Papers by Muhammad Hossain
Turkish Journal of Biology
The strawberry (Fragaria sp.) is one of the most popular fruits in the world. It is eaten raw or ... more The strawberry (Fragaria sp.) is one of the most popular fruits in the world. It is eaten raw or used in making juice, desserts, jam, syrup, and wine. The leaves are used in blended herbal tea. Leaves and roots are believed to have medicinal properties. The fruit juice is used externally to counteract sunburn, skin blemishes, and discolored teeth (1).
PLOS ONE, 2021
Obesity is an enduring medical issue that has raised concerns around the world. Natural plant ext... more Obesity is an enduring medical issue that has raised concerns around the world. Natural plant extracts have shown therapeutic potential in preventing oxidative stress and inflammation related to obesity complications. In this study,Senna alexandrinaMill. leaves were utilized to treat high-fat diet-related metabolic disorders and non-alcoholic fatty liver diseases. Plasma biochemical assays were conducted to determine the lipid profiles and oxidative stress parameters, and the gene expression of antioxidant enzymes and inflammatory mediators was measured. Histological stained livers of high-fat diet-fed rats were observed.S.alexandrinaleaf powder supplementation prevented the increase in cholesterol and triglyceride levels in high-fat diet-fed rats. Moreover,S.alexandrinaleaves also reduced lipid peroxidation and nitric oxide production in these rats. Prevention of oxidative stress byS.alexandrinaleaf supplementation in high-fat diet-fed rats is regulated by enhancing the antioxidant...
Cholera can result in the expulsion of important microbiota from the gut and result in death if l... more Cholera can result in the expulsion of important microbiota from the gut and result in death if left untreated. The disease transmits mainly via drinking water carrying Vibrio cholerae; and household contacts (HHC) of cholera patients are at elevated risk during the first week of infection. The gut microbiota profiles of HHC-children of cholera patients at Dhaka city slums were investigated before (day 0) and after (day 8) delivery of chlorinated water as part of the cholera-hospital-based intervention for 7 days (CHoBI7), a randomized controlled trial. Results of sequencing and analysis of bacterial community DNA revealed the predominance of two bacterial phyla: Bacteroidetes and Firmicutes at day 0 with a relative abundance of 62 ± 6 (mean ± SEM %) and 32 ± 7, respectively. The pattern reversed at day 8 with a decreased relative abundance of Bacteroidetes (39 ± 12) and an increased abundance of Firmicutes (49 ± 12). Of 65 bacterial families confirmed at day 0, six belonging to Pro...
Current Pollution Reports, 2021
The episodic outbreak of COVID-19 due to SARS-CoV-2 is severely affecting the economy, and the gl... more The episodic outbreak of COVID-19 due to SARS-CoV-2 is severely affecting the economy, and the global count of infected patients is increasing. The actual number of patients had been underestimated due to limited facilities for testing as well as asymptomatic nature of the expression of COVID-19 on individual basis. Tragically, for emerging economies with high population density, the situation has been more complex due to insufficient testing facilities for diagnosis of the disease. However, the recent reports about persistent shedding of viral RNA of SARS-CoV-2 in the human feces have created a possibility to track the prevalence and trends of the disease in communities, known as wastewater-based epidemiology (WBE). In this article, we highlight the current limitations and future prospects for WBE to manage pandemics.
Scientific Reports, 2020
Escherichia coli is a pathogen commonly encountered in clinical laboratories, and is capable of c... more Escherichia coli is a pathogen commonly encountered in clinical laboratories, and is capable of causing a variety of diseases, both within the intestinal tract (intestinal pathogenic strains) and outside (extraintestinal pathogenic E. coli, or ExPEC). It is associated with urinary tract infections (UTIs), one of the most common infectious diseases in the world. This report represents the first comparative analysis of the draft genome sequences of 11 uropathogenic E. coli (UPEC) strains isolated from two tertiary hospitals located in Dhaka and Sylhet, Bangladesh, and is focused on comparing their genomic characteristics to each other and to other available UPEC strains. Multilocus sequence typing (MLST) confirmed the strains belong to ST59, ST131, ST219, ST361, ST410, ST448 and ST4204, with one of the isolates classified as a previously undocumented ST. De novo identification of the antibiotic resistance genes blaNDM-5, blaNDM-7, blaCTX-M-15 and blaOXA-1 was determined, and phenotypi...
