Dr Md Shahidul Islam

Abstract: The 5' end of the major RNA transcript of the LEE1 operon of enterohaemorrhagic Escherichia coli contains ~170 bases before the AUG translation start codon of the first recognised gene, ler. This unusually long leader sequence carries three potential alternative AUG start codons. Using a lac fusion expression vector, we confirmed that the ler gene AUG is functional for translation initiation, and we checked for translation initiation at the three alternative AUG codons. Whilst two of the alternative AUG codons appear incompetent for translation initiation, we detected strong initiation at the third AUG, which is followed by one AAA codon and a UAG stop codon. The location of this very short two-codon open reading frame with respect to the ler translation start appears critical. Hence mutations that destroy the UAG stop codon, or short deletions between the UAG stop codon and the ler translation initiation region, result in big effects on ler expression. In the context of the full length LEE1 operon leader sequence, translation of this very short two-codon open reading frame is necessary for optimal expression of the ler gene and for the subsequent interactions of enterohaemorrhagic Escherichia coli with host target cells.

Abstract: Expression of the genes in the locus of enterocyte effacement (LEE) in enterohaemorrhagic Escherichia coli is primarily co-ordinated by expression of the LEE1 operon. GrlA is a LEE-encoded transcription regulator that has been proposed to be involved in the regulation of expression of the LEE1 operon. We describe a simple plasmid-based system to investigate the LEE1 operon regulatory region and to study GrlA-dependent effects. We report that GrlA can activate transcription initiation at the LEE1 P1 promoter by binding to a target located within the 18-base-pair spacer between the promoter -10 and -35 elements, which were defined by mutational analysis. Shortening this spacer to 17 base pairs increases P1 promoter activity and short-circuits GrlA-dependent activation. Hence, at the P1 promoter, the action of GrlA resembles that of many MerR family transcription activators at their target promoters.

Abstract: Transcription of the LEE1 operon in the locus of enterocyte effacement of enterohaemorrhagic Escherichia coli is due to the P1 promoter. Mutational and biochemical analyses reveal the existence of an overlapping promoter, designated P1A, which can drive transcript initiation 10 bp upstream of the P1 promoter transcript start point. Because of the overlap between P1 and P1A, P1A activity is unmasked only when the P1 promoter is inactivated by mutation. In the present paper, we report that mutation of the P1-10 element is less effective in unmasking P1A promoter activity than mutation of the P1-35 element. This suggests that the P1 promoter -35 element, which corresponds to the consensus, can sequester RNA polymerase even when P1 is inactive and thereby prevent RNA polymerase from serving the P1A promoter. We propose that such promoter elements may play a role in enforcing specificity in bacterial regulatory regions that contain alternative possible promoters.

Abstract: Knowledge on genetic structure of a fish species is essential for assessing the genetic status and subsequently implementing programs on conservation of the genetic resources as well as selective improvement. Random amplified polymorphic DNA fingerprinting assay was applied to examine genetic variability in the freshwater mud eel, Monopterus cuchia, a vulnerable species in Bangladesh. Upon testing 40 random decamer primers four primers giving reproducible results were selected and used for generating DNA fingerprints from a total of 51 fish collected from the district of Mymensingh, Bangladesh. A total of 39 loci were scored, 30 of which were found to be polymorphic in nature. The average values of Nei’s gene diversity, Shannon’s Information Index and band sharing based similarity index were 0.285, 0.423 and 88.33% respectively indicating a substantial level of genetic diversity in the studied samples of the vulnerable species. Due to the scarcity of M. cuchia in Bangladesh only 51 individuals were examined in the study however the PCRRAPD fingerprinting technique has been found to be suitable for assessing the genetic structure of the freshwater mud eel that could be used as a baseline study for taking any program on conservation and stock improvement of this species.

Abstract: Genetic variation in 64 pointed gourd accessions was investigated using the Randomly Amplified Polymorphic DNA (RAPD). Out of 45 random primers screened five were selected, which gave 38 clear and bright fragments, out of which 30 (79.5%) fragments were considered polymorphic. The proportion of polymorphic loci across all loci was 96%. The number of bands per primer was five to eleven. The highest genetic distance 0.6419 was observed between the accession PG035 and PG051, PG035 and PG056 and PG035 and PG021. While the lowest genetic distance 0.00 was observed between the accessions PG042 and P043 and between PG042 and PG044. The UPGMA dendogram constructed based on RAPD analysis in 64 pointed gourd accessions were found to be grouped in twelve major clusters. Cluster VIII is a broad one which includes 21 accessions and only a single accession formed in cluster VII (PG021). RAPD analysis showed promise as an effective tool in estimating genetic polymorphism in different accessions of pointed gourd.

