High-throughput SNP genotyping by single-tube PCR with Tm-shift primers

Despite many recent advances in high-throughput single nucleotide polymorphism (SNP) genotyping technologies, there is still a great need for inexpensive and flexible methods with a reasonable throughput. Here we report substantial modifications and improvements to an existing homogenous allele-specific PCR-based SNP genotyping method, making it an attractive new option for researchers engaging in candidate gene studies or following up on genome-wide scans. In this advanced version of the melting temperature (Tm)-shift SNP genotyping method, we attach two GC-rich tails of different lengths to allele-specific PCR primers, such that SNP alleles in genomic DNA samples can be discriminated by the Tms of the PCR products. We have validated 306 SNP assays using this method and achieved a success rate in assay development of greater than 83% under uniform PCR conditions. We have developed a standalone software application to automatically assign genotypes directly from melting curve data. To demonstrate the accuracy of this method, we typed 592 individuals for 6 SNPs and showed a high call rate (>98%) and high accuracy (>99.9%). With this method, 6-10,000 samples can be genotyped per day using a single 384-well real-time thermal cycler with 2-4 standard 384-well PCR instruments.     

The flavonoid,quercetin, differentially regulates Th-1 (IFNgamma) and Th-2 (IL4) cytokine gene expression by normal peripheral blood mononuclear cells

Flavonoids are plant metabolites that are dietary antioxidants and exert significant anti-tumor, anti-allergic, anti-inflammatory and anti-viral effects. It is generally accepted that Th-1 derived cytokines such as IL-2, IFNgamma and IL-12 promote cellular immunity while Th-2 derived cytokines such as IL-4, IL-5, IL-6 exert negative immunoregulatory effects on cellular immunity while upregulating humoral immunity. The molecular mechanisms underlying the biological activities of flavonoids have not been elucidated. We hypothesize that the flavonoid, quercetin, exert significant anti-viral and anti-tumor effects possibly by modulating the production of Th-1 and Th-2 derived cytokines. Peripheral blood mononuclear cells (PBMC, 1 x 10(6) cells/ml) from normal subjects were cultured with different concentrations of quercetin (0.5-50 microM) for 24-72 h and supernates were quantitated for IFN-gamma and IL-4 by ELISA and antiviral activity of IFNgamma by bioassay. FACS analysis was done to determine the number of IFN-gamma and IL-4 positive cells and RT-PCR was done to quantitate gene expression. Quercetin significantly induces the gene expression as well as the production of Th-1 derived IFNgamma and the downregulates Th-2 derived IL-4 by normal PBMC. Further, quercetin treatment increased the phenotypic expression of IFNgamma cells and decreased IL-4 positive cells by FACS analysis, which corroborate with protein secretion and gene expression studies. These results suggest that the beneficial immuno-stimulatory effects of quercetin may be mediated through the induction of Th-1 derived cytokine, IFNgamma, and inhibition of Th-2 derived cytokine, IL-4.     

Characterization of hygromycin-resistant transformants of thermophilic fungus Thermomyces lanuginosus

Hygromycin-resistant stable transformants of the thermophilic fungus, Thermomyces lanuginosus, were obtained by electroporation of germinating aleurospores with a plasmid pMP6, coding for hygromycin resistance. Southern hybridization analysis revealed that the gene is integrated into the chromosome. The hygromycin-resistant transformants were characterized for morphological changes, growth response towards the presence of antagonistic metabolites (hygromycin, 2-deoxy-D-glucose, cylcoheximide, benlate and acriflavine) on plates and enzyme production (amylases, pectinases and xylanase) in shake flask cultures. A hygromycin-resistant transformant hyg 33 was characterized as non-sporulating, 2-deoxy-D-glucose-resistant, acriflavine-sensitive and xylanase hypo-producer and is being used as parental strain for breeding strains through protoplast fusion.     

