Evaluation of morphological traits, biochemical parameters and seeding availability pattern among Citrus limon 'Assam lemon' accessions across Assam

The Assam lemon is a highly valued Citrus cultivar known for its unique aroma, flavor, and appearance. This study aimed to investigate the morphological, seeding pattern and biochemical variations within 132 populations of Assam lemon from across 22 districts of Assam along with the control samples, with the objective to offer comprehensive understanding that could facilitate the improvement of breeding programs and further improvement of this important cultivar. Clustering based on UPGMA algorithm for morphological and seeding pattern data were analysed at population level, revealed two major clusters, where all the populations of Upper Assam districts were in the same cluster with the original stock (control population). The populations from Tinsukia and Dhemaji districts displayed more close similarities with the control population in comparison to populations of Upper Assam districts. Another interesting observation was regarding flowering patterns, while populations from Upper Assam districts excluding Golaghat district displayed both bisexual and unisexual flowers with less concentration of unisexual flowers, other remaining districts had bisexual and unisexual flowers of almost equal concentration. Unisexual flowers contained only the male reproductive organs with 40 anthers, while bisexual flowers had 36 anthers. Seeding patterns were examined across the districts, and it was found that populations from Tinsukia, Dhemaji, Lakhimpur, Dibrugarh, Jorhat, and the control population exhibited seedless characteristic while populations from other selected districts displayed a combination of seedless and seeded traits. Interestingly, Golaghat district appears as the linking district and showed availability of both seeded and seedless Assam lemon fruit, connecting the regions of Barak valley, Central, Lower, North and Upper Assam. Biochemical analysis showed significant variations across districts, however, the populations from Dhemaji, Tinsukia, Lakhimpur, Dibrugarh, and Jorhat districts displayed similarity with the control population. The study also investigated variability in soil nutrient content revealing substantial variation among the populations studied. This comprehensive investigation provides valuable insights into the morphological, seeding pattern, and biochemical diversity within the Assam lemon cultivar. These findings can be instrumental in breeding programs to enhance the cultivar, particularly in producing high-quality seedless fruits to meet consumer demands.

Genome-wide analysis of respiratory burst oxidase homolog (Rboh) genes in Aquilaria species and insight into ROS-mediated metabolites biosynthesis and resin deposition

Respiratory burst oxidase homolog (Rboh) generates reactive oxygen species (ROS) as a defense response during biotic and abiotic stress. In Aquilaria plants, wounding and fungal infection result in biosynthesis and deposition of secondary metabolites as defense responses, which later form constituents of fragrant resinous agarwood. During injury and fungal invasion, Aquilaria tree generates ROS species via the Rboh enzymes. Despite the implication of Rboh genes in agarwood formation, no comprehensive genomic-level study of the Rboh gene family in Aquilaria is present. A systematic illustration of their role during stress and involvement in initiating signal cascades for agarwood metabolite biosynthesis is missing. In this study, 14 Rboh genes were retrieved from genomes of two Aquilaria species, A. agallocha and A. sinensis, and were classified into five groups. The promoter regions of the genes had abundant of stress-responsive elements. Protein-protein network and in silico expression analysis suggested their functional association with MAPK proteins and transcription factors such as WRKY and MYC2. The study further explored the expression profiles of Rboh genes and found them to be differentially regulated in stress-induced callus and stem tissue, suggesting their involvement in ROS generation during stress in Aquilaria. Overall, the study provides in-depth insight into two Rboh genes, AaRbohC and AaRbohA, highlighting their role in defense against fungal and abiotic stress, and likely during initiation of agarwood formation through modulation of genes involved in secondary metabolites biosynthesis. The findings presented here offer valuable information about Rboh family members, which can be leveraged for further investigations into ROS-mediated regulation of agarwood formation in Aquilaria species.

Genome-wide investigation of Cytochrome P450 superfamily of Aquilaria agallocha: Association with terpenoids and phenylpropanoids biosynthesis

Agarwood is a dark resinous wood, produced when Aquilaria tree responds to wounding and microbial infection resulting in the accumulation of fragrant metabolites. Sesquiterpenoids and 2-(2-phenylethyl) chromones are the major phytochemicals in agarwood and Cytochrome P450s (CYPs) are one of the important enzymes in the biosynthesis of these fragrant chemicals. Thus, understanding the repertoire of CYP superfamily in Aquilaria can not only give insights into the fundamentals of agarwood formation, but can also provide a tool for the overproduction of the aroma chemicals. Therefore, current study was designed to investigate CYPs of an agarwood producing plant, Aquilaria agallocha. We identified 136 CYP genes from A. agallocha genome (AaCYPs) and classified them into 8 clans and 38 families. The promoter regions had stress and hormone-related cis-regulatory elements which indicate their participation in the stress response. Duplication and synteny analysis revealed segmental and tandem duplicated and evolutionary related CYP members in other plants. Potential members involved in the biosynthesis of sesquiterpenoids and phenylpropanoids were identified and found to be upregulated in methyl jasmonate-induced callus and infected Aquilaria trees by real-time quantitative PCR analyses. This study highlights the possible involvement of AaCYPs in agarwood resin development and their complex regulation during stress exposure.

Clinical outcomes in Covishield (ChAdOx1) and Covaxin (BBV-152) vaccinated individuals hospitalized with the Delta variant (B.1.617.2)

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The Delta variant of severe acute respiratory syndrome coronavirus-2 is the predominant variant causing breakthrough infections in India.

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Disease severity was significantly lower in vaccinated individuals.

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Mortality reduced by >50% in fully vaccinated (two doses) individuals.

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Vaccinated individuals had higher antibody levels and lower inflammatory markers.

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Vaccinated deceased individuals mounted a minimal antibody response.

Background

Covishield (ChAdOx) and Covaxin (BBV-152) are the mainstream vaccines against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) used in India and a few other countries.