Abstract: Understanding the genetic diversity at molecular level is a prerequisite in developing strategies for effective conservation and utilization of chicken genetic resources. We studied the genetic variation within and between Bangladeshi native (Naked Neck, Frizzle and Non-descriptive indigenous) and exotic (White Leghorn, Rhode Island Red, Commercial layer and broiler) chicken populations by Random Amplified Polymorphic DNA (RAPD). Four out of the 20 random primers exhibited sufficient variability for studied populations. The four primers yielded a total of 39 distinct bands, 25 of which were polymorphic. Estimation of polymorphic loci, intra-population similarity indices and Nei’s gene diversity suggested that genetic diversities within a population were high in non-descriptive, Frizzle, Naked Neck, Rhode Island Red and White Leghorn chicken populations compared to the commercial layer and broiler populations. The coefficient of gene differentiation (GST = 0.34) and gene flow (Nm = 0.98) values reflected a high level of population differences. UPGMA dendrogram segregated the chicken populations in various degree based on their genetic distance. The overall genetic distance among native chicken was relatively low comparison to the exotic populations. The results of present study might have significant impact on the breeding and conservation of native chicken genetic resources in Bangladesh.

Abstract: Microsatellite DNA markers have been increasingly used in genetic diversity studies. The present study reports on the characterization of genetic variation and differentiation in four different natural populations of the stinging catfish, Heteropneustes fossilis (Bloch), in Bangladesh, viz., Mymensingh, Netrakona, Narsingdi and Rangpur, using cross-species microsatellite DNA markers developed from the walking catfish, Clarias batrachus. Eighteen polymorphic alleles were found in the 128 diploid individuals (32 from each population), with nine alleles at each of the two loci analyzed. The Netrakona and Rangpur population deviated from the Hardy-Weinberg proportion at one locus. The population differentiation (FST) value between the Narsingdi and Netrakona population was found to be insignificant, while the values between all the other population pairs were found to be significant. The genetic distance values ranged between 0.165 and 0.626. The UPGMA dendrogram based on genetic distance resulted in two clusters: the Mymensingh population alone was in one cluster and the three other populations in the second cluster. This study revealed a fairly high level of genetic variation in the microsatellite loci within and between the four populations, and identified existence of distinct population groups of H. fossilis.

Abstract: Determining the genetic structure is essential for developing conservation and stock improvement plans. Four dinucleotide microsatellite loci were analysed to reveal population genetic structure of the Indian major carp,Labeo rohita collected from three major rivers namely the Halda, the Jamuna, and the Padma in Bangladesh. The four loci were polymorphic (P 95) in all the populations. The populations varied in the number and frequencies of alleles as well as heterozygosities in the loci analyzed. Population differentiation (F ST) value between the Halda and the Jamuna population was significant (P<0.05). Relatively high level of gene flow and low level ofF ST values were found between the Padma and the Jamuna population. The unweighted pair group method with averages (UPGMA) dendrogram based on genetic distance resulted in two clusters: the Halda population was alone in one cluster whereas the Jamuna and the Padma made another cluster. The results revealed a relatively low level of genetic variability in the river populations of L. rohita in Bangladesh.

Abstract: Genetic variation is a key component for improving a stock through selective breeding programs. Randomly amplified polymorphic DNA (RAPD) markers were used to assess genetic variation in three wild population of the catla carp (Catla catla Hamilton 1822) in the Halda, Jamuna and Padma rivers and one hatchery population in Bangladesh. Five decamer random primers were used to amplify RAPD markers from 30 fish from each population. Thirty of the 55 scorable bands were polymorphic, indicating some degree of genetic variation in all the populations. The proportion of polymorphic loci and gene diversity values reflected a relatively higher level of genetic variation in the Halda population. Sixteen of the 30 polymorphic loci showed a significant (p < 0.05, p < 0.01, p < 0.001) departure from homogeneity and the FST values in the different populations indicated some degree of genetic differentiation in the population pairs. Estimated genetic distances between populations were directly correlated with geographical distances. The unweighted pair group method with averages (UPGMA) dendrogram showed two clusters, the Halda population forming one cluster and the other populations the second cluster. Genetic variation of C. catla is a useful trait for developing a good management strategy for maintaining genetic quality of the species.

