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  1. Article ; Online: Bioinformatics approaches identified dasatinib and bortezomib inhibit the activity of MCM7 protein as a potential treatment against human cancer

    Abdus Samad / Md. Amdadul Huq / Md. Shahedur Rahman

    Scientific Reports, Vol 12, Iss 1, Pp 1-

    2022  Volume 16

    Abstract: Abstract Minichromosome Maintenance Complex Component 7 (MCM7) is a key component of the DNA replication licensing factor and hexamer MCM (MCM2–7) complex that regulates the DNA replication process. The MCM7 protein is associated with tumor cell ... ...

    Abstract Abstract Minichromosome Maintenance Complex Component 7 (MCM7) is a key component of the DNA replication licensing factor and hexamer MCM (MCM2–7) complex that regulates the DNA replication process. The MCM7 protein is associated with tumor cell proliferation that plays an important role in different human cancer progression. As the protein is highly expressed during the cancer development process, therefore, inhibition of the protein can be utilized as a treatment option for different human cancer. However, the study aimed to identify potential small molecular drug candidates against the MCM7 protein that can utilize treatment options for human cancer. Initially, the compounds identified from protein-drugs network analysis have been retrieved from NetworkAnalyst v3.0 server and screened through molecular docking, MM-GBSA, DFT, pharmacokinetics, toxicity, and molecular dynamics (MD) simulation approach. Two compounds namely Dasatinib (CID_3062316) and Bortezomib (CID_387447) have been identified throughout the screening process, which have the highest negative binding affinity (Kcal/mol) and binding free energy (Kcal/mol). The pharmacokinetics and toxicity analysis identified drug-like properties and no toxicity properties of the compounds, where 500 ns MD simulation confirmed structural stability of the two compounds to the targeted proteins. Therefore, we can conclude that the compounds dasatinib and bortezomib can inhibit the activity of the MCM7 and can be developed as a treatment option against human cancer.
    Keywords Medicine ; R ; Science ; Q
    Subject code 500
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Identification of genetic biomarkers, drug targets and agents for respiratory diseases utilising integrated bioinformatics approaches

    Fee Faysal Ahmed / Arnob Dip Das / Mst. Joynab Sumi / Md. Zohurul Islam / Md. Shahedur Rahman / Md. Harun Rashid / Salem A. Alyami / Naif Alotaibi / A. K. M. Azad / Mohammad Ali Moni

    Scientific Reports, Vol 13, Iss 1, Pp 1-

    2023  Volume 14

    Abstract: Abstract Respiratory diseases (RD) are significant public health burdens and malignant diseases worldwide. However, the RD-related biological information and interconnection still need to be better understood. Thus, this study aims to detect common ... ...

    Abstract Abstract Respiratory diseases (RD) are significant public health burdens and malignant diseases worldwide. However, the RD-related biological information and interconnection still need to be better understood. Thus, this study aims to detect common differential genes and potential hub genes (HubGs), emphasizing their actions, signaling pathways, regulatory biomarkers for diagnosing RD and candidate drugs for treating RD. In this paper we used integrated bioinformatics approaches (such as, gene ontology (GO) and KEGG pathway enrichment analysis, molecular docking, molecular dynamic simulation and network-based molecular interaction analysis). We discovered 73 common DEGs (CDEGs) and ten HubGs (ATAD2B, PPP1CB, FOXO1, AKT3, BCR, PDE4D, ITGB1, PCBP2, CD44 and SMARCA2). Several significant functions and signaling pathways were strongly related to RD. We recognized six transcription factor (TF) proteins (FOXC1, GATA2, FOXL1, YY1, POU2F2 and HINFP) and five microRNAs (hsa-mir-218-5p, hsa-mir-335-5p, hsa-mir-16-5p, hsa-mir-106b-5p and hsa-mir-15b-5p) as the important transcription and post-transcription regulators of RD. Ten HubGs and six major TF proteins were considered drug-specific receptors. Their binding energy analysis study was carried out with the 63 drug agents detected from network analysis. Finally, the five complexes (the PDE4D-benzo[a]pyrene, SMARCA2-benzo[a]pyrene, HINFP-benzo[a]pyrene, CD44-ketotifen and ATAD2B-ponatinib) were selected for RD based on their strong binding affinity scores and stable performance as the most probable repurposable protein-drug complexes. We believe our findings will give readers, wet-lab scientists, and pharmaceuticals a thorough grasp of the biology behind RD.
    Keywords Medicine ; R ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2023-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Strategic development of metal doped TiO2 photocatalysts for enhanced dye degradation activity under UV–Vis irradiation

    Marzia Sultana / Atol Mondal / Sumon Islam / MOST. Afroza Khatun / Md. Hafezur Rahaman / Ashok Kumar Chakraborty / Md. Shahedur Rahman / Md Mahfuzur Rahman / Alam S.M. Nur

    Current Research in Green and Sustainable Chemistry, Vol 7, Iss , Pp 100383- (2023)

    A review

    2023  

    Abstract: This review article discusses the potential of using metal-doped TiO2 as a photocatalyst for dye degradation in water. TiO2 is a promising photocatalyst but is limited due to its fast electron-hole recombination rate and vast bandgap energy. Metal ... ...