Recently the first genome sequence for a Severe acute respiratory syndrome coronavirus 2 or SARS-... more Recently the first genome sequence for a Severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2 isolate from Bangladesh became available. The sequencing was carried out by the Child Health Research Foundation and provided the first insight into the genetic details of the viral strain responsible for the SARS-CoV-2 infections in Bangladesh. Here we carried out a comparative study were we explored the phylogenetic relationship between the Bangladeshi isolate with other isolates from different parts of the world. Afterwards we identified single nucleotide variants in the Bangladeshi isolate, using the Wuhan virus reference sequence. We found a total of 9 variants in the Bangladeshi isolate using 2 separate tools. Barring 2, the rest of these variants were also observed in other isolates from different countries. Most of the variants occurred in the ORF1ab gen. Another noteworthy finding was a sequence of three consecutive variants in the N protein gene that were observed in othe...
Whole-genome sequencing (WGS) is a comprehensive method for analysing entire genomes and this has... more Whole-genome sequencing (WGS) is a comprehensive method for analysing entire genomes and this has been instrumental in characterizing the single nucleotide polymorphisms associated with different diseases including cancer, diabetes, cardiovascular diseases and many others. In this paper we undertake a pilot study for sequencing four Bangladeshi individuals and profiling their single nucleotide variants. Our findings shed possible light on specific biological pathways effected by such variants in this population.
The Severe Acute Respiratory Syndrome Coronavirus 2 or COVID-19 has been the cause of a global pa... more The Severe Acute Respiratory Syndrome Coronavirus 2 or COVID-19 has been the cause of a global pandemic in 2020. With the numbers infected rising well above a 100,000 and confirmed deaths above 4000, it has become the paramount health concern for the global community at present. The COVID-19 genome has since been sequenced and its predicted proteome identified. In this study, we looked at the expected COVID-19 proteins and compare them to its close relative, the Severe Acute Respiratory Syndrome-Related Coronavirus. In particular we focussed on the M protein which is known to play a significant role in the virion structure of Coronaviruses. The rationale here was that since the major risk factor associated with COVID-19 was its ease of spread, we wished to focus on the viral structure and architecture to look for clues that may indicate structural stability, thus prolonging the time span for which it can survive free of a host. As a result of the study, we found some rather interest...
FEMS Microbiology Letters, 2020
Morganella morganii, a gram negative, facultative anaerobic bacterium belonging to the Proteeae t... more Morganella morganii, a gram negative, facultative anaerobic bacterium belonging to the Proteeae tribe of the Morganellaceae family, is an unusual opportunistic pathogen mainly responsible for nosocomial and urinary tract infections. While cattle have long been established as a source of a few zoonotic pathogens, no such data has been recorded for M. morganii despite its ubiquitous presence in nature and a number of animal hosts. In this study, draft genomes were produced of three M. morganii isolates from Bangladeshi cattle. The three isolates, named B2, B3 and B5, possessed an average genome size of 3.9 Mp, a GC% of ∼51% and pan and core genomes of 4637 and 3812 genes, respectively. All strains were bearers of the qnrD1 carrying plasmid Col3M and possessed roughly similar virulence profiles and prophage regions. The strains also carried genes that were unique when compared with other publicly available M. morganii genomes. Many of these genes belonged to metabolic pathways associat...
RNA editing is a form of post-transcriptional modification that results in changes to the messeng... more RNA editing is a form of post-transcriptional modification that results in changes to the messenger RNA sequence. At the onset of the study we focused on detecting the changes in RNA editing patterns in cell lines exposed to hypoxic conditions followed by the detection of changes in RNA editing patterns in the fetuses of preeclamptic mothers using publicly available RNA sequence data from the NCBI SRA database. The results showed an increase in RNA editing activity in hypoxic cell lines and a decrease in RNA editing activity in the fetuses with preeclamptic mothers. A total of 85 genes common in the cell lines and 33 in the fetus disease models and not present in controls were identified as harboring editing sites in exonic, downstream, upstream or splicing regions. Subsequently we focused on unique editing sites in genes and categorized in order of relevance to Preeclampsia as A, B and C (A being most closely related to the disease and C the least). The genes implicated ones involv...
