Biology subjects

Rahman, M. M.

Publications and source records attributed to Rahman, M. M..

66 records · Page 4Linked to original sources

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↗

bioRxiv2020

Antimicrobial Resistance Profile and mcr-1 gene Detection in Salmonella Isolates from Poultry in Bangladesh: Molecular and Bioinformatics Characterization

Antimicrobial resistance gene mcr-1 has been disseminated globally since its first discovery in Southern China in late 2015. However, the mcr-1 gene had not been identified previously in Salmonella isolates from poultry in Bangladesh. Here, we aimed to explore antimicrobial resistance gene mcr-1 in Salmonella isolates. Eighty two Salmonella isolates were isolated and characterized from suspected poultry specimens received from different zones of the country. A phenotypic disc diffusion assay with 15 antimicrobial agents was performed following CLSI standard. The disk diffusion assay showed that, all of the isolates presented high resistance to colistin (92.68%), oxytetracycline (86.59%), co-trimoxazole (76.83%), ciprofloxacin (73.17%) and enrofloxacin (65.85%). Further, randomly selected 10 Salmonella isolates were analyzed by polymerase chain reaction (PCR) targeting genus-specific invA and antimicrobial (colistin) resistance mcr-1 genes. Five were confirmed for the presence of the mcr-1 gene belonging to Salmonella spp. Further, sequencing followed by phylogenetic analysis revealed divergent evolutionary relation between the LptA and MCR proteins rendering them resistant to colistin. Three-dimensional homology structures of MCR-1 proteins were constructed and verified using different bioinformatics tools. Moreover, molecular docking interactions suggested that, MCR-1 and LptA share a similar substrate binding cavity which could be validated for the functional analysis. The results represent here is the first molecular and in silico analysis of colistin resistance mcr-1 gene of Salmonella in poultry in Bangladesh, which may emphasize the importance of the study on antibiotic resistance genes requiring for national monitoring and strategic surveillance in the country.

microbiology↗

bioRxiv2020

Microbiological water quality of Managed Aquifer Recharge systems in the salinity-prone southwest coastal Bangladesh

Managed aquifer recharge (MAR), a hydro-geological intervention designed to dilute groundwater salinity, pumps pond water treated through a slow sand filter into the underground aquifers. We evaluated the microbiological safety of the resulting MAR water at sites from three districts in southwest coastal Bangladesh. We collected monthly paired pond-MAR water samples from July 2016-June 2017 and enumerated fecal coliforms and E. coli using the IDEXX quanti-tray technique, by the most probable number (MPN) method. We used WHO risk categories for microbiological quality; no risk (<1 MPN), low risk (1-10 MPN) and moderate to high risk (>10 MPN per 100 mL water). We estimated the difference in mean log10 MPN in pond and MAR water using linear mixed effect models with random intercepts and cluster adjusted robust standard error. Almost all pond water samples (292/299, 98%) had moderate- to high-risk level (>10 MPN) fecal coliforms and E. coli (283/299, 95%). In contrast, 81% (242/300) of MAR water samples had no or low risk level fecal coliforms (0-10 MPN), of which 60% (179/300) had no fecal coliforms. We detected no or low risk level E. coli in 94% (283/300) of MAR water samples of these 80% (240/300) had no E. coli. MAR samples had lower mean log10 MPN fecal coliforms (-2.37; 95% CI: -2.56, -2.19) and E. coli (-2.26; 95% CI: - 2.43, -2.09) than pond water; microbial reductions remained consistent during the wet (May-October) and dry seasons. MAR-systems provided water with reduced fecal indicator bacteria compared to infiltered pond water.

