Biology subjects

Hasan, M. R.

Publications and source records attributed to Hasan, M. R..

5 recordsLinked to original sources

bioRxiv2020

Virome-wide serological profiling reveals association of herpesviruses with obesity

The relationship between viral infection and obesity has been known for several decades but epidemiological data related to obesity is limited to only a few viral pathogens. To identify associations between viral infections and obesity, a high-throughput virome-wide serological profiling tool, VirScan, was used to measure antibody responses to a wide range of viruses. Serum specimens from 457 Qatari adults (lean=184;obese=273) and 231 Qatari children (lean=111;obese=120) were assessed by VirScan. Pediatric specimens were simultaneously tested by conventional serology for several herpesviruses to validate VirScan results. Viral association with obesity was determined by calculation of odds ratio (OR) and p-values from Fisher test, and by multivariate regression analysis to adjust for age and gender, with Bonferroni correction for multiple testing. Comprehensive serological profiling of Qatari adult population with VirScan revealed positive and negative associations (p<0.05) of antibody responses to members of Herpesviridae and Picornaviridae families, respectively, with obesity. After adjusting p-values for multiple comparisons, only herpes simplex virus 1 (HSV-1) and Rhinovirus A were positively (OR=3.3; 95%CI 2.15-4.99; p=2.787E-08) and negatively (OR=0.4; 95%CI 0.26-0.65; p=1.175E-03) associated with obesity. At the peptide level, higher prevalence of antibodies against several peptide epitopes of HSV-1/2 was positively (OR=2.35-3.82; p[≤]3.981E-05) associated with obesity. No such associations were seen at the species or peptide levels in the pediatric population. By multivariate regression analysis, HSV-1 was independently associated with obesity irrespective of age and gender. These findings are in agreement with limited data on the adipogenic properties of HSV-1 observed in vitro. ImportanceThe state of Qatar has one of the highest rates of obesity and associated morbidities in the world. Although obesity is predominantly caused by the intake of high calorie diet and reduced physical activities, other factors including infections with certain viruses have been reported. Among these viruses, human adenoviruses were widely studied but epidemiological data for other viruses in relation to human obesity are limited. Here, we studied the association of obesity in Qatari adults and children with a wide range of viral pathogens using VirScan, a virome-wide serological profiling tool. Our results indicate significant association HSV-1 with obesity in the adult population only. Furthermore, we have identified a set of HSV peptides as candidate obesogenic factors for future studies.

microbiology↗

bioRxiv2020

Endemic human coronaviruses induce distinct antibody repertoires in adults and children

Four endemic human coronaviruses (HCoVs) are commonly associated with acute respiratory infection in humans. B cell responses to these "common cold" viruses remain incompletely understood. Here we report a comprehensive analysis of CoV-specific antibody repertoires in 231 children and 1168 adults using phage-immunoprecipitation sequencing. Seroprevalence of antibodies to endemic HCoVs ranged between ~4 and 27% depending on the species and cohort. We identified at least 136 novel linear B cell epitopes. Antibody repertoires against endemic HCoVs were qualitatively different between children and adults in that anti-HCoV IgG specificities more frequently found among children targeted functionally important and structurally conserved regions of the spike, nucleocapsid and matrix proteins. Moreover, antibody specificities targeting the highly conserved fusion peptide region and S2 cleavage site of the spike protein were broadly cross-reactive with peptides of epidemic human and non-human coronaviruses. In contrast, an acidic tandem repeat in the N-terminal region of the Nsp3 subdomain of the HCoV-HKU1 polyprotein was the predominant target of antibody responses in adult donors. Our findings shed light on the dominant species-specific and pan-CoV target sites of human antibody responses to coronavirus infection, thereby providing important insights for the development of prophylactic or therapeutic monoclonal antibodies and vaccine design.

immunology↗

bioRxiv2020

Isolation and characterization of two bacterial strains from textile effluents having Malachite Green dye degradation ability