Potential role of nicotinamide analogues against SARS-COV-2 target proteins

Background and objectiveCoronavirus 2019 (COVID-19) is caused by ‘severe acute respiratory syndrome coronavirus 2′ (SARS-CoV-2), first reported in Wuhan, China in December 2019, which eventually became a global disaster. Various key mediators have been reported in the pathogenesis of COVID-19. However, no effective pharmacological intervention has been available to combat COVID-19 complications. The present study screens nicotinamide riboside (NR) and nicotinamide mononucleotide (NMN) as potential inhibitors of this present generation coronavirus infection using an in-silico approach.Materials and methodsThe SARS-CoV-2 proteins (nucleocapsid, proteases, post-fusion core, phosphatase, endoriboruclease) and ACE-2 protein were selected. The 2D structure of nicotinamide ribonucleoside and nicotinamide ribonucleotide was drawn using ChemDraw 14.0 and saved in .cdx format. The results were analyzed using two parameters: full fitness energy and binding free energy (ΔG).ResultsThe full fitness energy and estimated ΔG values from docking of NM, and NMN with selected SARS-CoV-2 target proteins, ADMET prediction and Target prediction indicate the interaction of NR and NMN in the treatment of COVID-19.ConclusionsBased on full fitness energy and estimated ΔG values from docking studies of NM and NAM with selected SARS-CoV-2 target proteins, ADME prediction, target prediction and toxicity prediction, we expect a possible therapeutic efficacy of NR in the treatment of COVID-19.Keyword: COVID-19, SARS-CoV-2, Molecular docking, Poly (ADP-ribose) polymerase enzyme, Nicotinamide     

Focus: Addiction: Marijuana for Glaucoma: A Recipe for Disaster or Treatment?

Marijuana has been shown to lower intraocular pressure (IOP) but with limited duration of action and numerous adverse effects. Use of marijuana to lower IOP as a means of glaucoma treatment would require frequent use throughout the day, leading to significant adverse effects, possible progression toward Cannabis Use Disorder (CUD), and/or withdrawal symptoms. The treatment of glaucoma based on the cannabis plant or drugs based on the cannabinoid molecule should be considered carefully before being prescribed. Considerations should include the adverse physical and psychological adverse effects, including substance abuse. Currently, the deleterious effects of marijuana outweigh the benefits of its IOP-lowering capacity in most glaucoma patients. Under extremely rare circumstances, a few categories of glaucoma patients may be potential candidates for treatment with medical marijuana. Further studies on alternate routes and more focused means of cannabinoid molecule delivery to the eye for glaucoma treatment are needed.     

Short Note: Biodegradation of chlorobenzoates by Actinomycetes

Of the nine actinomycete strains screened for their ability to grow on isomeric chlorobenzoates (Cba), Corynebacterium liquefaciens, a sewage isolate, was able to maximally metabolize 3.2mM 2- and 3-Cba in presence of 0.25mM glucose as co-substrate. The degradation of 2-Cba and 3-Cba was 70.3% and 79.37% (w/v), respectively, under optimized conditions.     

Affinity of human leukocyte interferon for polyribonucleotides.

Human leukocyte interferon (HL-IF)binds to AGPOLY(A)TM, AGPOLY(U)TM and AGPOLY(I)TM. The bound interferon could be displaced from all three polyribonucleotides by including sodium chloride in the eluant. The nature of interaction of HL-IF with polyribonucleotides is electrostatic and not hydrophobic since its binding was not prevented in the presence of 50% ethylene glycol. The binding of HL-IF on AGPOLY(I)TM is stronger at lower pH since an increase in ionic strength is required to displace it.     

Prevalence of Pulmonary Tuberculosis among Adults in a North Indian District

BackgroundRecent population prevalence estimates of pulmonary tuberculosis (PTB) are not available for several areas in India. We conducted a field-based population survey at a north Indian district to estimate point prevalence of bacteriologically positive PTB.MethodsA stratified cluster sampling design was used to conduct the survey in both urban and rural areas within the district. All adults aged more than 15 years, in 18 rural and 12 urban clusters of 3000 subjects each, were interviewed using a symptom card. Two sputum samples were collected from all persons having symptoms suggestive of PTB, or history of antitubercular treatment, for smear microscopy for acid-fast bacilli and mycobacterial culture. Those having at least one sputum specimen positive on microscopy and/or culture were categorized as having PTB. Prevalence was estimated after adjusting for cluster sampling and incomplete data (through individual level analysis with robust standard error).ResultsOf 91,030 eligible adult participants (47,714 men and 43,316 women), 85,770 (94.2%) completed the symptom cards. Of them, 2,898 persons were considered eligible for sputum examination and 2,839 (98.0%) provided at least one sample. Overall, 21 persons had bacteriologically positive PTB, and cluster level prevalence was estimated at 24.5 per 100,000 population (95% CI 12.8–36.2). Individual level analysis with robust standard error yielded a prevalence estimate of 24.1 per 100,000 populations (95% CI 12.8–35.4).ConclusionThe observed prevalence of bacteriologically positive PTB in this district is lower than empiric national estimates, probably as a result of successful implementation of tuberculosis control measures in the area.