Specific and complete human genome amplification with improved yield achieved by phi29 DNA polymerase and a novel primer at elevated temperature

<p>Abstract</p> <p>Backgrounds</p> <p>Whole genome amplification (WGA) is a practical solution to eliminate molecular analysis limitations associated with genomic DNA (gDNA) quantity. Different methods have been developed to amplify the whole genome, including primer extension preamplification (PEP), degenerate oligonucleotide primed PCR (DOP-PCR), and multiple displacement amplification (MDA). Each of these methods has its own merits and limitations.</p> <p>Findings</p> <p>Effects of primer length and composition on amplification quality and quantity were explored in this study at two different temperatures (30°C & 40°C). New primer designs combined with elevated amplification temperature has significantly improved MDA as measured by amplification yield, genome coverage, and allele drop out (ADO) analysis. A remarkable finding was the comprehensive amplification, at 30°C & 40°C, of the human whole genome via the use of GGGCAGGA*N*G hotspot recombination consensus primer. Amplification was characterized by Affymetrix 10K SNP chip analysis. Finally, the use of new primer designs has suppressed the template-independent DNA amplification (TIDA) both at 30°C and 40°C.</p> <p>Conclusion</p> <p>The use of new primers in this study combined with elevated incubation temperatures in MDA has remarkably improved the specificity, amplification yield, and suppressed TIDA.</p

Effect of Ca2+ Channel Block on Glycerol Metabolism in Dunaliella salina under Hypoosmotic and Hyperosmotic Stresses

The effect of Ca2+ channel blockers on cytosolic Ca2+ levels and the role of Ca2+ in glycerol metabolism of Dunaliella salina under hypoosmotic or hyperosmotic stress were investigated using the confocal laser scanning microscope (CLSM). Results showed that intracellular Ca2+ concentration increased rapidly when extracellular salinity suddenly decreased or increased, but the increase could be inhibited by pretreatment of Ca2+ channel blockers LaCl3, verapamil or ruthenium red. The changes of glycerol content and G3pdh activity in D. salina to respect to hypoosmotic or hyperosmotic stress were also inhibited in different degrees by pretreatment of Ca2+ channel blockers, indicating that the influx of Ca2+ via Ca2+ channels are required for the transduction of osmotic signal to regulate osmotic responses of D. salina to the changes of salinity. Differences of the three blockers in block effect suggested that they may act on different channels or had different action sites, including influx of Ca2+ from the extracellular space via Ca2+ channels localized in the plasma membrane or from intracellular calcium store via the mitochondrial. Other Ca2+-mediated or non-Ca2+-mediated osmotic signal pathway may exist in Dunaliella in response to hypoosmotic and hyperosmotic stresses

Weak or no association of TCF7L2 variants with Type 2 diabetes risk in an Arab population

<p>Abstract</p> <p>Background</p> <p>The rs7903146 and rs12255372 variants of <it>TCF7L2 </it>have been strongly associated with type 2 diabetes (T2D) risk in most populations studied to date. Meta-analysis of 27 different studies has resulted in a global OR of 1.46 [1.42–1.51] (rs7903146 variant). Thus far, despite a high incidence of T2D, the role of this variant in Arabs has not been established.</p> <p>Methods</p> <p>We performed a case-control association study using 522 Saudi T2D patients (WHO criteria), and 346 controls (age > 60; fasting plasma glucose < 7 mmol/L). Genotyping was performed by pyrosequencing. Statistical analyses were performed using SPSS version 13.0 for Windows (SPSS, Chicago, IL, USA).</p> <p>Results</p> <p>For rs7903146, the T allele frequency of the cases (0.415) was not different from that observed in the controls (0.405). The crude odds ratio (OR) was 1.04 with a 95% CI of 0.86–1.27 (P = 0.675). For rs12255372, the T allele frequency of the cases (0.368) was not different from that observed in the controls (0.355). Retrospective power calculations based upon an OR of 1.46 reported in a comprehensive meta-analysis of <it>TCF7L2 </it>risk, indicated this study was sufficiently powered (96.92%; α = 0.05) to detect an effect of similar magnitude to that reported for rs7903146.</p> <p>Conclusion</p> <p>Our study is consistent with weak or no association of T2D in Arabs with the two <it>TCF7L2 </it>variants, however it cannot rule out an effect of other SNPs in this gene. Future studies in this population are required to confirm our findings and may indicate the presence of yet to be defined genetic risk factors for T2D.</p

Investigation of genetic variation and lifestyle determinants in vitamin D levels in Arab individuals

Background: Differences in the concentrations of circulating 25-hydroxyvitamin D [25(OH)D] are associated with a wide range of health outcomes; however, most studies on genetic variants that impact 25(OH)D levels have been conducted in European populations. Here we aimed to identify common genetic variants that affect vitamin D concentrations in individuals of self-reported Arab ethnicity. Methods: The study included 1151 Arab subjects living in Kuwait. Common variants of single-nucleotide polymorphisms and genes previously associated with vitamin D levels, such as GC, PDE3B, CYP2R1, and NADSYN1, were genotyped. Raw vitamin D level data were corrected for age, body mass index, and sex and then normalized. Regression tree analyses were performed to identify the impact of genetic variants on vitamin D levels. Results: Compared with other gene variants, the GC gene variants exhibited the greatest impact on vitamin D levels in our study population, of which rs2298850 had the lowest p value (0.003). Individuals homozygous for the derived allele C had lower vitamin D levels. Analyses of the interaction between the number of years for which the subjects had lived in Kuwait and genetic variation in the GC gene showed that those with the CC genotype of rs2298850 who had lived in Kuwait for &lt; 51 years had a mean 25(OH)D level of 10 ng/ml, whereas those who were homozygous for the ancestral allele had a mean 25(OH)D level of 17 ng/ml. Furthermore, subjects who had lived in Kuwait for &gt; 51 years had higher vitamin D levels (mean 28 ng/ml) regardless of the genotype of their GC gene. Conclusions: The GC gene may play a major role in determining vitamin D levels in Arab populations

The demographic and clinical characteristics of leprosy in Saudi Arabia

Summary: Leprosy is a chronic disease caused by Mycobacterium leprae. Although the occurrence of leprosy has declined in Saudi Arabia, it has not yet been eradicated. To our knowledge, this descriptive retrospective study is the first to assess the clinical presentation of leprosy at the time of diagnosis in Saudi Arabia. All study subjects were leprosy patients admitted to Ibn Sina hospital, the only referral hospital for leprosy in Saudi Arabia, between January 2000 and May 2012. A total of 164 subjects, the majority of whom (65%) were between 21 and 50 years of age, were included, and the male-to-female ratio was 2.8:1. Of these 164 patients, 63% were Saudis, and 77% of all admitted patients were from the western region. Lepromatous leprosy was observed most frequently (33%), and 31% of cases had a positive history of close contact with leprosy. At the time of diagnosis, 84% of all subjects presented with skin manifestation. The prevalence of neurological deficit at the time of diagnosis was 87%. Erythema nodosum leprosum (E.N.L.) developed in only 10% of all subjects. Further studies are needed to determine the clinical characteristics pertaining to each type of leprosy in the region, and training courses in caring for and diagnosing patients with leprosy should be organized for health workers. Keywords: Leprosy, Hansen's disease, Epidemiology, Saudi Arabia, Infectious diseas