microbiology↗

bioRxiv2020

Gold-standard diagnostics are tarnished by lytic bacteriophage

BackgroundA fundamental clinical and scientific concern is how lytic bacteriophage, as well as antibiotics, impact diagnostic positivity. MethodsCholera was chosen as a model disease to investigate this important question. Patients with diarrheal disease were enrolled at two remote hospitals in Bangladesh. Diagnostic performance was assessed as a function of lytic bacteriophage detection, as well as exposure to the first-line antibiotic azithromycin detected by mass spectrometry. ResultsAmong diarrheal samples positive by nanoliter quantitative PCR for Vibrio cholerae (n=78/849), the odds that a rapid diagnostic test (RDT) or qPCR was positive was reduced by 89% (OR 0.108; 95%CI 0.002-0.872) and 87% (OR 0.130; 95%CI 0.022-0.649) when lytic bacteriophage were detected, respectively. The odds that a rapid diagnostic test (RDT) or qPCR was positive was reduced by more than 99% (OR 0.00; 95% CI: 0.00-0.28) and 89% (OR 0.11; 95% CI: 0.03-0.44) when azithromycin was detected, respectively. ConclusionsEstimations of cholera burden may improve by accommodating for the negative effect of antimicrobial exposure on diagnostic positivity. Furthermore, the findings herein challenge our current approach to interpreting and developing bacterial diagnostics given variable rates of lytic bacteriophage and antibiotic exposure.

microbiology↗

bioRxiv2019

iPromoter-BnCNN: a Novel Branched CNN Based Predictor for Identifying and Classifying Sigma Promoters

MotivationPromoter is a short region of DNA which is responsible for initiating transcription of specific genes. Development of computational tools for automatic identification of promoters is in high demand. According to the difference of functions, promoters can be of different types. Promoters may have both intra and inter class variation and similarity in terms of consensus sequences. Accurate classification of various types of sigma promoters still remains a challenge. ResultsWe present iPromoter-BnCNN for identification and accurate classification of six types of promoters -{sigma} 24,{sigma} 28,{sigma} 32,{sigma} 38,{sigma} 54,{sigma} 70. It is a CNN based classifier which combines local features related to monomer nucleotide sequence, trimer nucleotide sequence, dimer structural properties and trimer structural properties through the use of parallel branching. We conducted experiments on a benchmark dataset and compared with six state-of-the-art tools to show our supremacy on 5-fold cross-validation. Moreover, we tested our classifier on an independent test dataset. AvailabilityOur proposed tool iPromoter-BnCNN web server is freely available at http://103.109.52.8/iPromoter-BnCNN. The runnable source code can be found here. Contactrafeed@cse.uiu.ac.bd Supplementary informationSupplementary data (benchmark dataset, independent test dataset, model files, structural property information, attention mechanism details and web server usage) are available at Bioinformatics. online.

genomics↗

bioRxiv2019

Immunoinformatic and dynamic simulation-based designing of a multi-epitope vaccine against emerging pathogen Elizabethkingia anophelis

Elizabethkingia anophelis is an emerging human pathogen causing neonatal meningitis, catheter-associated infections and nosocomial outbreaks with high mortality rates. Besides, they are resistant to most antibiotics used in empirical therapy. In this study, therefore, we used immunoinformatic approaches to design an epitope-based vaccine against E. anophelis as an alternative preventive measure. Initially, T-cell (CTL and HTL) and B-cell (LBL) epitopes were predicted from the highest antigenic protein. The CTL and HTL epitopes together had a population coverage of 99.97% around the world. Eventually, 6 CTL, 7 HTL, and 2 LBL epitopes were selected and used to construct a multiepitope vaccine. The vaccine protein was found to be highly immunogenic, non-allergenic, and non-toxic. Codon adaptation and in silico cloning were performed to ensure better expression within E. coli K12 host system. The stability of the vaccine structure was also improved by disulphide bridging. In addition, molecular docking and dynamic simulation revealed good and stable binding affinity between the vaccine and receptor. The immune simulation showed higher levels of T-cell and B-cell activities which was in coherence with actual immune response. Repeated exposure simulation resulted in higher clonal selection and faster antigen clearance. Nevertheless, experimental validation is required to ensure the immunogenic potency and safety of this vaccine to control E. anophelis infection in the future.

bioinformatics↗

bioRxiv2019

Megacities as drivers of national outbreaks: the role of holiday travel in the spread of infectious diseases

Human mobility connects populations and can lead to large fluctuations in population density, both of which are important drivers of epidemics. Measuring population mobility during infectious disease outbreaks is challenging, but is a particularly important goal in the context of rapidly growing and highly connected urban centers in low and middle income countries, which can act to amplify and spread local epidemics nationally and internationally. Here, we combine estimates of population movement from mobile phone data for over 4 million subscribers in the megacity of Dhaka, Bangladesh, one of the most densely populated cities globally. We combine mobility data with epidemiological data from a household survey, to understand the role of population mobility on the spatial spread of the mosquito-borne virus chikungunya within and outside Dhaka city during a large outbreak in 2017. The peak of the 2017 chikungunya outbreak in Dhaka coincided with the annual Eid holidays, during which large numbers of people traveled from Dhaka to their native region in other parts of the country. We show that regular population fluxes around Dhaka city played a significant role in determining disease risk, and that travel during Eid was crucial to the spread of the infection to the rest of the country. Our results highlight the impact of large-scale population movements, for example during holidays, on the spread of infectious diseases. These dynamics are difficult to capture using traditional approaches, and we compare our results to a standard diffusion model, to highlight the value of real-time data from mobile phones for outbreak analysis, forecasting, and surveillance.