Journal of Tuberculosis Research, 2018
Background: The number of reported MDR-TB cases has been increasing in recent years. Objectives: ... more Background: The number of reported MDR-TB cases has been increasing in recent years. Objectives: To describe the epidemiological profile of MDR-TB cases in Bangladesh. Design: This was a descriptive cross-sectional study. Settings: The study was conducted among the multi drug resistant tuberculosis patient admitted in the National Institute of Diseases of the Chest and Hospital (NIDCH) Dhaka, Bangladesh. Samples: 148 confirmed cases of MDR-TB. Materials and Methods: Hospital admitted MRD-TB cases were randomly chosen from the above mentioned hospital. Semi-structured and pretested questionnaire were introduced by researcher. Clinical and treatment data i.e. duration of TB drug intake, report of sputum, X-ray and blood test etc. were extracted from the hospital record. Results: Study found, majority of the participants (56.1%) were in the age group of 16-30 years. 64.2% of the study subjects were married. Majority of the participants education were whether under primary or primary level. 24.3% participant's family member and 14.5% of neighbor were having TB. Most common comorbidity were diabetes, pulmonary infection, hearing loss, psychiatric symptoms, chest pain, joint pain etc. 63.5% respondent had high degree of AFB for sputum positivity and more than 98% had positive finding in X-ray chest. On an average ESR was low and also few cases of extremely low ESR were found. 71.6% were under twenty four months regimen. Conclusion: We can conclude that, many possible factors for MDR-TB.
Major Depressive Disorder (MDD) is one of the most significant psychiatric disorders in the world... more Major Depressive Disorder (MDD) is one of the most significant psychiatric disorders in the world today. Its incidence is widespread in society and its heavy adverse impact on the quality of life is well documented. Previously genetic studies on MDD had identified a hereditary component of the disease as well as crediting RNA editing with a role in its development. The later due to an overexpression of a heavily edited isoform of the Serotonin 2c receptor. Here we used publicly available RNA sequence data from suicide patients diagnosed with MDD as well as controls for identifying RNA editing sites unique to MDD. After variant calling and several steps of filtering, we identified 142 unique RNA editing sites in the MDD patients. These included intronic, downstream, UTR3 and exonic edits. The latter comprising several amino acid changes in the encoded protein. The genes implicated to be uniquely edited in MDD included the aforementioned and previously implicated Serotonin 2c receptor...
Virusdisease, 2018
Influenza A virus subtype H3 is a threat to public health and it is important to understand the e... more Influenza A virus subtype H3 is a threat to public health and it is important to understand the evolution of the viruses for the surveillance and the selection of vaccine strains. Comparative analysis of four Bangladeshi isolates with isolates circulating other parts of the world based on three candidate genes hemagglutinin (HA), neuraminidase (NA), matrix protein (MA) showed no evidence of significant distinct subclade of viruses circulating in the country over the period of study. Despite these findings, we found N161S substitution in all four H3N2 influenza stains resulting in the gain of NSS160-162 glycosylation site. All H3N2 Influenza subtypes in the study had amino acid substitution at position 31 on the M2 protein (Aspartic acid to Asparagine) which is known to be responsible for amantadine drug resistance.
Genome announcements, Jan 8, 2018
We report here the first draft genome sequence of the non-O1/non-O139strain VcN1, isolated from D... more We report here the first draft genome sequence of the non-O1/non-O139strain VcN1, isolated from Dhaka, Bangladesh. The data submitted to GenBank for this strain will contribute to advancing our understanding of this environmentally disseminated bacterium, including its virulence and its evolution as an important pathogen.
BMC genomics, Jan 23, 2015
Streptococcus uberis, a Gram-positive, catalase-negative member of the family Streptococcaceae is... more Streptococcus uberis, a Gram-positive, catalase-negative member of the family Streptococcaceae is an important environmental pathogen responsible for a significant proportion of subclinical and clinical bovine intramammary infections. Currently, the genome of only a single reference strain (0140J) has been described. Here we present a comparative analysis of complete draft genome sequences of an additional twelve S. uberis strains. Pan and core genome analysis revealed the core genome common to all strains to be 1,550 genes in 1,509 orthologous clusters, complemented by 115-246 accessory genes present in one or more S. uberis strains but absent in the reference strain 0140J. Most of the previously predicted virulent genes were present in the core genome of all 13 strains but gene gain/loss was observed between the isolates in CDS associated with clustered regularly interspaced short palindromic repeats (CRISPRs), prophage and bacteriocin production. Experimental challenge experiment...
Effects of colour illumination on multiple shoot regeneration from runner tip explants of strawbe... more Effects of colour illumination on multiple shoot regeneration from runner tip explants of strawberry were studied. Six colour (mixed, white, red, yellow, blue and green) illuminations were used in this study and among them mixed colour illumination showed the high percentage of shoot proliferation. Fresh and dry weights were also significantly higher under the mixed colour condition. Proliferated shoots showed 100% rooting in half strength of MS media. Plantlets were established successfully in soil.
