BackgroundIn addition to HLA genetic incompatibility, non-HLA difference between donor and recipients of transplantation leading to allograft rejection are now becoming evident. We aimed to create a unique genome-wide platform to facilitate genomic research studies in transplant-related studies. We designed a genome-wide genotyping tool based on the most recent human genomic reference datasets, and included customization for known and potentially relevant metabolic and pharmacological loci relevant to transplantation.MethodsWe describe here the design and implementation of a customized genome-wide genotyping array, the ‘TxArray’, comprising approximately 782,000 markers with tailored content for deeper capture of variants across HLA, KIR, pharmacogenomic, and metabolic loci important in transplantation. To test concordance and genotyping quality, we genotyped 85 HapMap samples on the array, including eight trios.ResultsWe show low Mendelian error rates and high concordance rates for HapMap samples (average parent-parent-child heritability of 0.997, and concordance of 0.996). We performed genotype imputation across autosomal regions, masking directly genotyped SNPs to assess imputation accuracy and report an accuracy of >0.962 for directly genotyped SNPs. We demonstrate much higher capture of the natural killer cell immunoglobulin-like receptor (KIR) region versus comparable platforms. Overall, we show that the genotyping quality and coverage of the TxArray is very high when compared to reference samples and to other genome-wide genotyping platforms.ConclusionsWe have designed a comprehensive genome-wide genotyping tool which enables accurate association testing and imputation of ungenotyped SNPs, facilitating powerful and cost-effective large-scale genotyping of transplant-related studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-015-0211-x) contains supplementary material, which is available to authorized users.

Introduction: Few reports about the prevalence and genetic basis of extended spectrum beta-lactamases (ESBLs) are available from Saudi Arabia. We sought to determine the prevalence of ESBL-producing Enterobacteriaceae in a university hospital in eastern Saudi Arabia and to characterize the ESBLs produced by these isolates at the molecular level. Methodology: All clinical isolates of Escherichia coli, Klebsiella spp., and Proteus spp. collected over two years were evaluated for susceptibility to a panel of antimicrobials and were analyzed for the ESBL phenotype using screening and confirmatory tests. ESBL-positive isolates were then screened for the presence of genes encoding CTX-M, SHV, and TEM beta-lactamases by PCR. Results and conclusions: The overall prevalence of ESBL-producing isolates was 4.8% (253/5256). Most isolates (80%) were from the inpatient department. The ESBL phenotype was more frequently detected in K. pneumonia. CTX-M genes were the most prevalent ESBL genes, detected in 82% of the studied isolates. The ESBL producers demonstrated a high multidrug resistance rate (96.6%). In transconjugation assay, the same ESBL gene pattern was transmitted from 29.7% of K. pneumoniae donors to the recipient strain, and the latter exhibited concomitant decreased aminoglycosides and co-trimoxazole susceptibility. We observed the presence of ESBL screenpositive but confirmatory-negative isolates (8.9%). Phenotypic tests for the production of AmpC β-lactamase tested positive in 52% of these isolates. Further studies are needed for appropriate detection of concomitant ESBL and AmpC enzyme production among such isolates. Continued surveillance and judicious antibiotic usage together with the implementation of efficient infection control measures are absolutely required.

The discovery of induced pluripotent stem cells (iPSCs) has made an invaluable contribution to the field of regenerative medicine, paving way for identifying the true potential of human embryonic stem cells (ESCs). Since the controversy around ethicality of ESCs continue to be debated, iPSCs have been used to circumvent the process around destruction of the human embryo. The use of iPSCs have transformed biological research, wherein increasing number of studies are documenting nuclear reprogramming strategies to make them beneficial models for drug screening as well as disease modelling. The flexibility around the use of iPSCs include compatibility to non-invasive harvesting, and ability to source from patients with rare diseases. iPSCs have been widely used in cardiac disease modelling, studying inherited arrhythmias, neural disorders including Alzheimer’s disease, liver disease, and spinal cord injury. Extensive research around identifying factors that are involved in maintaining the identity of ESCs during induction of pluripotency in somatic cells is undertaken. The focus of the current review is to detail all the clinical translation research around iPSCs and the strength of its ever-growing potential in the clinical space.

The present work was aimed to study the activity of nano-particulated ZnO and nano Pd doped nano-ZnO against Aspergillus and Candida species, commonly contaminating the water supply systems. Micro-ZnO was purchased from the market (Aldrich, USA) while nano ZnO were synthesized using sole gel and precipitation methods and their morphology was determined using XRD and TEM techniques. The average grain size of nano-ZnO estimated by these techniques was 30 nm and 20 nm, respectively. The doping of nano-ZnO with 5 % Pd was achieved by a thermal decomposition method and its morphology; as characterized by XRD, TEM and FESEM techniques; gave an average grain size of 35 nm. Serial dilutions of nano-ZnO doped with 5 % Pd, pure nano-ZnO and micro-ZnO (as a control) were prepared from 10 mg/mL stock solution of each in dermasel agar (OXOID), inoculated with standard strains of Candida albicans and Aspergillus niger and incubated at 37°C for 24 and 48 hours, respectively. Their antimicrobial effect was compared by the minimal inhibitory concentration (MIC), determined as the dilution giving a negligible growth of microorganism. Nano-ZnO doped with 5 % nano-Pd, pure nano-ZnO and micro-ZnO, showed antifungal activity against Aspergilus niger with an MIC of 1.25, 2.5 and 5mg/mL, respectively. However, Candida albicans yeasts were relatively resistant to these compounds, with an MIC of 2.5, 5 and 10 mg/mL for Pd doped nano-ZnO, nano-ZnO and micro-ZnO, respectively. Thus nano-ZnO was twice as potent in killing Aspergillus, as compared to its non-nano-counterpart and loading of nano-ZnO with 5 % nano-Pd further increased its activity, four times that of micro-ZnO. Further investigations are needed to confirm the potential use of nano-ZnO and its doping with nano-Pd in the treatment of water supply systems and food preservation.

Drug users and particularly, injecting drug users, are at increased risk for infection with hepatitis C virus (HCV). The aims of the study were to simultaneously detect HCV core antigen and specific antibodies in sera from Saudi drug users using the new HCV combination assay and to compare this data with HCV core antigen, anti-HCV antibodies and HCV RNA data from the same patients. A total of 297 patients who are followed up or admitted to a drug rehabilitation hospital over a period of 3 years were included in this study. Samples were analyzed using the new HCV Ag/Ab combination assay (Meurex), HCV core Ag assay, HCV antibodies and with the HCV RNA assay. Out of the 297 samples from Saudi drug users, 111 samples (37.4%) have detectable HCV core Ag, 112 samples (37.7%) have detectable HCV antibodies, 118 have detectable HCV RNA, and 116 samples were positive by the HCV Ag/Ab combination assay (39.1%). Out of the 116 samples, HCV core Ag was detected in 110 samples (94.8%), HCV antibodies were detected in 111 (95.7%) samples and HCV RNA was detected in 114 samples (98.3%). In the control group (n = 305), only 2 (0.66%) blood donor were positive by HCV antibodies assay, HCV RNA assay as well as HCV Ag/Ab combination assay. The new HCV Ag/Ab combination assay may well improve the overall quality of diagnosis of HCV infection especially in high risk population such as drug users that necessitates rigorous testing.