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Malaysian Journal of Biochemistry & Molecular Biology M J B M B
The official publication of the Malaysian Society for Biochemistry & Molecular Biology (MSBMB) E-ISSN 2600-9005
Indexed by SCOPUS and Malaysian Citation Index (MYCITE)
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About MJBMB
Malaysian Journal of Biochemistry and Molecular Biology (MJBMB) was founded by the Malaysian Society for Biochemistry and Molecular Biology (MSBMB) in the year 1997. It was published two times a year prior to 2010. From 2016 onwards, the journal will be published ONLINE 3 times per year, in April, August and December. The journal publishes research papers in all areas of biochemistry, biophysics and molecular biology, which include DNA and RNA biology, gene expression, glycobiology, enzymology, protein structure and function, lipid chemistry, membranes, immunology, plant biochemistry and physiology, microbiology, immunology, natural product chemistry, biomedical science, research methods and bioinformatics. Indexing
SCOPUS MyCITE (Malaysian Citation Index)
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Dr. Azzreena Mohamad Azzeme 0 0 1 1 3 9 1 Managing Editor Email : [email protected]
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Malaysian Journal of Biochemistry & Molecular Biology M J B M B
The official publication of the Malaysian Society for Biochemistry & Molecular Biology (MSBMB) E-ISSN 2600-9005
Indexed by SCOPUS and Malaysian Citation Index (MYCITE)
Home About This Journal Past Issues Editorial Board For Authors Contact Us
Chief Editor Managing Editor
Noor Azmi Shaharuddin Azzreena Mohamad Azzeme Department of Biochemistry Department of Biochemistry Faculty of Biotechnology and Faculty of Biotechnology and Biomolecular Sciences Biomolecular Sciences Universiti Putra Malaysia 4300 Universiti Putra Malaysia 43400 UPM Serdang, Selangor MALAYSIA MALAYSIA [email protected] [email protected]
(Plant Biotechnology; Transcriptomics) (Plant Biochemistry and Biotechnology)
Associate Editors
Mohd Ezuan Khayat Noor Dina Muhd Noor Mohd Badrin Hanizam Ph.D., University of Manchester, Shafinaz Abd Gani Ph.D., University of Hyogo, Abdul Rahim United Kingdom Ph.D., Universiti Putra Malaysia (Animal Cell Biochemistry) Jepun (Drug Development; Drug Ph.D., Imperial College London, (Structural Biology; Protein Toxicology) United Kingdom Crystallization) (Cell Metabolomics; Nutritional Biochemistry)
Editorial Board Members
Sandy Hwe San Loh Yuh-Fen Pung Ho Chai Ling University of Nottingham University of Nottingham Malaysia Faculty of Biotechnology and Malaysia Room B1B20 Block B1 Biomolecular Sciences Room B1A22 Block B1 Malaysia Campus Universiti Putra Malaysia Malaysia Campus Jalan Broga 43400 UPM Serdang, Selangor Jalan Broga 43500 Semenyih https://msbmb2010.wixsite.com/mjbmb/editorial-board 1/3 11/29/2020 Editorial Board | mjbmb Jalan Broga 43500 Semenyih MALAYSIA 43500 Semenyih Selangor Darul Ehsan This site was designed with theSelangor .c oDarulm w eEhsanbsite builder. Create your website tMalaodayysia. Start Now Malaysia (Plant Genetics; Cell and (Mitochondrial bioenergetics; Oxidative Molecular Biology) (Virology and molecular stress; Obesity and diabetes; Vascular biology) biology)
Sheila Nathan Dhrubajyoti Darakhshan Jabeen Haleem School of Biosciences & Chattopadhyay Dr Pajwani Center for Molecular Biotechnology Amity University Medicine and Drug Research Faculty of Science and Department of Biochemistry International Center for Technology and Biotechnology Chemical and Biological Universiti Kebangsaan Malaysia Calcutta University, Kolkata, Sciences Selangor D.E., MALAYSIA INDIA. University of Karachi, PAKISTAN (Neuroscience; Molecular (Microbial Genomics; Molecular (Biochemistry; Virology; Neuropharmacology) Biology) Metagenomics)