Abstract:

Abstract: Six indigenous aromatic rice cultivars, viz. Badshabhog, Kalijira, Kataribhog, Radhunipagal, Tulshimala and Ukunmadhu were subjected to random amplified polymorphic DNA (RAPD) analysis. Polymerase chain reaction (PCR) with three arbitrary decamer oligonucleotide primers applied to the six cultivars produced a total of 22 RAPD markers of which 86.36% were polymorphic. The size range of the amplified DNAs was mostly between 230-1353 bp. The proportion of polymorphic loci and Nei’s gene diversity values were 54.55% and 0.231 for Ukunmadhu, 50.00% and 0.204 for Badshabhog, 45.45% and 0.207 for Tulshimala, 45.45% and 0.187 for Kataribhog, 45.45% and 0.181 for Radhunipagal and 40.91% and 0.173 for Kalijira. Lowest intra-cultivar similarity index, highest proportion of polymorphic loci and Nei’s gene diversity values reflected that the Ukunmadhu was found to be more diversified cultivar compared to the others. The coefficient of gene differentiation (Gst) and gene flow (Nm) values across all the loci were 0.42 and 0.71 respectively, indicating the existence of high level of genetic variation among the six local aromatic rice cultivars. The Unweighted Pair Group Method of Arithmetic Mean (UPGMA) dendrogram based on Nei’s genetic distance grouped the six cultivars into two main clusters with mean genetic distance of 0.23. In cluster 1, two short medium grain type cultivars Badshabhog and Kalijira grouped together in sub-cluster I with genetic distance of 0.077 and medium slender type Kataribhog segregated to subcluster II while, in cluster 2, short medium grain type Tulshimala and Ukunmadhu grouped together with genetic distance of 0.092. The RAPD analysis offers a rapid and reliable method for the estimation of variability and relationship between different aromatic rice cultivars which could be utilized by the breeders for further improvement of aromatic rice genotypes

Abstract: Random Amplified Polymorphic DNA (RAPD) assay was performed to estimate genetic polymorphism in six different rice (Oryza sativa L.) cultivars viz. Basmati 370, DM 25, IRATOM 24, Binadhan 6, TNDB 100 and Y 1281. Three out of the 15 decamer random primers showed amplification of genomic DNA in 24 individuals. The primers produced a total of 26 bands of which 14 were polymorphic. Proportion of polymorphic bands and gene diversity estimates were 26.92% and 0.09 for Basmati 370, 11.54% and 0.04 for DM 25, 11.54% and 0.05 for IRATOM 24, 7.69% and 0.02 for Binadhan 6 and 23.08% and 0.11 for TNDB 100 whereas Y 1281 cultivar was monomorphic indicating the existence of high level of intra cultivar genetic variation in Basmati 370 and TNDB, respectively 100. High levels of population differentiation (GST = 0.75) and low levels of gene flow (Nm = 0.16) estimates across all the loci indicate sufficient existence of genetic variation among these six cultivars. Low intra cultivar variation and significant differentiation in different cultivar pairs was observed at a number of loci. Nei’s genetic distances estimated among the different pairs of cultivars were correlated with geographical distances. The UPGMA dendrogram based on Nei’s genetic distance clubbed the cultivars into three clusters. RAPD analysis showed promise as an effective tool in estimating genetic polymorphism in different rice cultivars.

Abstract: Information on genetic variation is essential for conservation and stock improvement programs. Seven dinucleotide microsatellite loci were analyzed to reveal genetic variability in three wild populations (Kella beel, Hakaluki haor, and Shobornokhali beel) and one hatchery population of the freshwater walking catfish, Clarias batrachus, in Bangladesh. Upon PCR amplification, the alleles were separated on polyacrylamide gel using a sequencing gel electrophoresis system and visualized by the silver-staining method. The loci were polymorphic (P95) in all the populations. Differences were observed in number and frequency of alleles as well as heterozygosity in the studied populations. Current gene diversity (He) was higher than expected under mutation-drift equilibrium, significantly in the Hakaluki haor and Shobornokhali beel populations, indicating a recent genetic bottleneck. Population differentiation (FST) values were significant (P<0.05) in all the population pairs. A relatively high level of gene flow and a low level of FST values were found between wild population pairs compared to hatchery-wild pairs. The unweighted pair group method with averages dendrogram based on genetic distance resulted in two major clusters: the hatchery population was alone in one cluster whereas the three wild populations made another cluster. The results reflect some degree of genetic variability in C. batrachus populations indicating potentialities for improving this species through a selective breeding program. The results revealed a recent bottleneck in some wild populations of C. batrachus. Protection of habitat may help increase the population size and lower the risk of vulnerability of the species in the future.

