Evaluating the possibility of detecting evidence of positive selection across Asia with sparse genotype data from the HUGO Pan-Asian SNP Consortium

10.1186/1471-2164-15-332BMC Genomics151-BGME

Detection of pathological myopia by PAMELA with texture-based features through an SVM approach

10.1260/2040-2295.1.1.1Journal of Healthcare Engineering111-1

Dataset on gene expression in the elderly after Mindfulness Awareness Practice or Health Education Program

It has been reported that relaxation techniques can improve physical health and cognitive function. A number of studies involving different types of relaxation practices showed changes in expression of genes. We investigated the gene expression pattern of a cohort of elderly subjects of Asian descent after weekly (for the first three months) and monthly (for the subsequent six months) intervention. Sixty consenting elderly subjects (aged 60–90 years) with mild cognitive impairment were assigned to either the Mindfulness Awareness Practice (MAP) or Health Education Program (HEP) group in a randomized controlled trial to assess the effectiveness of the programs in preventing further cognitive decline and evaluate the influence on neurological, cellular and biochemical factors. Blood samples were collected before the start of intervention and after nine months for gene expression profiling using Affymetrix Human Genome U133 Plus 2.0 arrays. The dataset is publicly available for further analyses

Predictors of allergen sensitization in Singapore children from birth to 3 years

10.1186/s13223-016-0161-xAllergy, asthma, and clinical immunology : official journal of the Canadian Society of Allergy and Clinical Immunology121Article number 56GUSTO (Growing up towards Healthy Outcomes

A metabolite-derived protein modification integrates glycolysis with KEAP1-NRF2 signalling.

Mechanisms that integrate the metabolic state of a cell with regulatory pathways are necessary to maintain cellular homeostasis. Endogenous, intrinsically reactive metabolites can form functional, covalent modifications on proteins without the aid of enzymes1,2, and regulate cellular functions such as metabolism3-5 and transcription6. An important 'sensor' protein that captures specific metabolic information and transforms it into an appropriate response is KEAP1, which contains reactive cysteine residues that collectively act as an electrophile sensor tuned to respond to reactive species resulting from endogenous and xenobiotic molecules. Covalent modification of KEAP1 results in reduced ubiquitination and the accumulation of NRF27,8, which then initiates the transcription of cytoprotective genes at antioxidant-response element loci. Here we identify a small-molecule inhibitor of the glycolytic enzyme PGK1, and reveal a direct link between glycolysis and NRF2 signalling. Inhibition of PGK1 results in accumulation of the reactive metabolite methylglyoxal, which selectively modifies KEAP1 to form a methylimidazole crosslink between proximal cysteine and arginine residues (MICA). This posttranslational modification results in the dimerization of KEAP1, the accumulation of NRF2 and activation of the NRF2 transcriptional program. These results demonstrate the existence of direct inter-pathway communication between glycolysis and the KEAP1-NRF2 transcriptional axis, provide insight into the metabolic regulation of the cellular stress response, and suggest a therapeutic strategy for controlling the cytoprotective antioxidant response in several human diseases

Hospital-based Diagnosis of Hemorrhagic Fever, Encephalitis, and Hepatitis in Cambodian Children

Surveillance was conducted for three clinical syndromes (hemorrhagic fever, encephalitis, and hepatitis) in Cambodian children admitted to the National Pediatric Hospital in Phnom Penh from July 1996 through September 1998. Acute- and convalescent-phase sera, and cerebrospinal fluid, when applicable, underwent diagnostic evaluation for infections with Dengue virus (DENV), Japanese encephalitis virus (JEV), and Hepatitis A, B, C, and E viruses. Of 621 children admitted with hemorrhagic fever, 499 (80%) were confirmed to have either primary or secondary DENV infection. DENV rates were as high as 10.6/100 hospital admissions in September 1998. Of 50 children with clinical encephalitis, 9 (18%) had serologic evidence of JEV infection. Forty-four children had clinical hepatitis, most (55%) due to Hepatitis A virus (HAV). One patient had Hepatitis B virus, and no patients had hepatitis C or E. This study identified a large number of children with vaccine-preventable diseases (JEV and HAV)

Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1

Sequencing of the complete genome of Anoxybacillus flavithermus reveals enzymes that are required for silica adaptation and biofilm formation

Papillary fibroelastoma of the aortic valve - a case report and literature review