Kok Yih Yih Lim Yang Mooi FUNG SHIN YEE School of Health Sciences, Faculty of Medicine & Health Department of Molecular Division of Applied Biomedical Sciences Medicine Sciences and Biotechnology, Universiti Tunku Abdul Rahman Faculty of Medicine International Medical University Kajang, Selangor D.E., University of Malaya 126, Jln Jalil Perkasa 19, Bukit MALAYSIA Jalan Universiti, 50603 Kuala Jalil, 57000 Kuala Lumpur Lumpur, Wilayah Persekutuan (Cancer chemoprevention, Cell Kuala Lumpur (Algal Biotechnology) Biology & Phytochemistry) (Toxinology and toxicology; Biochemistry)
Anthony Ho S.H. Hwang Jung Shan Hasidah Mohd. Sidek School of Biosciences Department of Medical School of Biosciences & Taylor's University Sciences, Sunway University Biotechnology Selangor D.E., 5, Jalan Universiti, Bandar Faculty of Science and Technology MALAYSIA Sunway, 47500 Petaling Jaya, Universiti Kebangsaan Malaysia Selangor Selangor D.E., MALAYSIA (Cancer Biology; Bioactive compounds) (Immunotoxinology; Genetic (Natural products; Biochemistry) polymorphism)
Mohd Firdaus Raih Muhammad Fazril School of Biosciences & Ng Chyan Leong Mohamad Razif Biotechnology Institute of Systems Biology Department of Molecular Faculty of Science and Universiti Kebangsaan Malaysia Medicine, Faculty of Medicine, Technology Selangor D.E., MALAYSIA University of Malaya Universiti Kebangsaan Malaysia Kuala Lumpur, Malaysia Selangor D.E., Malaysia (Structural Biology; Molecular
Biology) (Synthetic Biology; RNA- (Bioinformatics, Computational binding proteins) Biology, RNA Biology)
Adeline Chia Yoke Yin Renee Lim Lay Hong School of Biosciences Faculty of Applied Sciences Taylor's University UCSI University,Kuala Lumpur, Selangor D.E., Malaysia MALAYSIA
(Recombinant allergens; (Translational Medicine, Drug Probiotics, Obesity and gene Discovery & Development, variants, Molecular Biology) Endocrinology & Reproductive systems)
Enquiries:
Dr. Azzreena Mohamad Azzeme 0 0 1 1 3 8 9 https://msbmb2010.wixsite.com/mjbmb/editorial-board 2/3 11/29/2020 Editorial Board | mjbmb Dr. Azzreena Mohamad Azzeme 0 0 1 1 3 8 9 This site was designed with the .com website builder. Create your website today. Start Now Managing Editor Email : [email protected]
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Malaysian Journal of Biochemistry & Molecular Biology M J B M B
The official publication of the Malaysian Society for Biochemistry & Molecular Biology (MSBMB) E-ISSN 2600-9005
Indexed by SCOPUS and Malaysian Citation Index (MYCITE)
Home About This Journal Past Issues Editorial Board For Authors Contact Us
December 2019 Malay. J. Biochem. Mol. Biol. (2019) 22 (3) TABLE OF CONTENTS
Page 1-7 Nur Nadhirah Zakaria, Ahmad Fareez Ahmad Roslee, Azham Zulkharnain, Claudio Gomez-Fuentes, Mansur Abdulrasheed, Suriana Sabri, Nancy Calisto-Ulloa and Siti Aqlima Ahmad
BACTERIAL GROWTH AND DIESEL BIODEGRADATION IN THE PRESENCE OF As, Cu AND Pb BY ANTARCTIC MARINE BACTERIA
Abstract Antarctica is considered to be low-impacted by anthropogenic activities despite the rising activities occurring in the Southern Ocean. Rising human activities from within Antarctica and external sources resulted in hydrocarbon and heavy metal pollution and create more and more evidence on how much anthropogenic pollution has influenced the southern polar region. Bioremediation possibilities in these parts are very limited in terms of maximum efficiency due to its unique climatic conditions. Furthermore, heavy metals come hand in hand with hydrocarbon pollution and there is a call to obtain. In the present study, diesel degradation was inhibited the most by Pb (31.75%), As (34.35%) and lastly Cu (48.91%) in comparison to control flask (65.19%). Bacterial growth was most inhibited by Cu. Pb had little effect to the growth of bacteria in comparison to As and Cu. Growth rates were obtained by fitting the Exponential mathematical model to the data and obtaining individual growth rates and measures of good fit. ANOVA analysis of the growth obtained P values of control, As and Pb to be <0.05 while Cu gave a P>0.05.
