Papers by Mohammad Shamsur Rahman
Dhaka University Journal of Biological Sciences, 2015
Thai pangas, Pangasius hypophthalmus fingerlings were reared for 60 days in laboratory condition ... more Thai pangas, Pangasius hypophthalmus fingerlings were reared for 60 days in laboratory condition to investigate the effects of feeding frequency on the growth performance. The fish fingerlings in three treatments were fed with two, three and four times a day, respectively. During the feeding trial, growth and feed utilization were assessed by condition factor (K), average daily gain (ADG), specific growth rate (SGR) and feed conversion ratio (FCR). Significantly lower FCR 1.81 ± 0.02 and higher ADG 0.38 ± 0.02 and SGR 2.20 ± 0.02% were found in fish fed thrice a day than that of other treatments (p < 0.05). Highest condition factor 1.69 ± 0.13 was found in fish fed four times a day while the lowest condition factor 0.77 ± 0.03 was detected in fish fed twice a day. Moisture content of Thai pangas in treatment T1, T2 and T3 were 79.23 ± 0.77, 78.08 ± 0.85 and 77.84 ± 0.17%, respectively. The crude protein, crude lipid and ash contents were 16.11 ± 0.00 to 16.38 ± 0.08%, 3.22 ± 0.27...
Ecological Genetics and Genomics, 2022
BMC Bioinformatics, 2021
Background Proteins are integral part of all living beings, which are building blocks of many ami... more Background Proteins are integral part of all living beings, which are building blocks of many amino acids. To be functionally active, amino acids chain folds up in a complex way to give each protein a unique 3D shape, where a minor error may cause misfolded structure. Genetic disorder diseases i.e. Alzheimer, Parkinson, etc. arise due to misfolding in protein sequences. Thus, identifying patterns of amino acids is important for inferring protein associated genetic diseases. Recent studies in predicting amino acids patterns focused on only simple protein misfolded disease i.e. Chromaffin Tumor, by association rule mining. However, more complex diseases are yet to be attempted. Moreover, association rules obtained by these studies were not verified by usefulness measuring tools. Results In this work, we analyzed protein sequences associated with complex protein misfolded diseases (i.e. Sickle Cell Anemia, Breast Cancer, Cystic Fibrosis, Nephrogenic Diabetes Insipidus, and Retinitis Pi...
Background Due to its rapid lethal effect in the early stage of shrimp, acute hepatopancreatic ne... more Background Due to its rapid lethal effect in the early stage of shrimp, acute hepatopancreatic necrosis disease (AHPND) causing great economic losses, since it first outbreak in southeast China in 2009. Vibrio parahaemolyticus , carrying the pir A and pir B toxin genes is known to cause AHPND in shrimp. The overall objective of this study was to sequence whole genome of AHPND positive V. parahaemolyticus strains isolated from shrimp ( Peneaus monodon ) of south-west region of Bangladesh in 2016 and 2017 and characterize the genomic features and emergence pattern of this marine pathogen. Results Two targeted AHPND positive V. parahaemolyticus strains were confirmed using PCR with 16S rRNA, ldh , AP3 and AP4 primers. The assembled genomes of strain MSR16 and MSR17 were comprised of total 5,393,740 bp and 5,241,592 bp, respectively. From annotation, several virulence genes involved in chemotaxis and motility, EPS type II secretion system, Type three secretion system-1 (TTSS-1) and its ...
Asia-Pacific Journal of Rural Development, 2009
markets of Dhaka ese markets in which only 15 per cent was found to tter-cum-sellers. Estimated t... more markets of Dhaka ese markets in which only 15 per cent was found to tter-cum-sellers. Estimated total yield of dry scales found was 390 mt which could be increased by 9-folds. The expected potential harvest of maws could be increased by 2-folds while PG by 28-folds of the present. Total value of the current harvest of dry scales, maws and PG found was US$604,615 which would be increased by 3.5-folds if the entire yield can be harvested. This study has clearly shown the potential economic importance of the nonconventional fishery by-products of Dhaka City that may improve the livelihoods of the poor cutters and cutter-sellers. 1.0 Introduction 1.1 Background Bangladesh has earned the ever highest foreign currency US$410 million in 2004-2005 from fishery sub-sector in which the contribution of fishery byproducts was 0.02 per cent. However, the earnings from shark fins and fish maws 1 (major parts of non-conventional by-products) have been surprisingly decreasing. The export of shark fins and fish maws dropped from 172.