Objective

To assess the clinical outcomes of patients hospitalized with coronavirus disease 2019 (COVID-19) who had been vaccinated with either Covishield or Covaxin.

Methods

This prospective, single-centre, observational cohort study of 1160 patients hospitalized with COVID-19 was conducted between April and June 2021. Severity of disease at admission and during hospitalization, requirement for intensive care unit (ICU) admission and ventilatory support, inflammatory markers (C-reactive protein, ferritin, lactate dehydrogenase, D-dimer), neutralizing antibody levels and mortality were assessed in vaccinated and unvaccinated patients.

Results

More than 90% of patients in this study harboured the Delta variant (Pango lineage B.1.617.2) of SARS-CoV-2. Severity of disease at admission and during hospitalization (3.44% vs 7.51%; P=0.0032) and requirement for ICU admission and ventilatory support (2.83% vs 5.86%; P=0.0154) were significantly lower in vaccinated patients compared with unvaccinated patients. Vaccinated patients also had significantly (P<0.0001) higher antibody levels and lower inflammatory marker levels compared with unvaccinated patients. A subset of vaccinated, deceased patients mounted minimal antibody response [‘non-responders’: 4.53 (standard deviation 1.40) AU/mL].

Conclusion

These results demonstrate the effectiveness of Covishield and Covaxin against severe disease in patients hospitalized with COVID-19 with breakthrough infections caused by the Delta variant. Strategies targeting non-responders are desirable to minimize morbidity and mortality.

Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes

During the course of the COVID-19 pandemic, large-scale genome sequencing of SARS-CoV-2 has been useful in tracking its spread and in identifying variants of concern (VOC). Viral and host factors could contribute to variability within a host that can be captured in next-generation sequencing reads as intra-host single nucleotide variations (iSNVs). Analysing 1347 samples collected till June 2020, we recorded 16 410 iSNV sites throughout the SARS-CoV-2 genome. We found ∼42% of the iSNV sites to be reported as SNVs by 30 September 2020 in consensus sequences submitted to GISAID, which increased to ∼80% by 30th June 2021. Following this, analysis of another set of 1774 samples sequenced in India between November 2020 and May 2021 revealed that majority of the Delta (B.1.617.2) and Kappa (B.1.617.1) lineage-defining variations appeared as iSNVs before getting fixed in the population. Besides, mutations in RdRp as well as RNA-editing by APOBEC and ADAR deaminases seem to contribute to the differential prevalence of iSNVs in hosts. We also observe hyper-variability at functionally critical residues in Spike protein that could alter the antigenicity and may contribute to immune escape. Thus, tracking and functional annotation of iSNVs in ongoing genome surveillance programs could be important for early identification of potential variants of concern and actionable interventions.

Genome-wide detection and classification of terpene synthase genes in Aquilaria agallochum

Agarwood, one of the precious woods in the globe, is produced by Aquilaria plant species during an upshot of wounding and infection. Produced as a defence response, the dark, fragrant resin gets secreted in the plant's duramen, which is impregnated with fragrant molecules with the due course. Agarwood has gained worldwide popularity due to its high aromatic oil, fragrance, and pharmaceutical value, which makes it highly solicited by numerous industries. Predominant chemical constituents of agarwood, sesquiterpenoids, and 2-(2-phenylethyl) chromones have been scrutinized to comprehend the scientific nature of the fragrant wood and develop novel products. However, the genes involved in the biosynthesis of these aromatic compounds are still not comprehensively studied in Aquilaria. In this study, publicly available genomic and transcriptomics data of Aquilaria agallochum were integrated to identify putative functional terpene synthase genes (TPSs). The in silico study enabled us to identify ninety-six TPSs, of which thirty-nine full-length genes were systematically classified into TPS-a, TPS-b, TPS-c, TPS-e, TPS-f, and TPS-g subfamilies based on their gene structure, conserve motif, and phylogenetic comparison with TPSs from other plant species. Analysis of the cis-regulatory elements present upstream of AaTPSs revealed their association with hormone, stress and light responses. In silico expression studies detected their up-regulation in stress induced tissue. This study provides a basic understanding of terpene synthase gene repertoire in Aquilaria agallochum and unlatches opportunities for the biochemical characterization and biotechnological exploration of these genes.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01040-z.

An overview of basic molecular biology of SARS-CoV-2 and current COVID-19 prevention strategies

Coronavirus Disease 2019 (COVID-19) manifests as extreme acute respiratory conditions caused by a novel beta coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) which is reported to be the seventh coronavirus to infect humans. Like other SARS-CoVs it has a large positive-stranded RNA genome. But, specific furin site in the spike protein, mutation prone and phylogenetically mess open reading frame1ab (Orf1ab) separates SARS-CoV-2 from other RNA viruses. Since the outbreak (February-March 2020), researchers, scientists, and medical professionals are inspecting all possible facts and aspects including its replication, detection, and prevention strategies. This led to the prompt identification of its basic biology, genome characterization, structural and expression based functional information of proteins, and utilization of this information in optimizing strategies to prevent its spread. This review summarizes the recent updates on the basic molecular biology of SARS-CoV-2 and prevention strategies undertaken worldwide to tackle COVID-19. This recent information can be implemented for the development and designing of therapeutics against SARS-CoV-2.

Tissue-specific transcriptome recovery on withdrawal from chronic alcohol exposure in zebrafish

Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have documented altered behavior and physiology in zebrafish exposed to alcohol. In this work, we have identified the changes in the zebrafish transcriptome in response to chronic alcohol exposure. We have further followed the extent of transcriptional recovery upon withdrawal from alcohol and found evidence of tissue-specific responses. Our results indicate a greater extent of recovery of the brain transcriptome compared to the liver. We identify two distinct classes of genes in response to withdrawal from alcohol exposure - those that recover their pre-alcohol expression profile versus those that retain altered expression even after the fish are removed from the alcohol environment. Finally, we have examined gender-specific responses to alcohol exposure in zebrafish and find evidence for distinct alcohol tolerance levels. Upon chronic alcohol exposure, a higher percentage of genes show perturbation in expression profile in males compared to females. Female fish also recover better with more genes regaining the control expression level upon withdrawal from alcohol. Overall, our work identifies genes and pathways perturbed by exposure to alcohol, and demonstrates the extent of gender- and tissue-specific transcriptional changes associated with chronic alcoholism and withdrawal.