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Page 8 - 15 Syazani Darham, Claudio Gomez-Fuentes, Azham Zulkharnain, Suriana Sabri, Nancy Calisto-Ulloa, Nicolás Ramírez-Moreno and Siti Aqlima Ahmad
ISOLATION AND IDENTIFICATION OF MOLYBDENUM-REDUCING COLD-ADAPTED MARINE BACTERIA ISOLATED FROM BERNARDO O’HIGGINS RIQUELME BASE STATION, ANTARCTICA
Abstract Molybdenum (Mo) pollution is an emerging problem in some parts of the world. Traces of Mo can be found in the soil and snow even in the most remote part on earth, Antarctica. Bioremediation of Mo using microorganisms has been an up-and-coming alternative in cleaning up Mo from the environment. Mo reduction is a process that transforms sodium molybdate with an oxidation state of 5+ or 6+ to Mo-blue, a less toxic form of the compound. The objectives of this research are to screen, isolate and identify the best cold-adapted Mo-reducing bacterial strain isolated from marine water samples at Bernardo O’Higgins Riquelme Base Station, Antarctica. A total of 11 psychrotolerant strains were seen able to reduce Mo and further studied to determine their taxonomic position using phylogenetic analysis. Based on 16S rRNA identification, the strains were identified as Shewanella sp., Staphylococcus sp. and Marinomonas sp. This study suggests the potential use of the best Mo-reducing cold- adapted bacteria, strain Marinomonas sp. strain AQ5-A9, on the remediating of Mo in the Antarctic region.
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This site was designed with the .com website builder. Create your website today. Start Now Page 16 - 19 M. Ali Sarong , S. Supriyatno, Asiah M.D., Mimie Saputri, S. Safika, Asri Mursawal, Wenni Novita Sari & Agung S. Batubara
DNA HOMOLOGICAL ANALYSIS OF THE GELOINA SHELL IN REULEUNG LEUPUNG MANGROVE ECOSYSTEM, ACEH BESAR DISTRICT, ACEH PROVINCE, INDONESIA
Abstract
Three species of Geloina shells were found in the Reuleung Leupung mangrove ecosystem area, Aceh Besar District, Indonesia which consists of Geloina erosa, G. expansa, and G. coaxana. The phylogenetic relationship of the three closely related species is currently not established. In this study, we analyze the DNA sequence homology of the three Geloina species and compare them with other mangrove shells species stored at NCBI GenBank. The research activities were conducted from July to September 2017, in the area of the Reuleng Leupung mangrove ecosystem where Geloina shells were obtained using destructive sampling method. The results showed that the three Geloina shells have a high similarity with Polymesoda carolina Voucher, Cyrenoida floridana Partial, Cyrenoida floridana Voucher, Glauconome rugosa Voucher, Corbicula fluminea, Glauconome viren Partial, where a very close level of phylogenetic relationship was shown at Polymesoda carolina Voucher sequence homology of 99%. We conclude that due to 99% DNA homology between G. erosa, G. expansa, and G. coaxan and Polymesoda carolina, they are of the same species.
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Page 20 - 24 Ilham Abd Allah Ali Al-Saleem
Celiac Disease and Risk of Lymphoma
Abstract Celiac disease (CD) is a popular autoimmune systemic defect producing from consumption of gluten that stores a protein of barley, wheat and rye. A few numbers of individual’s celiac disease continuous atrophy of villous with a raise of mucosa intraepithelial lymphocytes (IELs) in an intestine, regardless of a rigorous gluten free diets GFD termed refractory celiac disease (RCD). Precocious detection and treatment could be related to avoid disease problems as a malignant lymphoma. The purposes of this research are to epitomize the accessible facts on the (CD) history related to lymphoma, the lymphoma kinds associated with CD , the methods that gluten excite enteropathy- associated T-cell lymphoma and celiac disease molecular grounds associated with lymphoma.