    Abstract This review article discusses the potential of using metal-doped TiO2 as a photocatalyst for dye degradation in water. TiO2 is a promising photocatalyst but is limited due to its fast electron-hole recombination rate and vast bandgap energy. Metal dopants have enhanced the photocatalytic activity of TiO2, especially noble metal doping, due to the synergistic effects between the metal dopants and TiO2. The review summarizes experimental studies on photocatalytic dye degradation using metal-doped TiO2 and compares the degradation performance between doped and undoped TiO2. The authors emphasize the importance of understanding the interaction between metal dopants and TiO2 to improve the dye degradation activity and stability of metal-doped TiO2. The article highlights the optimum dopant concentration and preparation methods that can improve the textural or surface properties of doped TiO2 and enhance dye degradation capacity.
    Keywords Photocatalytic activity ; Water pollution ; Metal-doped TiO2 ; Dye degradation ; UV–Vis irradiation ; Chemistry ; QD1-999
    Subject code 620
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: In Silico Analysis of the Antigenic Properties of Iron-Regulated Proteins against Neisseria meningitidis

    Md. Shahedur Rahman / Chayon Biswas / Polash Kumar Biswas / Md. Ashraful Kader / S. M. Nur Alam / Christian Sonne / Ki-Hyun Kim

    Applied Sciences, Vol 10, Iss 6113, p

    2020  Volume 6113

    Abstract: Neisseria meningitidis is a commensal pathogen that causes infectious cerebrospinal disease in people of all ages. The multivariate role of six disease-causing polysaccharide serotypes is found to play a crucial role in developing vaccines (or general ... ...

    Abstract Neisseria meningitidis is a commensal pathogen that causes infectious cerebrospinal disease in people of all ages. The multivariate role of six disease-causing polysaccharide serotypes is found to play a crucial role in developing vaccines (or general treatment strategies) to treat this emerging pathogen. Iron is a crucial transition metal for N. meningitidis . Proteomic analysis data could be valuable for vaccine design. Here, we conduct a comparative study using computational bioinformatic tools to identify the most effective iron-regulated outer membrane proteins (OMPs) as immunogenic targets for a potential vaccine against N. meningitidis . The basic properties of N. meningitidis OMPs are explored for flexibility, solubility, hydrophilicity, beta-turns, and overall antigenic probability. Results of our study suggest that iron-regulated OMPs are flexible and soluble in water with high densities of conformational B-cell epitopes. As such, they can be recommended as a novel candidate for a vaccine against N. meningitidis both in vitro and in vivo .
    Keywords Neisseria meningitidis ; vaccine development ; epidemic disease ; immunogenicity ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
    Subject code 570
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Combined effect of salt stress and Xanthomonas axonopodis pv citri on citrus (Citrus aurantifolia)

    Shahran Ahmed Nayem / M. Salahuddin M. Chowdhury / Nazneen Sultana / Gazi Ziaul Haque Masum / Md. Shahedur Rahman / Mohammad Abu Hena Mostofa Jamal

    Heliyon, Vol 6, Iss 2, Pp e03403- (2020)

    2020  

    Abstract: Xanthomonas axonopodis pv citri (Xac) and salt stress are two crucial hindrances to citrus production. The effect of continuous salt application and Xac infection in citrus has been investigated. Citrus plants were exposed to salt stress by irrigating ... ...