SARS-CoV-2 genomics: An Indian perspective on sequencing viral variants

Since its emergence as a pneumonia-like outbreak in the Chinese city of Wuhan in late 2019, the novel coronavirus disease COVID-19 has spread widely to become a global pandemic. The first case of COVID-19 in India was reported on 30 January 2020 and since then it has affected more than ten million people and resulted in around 150,000 deaths in the country. Over time, the viral genome has accumulated mutations as it passes through its human hosts, a common evolutionary mechanism found in all microorganisms. This has implications for disease surveillance and management, vaccines and therapeutics, and the emergence of reinfections. Sequencing the viral genome can help monitor these changes and provides an extraordinary opportunity to understand the genetic epidemiology and evolution of the virus as well as tracking its spread in a population. Here we review the past year in the context of the phylogenetic analysis of variants isolated over the course of the pandemic in India and highlight the importance of continued sequencing-based surveillance in the country.

Transcriptomic dataset of zebrafish tissues following chronic alcohol exposure and withdrawal

Alcohol is a psychoactive substance which has detrimental health effects upon consumption. Transcriptome profiling can provide insights into the dynamic changes in global gene expression profiles induced by chronic alcohol exposure and withdrawal. Male and female zebrafish were continually exposed to 0.5% ethanol for a period of 9 weeks. Upon completion of alcohol treatment, the fish were subjected to a withdrawal program for 9 weeks. Brain and liver tissues of control, alcohol exposed and withdrawal fish were isolated and the extracted RNA was sequenced on Illumina HiSeq 2000. The resultant paired end reads were mapped to the zebrafish reference genome (danRer10). The mapped transcripts were quantified for their expression and subjected to differential expression analysis across the three conditions. Gene ontology enrichment analysis of the differentially regulated genes was carried out to identify affected biological processes. The data for this project is available as a GEO dataset under Accession number GSE143416. The gene expression data discussed here accompanies the research article entitled ‘Tissue-specific transcriptome recovery on withdrawal from chronic alcohol exposure in zebrafish’.

A Distinct Phylogenetic Cluster of Indian Severe Acute Respiratory Syndrome Coronavirus 2 Isolates

BACKGROUND

From an isolated epidemic, coronavirus disease 2019 has now emerged as a global pandemic. The availability of genomes in the public domain after the epidemic provides a unique opportunity to understand the evolution and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus across the globe.

METHODS

We performed whole-genome sequencing of 303 Indian isolates, and we analyzed them in the context of publicly available data from India.

RESULTS

We describe a distinct phylogenetic cluster (Clade I/A3i) of SARS-CoV-2 genomes from India, which encompasses 22% of all genomes deposited in the public domain from India. Globally, approximately 2% of genomes, which to date could not be mapped to any distinct known cluster, fall within this clade.

CONCLUSIONS

The cluster is characterized by a core set of 4 genetic variants and has a nucleotide substitution rate of 1.1 × 10-3 variants per site per year, which is lower than the prevalent A2a cluster. Epidemiological assessments suggest that the common ancestor emerged at the end of January 2020 and possibly resulted in an outbreak followed by countrywide spread. To the best of our knowledge, this is the first comprehensive study characterizing this cluster of SARS-CoV-2 in India.

Sperm methylome alterations following yoga-based lifestyle intervention in patients of primary male infertility: A pilot study

A majority of the cases of primary male infertility are idiopathic with the underlying molecular mechanisms contributing to the pathophysiology as yet unknown. Effects of the environment can alter the sperm epigenome thereby impacting male reproductive health. Epigenetic mechanisms are crucial to understanding health and disease, and methylome alterations are now known to have far-reaching clinical implications. Here, we report the results from our pilot study, a first of its kind analysis of the effect of the traditional practice of yoga on human sperm quality. We find marked improvement in sperm characteristics in patients of idiopathic male infertility following a supervised 21-day yoga regimen. Furthermore, next-generation sequencing-based methylome analysis reveals alterations in the sperm epigenome of these patients. We find that the practice of yoga is associated with DNA methylation changes at nearly 400 genes, 147 of which were hypermethylated while 229 were hypomethylated. These included promoters of several genes linked to maintenance of fertility and genomic integrity. This novel piece of work draws a direct link between positive lifestyle practices and male reproductive health.

Determination of individual type 2 diabetes risk profile in the North East Indian population & its association with anthropometric parameters

Background & objectives:

Diabetes genomics research has illuminated single nucleotide polymorphism (SNP) in several genes including, fat mass and obesity associated (FTO) (rs9939609 and rs9926289), potassium voltage-gated channel subfamily J member 11 (rs5219), SLC30A8 (rs13266634) and peroxisome proliferator-activated receptor gamma 2 (rs1805192). The present study was conducted to investigate the involvement of these polymorphisms in conferring susceptibility to type 2 diabetes (T2D) in the North East Indian population, and also to establish their association with anthropometric parameters.

Methods:

DNA was extracted from blood samples of 155 patients with T2D and 100 controls. Genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing. To confirm the association between the inheritance of SNP and T2D development, logistic regression analysis was performed.