ecology↗

bioRxiv2019

Bioaccumulation of heavy metals in commercially important fish species from the tropical river estuary suggests higher potential child health risk than adults

The Karnaphuli, a major river of Bangladesh, located off the coast of Chittagong in the Bay of Bengal is largely exposed to the heavy metal pollutants, which may be toxic to humans and aquatic fauna. The estuary is a striking example of a site where human pressure and ecological values collide with each other. In spite of being a major supplier of fish food for local community, there has been no study carried out to date to assess the potential human health risk due to heavy metal contamination in the fish species from this estuary. Therefore, the aim of present study was to assess bioaccumulation status and the potential human health risk evaluation for local consumers. Six commercially important fish species, Apocryptes bato, Pampus chinensis, Hyporhamphus limbatus, Liza parsia, Mugil cephalus, and Tenualosa toil from the Karnaphuli River estuary were collected to analyze heavy metals concentration level. Heavy metals As, Pb, Cd, Cr and Cu were detected from the samples using inductively coupled plasma mass spectrometry (Model: ELAN9000, Perkin-Elmer, Germany). The hierarchy of the measured concentration level of the metals was as follows: Pb (mean: 13.88, range: 3.19 - 6.19) > Cu (mean: 12.10, range: 10.27 - 16.41) > As (mean: 4.89, range: 3.19 - 6.19) > Cr (mean: 3.36, range: 2.46 - 4.17) > Cd (mean: 0.39, range: 0.21 - 0.74). The Fultons condition factor denoted that organisms were particularly in better condition and most of the species were in positive allometric growth. The Bioaccumulation factors (BAFs) observed in the species of the contaminants were organized in the following ranks: Cu (1971.42) > As (1042.93) > Pb (913.66) > Cr (864.99) > Cd (252.03), and among all the specimens, demersal fish, A. bato corresponded to the maximum bio-accumulative organism. Estimated daily intake (EDI), target hazard quotient (THQ) and carcinogenic risk (CR) assessed for human health risk implications suggest that the values are within the acceptable threshold for all sorts of consumers. Hence none of them would experience non-carcinogenic and carcinogenic health effect for the ingestion of the fishes. However, children are shown to be largely susceptible than adults to non-carcinogenic and carcinogenic health effect due to the consumption of fish. Therefore, an appropriate guidlines and robust management measures needed to be taken to restore the estuarine health condition for greater benefit of the quality of fish products for local consumption.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC=\"FIGDIR/small/681478v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (28K):\norg.highwire.dtl.DTLVardef@802d07org.highwire.dtl.DTLVardef@10c300eorg.highwire.dtl.DTLVardef@126f608org.highwire.dtl.DTLVardef@e28cf0_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2018

Trends and projections of universal health coverage indicators in Ghana, 1995-2030: A national and subnational study

Ghana has made significant stride towards universal health coverage (UHC) by implementing the National Health Insurance Scheme (NHIS) in 2003. This paper investigates the progress of UHC indicators in Ghana from 1995 to 2030 and makes future predictions up to 2030 to assess the probability of achieving UHC targets. National representative surveys of Ghana were used to assess health service coverage and financial risk protection. The analysis estimated the coverage of 13 prevention and four treatment service indicators at the national level and across wealth quintiles. In addition, this analysis calculated catastrophic health payments and impoverishment to assess financial hardship and used a Bayesian regression model to estimate trends and future projections as well as the probabilities of achieving UHC targets by 2030. Wealth-based inequalities and regional disparities were also assessed. At the national level, 14 out of the 17 health service indicators are projected to reach the target of 80% coverage by 2030. Across wealth quintiles, inequalities were observed amongst most indicators with richer groups obtaining more coverage than their poorer counterparts. Subnational analysis revealed while all regions will achieve the 80% coverage target with high probabilities for prevention services, the same cannot be applied to treatment services. In 2015, the proportion of households that suffered catastrophic health payments and impoverishment at a threshold of 25% non-food expenditure were 1.9% (95%CrI: 0.9-3.5) and 0.4% (95%CrI: 0.2-0.8), respectively. These are projected to reduce to less than 0.5% by 2030. Inequality measures and subnational assessment revealed that catastrophic expenditure experienced by wealth quintiles and regions are not equal. Significant improvements were seen in both health service coverage and financial risk protection as a result of NHIS. However, inequalities across wealth quintiles and at the subnational level continue to be cause of concerns. Further efforts are needed to narrow these inequality gaps.