PeerJ, 2014
The aim of this study was to determine the prevalence of amoebic infection in nonhuman primates (... more The aim of this study was to determine the prevalence of amoebic infection in nonhuman primates (NHPs) from six Zoological gardens in the United Kingdom. Initially, 126 faecal samples were collected from 37 individually identified NHPs at Twycross Zoo, UK, and were subjected to microscopic examination. A subsequent, nationwide experiment included 350 faecal samples from 89 individually identified NHPs and 73 unidentified NHPs from a number of UK captive wildlife facilities: Twycross Zoo (n = 60), Colchester Zoo (n = 3), Edinburgh Zoo (n = 6), Port Lympne Wild Animal Park (n = 58), Howletts Wild Animal Park (n = 31), and Cotswold Wildlife Park (n = 4). Samples were examined by PCR and sequencing using four specific primer sets designed to differentiate between the pathogenic E. histolytica, the non-pathogenic E. dispar, and non-pathogenic uninucleate cystproducing Entamoeba species. In the first experiment, Entamoeba was detected in 30 primates (81.1%). Six (16.2%) primates were infected with E. histolytica species complex. The highest carriage of Entamoeba species was found in Old World Colobinae primates. In the nationwide experiment, molecular analysis of faecal samples revealed notable rates of Entamoeba infection (101 samples, 28.9%), including one sample infected with E. histolytica, 14 samples with E. dispar, and 86 samples with uninucleated-cyst producing Entamoeba species. Sequences of positive uninucleatedcyst producing Entamoeba samples from Twycross Zoo clustered with the E. polecki reference sequences ST4 reported in Homo sapiens, and are widely separated from other Entamoeba species. These findings suggest a low prevalence of the pathogenic Entamoeba infection, but notable prevalence of non-pathogenic E. polecki infection in NHPs in the UK.
Case Reports in Endocrinology, 2013
Adrenocortical tumors (ACTs) causing Cushing's syndrome are extremely rare in children and adoles... more Adrenocortical tumors (ACTs) causing Cushing's syndrome are extremely rare in children and adolescents. Bilateral macronodular adrenocortical disease which is a component of the McCune-Albright syndrome is the most common cause of endogenous Cushing's syndrome. We report the case of a boy with Cushing's syndrome who presented with obesity and growth retardation. The child was hypertensive. The biochemical evaluation revealed that his serum cortisol levels were 25.80 g/dL, with a concomitant plasma ACTH level of 10.0 pg/mL and nonsuppressed serum cortisol on high-dose dexamethasone suppression test (HDDST) to be 20.38 g/dL. Computed tomography of the abdomen demonstrated a 8 × 6 × 5 cm left adrenal mass with internal calcifications. Following preoperative stabilization, laparotomy was carried out which revealed a lobulated left adrenal mass with intact capsule weighing 120 grams. Histopathological examination revealed a benign cortical neoplastic lesion, suggestive of adrenal adenoma; composed of large polygonal cells with centrally placed nuclei and prominent nucleoli without capsular and vascular invasion. On the seventh postoperative day, cortisol levels were within normal range indicating biochemical remission of Cushing's syndrome. On followup after three months, the patient showed significant clinical improvement and had lost moderate amount of weight and adrenal imaging was found to be normal.
Bangladesh Journal of Microbiology, 2010
Although the involvement of intestinal bacteria in the degradation of lignocellulosic materials i... more Although the involvement of intestinal bacteria in the degradation of lignocellulosic materials is poorly understood xylanolytic activity of termite has been studied extensively. The present study was designed to identify potential xylanolytic bacteria from termite intestine and the isolated bacterium was studied with a view to preparing low cost medium and optimizing the cultural conditions in Dubos liquid medium. The bacterium produced highest activity of the enzyme (0.86 U/ml) on birchwood xylan as carbon substrate. Wheat bran a relatively cheap lignocellulosic material was found as good inducer of the enzyme. When grown on 4% wheat bran in Dubos liquid medium with an initial pH 6.0 under shaking incubation at 200 rpm at 40°C for 24 h, the bacterium produced the maximum activity of the extracellular xylanase (1.5 U/ml). These results strongly indicated that the bacterium from the intestine in termite is able synthesize xylanase activity on various substrate and the enzyme product...
Scientia Horticulturae, 2009
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Papers by Muhammad Hossain