commercially available kits, followed by genotyping. Ophthalmic examinations were performed in the USA and Sweden by two board-certified veterinary ophthalmologists. Results A greater variation in the age of onset and progression of the disease was observed compared to that previously described. An excellent correlation between genotype and phenotype was observed. A population genetic survey revealed that the rdAc allele is in moderate abundance in the Abyssinian breed in Europe and Australia. Surprisingly, homozygosity for the mutant allele was observed in a Siamese cat with ophthalmoscopic findings similar to those originally described for affected rdAc individuals. Conclusions Alertness to the potential of rdAc is needed on the part of the veterinary ophthalmology community, not only in Abyssinian and Somali cats but possibly also in other related cat breeds.