Abstract: Characterization of different strains of common carp (Cyprinus carpio L.) using molecular markers is essential for the management of this fish in respect to the evaluation of the potential genetic effects induced by hatchery operations and the genetic improvement of carp varieties. Five microsatellite loci (MFW1, MFW2, MFW11, MFW15 and MFW20) were analyzed for the molecular characterization of four common carp strains, i.e. scaled carp, mirror carp, red carp and koi carp. We observed differences in heterozygosities and the average numbers of alleles but not in polymorphic loci (P95) among the strains. Koi carp displayed the highest level of variability in terms of heterozygosity. The Nm values and the FST values indicated a low level of gene flow and high level of differentiation among the strains. The highest genetic distance was observed between the scaled carp and the koi carp whilst the lowest genetic distance was found between the red- and koi carp. The unweighted pair group method with averages (UPGMA) dendrogram resulted in two clusters, one containing only the scaled carp and the other the remaining three varieties. Microsatellite markers have been found to be effective tools for characterization of different strains of common carp.

Abstract: Random Amplified Polymorphic DNA (RAPD) analysis was used to study the genetic diversity of six cultivars of potato. Amplification with three decamer random primers generated 35 RAPD markers of which 33 (94.29%) were polymorphic. The proportion of polymorphic loci and the gene diversity estimates were 14.29% and 0.068, 8.57% and 0.138, 17.14% and 0.075, 51.43% and 0.217 and 54.29% and 0.245 for Cardinal, Diamant, Heera, Raja and TPS, respectively. The results indicated that relatively high level of genetic variation was observed in the TPS and Raja cultivars compared to other cultivars studied. No intra-cultivar genetic variation was observed in the Ailsa cultivar. The high level of cultivar differentiation (GST = 0.634) and low level of gene flow (Nm = 0.289) across all loci reflected that the level of genetic divergence among six cultivars was high. The UPGMA dendrogram based on the Nei`s genetic distances segregated the cultivars into three clusters: Ailsa and Heera made one cluster, Cardinal and TPS made another cluster whereas Diamant and Raja grouped into another cluster. The RAPD markers were found to be useful in studying genetic diversity of potato cultivars.

Abstract: Information on the genetic structure of cultured fish species is essential for optimising fisheries management and stock improvement programs. Eight microsatellite loci (Cc6, Cc7, Cc8, Cc9, Ccat C3, Ccat A12, Ccat G1, and Ccat G2) were analysed to study the genetic variation in three river populations, (the Halda, Jamuna, and Padma rivers) and one hatchery population of Catla catla. Seven of the eight loci analysed were polymorphic in all the populations. Locus Ccat G2 had the highest numbers of alleles (8), while the locus Cc9 had the lowest (2). Differences were observed in heterozygosities and average numbers of alleles among the four populations; however, no difference was observed in proportion of polymorphic loci (P95) among the populations. All the studied populations deviated from Hardy–Weinberg equilibrium proportions at a number of loci, mostly due to the deficiency of heterozygosities. A low level of population differentiation (FST) was observed among populations; however, significant differentiation was evident only between the Halda and hatchery populations. The genetic distance computed by Nei [M. Nei, Genetic distance between populations. Am. Nat. 106, 1972, 283–292.] between the Halda and the other three populations was higher than the genetic distances between all other population pairs. The study revealed a relatively low level of genetic variation at microsatellite loci within and between catla populations, with genetic variation in the hatchery population lower than the river populations. Knowledge of genetic structure of the major river populations and a typical hatchery population is helpful for management of the populations in order to maintain their genetic quality.

Abstract:

Abstract:

Abstract: The aim of the research was to find out the effective antibiotic(s) against Escherichia coli and to observe the relationship between the plasmids to the antibiotic resistant pattern found by antibiotic sensitivity tests. For these forty water samples were collected from different sources including river, pond, tap and drain for isolation and identification of pure E. coli. The overall recovery rate of E. coli from water samples was 45%. The highest recovery rate was found from drain water (70%). The pure cultures were subjected to observe the antibiotic resistant pattern by commonly used ten antibiotic disks. All the isolates were found resistant to Penicillin G (94.45%) but 50% isolates were resistant to Amoxicillin. The isolates were highly sensitive to other antibiotics as Ciprofloxacin (88.89%), Chloramphenicol (72.22%), Norfloxacillin (88.33%) and Tetracycline (61.11%). The isolates exhibited moderate sensitivity to Ampicillin (44.44%), Gentamicin (77.78%), Streptomycin (33.33%). Only 22.22, 27.78, 27.78, 16.67, 11.11 and 16.67% of the isolates were recorded to show moderate sensitivity to Amoxycillin, Tetracycline, Chloramphenicol, Cephradin, Ciprofloxacin and Norfloxacillin, respectively. Plasmid profile analysis of 18 isolates were done by 0.8% agarose gel electrophoresis. A total of 11 different plasmid bands of different size were observed by careful eye estimation with the comparison to reference marker. The size of the bands range from 2.4 to 40 kb and at best 5 plasmid bands were found. There was no plasmid in only one isolate. There was no relation found between the plasmid band pattern in agarose gel and antibiotic resistance of E. coli.