Results:

For the rs9939609 variant (FTO), the dominant model AA/(AT+TT) revealed significant association with T2D [odds ratio (OR)=2.03, P=0.021], but was non-significant post correction for multiple testing (P=0.002). For the rs13266634 variant (SLC30A8), there was considerable but non-significant difference in the distribution pattern of genotypic polymorphisms between the patients and the controls (P=0.004). Significant association was observed in case of the recessive model (CC+CT)/TT (OR=4.56 P=0.001), after adjusting for age, gender and body mass index. In addition, a significant association (P=0.001) of low-density lipoprotein (mg/dl) could be established with the FTO (rs9926289) polymorphism assuming dominant model.

Interpretation & conclusions:

The current study demonstrated a modest but significant effect of SLC30A8 (rs13266634) polymorphisms on T2D predisposition. Considering the burgeoning prevalence of T2D in the Indian population, the contribution of these genetic variants studied, to the ever-increasing number of T2D cases, appears to be relatively low. This study may serve as a foundation for performing future genome-wide association studies (GWAS) involving larger populations.

Discordance in Xpert® MTB/RIF assay results among low bacterial load clinical specimens in Bangladesh

BACKGROUND

The Xpert® MTB/RIF assay detects Mycobacterium tuberculosis (MTB) and rifampicin (RIF) resistance. RIF-resistant (RIF-R) MTB cases detected using Xpert on sputum specimens at three private-sector TB screening centres in Dhaka, Bangladesh, were subjected to consecutive confirmatory Xpert testing, the results of which were MTB-positive/RIF-susceptible, MTB-positive/RIF-indeterminate or MTB-negative.

OBJECTIVE

To assess the possible causes of discordant MTB and RIF-R results.

METHODS

Discordant confirmatory Xpert test results were subjected to further investigations using the GenoType® MTBDRplus assay, culture and rpoB gene sequencing.

RESULTS

The confirmatory Xpert test was performed on a remnant or a second specimen collected from individuals with an initial RIF-R result (n = 69); 22 (32%) results were discordant, 20 of which had an 'MTB detected-very low' result. Further investigations were mostly concordant with the confirmatory Xpert test. Average variability in paired cycle threshold (Ct) values were higher in 'MTB detected-very low' results vs. specimens with low, medium or high detected MTB results (P < 0.05); discordant results were mostly observed in specimens with 'MTB detected-very low' (20/22).

CONCLUSIONS

Repeating the Xpert test and comparing with other available tests should be considered in case of 'MTB detected-very low, RIF resistance detected' results on Xpert.

Effects of Resveratrol and Mangiferin on PPARγ and FALDH Gene Expressions in Adipose Tissue of Streptozotocin-Nicotinamide-Induced Diabetes in Rats

Type 2 diabetes (T2D) is characterized by insufficient insulin secretion by the pancreatic beta cells and insulin resistance in liver, skeletal muscle, and white adipose tissue. Adipose tissue plays a major role in glucose homeostasis and lipid metabolism. Dietary antioxidants such as resveratrol and mangiferin may offer some protection against the early stage of diabetes mellitus. Therefore, an attempt has been made to investigate the effects of resveratrol and mangiferin on biochemical parameters and molecular mechanism of PPARγ and FALDH gene expression in adipose tissue of streptozotocin- (STZ-) nicotinamide- (NA-) induced diabetic rats. Albino Wister rats were randomly divided into five groups: control rats (Group 1), diabetic control rats (Group 2), diabetic rats given resveratrol (40 mg/kg body weight per day; Group 3), diabetic rats given mangiferin (40 mg/kg body weight per day; Group 4), diabetic rats given glibenclamide (0.6 mg/kg body weight per day; Group 5). Serum biochemical parameters-total cholesterol (TC), total triglyceride (TG), low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, glycosylated hemoglobin (HbA1c), urea, and uric acid were analyzed. We found that the oral administration of resveratrol and mangiferin to STZ-NA-induced diabetic rats for 30 days showed the significant protective effect on all the biochemical parameters. A significant reduction in blood glucose and HbA1c levels was observed in rats treated with 40 mg/kg body weight per day of resveratrol or mangiferin. Moreover, both these antioxidants showed significant enhancement of PPARγ and FALDH gene expression in rat adipose tissue compared to control rats.

Comparative analysis of different dietary antioxidants on oxidative stress pathway genes in L6 myotubes under oxidative stress

Enhanced oxidative stress plays an important role in the progression and onset of diabetes and its complications. Strategies or efforts meant to reduce the oxidative stress are needed which may mitigate these pathogenic processes. The present study aims to investigate the in vitro ameliorative potential of nine antioxidant molecules in L6 myotubes under oxidative stress condition induced by 4-hydroxy-2-nonenal and also to comprehend the gene expression patterns of oxidative stress genes upon the supplementation of different antioxidants in induced stress condition. The study results demonstrated a marked increase in the level of malondialdehyde and protein carbonyl content with a subsequent increase in the free radicals that was reversed by the pretreatment of different dietary antioxidant. From the expression analysis of the oxidative stress genes, it is evident that the expression of these genes is modulated by the presence of antioxidants. The highest expression was found in the cells treated with Insulin in conjugation with an antioxidant. Resveratrol is the most potent modulator followed by Mangiferin, Estragole, and Capsaicin. This comparative analysis ascertains the potency of Resveratrol along with Insulin in scavenging the reactive oxygen species (ROS) generated under induced stress conditions through antioxidant defense mechanism against excessive ROS production, contributing to the prevention of oxidative damage in L6 myotubes.

Multidrug-resistant tuberculosis in Bangladesh: results from a sentinel surveillance system

BACKGROUND

Multidrug-resistant tuberculosis (MDR-TB) is a serious obstacle to successful TB control. The 2010-2011 Bangladesh Drug Resistance Survey (DRS) showed MDR-TB prevalence to be 7% overall, 1.4% in new and 28.5% in previously treated patients. We aimed to determine the rate of MDR-TB in selected sentinel sites in Bangladesh.