Bangladesh Journal of Zoology, 2017
Gelatin was extracted from the scales of catla (Catla catla), rohu (Labeo rohita), grass carp (Ct... more Gelatin was extracted from the scales of catla (Catla catla), rohu (Labeo rohita), grass carp (Ctenopharyngodon idella), and their mixed type. However, amino acid of the gelatin extracted from the scales of catla and rohu was profiled. While grass carp (0.78 ± 0.03) and mixed scales (0.78 ± 0.02) yielded similar level of gelatin, rohu had the lowest recovery (0.61 ± 0.05). Scales of catla had 0.72 ± 0.06% gelatin. Of the total 14 amino acids, the highest level of glutamic acid (6.58%) was found in the gelatin extracted from the scales of catla with the lowest level of leucine (0.76%). Gelatin extracted from rohu had the highest percent of glutamic acid (6.14) with lowest percent of leucine (0.59). Of the 10 EAAs, 8 were found in the gelatin extracted from the scales of catla and rohu. While the highest per cent of lysine (4.15) was found in the gelatin extracted from the scales of rohu, the lowest per cent (0.59) was leucine. Quantification of fish scales from the fish markets of Ba...
Oriental Pharmacy and Experimental Medicine, 2008
The plant Eclipta prostrata, a member of the Compositae family, has folkloric reputation of being... more The plant Eclipta prostrata, a member of the Compositae family, has folkloric reputation of being used as a medicinal agent in Bangladesh. In the present investigation, attempt was taken to explore the antimicrobial potency and cytotoxicity of its extractives and purified compounds. The methanolic extract of the whole plant, its n-hexane, carbon tetrachloride, chloroform, aqueous soluble fractions and two purified compounds, eclalbasaponin I (1) and II (2), obtained from Eclipta prostrata were subjected to screening for inhibition of microbial growth by the disc diffusion method at 300 and 100 µg/disc for extracts and pure compounds, respectively. In this case, the carbon tetrachloride and chloroform soluble fractions of the methanolic extract appeared very potent in terms of both zone of inhibition and spectrum of activity. However, all the extractives were also subjected to brine shrimp lethality bioassay for preliminary cytotoxicity evaluation. Here, the carbon tetrachloride soluble fraction of methanolic extract revealed the strongest cytotoxicity having LC 5 0 of 1.318 µg/ml.
Oriental Pharmacy and Experimental Medicine, 2009
Amoora cucullata (Meliaceae), a mangrove plant, has folkloric reputation as a medicinal agent in ... more Amoora cucullata (Meliaceae), a mangrove plant, has folkloric reputation as a medicinal agent in Bangladesh. In this study, the n-hexane, ethyl acetate and methanolic extracts of the stem bark of this plant were subjected to microbiological investigation and brine shrimp lethality bioassay. In case of antimicrobial screening, the ethyl acetate and methanolic extracts appeared to be potent in terms of both zone of inhibition and spectrum of activity showing the average zones of inhibition 8-14 mm and 9-16 mm, respectively. In the brine shrimp lethality bioassay, the methanolic extract demonstrated highest cytotoxicity having LC 5 0 of 0.549 µg/ml, whereas the ethyl acetate and n-hexane extract showed LC 5 0 of 7.943 and 17.180 µg/ml, respectively.
Bangladesh Pharmaceutical Journal, 2015
Cyclooxygenase-2 (COX-2) is an inducible enzyme that causes inflammation. COX-2 inhibitors are cl... more Cyclooxygenase-2 (COX-2) is an inducible enzyme that causes inflammation. COX-2 inhibitors are clinically effective anti-inflammatory agents with less gastrointestinal and renal toxicities. However, they lack anti-thrombotic activity and hence lead to increased incidences of adverse cardiovascular thrombotic events, including myocardial infarction. Therefore, there is still need to develop COX-2 inhibitors with better therapeutic effects and tolerability. The aim of the present study is to explore the anti-inflammatory activity of five lichen metabolites by conducting virtual screenings. In this regard, molecular docking simulations were carried out for the lichen metabolites namely atranorin, diffractic acid, lecanoric acid, salazinic acid and usnic acid with human COX-2 enzyme and the docked results were compared with the standard reference ligands (Celecoxib and Rofecoxib). Among all the docked ligands, the lecanoric acid demonstrated best binding affinity -9.83 kcal/mol followed...