    Abstract Xanthomonas axonopodis pv citri (Xac) and salt stress are two crucial hindrances to citrus production. The effect of continuous salt application and Xac infection in citrus has been investigated. Citrus plants were exposed to salt stress by irrigating with 50 mM, 100 mM, 150 mM, and 200 mM NaCl solution on weekly basis and challenged by Xac. Salt stress affected the defense response of Citrus plants to Xac and therefore lesion diameter and disease severity were gradually increased at higher salt concentration. Meanwhile, accumulation of Na+ and Cl− in the leaves were also increased with the increase of salt concentration. Besides, physiological performance (PP) of plants was estimated based on the parameters such as net assimilation rate, chlorophyll content, stomatal conductance, transpiration rate and intercellular CO2 concentration. The PP of sole Xac treated plants was gradually increased and maintained up to end of the experiment, whereas plants treated with Xac+50 mM and Xac+100 mM NaCl showed the highest PP up to 30 days after inoculation and then decreased. However, the PP of Xac+150 mM and Xac+200 mM NaCl treated plants gradually decreased till the end of experiment. Similarly, the PP of 200 mM NaCl treated plants declined continuously. Interestingly, the PP in 50 mM and 100 mM NaCl treated plants was higher initially and then decreased at 30 DAI to 40 DAI. This study revealed that citrus canker disease development was enhanced by salt stress. In addition, the physiological performance of the plants was enhanced by Xac and Xac + moderate salt stress but then demolished under severe salt stress.
    Keywords Agriculture ; Plant biology ; Salt stress ; Chlorophyll content ; Net assimilation rate ; Intercellular CO2 concentration ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
    Subject code 580 ; 630
    Language English
    Publishing date 2020-02-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Prognostic and clinico-pathological significance of BIN1 in breast cancer

    Subbroto Kumar Saha / Md. Ashraful Kader / Kazi Abdus Samad / Krishno Chandra Biswas / Md. Ataur Rahman / Md. Anwar Khasru Parvez / Md. Shahedur Rahman

    Informatics in Medicine Unlocked, Vol 19, Iss , Pp 100327- (2020)

    2020  

    Abstract: Bridging integrator 1 (BIN1) is a potential tumor suppressor that behaves as silent or misplaced in breast, prostate, skin, lung, and colon cancers. Previous studies noted decreased BIN1 expression in breast cancer (BC). Despite this, BIN1's role in ... ...

    Abstract Bridging integrator 1 (BIN1) is a potential tumor suppressor that behaves as silent or misplaced in breast, prostate, skin, lung, and colon cancers. Previous studies noted decreased BIN1 expression in breast cancer (BC). Despite this, BIN1's role in breast cancer is not well understood and remains to be elucidated. Here, we computationally analyzed BIN1 expression and its prognostic role in BC using various databases. Specifically, we found a down-regulated expression profile for the BIN1 gene in different BC subtypes using Oncomine, TCGA, and bcGenExMiner v4.2 web. The expression of BIN1 was found to be associated with various clinico-pathological conditions including estrogen receptor (ER), progesterone receptor (PR) basal-like subtype, and triple-negative breast cancer (TNBC) based on analysis of the bcGenExMiner v4.2 and TCGA databases. In addition to mRNA expression, the correlation between mRNA expression and BIN1 promoter methylation was established using TCGA datasets from UCSC Xena and ULCAN web, and we subsequently examined the relationship of BIN1 promoter methylation with different clinico-pathological conditions in BC patients. Data mining via Kaplan-Meier plotter indicated a positive association between lower BIN1 expression and low BC patient survival and various clinico-pathological conditions in BC patients. Furthermore, we identified a list of genes co-expressed with BIN1 in BC using TCGA data from the ULCAN web. Among the co-expressed genes, glycophorin C (GYPC) had the most predominant positive correlation. This correlation was further confirmed in BC using UCSC Xena and bcGenExMiner v4.2 webs. Overall, this study establishes that attenuated BIN1 expression might induce progression and poor prognosis in BC patients with GYPC association. This could be useful for clinical BC therapy.
    Keywords BIN1 ; Methylation ; Breast cancer ; Prognosis ; GYPC ; Oncomine ; Computer applications to medicine. Medical informatics ; R858-859.7
    Subject code 616
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Antibacterial activities of green tea crude extracts and synergistic effects of epigallocatechingallate (EGCG) with gentamicin against MDR pathogens

    Md. Anowar Khasru Parvez / Karabi Saha / Juairia Rahman / Rahath Ara Munmun / Md. Atikur Rahman / Shuvra Kanti Dey / Md. Shahedur Rahman / Sohidul Islam / Mohammad Hossain Shariare

    Heliyon, Vol 5, Iss 7, Pp e02126- (2019)

    2019  

    Abstract: Plant extracts and their purified compounds were examined for synergistic antimicrobial activity using selected multi-drug resistant (MDR) pathogens. The study aims to investigate the antibacterial activity of green tea (Camellia sinensis) and its ... ...