METHODS

Fourteen hospitals from the seven divisions in Bangladesh were selected as sentinel surveillance sites. Newly registered TB patients were systematically enrolled from August 2011 to December 2014. Sputum specimens were processed for culture and drug susceptibility testing by the proportion method using Löwenstein-Jensen medium.

RESULTS

Specimens from 1906 (84%) of 2270 enrolled patients were analysed. Isolates from 61 (3.2%) were identified as having MDR-TB. The proportion of MDR-TB was 2.3% among new and 13.8% among previously treated TB patients (P < 0.001). The overall proportion of MDR-TB was 3.2%:3.5% in males and 2.3% in females; by age, the MDR-TB rate was highest (5.2%) in those aged 65 years.

CONCLUSIONS

The high proportion of MDR-TB among new patients found in this sentinel surveillance significantly differs from that reported in the DRS. While the sentinel surveillance sites were not designed to be nationally representative, it is worrying to observe a higher number of MDR-TB cases among new patients.

Potential exposure to Australian bat lyssavirus is unlikely to prevent future bat handling among adults in South East Queensland

Despite ongoing public health messages about the risks associated with bat contact, the number of potential exposures to Australian bat lyssavirus (ABLV) due to intentional handling by members of the general public in Queensland has remained high. We sought to better understand the reasons for intentional handling among these members of the public who reported their potential exposure to inform future public health messages. We interviewed adults who resided in a defined geographic area in South East Queensland and notified potential exposure to ABLV due to intentional handling of bats by telephone between 1 January 2012 and 31 December 2013. The participation rate was 54%. Adults who reported they had intentionally handled bats in South East Queensland indicated high levels of knowledge and perception of a moderately high risk associated with bats with overall low intentions to handle bats in the future. However, substantial proportions of people would attempt to handle bats again in some circumstances, particularly to protect their children or pets. Fifty-two percent indicated that they would handle a bat if a child was about to pick up or touch a live bat, and 49% would intervene if a pet was interacting with a bat. Future public health communications should recognize the situations in which even people with highrisk perceptions of bats will attempt to handle them. Public health messages currently focus on avoidance of bats in all circumstances and recommend calling in a trained vaccinated handler, but messaging directed at adults for circumstances where children or pets may be potentially exposed should provide safe immediate management options.

Bioremoval of lead using Pennisetum purpureum augmented with Enterobacter cloacae-VITPASJ1: A pot culture approach

Lead is a toxic heavy metal discharged into the ecosystem from various industries. Biological remediation strategies have been effective in the bioremoval of lead. In our current study, a phytobacterial system using Pennisetum purpureum along with lead-resistant bacterium (LRB) was employed for the uptake of lead. The LRB was obtained from lead-contaminated sites. The isolate VITPASJ1 was found to be highly tolerant to lead and was identified as an effective plant growth-promoting bacterium. The 16S rRNA sequencing revealed VITPASJ1 to be the closest neighbour of Enterobacter cloacae. The lead-resistant gene pbrA in the plant and the bacterium were amplified using a specific primer. The uptake of lead was studied by phytoremediation and rhizoremediation set-ups where the soil was supplemented with various concentrations of lead (50, 100, 150 mg/kg). The plants were uprooted at regular intervals, and the translocation of lead into the plant was determined by atomic absorption spectroscopy. The root length, shoot height and chlorophyll content were found to be higher in the rhizoremediation set-up when compared to the phytoremediation set-up. The scanning electron microscopic micrographs gave a clear picture of increased tissue damage in the root and shoot of the phytoremediation set-up as compared to the rhizoremediation set-up with LRB.

Comparison of TaqMan(®) Array Card and MYCOTB(TM) with conventional phenotypic susceptibility testing in MDR-TB

BACKGROUND

Although phenotypic drug susceptibility testing (DST) is endorsed as the standard for second-line drug testing of Mycobacterium tuberculosis, it is slow and laborious.

METHODS

We evaluated the accuracy of two faster, easier methodologies that provide results for multiple drugs: a genotypic TaqMan(®) Array Card (TAC) and the Sensititre(®) MYCOTB(TM) plate. Both methods were tested at three central laboratories in Bangladesh, Tanzania, and Thailand with 212 multidrug-resistant tuberculosis (MDR-TB) isolates and compared with the laboratories' phenotypic method in use.

RESULTS

The overall accuracy for ethambutol, streptomycin, amikacin, kanamycin, ofloxacin, and moxifloxacin vs. the phenotypic standard was 87% for TAC (range 70-99) and 88% for the MYCOTB plate (range 76-98). To adjudicate discordances, we re-defined the standard as the consensus of the three methods, against which the TAC and MYCOTB plate yielded 94-95% accuracy, while the phenotypic result yielded 93%. Some isolates with genotypic mutations and high minimum inhibitory concentration (MIC) were phenotypically susceptible, and some isolates without mutations and low MIC were phenotypically resistant, questioning the phenotypic standard.

CONCLUSIONS

In our view, the TAC, the MYCOTB plate, and the conventional phenotypic method have similar performance for second-line drugs; however, the former methods offer speed, throughput, and quantitative DST information.

