A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip® whole-genome resequencing platform

DNA resequencing arrays enable rapid acquisition of high-quality sequence data. This technology represents a promising platform for rapid high-resolution genotyping of microorganisms. Traditional array-based resequencing methods have relied on the use of specific PCR-amplified fragments from the query samples as hybridization targets. While this specificity in the target DNA population reduces the potential for artifacts caused by cross-hybridization, the subsampling of the query genome limits the sequence coverage that can be obtained and therefore reduces the technique's resolution as a genotyping method. We have developed and validated an Affymetrix Inc. GeneChip® array-based, whole-genome resequencing platform for Francisella tularensis, the causative agent of tularemia. A set of bioinformatic filters that targeted systematic base-calling errors caused by cross-hybridization between the whole-genome sample and the array probes and by deletions in the sample DNA relative to the chip reference sequence were developed. Our approach eliminated 91% of the false-positive single-nucleotide polymorphism calls identified in the SCHU S4 query sample, at the cost of 10.7% of the true positives, yielding a total base-calling accuracy of 99.992%.     

Design and operation of a simple continuous-culture apparatus

A versatile and simple continuous-culture apparatus is described. With this apparatus, independent control of limiting growth factors and other nutrilites is possible and the conditions of each experiment are reproducible. In view of the synchronized speed of the feeder syringes, flow variation troubles are not encountered. The device allows the performance of growth experiments at different dilution rates simultaneously in a single run which makes the comparison of the results more reliable. The operation of the device has been tested successfully with a study of adenine deaminase induction in yeast.     

Immobilized Peptide on the Surface of Poly l-DOPA/Silica for Targeted Delivery of 5-Fluorouracil to Breast Tumor

International Journal of Peptide Research and Therapeutics - Chemotherapy using drug delivery systems can target tumor cells selectively and do not affect normal cells. In this paper, a specific...     

Urinary and air biomonitoring of occupational exposure to benzene in oil pit workers

Abstract

The purpose of this study is to evaluate the personal exposure to benzene and its relationship with biomonitoring and quantitative risk assessment among the personnel working and living near oil pits. This study was conducted in one of oil subsidiary companies in Kharg in 2017. Airborne benzene exposure was evaluated over 8-h periods during work-shift by using personal active samplers. Urinary O-Cresol levels were determined using GC-FID for separation and detection. The highest mean concentration of airborne benzene was at monitoring location, A (0.53?ppm), monitoring location H (0.59?ppm) in the spring, monitoring location M (0.72?ppm) and monitoring location P (0.8?ppm) in the summer, which was more than suggested by the American Conference of Governmental Industrial Hygienists. No direct linear relationship was found between the concentration of airborne benzene, age, work experience, urinary creatinine, and O-Cresol in this study (p?>?.05). No significant difference was observed between urinary O-Cresol and benzene in occupational groups and different seasons (p?>?.05). The highest mean quantitative risk of cancers was observed in summer (1.21?±?0.47). According to the results of this study, urinary biomarker O-Cresol is not a suitable measure for evaluating exposure to environmental benzene.     

Effect of the conditioned medium of mesenchymal stem cells on the expression levels of P2X4 and P2X7 purinergic receptors in the spinal cord of rats with neuropathic pain

Purinergic Signalling - Recent studies have shown that mesenchymal stem cells (MSCs) and their conditioned medium (CM) have potential therapeutic effects in animal models of neuropathic pain (NP)....     

New Insight into the Interactions of Arbutin with Mushroom Tyrosinase

The Protein Journal - As a safe substitute for hydroquinone, β-arbutin, a natural plant substance, and its synthetic counterpart, α-arbutin, are used in depigmentation formulations....