Water pollution from textile effluent is now one of the major issues all over the world. Malachite Green dye of the triphenylmethane group is a key component of textile effluents. This study aimed to isolate and identify potential Malachite Green dye degrading bacteria from textile effluents. Different growth and culture parameters such as temperature, pH, inoculum-size and dye concentration were optimized to perform the dye-degradation assay using different concentrations of Malachite Green dye in mineral salt medium. A photo-electric-colorimeter was used to measure the decolorizing activity of bacteria at different time intervals after aerobic incubation. Two competent bacterial strains of Enterobacter spp. (CV-S1 and CM-S1) were isolated from textile effluents showing potential degradation efficiency against Malachite Green dye. The RAPD analysis and 16S rRNA sequencing confirmed the genetical difference of the isolated strains Enterobacter sp. CV-S1 and Enterobacter sp. CM-S1. The two bacterial strains CV-S1 and CM-S1 showed complete Malachite Green dye degradation up to 15 mg/l under shaking condition with 5% (v/v) inoculums at pH 6.50 and temperature 35{degrees}C within 72 and 144 hours respectively. These findings indicate that the two potential bacterial strains can be used in large scale treatment of textile effluents in the future.

microbiology↗

bioRxiv2019

A Metagenomics - Based Diagnostic Approach for Central Nervous System Infections in Hospital Acute Care Setting

The etiology of central nervous system (CNS) infections such as meningitis and encephalitis remains unknown in a large proportion of cases partly because the diversity of pathogens that may cause CNS infections greatly outnumber available test methods. Here we present a metagenomic next generation sequencing (mNGS) based approach for broad-range detection of pathogens associated with CNS infections, which is suitable for application in the acute care hospital setting. Using an Illumina MiSeq benchtop sequencer and the IDseq pipeline for identifying pathogens in metagenomic sequence data, we show that the analytical sensitivity of mNGS to detect pathogens is comparable to that of PCR in simulated cerebrospinal fluid (CSF) specimens. We then applied this method for pathogen detection in 74 CSF specimens from patients with suspected CNS infections that were previously tested by culture and/or PCR. Diagnostic accuracy, sensitivity and specificity of mNGS approach with reference to conventional methods were all 95%. Furthermore, confirmatory testing on specimens that gave discrepant results were mostly in favor of the mNGS assay. The clinical application of mNGS holds promise to benefit patients with CNS infections of unknown etiology.

pathology↗

bioRxiv2018

A novel real-time PCR assay panel for detection of common respiratory pathogens in a convenient, strip-tube array format

Commercial multiplex assays, built on different chemistries and platforms are widely available for simultaneous detection of pathogens that cause respiratory infections. However, these tests are often difficult to implement in a resource limited setting because of high cost. In this study, we developed and validated a method for simultaneous testing of common respiratory pathogens (Respanel) by real-time PCR in a convenient, strip-tube array format. Primers and probes for sixteen PCR assays were selected from the literature or newly designed. Following optimization of individual PCR assays, strip-tube arrays were prepared by dispensing primer-probe mixes (PPM) into two sets of 8-tube strips. Nucleic acid extracts from specimens were mixed with PCR master mix, and dispensed column-wise into 2X8-wells of a 96-well plate. PPMs from strip-tubes were then added to the wells using a multichannel pipette for real-time PCR. Individual PCR assays were optimized using previously known specimens (n=397) with 91%-100% concordance with culture, DFA or PCR results. Respanel was then tested in a routine manner at two different sites using specimens (n=147) previously tested by Qiagen Resplex I&II or Fast-Track Diagnostics Respiratory Pathogens 21 assays. The sensitivity, specificity and accuracy of Respanel were 94%, 95% and 95%, respectively, against Resplex and 88%, 100% and 99%, respectively, against FTDRP21. Respanel detected 48% more pathogens (p<0.05) than Resplex but the rate of pathogen detection was not significantly different from FTDRP21. Respanel is a convenient and inexpensive assay that is more sensitive than Resplex and comparable to FTDRP21 for the detection of common respiratory pathogens.

pathology↗