Detection of Cervical Cancer through Visual Inspection of Cervix with Acetic Acid (VIA) and Colposcopy at Mymensingh Medical College Hospital

Cervical cancer is the second most common cause of cancer related morbidity and mortality in women with 50% mortality rate. It is preventable if cervical cellular changes are detected and managed at early stage. This was a retrospective study conducted at VIA center of outpatient department and Colposcopy clinic at in-patient department of Mymensingh Medical College Hospital, Bangladesh covering a period from September 2013 to November 2014. Objective of this study was detection of cervical cancer and precancerous condition amongst patients reported to VIA center and Colposcopy clinic. In primary screening at VIA Center, total respondents were 3604, their mean age was 35.9 and highest were in the age group 31 to 40 years. At VIA center, 110(3.05%) were found positive and highest were between 31 to 40 years. In Colposcopy Clinic, out of 700 patients, 51.7% were CIN 1, 4.9% CIN 2, 1.4% CIN 3, invasive carcinoma was 0.3% and unsatisfactory or inconclusive were 34.3%. Most of the respondents were housewives and majority had poor monthly income. Amongst respondents, 72.1% were from rural area and Colposcopic findings revealed in 62.5% abnormal cervical changes, 46.5% were from rural area. Mean age at marriage or age at first coitus was found 16.25 years and 92.7% were in 11 to 20 years. Maximum abnormal cervical findings including CIN were between the ages ranged from 11 to 20 years of marriage age. In patients having 1 - 5 number of child having abnormal (58%) cervical changes, 48% were CIN 1. Histopathology reports found 19.6% CIN 1 (Total CIN 20.7%), cervical carcinoma 1.3%, inflammatory 7.0% and 0.42% cases were reported normal. Amongst 438 histopathology advised cases, 230 respondent's reports with patients were not available. VIA followed by Colposcopy has been a feasible, easy and reliable tools for screening cervical cancer in Bangladesh.

Relationship between Abnormal Cardiotocography and Fetal Outcome

Aims: This study aimed to determine the frequency of abnormal cardiotocography during labour and to evaluate the significance of these patterns in determining fetal well-being.Methods: This was cross-sectional study undertaken at sir Ganga Ram Hospital, Lahore from September 2009-September 2010. Hundred admitted pregnant women were enrolled for the study. Admission cardiotocography was done for 30 minutes in left lateral position and labeled as normal, suspicious or pathological. Suspicious pattern cardiotocography was repeated after hydration with 1000ml intavenous fluid and oxygen inhalation, if remained suspicious then action for delivery was taken. Mode of delivery was dependent on stage of labour.Results: Twenty three women had suspicious CTG traces and 77 had pathological.It was noticed that  the percentage of various mode of dellivery were not much different among suspicious and pathological CTG groups  with p value 0.668.The Apgar score observed as per mode delivery reveal that there was no  significant  association between Apgar score at 1 min and mode of delivery with pvalue 0.889. The association of poor Apgar in pathological CTG group was significant with p value 0.006. Fifteen (15.6%) neonates needed resuscitation and 81 (84.4%)did not require resuscitation.Conclusions: Abnormal CTG influence the fetal outcome, ie poor Apgar score at 1 min and 5 minutes, increased rate of caesarean section and neonatal resuscitation.

Smear Positive Tuberculosis amongst Suspects Reported to DOTS Corner of Mymensingh Medical College Hospital, Bangladesh

Sputum microscopy still remains the primary tool for the laboratory diagnosis of tuberculosis. A retrospective study was conducted in the directly observed treatment, short-course (DOTS) corner of Mymensingh Medical College Hospital (MMCH), in Bangladesh from May 2013 to May 2014. The study was designed to evaluate the extent of smear positive microscopy including multi-drug resistance (MDR) amongst tuberculosis suspected cases. A total of 2,361 Pulmonary Tuberculosis (PTB) suspects were noticed to DOTS corner during this period, with the mean age of 43 years. The male female ratio was 2.02:1 and the smear positivity rate was about 10%. Study found majority of the suspects were in the economically productive year of life 20-70 years. Smear negative suspects were not re-evaluated further, though smear negativity does not rule out absence of tuberculosis. Extra pulmonary or non tuberculous mycobacteria were not evaluated in this study. Twenty two patients 0.9% of total 2361 were identified as MDR during the study period where 61 clinically highly suspected cases were sent for GeneXpert that seems to be much lesser than the national rate (3.6% in new cases and 19% in retreated cases). The smear positivity rate of all three (1st, 2nd and 3rd) smear was 94.5%, all the second smear was 100% positive and the third were 95.47% positive. It is evident from this study that two smear microscopy was found sufficiently reliable to diagnose TB. However, further in depth prospective study might be undertaken to ascertain the scenario of this chronic diseases.

Molecular epidemiology of tuberculosis in rural Matlab, Bangladesh

OBJECTIVE

To characterise and classify clinical isolates collected from tuberculosis (TB) patients in rural Bangladesh and to investigate the mode of transmission.

DESIGN

An epidemiological study using a combination of conventional and molecular methods was performed in a rural population of Bangladesh. A total of 168 clinical isolates were collected from TB patients. Deletion analysis, used for rapid differentiation of members of the Mycobacterium tuberculosis complex, spoligotyping and variable number tandem repeats of mycobacterial interspersed repetitive units (VNTR-MIRU) typing were used.

RESULTS

Deletion analysis identified all isolates as M. tuberculosis and further divided them into 109 strains (65%) carrying the M. tuberculosis deletion region 1 (TbD1-intact or 'ancestral' strains) and 59 strains (35%) lacking this region (TbD1 or 'modern' strains). MIRU analyses showed that 149 strains (89%) had unique patterns, whereas 19 strains (11%) clustered into eight groups. The largest cluster comprised five TbD1 strains of the Beijing type. The rate of recent transmission was estimated to be 6.5%.

CONCLUSIONS

Our results suggest that TB in rural Bangladesh is caused primarily by reactivation of latent infections involving TbD1 intact strains, overlaid with the recent emergence of Beijing strain clusters that include multidrug-resistant isolates.