Abstract: Random Amplified polymorphic DNA (RAPD) technique was used to examine the population structure of three population viz. Satpaika, Nalgaira and Gaffargaon of mottled nandus (Nandus nandus) of the old Brahmaputra river basin. Eleven polymorphic loci were detected using three decamer random primers. The percentage of polymorphic loci were 33, 32 and 40 while the Nei's genetic diversities were 0.129, 0.116, and 0.156 for the Satpaika, Nalgaira, and Gaffargaon populations, respectively. The coefficient of gene differentiation (Gst) and estimate of gene flow per generation (Nm) were found to be 0.088 and 5.16 respectively indicating a low level of genetic divergence among populations. Only one locus causing significant (P95) departure from homogeneity across all populations also supported the above findings. Nevertheless, the priliminary study revealed that RAPD technique could be an effective tool in the assessment of population genetic structure of mottled nandus.

Abstract: The genetic variations in three major river populations viz. the Halda, the Jamuna and the Padma of the Indian major carp, Catla catla were analyzed by Random Amplified Polymorphic DNA (RAPD) markers. Four decamer primerswere used for amplifying DNA of 10 individuals from each population. The proportion of polymorphic loci and the gene diversity estimates were 59.4 and 0.20 for the Halda, 37.5 and 0.14 for the Jamuna and 46.9 and 0.16 for the Padma populations respectively indicating the existence of a relatively high level of genetic variation in the Halda river population. The inter-population similarity indices, gene flow and genetic distance values indicated that the Jamuna-Padma population pair of catla was genetically closer than the Halda-Jamuna and the Halda-Padma population pairs in compliance with the geographical distances among them. The coefficient of gene differentiation (GST=0.13) reflects some degree of genetic differentiation among three populations of catla studied. The data suggest that the RAPD technique could be used to discriminate different river populations of catla.

Abstract:

Abstract: The level of genetic variation provides the raw material for selective improvement of a stock. Random amplified polymorphic DNA (RAPD) assay was used to assess the genetic variation in three rivers: the Halda, the Jamuna and the Padma as well as in one hatchery population of the commercially important Indian major carp, Labeo rohita. RAPD markers were amplified from DNA samples of 35 fish from each of the four populations using six decamer random primers. The polymorphic loci proportions were 0.33, 0.28, 0.28 and 0.26 and Nei's gene diversity values were 0.06, 0.07, 0.06 and 0.05 for the Halda, the Jamuna, the Padma and the hatchery populations, respectively. The pairwise population differentiation (FST) values indicated a low level of genetic differentiation between the population pairs. From the unweighted pair group method of arithmetic mean (UPGMA) dendrogram based on Nei's genetic distances a correlation between genetic affinities and geographical area was found. The populations were segregated into two groups: the Halda in one group and the Jamuna, the Padma and the hatchery in another group. Overall, the RAPD technique can be introduced as a tool in the population genetics of the rohu fish to provide information on their genetic stock structure.

Abstract: The genetic structure of three populations Hilsa shad (Tenualosa ilisha), belonging to three different ecological zones such as freshwater (Chandpur), brackish (Kuwakata) and marine (Cox’s Bazar) were studied by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) of mitochondrial DNA. Fifteen composite haplotypes, representing information from 7 restriction enzymes were generated for samples of 7 fish from each site. All populations have polymorphic haplotype and the haplotype diversity (h) of the three populations were 0.979, 0.979 and 0.918 for Chandpur, Kuwakata and Cox’s Bazar respectively. The intra-population nucleotide diversity was 36.75% in Chandpur and Kuwakata and 25.56% in Cox’s Bazar population. These indicate that the genetic variability of the present Hilsa shad population falls within the range of good condition and the genetic status of Hilsa shad does not appear to be affected, though the catch has decreased due to overexploitation and indiscriminate killing. Genetic distance between Chandpur and Kuwakata populations, Chandpur and Cox’s Bazar, Kuwakata and Cox’s Bazar were 0.0213, 0.1823 and 0.1610 respectively. UPGMA dendrogram shows that the Chandpur and Kuwakata populations are very close group and Cox’s Bazar population is a different group.