The prevalence of primary cardiac tumour ranges from 0.0017-0.28% and papillary fibroelastoma is rare but not uncommon benign cardiac neoplasm. Currently, with the advent of higher-resolution imaging technology especially transoesophageal echocardiography such cases being recognized frequently. The clinical presentation of these tumours varies from asymptomatic to severe ischaemic or embolic complications. We herein, present a 50-year-old female patient with a papillary fibroelastoma of the aortic valve arising from the endocardium of the right coronary cusp very close to the commissure between the right and non-coronary cusps. The patient presented with angina-like chest pain and was investigated using echocardiography and CT angiographic modalities in addition to the usual investigations. The differential diagnosis considered was a thrombus, myxoma, Lambl's excrescence and infective vegetation. The surgical management included a prompt resection of the tumour on cardiopulmonary bypass avoiding injury to the aortic valve. The patient recovered well. A review of the literature suggests that the cardiac papillary fibroelastoma is a rare but potentially treatable cause of embolic stroke and other fatal complications, therefore, a strong suspicion; appropriate use of imaging modality, preoperative anticoagulation and urgent surgical resection is warranted. Also, possibility of this diagnosis should be kept in mind while managing cardiac or valvular tumours

Genetic Variants on Chromosome 1q41 Influence Ocular Axial Length and High Myopia

As one of the leading causes of visual impairment and blindness, myopia poses a significant public health burden in Asia. The primary determinant of myopia is an elongated ocular axial length (AL). Here we report a meta-analysis of three genome-wide association studies on AL conducted in 1,860 Chinese adults, 929 Chinese children, and 2,155 Malay adults. We identified a genetic locus on chromosome 1q41 harboring the zinc-finger 11B pseudogene ZC3H11B showing genome-wide significant association with AL variation (rs4373767, β = −0.16 mm per minor allele, Pmeta = 2.69×10−10). The minor C allele of rs4373767 was also observed to significantly associate with decreased susceptibility to high myopia (per-allele odds ratio (OR) = 0.75, 95% CI: 0.68–0.84, Pmeta = 4.38×10−7) in 1,118 highly myopic cases and 5,433 controls. ZC3H11B and two neighboring genes SLC30A10 and LYPLAL1 were expressed in the human neural retina, retinal pigment epithelium, and sclera. In an experimental myopia mouse model, we observed significant alterations to gene and protein expression in the retina and sclera of the unilateral induced myopic eyes for the murine genes ZC3H11A, SLC30A10, and LYPLAL1. This supports the likely role of genetic variants at chromosome 1q41 in influencing AL variation and high myopia

Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia

<p>Abstract</p> <p>Background</p> <p>The phylum <it>Verrucomicrobia </it>is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. We have recently reported cultivation and initial characterization of an extremely acidophilic methanotrophic member of the <it>Verrucomicrobia</it>, strain V4, isolated from the Hell's Gate geothermal area in New Zealand. Similar organisms were independently isolated from geothermal systems in Italy and Russia.</p> <p>Results</p> <p>We report the complete genome sequence of strain V4, the first one from a representative of the <it>Verrucomicrobia</it>. Isolate V4, initially named "<it>Methylokorus infernorum</it>" (and recently renamed <it>Methylacidiphilum infernorum</it>) is an autotrophic bacterium with a streamlined genome of ~2.3 Mbp that encodes simple signal transduction pathways and has a limited potential for regulation of gene expression. Central metabolism of <it>M. infernorum </it>was reconstructed almost completely and revealed highly interconnected pathways of autotrophic central metabolism and modifications of C₁-utilization pathways compared to other known methylotrophs. The <it>M. infernorum </it>genome does not encode tubulin, which was previously discovered in bacteria of the genus <it>Prosthecobacter</it>, or close homologs of any other signature eukaryotic proteins. Phylogenetic analysis of ribosomal proteins and RNA polymerase subunits unequivocally supports grouping <it>Planctomycetes</it>, <it>Verrucomicrobia </it>and <it>Chlamydiae </it>into a single clade, the PVC superphylum, despite dramatically different gene content in members of these three groups. Comparative-genomic analysis suggests that evolution of the <it>M. infernorum </it>lineage involved extensive horizontal gene exchange with a variety of bacteria. The genome of <it>M. infernorum </it>shows apparent adaptations for existence under extremely acidic conditions including a major upward shift in the isoelectric points of proteins.</p> <p>Conclusion</p> <p>The results of genome analysis of <it>M. infernorum </it>support the monophyly of the PVC superphylum. <it>M. infernorum </it>possesses a streamlined genome but seems to have acquired numerous genes including those for enzymes of methylotrophic pathways <it>via </it>horizontal gene transfer, in particular, from <it>Proteobacteria</it>.</p> <p>Reviewers</p> <p>This article was reviewed by John A. Fuerst, Ludmila Chistoserdova, and Radhey S. Gupta.</p