Association of postpartum maternal morbidities with children's mental, psychomotor and language development in rural Bangladesh

Little is known from developing countries about the effects of maternal morbidities diagnosed in the postpartum period on children's development. The study aimed to document the relationships of such morbidities with care-giving practices by mothers, children's developmental milestones and their language, mental and psychomotor development. Maternal morbidities were identified through physical examination at 6-9 weeks postpartum (n=488). Maternal care-giving practices and postnatal depression were assessed also at 6-9 weeks postpartum. Children's milestones of development were measured at six months, and their mental (MDI) and psychomotor (PDI) development, language comprehension and expression, and quality of psychosocial stimulation at home were assessed at 12 months. Several approaches were used for identifying the relationships among different maternal morbidities, diagnosed by physicians, with children's development. After controlling for the potential confounders, maternal anaemia diagnosed postpartum showed a small but significantly negative effect on children's language expression while the effects on language comprehension did not reach the significance level (p=0.085). Children's development at 12 months was related to psychosocial stimulation at home, nutritional status, education of parents, socioeconomic status, and care-giving practices of mothers at six weeks of age. Only a few mothers experienced each specific morbidity, and with the exception of anaemia, the sample-size was insufficient to make a conclusion regarding each specific morbidity. Further research with a sufficient sample-size of individual morbidities is required to determine the association of postpartum maternal morbidities with children's development.

On-line capacity-building program on "analysis of data" for medical educators in the South Asia region: a qualitative exploration of our experience

BACKGROUND AND OBJECTIVE

In medical education, using the World Wide Web is a new approach for building the capacity of faculty. However, there is little information available on medical education researchers' needs and their collective learning outcomes in such on-line environments. Hence, the present study attempted: 1)to identify needs for capacity-building of fellows in a faculty development program on the topic of data analysis; and 2) to describe, analyze and understand the collective learning outcomes of the fellows during this need-based on-line session.

MATERIALS AND METHODS

The present research is based on quantitative (on-line survey for needs assessment) and qualitative (contents of e-mails exchanged in listserv discussion) data which were generated during the October 2009 Mentoring and Learning (M-L) Web discussion on the topic of data analysis. The data sources were shared e-mail responses during the process of planning and executing the M-L Web discussion. Content analysis was undertaken and the categories of discussion were presented as a simple non-hierarchical typology which represents the collective learning of the project fellows.

RESULTS

We identified the types of learning needs on the topic 'Analysis of Data' to be addressed for faculty development in the field of education research. This need-based M-L Web discussion could then facilitate collective learning on such topics as 'basic concepts in statistics', tests of significance, Likert scale analysis, bivariate correlation, and simple regression analysis and content analysis of qualitative data.

CONCLUSIONS

Steps like identifying the learning needs for an on-line M-L Web discussion, addressing the immediate needs of learners and creating a flexible reflective learning environment on the M-L Web facilitated the collective learning of the fellows on the topic of data analysis. Our outcomes can be useful in the design of on-line pedagogical strategies for supporting research in medical education.

Prevalence of sputum smear-positive tuberculosis in a rural area in Bangladesh

The objective of the study was to determine the prevalence of smear-positive tuberculosis (TB) in a rural area in Bangladesh at Matlab. A TB surveillance system was established among 106,000 people in rural Bangladesh at Matlab. Trained field workers interviewed all persons aged > or = 15 years to detect suspected cases of TB (cough > 21 days) and sputum specimens of suspected cases were examined for acid-fast bacilli (AFB). Of 59,395 persons interviewed, 4235 (7.1%) had a cough for > 21 days. Sputum specimens were examined for AFB from 3834 persons, 52 (1.4%) of them were positive for AFB. The prevalence of chronic cough and sputum positivity were significantly higher among males compared to females (P < 0.001). The population-based prevalence rate of smear-positive TB cases was 95/100,000 among persons aged > or = 15 years. Cases of TB clustered geographically (relative risk 5.53, 95% CI 3.19-9.59). The high burden of TB among rural population warrants appropriate measures to control TB in Bangladesh. The higher prevalence of persistent cough and AFB-positive sputum among males need further exploration. Factors responsible for higher prevalence of TB in clusters should be investigated.

Serum homocysteine concentration in patients with acute MI and chronic IHD

This was an observational study carried out in the Department of Biochemistry, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka; with the active co-operation of Coronary Care Unit (CCU) of BSMMU & National Institute of Cardiovascular Disease (NICVD), Dhaka. This study was carried out from March 2002 to January 2003. Total seventy (70) subjects were studied. Out of them 20 were of Acute MI, 20 were Chronic ischemic heart disease (CHD) and 30 were age and sex matched healthy controls. Hospitalized diagnosed patients were selected by taking history, clinical examination and several investigations like ECG. Echocardiogram, Angiogram and several enzymes assay. Several studies in many countries showed that serum homocysteine (Hcy) was elevated in IHD Patient. Cardiovascular disease is alarmingly increasing in Bangladesh. So our aim and objective of the study was to find out the association of serum Hcy with Acute MI and chronic ischemic heart disease (CHD) patients in our population. Mean Hcy level of Acute MI were 21.16 +/- 4.56 (micromol/l), 27.55 +/- 10.40 (micromol/l) and that of control was 13.03 +/- 10.51(micromol/l). Serum Hcy was significantly higher in both cases than control. But insignificant difference was found between AMI vs CHD (P> 0.05). Quantitative measurement of serum Hcy was measured by fluorescence polarization Immunoassay (FPIA) in IMX analyzer (Abbott-USA).

Serum zinc and copper levels in the maternal blood and cord blood of neonates

Estimation of serum zinc and copper in the maternal blood and cord blood of neonates was carried out to correlate the trace metals in the neonates and their mothers in relation to gestational age and birth weight. Sixty-five healthy neonates, both term and preterm and their mothers were selected. This cross sectional study was done at Azimpur Maternity Centre, Dhaka Medical College Hospital and Chemistry Division, Atomic Energy Centre, Dhaka, Bangladesh from July 1997 to June 1998. The estimation of trace metals was carried out by Atomic Absorption Spectrophotometry (AAS). The mean serum zinc levels in the maternal blood and cord blood were 0.47 +/- 0.24 microgram/ml and 0.85 +/- 0.33 microgram/ml respectively and the mean copper levels in the maternal blood and cord blood were 1.37 +/- 0.62 micrograms/ml and 0.31 +/- 0.32 microgram/ml respectively. Cord blood zinc level was significantly higher and cord blood copper level was significantly lower than the corresponding maternal blood levels. There was no significant correlation between gestational age and serum zinc levels in the cord or maternal blood. But significant inverse correlation was found between gestational age and serum levels of copper in the maternal and cord blood.

