Current Issue

 

Volume 28(1); 2020

 

Nuclease pre-treatment increases efficiency of whole genome sequencing of Influenza B virus in respiratory specimens
Wudtichai Manasatienkij, Piyawan Chinnawirotpisan, Weerayuth Kittichotirat, Sriluck Simasathien, Louis R. Macareo, Damon W. Ellison, Supapon Cheevadhanarak, Wiriya Rutvisuttinunt, Stefan Fernandez, Chonticha Klungthong
APJMBB 28 (1): 1-13
Article DOI: https://doi.org/10.35118/apjmbb.2020.028.1.01
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The use of next generation sequencing (NGS) directly on respiratory specimens to obtain viral whole genome sequence (WGS) enhances the capability for rapid and unbiased viral characterization. One of the challenges of using NGS directly in influenza-like illness (ILI) respiratory specimens is the higher proportion of host and bacterial genome compared to viral genetic materials found, which reduces the likelihood of obtaining complete viral genome sequences. This study aims to evaluate nuclease pretreatments prior to sequencing of influenza B virus directly from ILI respiratory specimens.  Sequence data were mapped to human, bacteria and influenza B viral genome. In the absence of any nuclease pretreatments, the sequence reads identified as Haemophilus influenzae, Haemophilus parainfluenzae, Neisseria meningitidis and Veillonella parvula were the most prominent genetic materials in respiratory specimens. Filtration followed by nuclease treatment reduced bacterial sequence reads by at least 70 folds in all 4 tested samples, supporting the direct application of NGS in ILI respiratory specimens. Although the pretreatment methods significantly reduced human genome sequences, the remaining human genome especially human rRNA still impact the number and proportion of the viral sequence reads.
Potential use of Pennisetum purpureum for phytoremediation and bioenergy production: a mini review
Nurul Atiqah Osman, Ahmad Muhaimin Roslan, Mohamad Faizal Ibrahim, Mohd Ali Hassan
APJMBB 28 (1): 14-26
Article DOI: https://doi.org/10.35118/apjmbb.2020.028.1.02
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Organic and/or heavy metal pollutants in soil and wastewater can be remediated by phytoremediation. Phytoremediation combines the disciplines of plant physiology, soil microbiology and soil chemistry. There are several ways by which plants extract, stabilize, filtrate, volatilize or degrade the contaminants. However, the effectiveness of phytoremediation relies upon the type of plant used. Pennisetum purpureum, commonly referred to as Napier grass, is one of the exceptional phytoremediators due to its rapid growth rate and ability to survive in highly contaminated soils. In the present review, the potential use and applicability of P. purpureum to remediate various contaminated areas was highlighted and comprehensively discussed, especially the five phytoremediation mechanisms involved (i.e., phytodegradation, phytoextraction, phytofiltration, phytostabilization, phytovolatilization). The application and management of P. purpureum
in soil and wastewater phytoremediation were also critically presented. The coupling of phytoremediation and bioenergy is the zero-waste concept that can be applied since P. purpureum contains high lignocellulosic content that can be utilized as carbon source for biofuel production, such as ethanol and butanol.
Plasma miR-126 levels and its genomic polymorphism SNP rs4636297 in Type 2 diabetes
Monireh Rezai, Shirin Shahbazi, Nasrin Mansournia
APJMBB 28 (1): 27-33
Article DOI: https://doi.org/10.35118/apjmbb.2020.028.1.03
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Since the variation of microRNAs expression has been described in type2 diabetes, we aimed to evaluate the plasma levels of miR-126 with known roles in the angiogenesis. Genomic polymorphism of miR-126 (SNP rs4636297) was also assessed as it is involved in the processing of pri-miR-126 to mature microRNA.Genotyping of the SNP rs4636297 was carried out by PCR-RFLP using HaeII enzyme. Real-time PCR assay was applied to assess miR-126 expression, which the fold change in gene expression was calculated by the Relative Expression Software Tool (REST). Data analysis was performed using exact-like logistic regression, Fisher exact test and the elrm package with the R software. Our data indicated that the group with BMI greater than 30 was at greater risk of diabetes (odds ratio=14.4, p value=0.00), compared