scientific communication and education↗

bioRxiv2018

Network-based genetic profiling, and therapeutic target identification of Thyroid Cancer

Pathogenic mechanisms that underlie malignant follicular thyroid carcinoma (FTC) development are poorly understood. To identify key genes and pathways driving malignant behaviour we employed a system biology-based integrative analyses comparing FTC transcriptomes with a similar but benign lesion, follicular thyroid adenoma (FTA). We identified differentially expressed genes (DEGs) in microarray gene expression datasets (n=52) of FTCs and FTA tissues. Pathway analyses of DEGs using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) resources revealed significant pathways, and pathway hub genes using protein-protein interactions (PPI). We identified 598 DEGs (relative to FTAs) in FTCs and 12 significant pathways with altered expression in FTC. 10 GO groups were significantly connected with FTC-high expression DEGs and 80 with low-FTC expression. PPI analysis identified 12 potential hub genes based on degree and betweenness centrality. Moreover, 10 transcription factors (TFs) were identified that may underlie DEG expression as well as a number of microRNA (miRNAs). Thus, we identified DEGs, pathways, TFs and miRNAs that reflect molecular mechanisms differing between FTC and benign FTA. These may constitute biomarkers that distinguish these lesions and, given the similarities and common origin of the lesions, they may also be indicators of malignant progression potential.

bioinformatics↗

bioRxiv2018

Oligomeric α-synuclein-specific degradation by HtrA2/Omi to bestow a neuroprotective function

Although the malfunction of HtrA2/Omi leads to Parkinsons disease (PD), the underlying mechanism has remained unknown. Here, we showed that HtrA2/Omi specifically removed oligomeric -Syn but not monomeric -Syn to protect oligomeric -Syn-induced neurodegeneration. Experiments using mnd2 mice indicated that HtrA2/Omi degraded oligomeric -Syn specifically without affecting monomers. Transgenic Drosophila melanogaster experiments of the co-expression -Syn and HtrA2/Omi and expression of genes individually also confirmed that pan-neuronal expression of HtrA2/Omi completely rescued Parkinsonism in the -Syn-induced PD Drosophila model by specifically removing oligomeric -Syn. HtrA2/Omi maintained the health and integrity of the brain and extended the life span of transgenic flies. Because HtrA2/Omi specifically degraded oligomeric -Syn, co-expression of HtrA2/Omi and -Syn in Drosophila eye maintained a healthy retina, while the expression of -Syn induced retinal degeneration. This work showed that the bacterial function of HtrA to degrade toxic misfolded proteins is evolutionarily conserved in mammalian brains as HtrA2/Omi.

neuroscience↗

bioRxiv2018

Extinction recall of fear memories formed before stress is not affected despite amygdalar hyperactivity

Stress is known to exert its detrimental effects not only by enhancing fear, but also by impairing its extinction. However, in earlier studies stress exposure invariably preceded both processes. Thus, compared to unstressed animals, stressed animals had to extinguish fear memories from higher levels of freezing caused by prior exposure to stress. Here we decouple the two processes to examine if stress specifically impairs fear extinction. Strikingly, when fear memories were formed before stress exposure, thereby allowing animals to initiate extinction from comparable levels of fear, recall of fear extinction was unaffected. Despite this we observed a persistent increase in theta activity in the BLA. Theta activity in the mPFC, by contrast, was normal. Stress also disrupted mPFC-BLA theta-frequency synchrony and directional coupling. Thus, in the absence of the fear-enhancing effects of stress, the expression of fear reflects normal regulation of mPFC activity, not stress-induced hyperactivity in the amygdala.

neuroscience↗