Bangladesh Journal of Zoology, 2015
Proximate composition and microbial quality of three aquarium fish feeds commonly found in Bangla... more Proximate composition and microbial quality of three aquarium fish feeds commonly found in Bangladesh were collected from fish feed market of Dhaka city. Significantly higher moisture content (2.12 ± 0.06%) was found in Super Nova TM fish feed while similar moisture content was detected in other two feeds (p<0.05). On the other hand ash content detected in Optimum TM and Osaka 2000 TM aquarium fish feed was significantly higher than that of Super Nova TM (10.67±0.19%) (p<0.05).Protein content found in Optimum TM (42.21 ± 0.12%) was significantly higher than that of Osaka 2000 TM and Super Nova TM (p<0.05). However, similar lipid content was found in Optimum TM (1.06 ± 0.03%) and Super Nova TM (1.13 ± 0.01%) aquarium fish feed which were significantly higher than that of Osaka 2000 TM (p<0.05). The Escherichia coli and Staphylococcus aureus were found in all feeds. However Vibrio sp was not found in any feed. Total bacterial count was significantly higher in Osaka 2000 TM feed than that of others (P<0.05). However S. aureus was significantly higher in Super Nova TM than that of others while E. coli count was significantly higher in Optimum TM fish feed than that of others (p<0.05). Nutritional quality of the aquarium fish feed was qualified to some extent to meet the minimum requirement of the aquarium fish while microbial quality indicates some degrees of deterioration which may cause diseases of the aquarium fishes. Thus proper storage condition, hygienic handling and processing should be maintained to prevent the microbial contamination in aquarium fish feeds. There should be a monitoring cell from the government to assess the quality of this expensive imported feeds for aquarist.
Bangladesh Journal of Pharmacology, 2009
Dillenia indica Linn. (Syn. P. lanigerum; chalta in Bangla; Family-Dilleniaceae) is a evergreen l... more Dillenia indica Linn. (Syn. P. lanigerum; chalta in Bangla; Family-Dilleniaceae) is a evergreen large shrub or small to medium-sized tree that grows all over the Bangladesh. It is reputed as a cooling beverage in fever, expectorant in cough mixture, tonic, laxative and astringent (Maniruzzaman, 1993). Previous phytochemical studies with D. indica species revealed the occurrences of a number of triterpenes (Banerji et al., 1975), flavanoids (Pavanasasivam et al., 1975). We, herein, report the isolation of lupeol (1), betulinaldehyde (2), betulinic acid (3) and stigmasterol (4) as well as the antimicrobial activity, cytotoxicity and anti-oxidant activity of extracts from D. indica. Materials and Methods General experimental procedure 1 H spectra were acquired using the Ultra Shield Bruker DPX 400 NMR instrument, and the chemical shifts are reported in ppm with respect to TMS or residual non deutarated solvent signal.
2010 13th International Conference on Computer and Information Technology (ICCIT), 2010
This paper presents an efficient O(n3) time algorithm for solving the seeded tree alignment probl... more This paper presents an efficient O(n3) time algorithm for solving the seeded tree alignment problem that finds the similarity score of two RNA secondary structures. In the seeded tree alignment problem, a large tree, representing an RNA secondary structure, is converted into a small tree known as seeded tree. After conversion, a comparison operation is being placed to find the similarity score of necessary seed pair of two seeded trees and finally the overall trees. The algorithm is more efficient than the best known algorithm that needs O(n3.5) time.
2013 IEEE 3rd International Conference on Computational Advances in Bio and medical Sciences (ICCABS), 2013
Proteins are known to interact with each other to perform living organism functions by forming fu... more Proteins are known to interact with each other to perform living organism functions by forming functional modules or protein complexes. Many community detection methods have been devised for the discovery of functional modules or protein complexes from protein interaction networks. One common problem in current agglomerative community detection approaches is that vertices with just one neighbor are often classified as separated clusters, which does not make sense biologically. Also, a major limitation of agglomerative techniques is that their computational efficiency do not scale well to large protein interaction networks (PINs). In this paper, we propose a new agglomerative algorithm, FAC-PIN, based on a local premetric of relative vertex-to-vertex clustering value and which addresses the above two issues. Our proposed FAC-PIN method has been applied to PIN of baker's yeast for validating functional modules and protein complexes. The preliminary computational results show that FAC-PIN can discover functional modules and protein complexes from PINs more accurately. As well as, we have also compared the computational times with HC-PIN and CNM algorithms. Our algorithm outperformed above algorithms. Our FAC-PIN algorithm is faster and accurate algorithm which is the current state-of-the-art agglomerative approach to complex prediction and functional module identification.