    Abstract Plant extracts and their purified compounds were examined for synergistic antimicrobial activity using selected multi-drug resistant (MDR) pathogens. The study aims to investigate the antibacterial activity of green tea (Camellia sinensis) and its purified compound epigallocatechingallate (EGCG). The synergistic relation of the compound with antibiotic was detected against selected potential Gram positive and Gram negative pathogens. Staphylococcus aureus and Escherichia coli were used as test pathogens which were resistant to different groups of antibiotics. After collection of fresh green tea leaves, samples were washed and air dried. EGCG is one of the bioactive compounds and was separated from tea plant. Antibacterial activity of EGCG and crude extracts of green tea were done by microdilution method (minimum inhibitory concentration and minimum bactericidal concentration). The synergistic effect of EGCG and gentamicin was determined. MIC value of green tea extract was found at 125 μg/mL in case of MDR E. coli, MDR S. aureus and their reference strains and MBC at 500 μg/mL against S. aureus. No MBC value was found against E. coli. EGCG showed better activity on Gram positive pathogen compared to that of Gram negative. MBC value of this compound was 1250 μg/mL for E. coli where 625 μg/mL for S. aureus. Strong synergistic relation (FICI 0.325) was found against pathogens in the combination of EGCG with gentamycin. The purified EGCG compound of green tea has great synergistic effect against MDR pathogens. More investigation is needed to know the inhibitory effect of these plant extracts and their components.
    Keywords Microbiology ; Pharmaceutical science ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
    Subject code 571
    Language English
    Publishing date 2019-07-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Antibacterial activity of combined medicinal plants extract against multiple drug resistant strains

    Rafiqul Islam / Md. Shahedur Rahman / Riad Hossain / Nazmun Nahar / Belal Hossin / Abir Ahad / Shaikh Mizanur Rahman

    Asian Pacific Journal of Tropical Disease, Vol 5, Iss Sup 1, Pp 151-

    2015  Volume 154

    Abstract: Objective: To find out the combined antibacterial efficacy of Aegle marmelos, Aphanamixis polystachya, Cuscuta reflexa and Aesclynomene indica against bacterial pathogens. Methods: Antibacterial potency of combined plant extracts has been tested against ... ...

    Abstract Objective: To find out the combined antibacterial efficacy of Aegle marmelos, Aphanamixis polystachya, Cuscuta reflexa and Aesclynomene indica against bacterial pathogens. Methods: Antibacterial potency of combined plant extracts has been tested against Bacillus subtilis IFO 3026, Sarcina lutea IFO 3232, Xanthomonas campestris IAM 1671, Escherichia coli IFO 3007, Klebsiella pneumoniae ATTC 10031, Proteus vulgaris MTCC 321 and Pseudomonas denitrificans KACC 32026 by disc diffusion assay. Commercially available standard antibiotic discs were also used to find out antibiotic resistance pattern of test organisms. Results: Among the test organisms, Escherichia coli, Proteus vulgaris, Klebsiella pneumoniae and Proteus denitrificans showed resistance against multiple commercially available antibiotics. On the other hand, these multiple drug resistant organisms showed susceptibility against combined plant extracts. Conclusions: These combined plants extracts showed synergistic antibacterial activity and could lead to new antibacterial drug designing.
    Keywords Aegle marmelos ; Aphanamixis polystachya ; Cuscuta reflexa ; Aesclynomene indica ; Antibacterial activity ; Disc diffusion assay ; Medicine ; R ; Arctic medicine. Tropical medicine ; RC955-962
    Language English
    Publishing date 2015-06-01T00:00:00Z
    Publisher Asian Pacific Journal of Tropical Disease Editorial Office
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article: Antibacterial Properties and Chemical Composition of Essential Oil from Aegle marmelos (L.) Corr. Leaves Growing in Bangladesh

    Jamal, Mohammad Abu Hena Mostofa / Hea-Jong Chung / Hyeon-Jin Kim / Md. Belal Hossain / Md. Shahedur Rahman / Satya Priya Sharma / Seong-Tshool Hong

    Journal of essential oil-bearing plants. 2017 Jan. 2, v. 20, no. 1

    2017  

    Abstract: Aegle marmelos is frequently used in Ayurveda medicine in countries of the Indian subcontinent like Bangladesh. The present study attempts to elucidate the antibacterial activity of A. marmelos leaves growing in Bangladesh (A. marmelos LBD) and to screen ...