with the BMI=19-25. The mean fold decrease in miR-126 gene expression in diabetic samples relative to normal samples was 0.653 (95% confidence interval: 0.012-18.765). All patients with the lowest levels of miR-126, had experienced diabetic complications. Considering the AA genotype as the reference, the odds ratio of diabetic complications for the GG and AG genotype were 1.2 and 1.43, respectively. miR-126 is one of the key factors in predisposition to diabetes and diabetic complication. Since the lowest expression of miR-126 leads to the diabetic complications it can be concluded that genetic predisposing factors should be considered in the management and treatment of Type 2 diabetes.
In-silico molecular docking study of novel derivatives of erlotinib in glioma
Deepika Tripathi, Sabiha Imran
APJMBB 28 (1): 33-38
Article DOI: https://doi.org/10.35118/apjmbb.2020.028.1.04
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Gliomas are primary brain tumours arises from the glial cells. Gliomas associated risk factor depend upon its degree of stage and grade. Erlotinib is a quinazoline derivative and antineoplastic agent that capacities as a Protein Kinase Inhibitor for Epidermal growth factor receptor (EGFR) related tyrosine kinase and widely used for treating non-small cell carcinoma. Erlotinib, (a tyrosine kinase inhibitor) has been found in the glioblastoma. ErbB (EGF family receptor tyrosine kinase) established to control cell survival, proliferation, migration, and differentiation. The ErbB receptor accounts for the restricted and redundant functions in the maintenance of tissues in adult mammals. Newly discovered drug targets and personalised treatments could be used to identify the characteristics of any individual’s tumorigenesis. To see the binding mode of deferent classes of erlotinib carefully chosen based on the structural comparison, we employed simulated screening and molecular docking based on the theory of evolution. The study consists of a simulated screening of around 3200 molecular derivatives of erlotinib and their molecular docking using a Lamarckian genetic algorithm. Molecular docking results showed binding energy ranging from -12.15 kcal/mol to -1.17 kcal/mol. Top 10 best-docked proteins were analyzed using UCSF Chimera and finding discovered the complicated atomic-scale properties between ligand and the target protein. Further wet lab study requires to study the actual binding as binding mode provided. To identify new inhibitors of EGFR with higher potency and specificity, additional information is needed for future designs molecules.
Transcriptome analysis of Phytophthora infestans and Colletotrichum coccodes in tomato to reveal resistance mechanisms
Abbas Saidi, Zahra Hajibarat, Zohreh Hajibarat
APJMBB 28 (1): 39-51
Article DOI: https://doi.org/10.35118/apjmbb.2020.028.1.05
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Tomato is considered as an important commercial crop and protective food and it’s yield is extremely affected by different pathogens. Such harmful pathogens severely affecting tomato include Phytophthora infestans (oomycete) and Colletotrichum coccodes (fungi). In this study, gene expression analysis was performed using the microarray datasets available in the public database to investigate differentially expressed genes DEGs under developmental and anatomy conditions and consequently constructing the predicted PPI (Protein-protein interaction) network. Here, a comparison of abundances revealed that 51 genes were differentially expressed due to oomycete and fungi stresses in tomato. Expression analysis revealed that Solyc06g007510.3 was up-regulated whereas Solyc05g008850.3 was down-regulated in all developmental stages and anatomy conditions to manage auxin metabolism under fungi and oomycete infections in tomato. The gene ontology included cellular metabolic and organic substance metabolic processes, cellular biosynthetic, organic substance biosynthetic, and cellular macromolecule metabolic process, chloroplast, intracellular membrane-bounded organelle, heterocyclic compound binding, organic cyclic compound binding, ion binding, binding, and catalytic activity.  Analysis of cis-elements illustrated that 12 most general cis-regulatory elements (CATT-box, TATA-box, MYB, MYC, ABRE, G-box, Box 4, AAGAA-motif, MBS, as-1, TGACG-motif, and CGTCA-motif) were identified in promoter region. The highest frequency of cis-elements included CATT-box and TATA-box in response to the pathogens at different growth stages in tomato. Our findings can provide a better insight to the regulatory mechanisms involved in response to fungi and oomycete infection in tomato which can aid to improve the efficiency of developing tomato varieties.