Dhaka University Journal of Pharmaceutical Sciences, 2007
A total of six N-substituted benzamides, eight isoindolinone derivatives and six isoquinolinone a... more A total of six N-substituted benzamides, eight isoindolinone derivatives and six isoquinolinone analogs have been screened against five Gram positive and twelve Gram negative bacteria as well as four human fungal pathogens. From the antimicrobial screening, it is evident that 2-iodo-N-subustituted tetrahydro-1-oxo isoquinoline-3-carboxylic acids showed very prominent activity at a concentration 200 µg/disc, while the N-subtituted-3-alkyl isoindolin-1-one acetates showed weak to moderate activity. At the same time, 2-iodo-N-subustituted benzamides revealed very poor activity. Key words: 2-iodo-N-substituted benzamide, Isoindolinone, Isoquinolinone, Antimicrobial assay, Disc diffusion. Dhaka Univ. J. Pharm. Sci. Vol.5(1-2) 2006 The full text is of this article is available at the Dhaka Univ. J. Pharm. Sci. website
2013 2nd International Conference on Advances in Electrical Engineering (ICAEE), 2013
Proteins are responsible for health disorder, evolution of species. These tasks are carried out b... more Proteins are responsible for health disorder, evolution of species. These tasks are carried out by forming functional modules. Each functional module possesses community structure. For identifying the functional modules, a lot of community detection or clustering algorithms are designed, but most of the algorithms suffer by either high computational time or inappropriate clustering results. We propose an algorithm based on relative vertex-to-vertex clustering value and agglomerative hierarchical method, known as Fast Protein Network Clustering algorithm. It is faster than existing algorithms and resolves the most common clustering problem-clustering any vertex (protein) of degree one from its neighbour. We also tested our algorithm with the most popular four algorithms in respect to functional module mapping and efficiency analysis. FPNC algorithm successfully outperformed existing algorithms which is the current state-of-the-art agglomerative approach to functional module identification.
Dhaka University Journal of Pharmaceutical Sciences, 2007
Dhaka Univ. J. Pharm. Sci. 6(1): 65-67, 2007 (June) The full text is of this article is available... more Dhaka Univ. J. Pharm. Sci. 6(1): 65-67, 2007 (June) The full text is of this article is available at the Dhaka Univ. J. Pharm. Sci. website
Dhaka University Journal of Pharmaceutical Sciences, 2009
A total of four compounds were isolated from the n-hexane soluble fraction of a methanolic extrac... more A total of four compounds were isolated from the n-hexane soluble fraction of a methanolic extract of the whole plant of Bryophyllum daigremontianum. The structures of the isolated compounds were elucidated as 11-oxo-epi-β-amyrin (1), 21-dehydrodesmosterol (2), 3,4-dihydroxy-cis-cinnamic acid (3), and p-hydroxy-benzaldehyde (4) by high field NMR analyses as well as by comparison with structurally related compounds. Key words: Bryophyllum daigremontianum, Crassulaceae, 11-oxo-epi-β-amyrin, 21-dehydrodesmosterol, 3,4-dihydroxy-cis-cinnamic acid, p-hydroxybenzaldehyde. doi: 10.3329/dujps.v7i2.2169 Dhaka Univ. J. Pharm. Sci. 7(2): 141-144, 2008 (December)
Stamford Journal of Microbiology, 2013
Present study was conducted to determine and quantify the occurrence of various types of microorg... more Present study was conducted to determine and quantify the occurrence of various types of microorganisms in raw and final products of Chapila (Gudusia chapra) and Tengra (Mystus vittatus) and also to enhance food safety with a view of promoting international trade. Raw and frozen Chapila and Tengra samleswere collected and the microbial analysis was conducted. In case of raw product of Chapila, the aerobic plate count (APC) was 2.6×105 cfu/g, whereas in frozen products, the load was estimated to be 4.0×105 cfu/g. Furthermore, while APC of raw Tengra was 2×105 cfu/g, the APCs were 3.3×106 cfu/g in frozen product. Total coliform in raw and frozen Chapila was found to be 36.00 ± 2.3 MPN/g and 7.2 ± 1.01 MPN/g, respectively and 27.00 ± 5.57 MPN/g and 9.4 ± 3.75 MPN/g, respectively were found in raw and frozen Tengra samples. Moreover, Fecal coliform in frozen samples of Chapila and Tengra was found within the acceptable limit (<3 MPN/g). Salmonella spp. and Vibrio cholerae were not de...
Pakistan Journal of Biological Sciences, 2003
Dhaka University Journal of Pharmaceutical Sciences, 2008
The cytotoxic activity of the methanolic extracts of 35 plant species, including 28 traditionally... more The cytotoxic activity of the methanolic extracts of 35 plant species, including 28 traditionally used plants of Bangladesh was evaluated by the brine shrimp lethality bioassay technique. Among these, 19 plant extracts exhibited significant toxicity to brine shrimps with LC50 less than 10 μg/ml.Key words: Cytotoxic activity, Brine shrimp lethality bioassay.DOI = 10.3329/dujps.v7i1.1217Dhaka Univ. J. Pharm. Sci. 7(1): 47-52, 2008 (June)
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Papers by Mohammad Shamsur Rahman