    Abstract Aegle marmelos is frequently used in Ayurveda medicine in countries of the Indian subcontinent like Bangladesh. The present study attempts to elucidate the antibacterial activity of A. marmelos leaves growing in Bangladesh (A. marmelos LBD) and to screen therapeutically important phytochemicals. The extracts of this plant’s leaves prepared with six organic solvents were tested for their antibacterial activity against Bacillus subtilis IFO 3026 , Escherichia coli IFO 3007 , Klebsiella pneumoniae ATTC 10031 , Proteus vulgaris MTTC 321 , Pseudomonas denitrificans KACC 32026 , Sarcinalutea IFO 3232, and Xanthomonas campestris IAM 1671. Inhibition of bacterial growth and the minimum inhibitory concentration (MIC) were assayed by the disk diffusion method. Essential oil of A. marmelos LBD was used for gas chromatographicmass spectrometric (GC-MS) analysis in order to determine its chemical composition. Among the six solvents, n-hexane and petroleum ether extracts showed a great potential of antibacterial activity against all the bacteria, with inhibition zones of 13.3±0.58 to 10±1.0 mm. whereas essential oil showed 12.33±1.53 mm to 9.33±0.58 mm inhibition zone. The MIC value was 32 μgD ml for petroleum ether, dichloromethane, n-hexane extracts and 16 μlD ml for essential oil of A. marmelos LBD. Eighteen chemical components were found after GC-MS analysis of essential oil of A. marmelos LBD. The major components of the essential oil are ledene oxide-(II) (18.16%); menthol, 12 -(butyn-3-one-1-yl), (1R, 2S, 5R) (7.04%); (-)-caryophyllene oxide (7.10%); and himachalol (6.15%). These phytochemicals were previously well known to have strong antibacterial activity, which explains why A. marmelos LBDis an effective antibacterial agent against various infectious diseases.
    Keywords Aegle marmelos ; antibacterial properties ; antibiotics ; Ayurvedic medicine ; Bacillus subtilis ; bacteria ; chemical composition ; disk diffusion antimicrobial test ; Escherichia coli ; essential oils ; gas chromatography-mass spectrometry ; hexane ; infectious diseases ; Klebsiella pneumoniae ; leaves ; menthol ; methylene chloride ; microbial growth ; minimum inhibitory concentration ; petroleum ; phytopharmaceuticals ; Proteus vulgaris ; Pseudomonas denitrificans ; solvents ; Xanthomonas campestris ; Bangladesh ; India
    Language English
    Dates of publication 2017-0102
    Size p. 155-174.
    Publishing place Taylor & Francis
    Document type Article
    ISSN 0976-5026
    DOI 10.1080/0972060X.2017.1308276
    Database NAL-Catalogue (AGRICOLA)

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  10. Article ; Online: Anti-bacterial Evaluation and Minimum Inhibitory Concentration Analysis of Oxalis corniculata and Ocimum santum against Bacterial Pathogens

    Md. Abu Hena Mostofa Jamal / Md. Mahboob Hossain Khan / Md. Shahedur Rahman

    Biotechnology, Vol 9, Iss 4, Pp 533-

    2010  Volume 536

    Abstract: In this present study, it is tried to find out the antimicrobial effect and Minimum Inhibitory Concentration (MIC) of Oxalis corniculata leaf and Ocimum sanctum leaf extract against clinical isolates from urine, stool and sputum and their successive ... ...

    Abstract In this present study, it is tried to find out the antimicrobial effect and Minimum Inhibitory Concentration (MIC) of Oxalis corniculata leaf and Ocimum sanctum leaf extract against clinical isolates from urine, stool and sputum and their successive comparison with commercially, available antibiotic discs. Powdered leaves were prepared and used for extraction with various solvents, viz., methanol, ethanol and chloroform in case of Oxalis corniculata and ethanol, methanol, n-hexane and petroleum spirit in case of Ocimum santum . All the solvent extracts were evaporated to dryness in air. Using the disc diffusion method, the bacterial growth were inhibited. Among the solvent extracts tested, methanol extract of Oxalis corniculata leaf showed higher antibacterial activity compared to Erythromycin and Nalidixic acid against Staphylococci sp. whereas the methanol extract of Ocimum sanctum leaf showed higher antibacterial activity compared to CIP-5 against Staphylococcus aureus . The best MIC values were recorded to be 256 μg mL -1 against Salmonella typhi for ethanol extract of Oxalis corniculata leaf and 128 μg mL -1 against Staphylococcus aureus for the methanol extract of Ocimum sanctum leaf.
    Keywords Oxalis corniculata ; antibacterial activity ; Medicinal plants ; Ocimum santum ; MIC ; Biotechnology ; TP248.13-248.65 ; Chemical technology ; TP1-1185 ; Technology ; T ; DOAJ:Biotechnology ; DOAJ:Life Sciences ; DOAJ:Biology and Life Sciences
    Subject code 580
    Language English
    Publishing date 2010-01-01T00:00:00Z
    Publisher Asian Network for Scientific Information
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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