Development of attenuated Vibrio parahaemolyticus mutant strains as potential live vaccines
Vu Thi Bich Huyen, Nguyen Xuan Viet, Pham Thi Tam, Man Hong Phuoc, Huynh Viet Tung, Nguyen Dang Quang, Do Thanh Van
APJMBB 28 (1): 52-67
Article DOI: https://doi.org/10.35118/apjmbb.2020.028.1.06
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Vibrio parahaemolyticus is a pathogenic Gram-negative bacterium that commonly infects numerous species of marine fishes. In this study, we obtained eight attenuated mutant strains by the selection of rifampicin-resistant V. parahaemolyticus from three wild-type strains. Among eight selected strains, four strains (L4650, A650, L4200 and A400) were widely attenuated by virulence analysis. Sequences of two genes, tlh and toxR, that related to virulence were analyzed. The results showed that seven attenuated strains were different in sequences of the tlh gene while there was no difference in sequence of toxR gene in comparison with that of wild-type strains. Three attenuated strains (L4650, L4200 and A650) had the nucleotide changes in tlh gene that resulted to the changes in the size of deduced amino acid sequences. In addition, rpoB gene coding for b-subunit of RNA polymerase that related to Rifampicin resistance was analyzed for all selected strains. Two strains (A650 and L4650) had the nucleotide changes in ropB sequence. To assess the potential use of the L4650 strain as a live attenuated vaccine, the groupers (Epinephelus coioides) were intraperitoneally injected with the L4650 strain and later challenged with the virulent wild-type strain at three different doses. Results showed the protection for L4650 strain vaccinated-fish produced relatively earlier than usual at 15 days post-vaccination with relative percent survival (RPS) values from 96.91-100%. At 60 days post-vaccination, the RPS values of vaccinated fish were 96.27-100%. Our results suggest the L4650 strain could become a potential vaccine candidate against V. parahaemolyticus for future studies.
Statistical optimization of an acid protease production by a local Aspergillus nigerMH109542 using a medium based on decommissioned dates
Malika Benkahoul, Amina Bramki, Aicha Belmessikh, Aicha Mechakra-Maza
APJMBB 28 (1): 68-76
Article DOI: https://doi.org/10.35118/apjmbb.2020.028.1.07
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The production of an acid protease by liquid fermentation is performed on a medium based on decommissioned dates by a local mold isolated from an extreme environment. The used mold is isolated from the thermal soil in Hammam Safsaf of Teleghma (Algeria). Phenotypic and molecular identification has shown that it is Aspergillus niger. This fungi strain exhibited exo-protease activity on milk agar. The fermentation medium based on decommissioned dates is enriched by other factors according to a statistical method; the plan of Plackett and Burman. This method (N = 8 experiments and N-1 factors) allowed the optimization of the enzyme production and the growth of the mold. The statistical analysis of the obtained results shows an increased enzyme activity (650.20U), in the presence of yeast extract and salts with probabilities p = 0.239 for the first and p = 0.190 for the second. Furthermore, the corn-steep-liquor (p = 0.229) and yeast extract (p = 0.053) present a significant effect on mold growth. In conclusion, the culture of A. niger on optimized medium gives good yields of biomass and proteolytic activity compared to the basal medium. These results are encouraging. In fact, the use of a cheap and available substrate such as decommissioned dates saves the cost price of fermentation on an industrial scale.

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3rd International Conference on Molecular Biology & Biotechnology

in conjunction with the 26th  Scientific Meeting of the Malaysian Society of Molecular Biology & Biotechnology (MSMBB) & UCSI University's 2nd Applied Science Symposium

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FOSTERING INNOVATION THROUGH RESEARCH

24-25th April 2019, UCSI University Kuala Lumpur

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