Identification of novel VirR/VirS-regulated genes in Clostridium perfringens

Novel genes that are regulated in Clostridium perfringens by the two-component regulatory system, VirR/VirS, were identified using a differential display method. A plasmid library was constructed from C. perfringens chromosomal DNA, and the plasmids were hybridized with cDNA probes prepared from total RNA of wild-type strain 13 and its virR mutant derivative TS133. Three clones were identified that carry newly identified VirR/VirS-regulated genes, two of which were positively regulated and one of which was negatively regulated. Genes located on the identified clones were deduced by nucleotide sequencing, and the target genes of the VirR/VirS system were identified with a set of Northern hybridizations. A 4.9 kb mRNA transcribing the metB (cystathionine gamma-synthase), cysK (cysteine synthase) and ygaG (hypothetical protein) genes was negatively regulated, whereas 1.6 and 6.0 kb transcripts encoding ptp (protein tyrosine phosphatase) and cpd (2',3'-cyclic nucleotide 2'-phosphodiesterase) respectively, were shown to be positively regulated by the VirR/VirS system. The other gene, hyp7, whose transcript was positively regulated by the VirR/VirS system, was shown to activate the transcription of the colA (kappa-toxin) and plc (alpha-toxin) genes, but not the pfoA (theta-toxin) gene in C. perfringens. These results suggested that the global regulatory system VirR/VirS could regulate various genes, other than toxin genes, both positively and negatively and that the hyp7 gene might encode a novel regulatory factor for toxin production in C. perfringens.

Genomic diversity in the pfoA region of the theta-toxin-deficient strains of Clostridium perfringens

The genomic structure of the pfoA-colA region in six theta-toxin-deficient strains of Clostridium perfringens was examined by Southern hybridization using the pfoR, pfoA, pbg, arcABDC and colA genes, encoding regulator for pfoA, theta-toxin, beta-galactosidase, arginine metabolism enzymes and kappa-toxin, respectively, as gene probes. It is suggested that the productivity of theta-toxin in these strains is diverse because of the multiple genetic backgrounds including single deletion of pfoA, large deletion of the pfoA-colA region and the putative point mutations.

Collagenase gene (colA) is located in the 3'-flanking region of the perfringolysin O (pfoA) locus in Clostridium perfringens

The 3'-flanking region of the beta-galactosidase gene (pbg), which is located downstream of the perfringolysin O gene (pfoA), and the 5'-flanking region of the collagenase gene (colA) of Clostridium perfringens strains NCTC8237 and 13, respectively, were analyzed. Southern analysis revealed that the colA gene is located 6.5 kb downstream of the pbg gene in the chromosome of C. perfringens. Sequence analysis showed that between the pbg and colA genes were the arcABDC and ahrC genes, whose putative products were quite similar to enzymes of the arginine deiminase pathway of Pseudomonas aeruginosa and the arginine repressor/activator of Bacillus subtilis, respectively. It is concluded that the genomic structure of the pfoA-colA region consists of pfoR-pfoA-ORF54-pbg-arcABDC-ahrC-colA.

Self care in health

The study "self care" was conducted in two Unions of one Upazila to assess prevalence, component and outcome of popular "self care" and their decision making process. Head of the family (500) and wives of the head of the family (500) were interviewed on alternate basis by trained interviewers on structured pretested questionnaire. Self care for remedial measure was universally practiced. Initial step related to treatment of diseases were "wait and see" (71.8%), "Self care" (18.4%), "Doctor/Homeopath" (9.8%). Self care was practiced by majority of the people in all other components. Those who reported "wait and see" as their first choice to deal with disease, about 79% waited for one day, 21% for two days. Education and income was found significant with practice of self care.

Validity of the 'Ten Questions' for screening serious childhood disability: results from urban Bangladesh

A survey of 2576 children aged two to nine years was carried out in Dhaka, Bangladesh, as part of a collaborative study to test the validity of a questionnaire (the Ten Questions) for screening severe childhood disabilities in community settings. Approximately 7% of the children were positive on the screen and this rate was slightly higher in boys than girls. The sensitivity, specificity and negative predictive value of the Ten Questions were perfect or nearly perfect for severe and moderate (serious) disabilities. The positive predictive value was only 22% for serious disabilities, but 70% of children classified as false positives were found to have mild disabilities or other conditions (such as ear infections) for which early detection and treatment could be beneficial. No major age or gender differences in the validity of the questionnaire were apparent, but this finding needs additional study and confirmation with studies based on larger samples. In general, the results indicate that the Ten Questions is a valid tool for screening serious disabilities in children and can potentially improve the efficiency of health services by reducing the number of children requiring attention from professionals. Future studies using the Ten Questions should foster greater attention to the dimensions of childhood disability as a public health problem in the less developed world.

Health situation of slum dwellers of metropolitan area of Dhaka

The study interviewed three hundred women, mostly the wives of the head of the household of urban slums. The study women were selected on random sampling basis. The knowledge of study women on preventive MCH care was good (39.7%) and about 21.7%, contacted some trained persons for advice on matters related to pregnancy and treatment of sickness. Almost all the deliveries were conducted at home by relations or neighbours (80.1%). Disease prevalence rate at the time of interview was 253/1000 population. Common diseases reported were fever 31.6%, intestinal problems 26.3%, measles 11.8%, skin diseases 7. 9%, chronic respiratory infection 9.2% and the rests were "others". About one third of the sick persons did not have any treatment. On the average 3.9 persons lived in one room of 2.4 x 4 metres. Source of water supply for drinking and other purposes was mostly municipal taps in a public place. Environmental sanitation for the area was poor.