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Page 25 - 32 Nor Nadia Fadiha Aizuddin, Izyanti Ibrahim, Rusliza Basir, Noor Embi & Hasidah Mohd Sidek
ANTI-MALARIAL AND CYTOKINE-MODULATING EFFECTS OF SODIUM TUNGSTATE IN MURINE MODELS OF CEREBRAL AND SEVERE MALARIA INVOLVE INHIBITION OF GSK3Β MEDIATED VIA ACTIVATION OF BOTH ERK AND Akt SIGNALING
Abstract Malaria remains a major global health problem, associated with high morbidity and mortality. Dysregulated production of pro-inflammatory mediators and cytokines is one of the factors that contribute to the pathogenesis of severe and cerebral malaria. Glycogen synthase kinase-3 (GSK3) which plays a pivotal role in regulating the production of pro- and anti-inflammatory cytokines is a potential target for anti-malarial therapeutics. Sodium tungstate (Na2WO4), which exhibits strong normoglycaemic effects, has been reported to cause phosphorylation of GSK3β. The present study aims to evaluate the anti-malarial and cytokine-modulating effects of Na2WO4 using Plasmodium berghei ANKA (PbA) and Plasmodium berghei NK65 (PbN), established models for cerebral and severe malaria respectively. Intraperitoneal administration of Na2WO4 into PbA- or PbN-infected mice resulted in dose- dependent chemo-suppression of parasitaemia. At 50 mg/kg body weight, Na2WO4 treatment resulted in suppression exceeding 60% and improved median survival time of infected mice (14 and 17 days for PbA- and PbN- infected animals compared to 7.5 and 12 days in non-treated control respectively). Na2WO4 treatment also significantly decreased (p>0.05) the serum levels of pro-inflammatory cytokines (TNF-α, IFN-ɤ and IL-18) whilst significantly increasing levels of anti-inflammatory cytokines (IL-10 and IL-4) in mice from both models of malarial infection. In addition, western analysis revealed that in the brain (PbA) and liver (PbN) of infected animals administered with Na2WO4, the intensities of pGSK3β (Ser9), pERK1/2 (Thr202/Tyr204), pp90RSK (Ser380) and pAkt (Ser473) were increased significantly whilst pNF-κB (Ser536) was decreased compared to controls. Taken together our results indicate that anti-malarial and cytokine-modulating effects of Na2WO4 observed involve at least in part the regulation of NF-κB through inhibition of GSK3β mediated via activation of ERK/p90RSK as well as Akt signaling. Our findings reiterate the importance of GSK3β as a molecular target for anti-malarial therapeutics.
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Page 38 - 42 Anton S. Tkachenko, Galina I. Gubina-Vakulyck, Oksana I. Kauk, Anatolii I. Onishchenko, Esmira V. Shekhovtsova & Oksana A. Nakonechna
CHANGES IN S100 PROTEIN EXPRESSION IN THE CEREBELLUM OF RATS ORALLY EXPOSED TO ENERGY DRINKS
Abstract The aim of our study was to assess the rate of S100 protein expression in the cerebellum of rats orally exposed to caffeinated energy drinks (CED) during 2 and 4 weeks. Twenty WAG rats were enrolled in the experiment. They were subdivided into three groups. The animals from group 1 and group 2 (n=7 in each) were orally exposed to a caffeinated energy beverage “Black” at a dose of 12 ml per kg of body weight during two and four weeks https://msbmb2010.wixsite.com/mjbmb/december-2019 2/5 11/29/2020 December 2019 | mjbmb caffeinated energy beverage Black at a dose of 12 ml per kg of body weight during two and four weeks, respectively. The control group consisted of 6 intact rats obtained drinking water instead of a caffeine-containing This site was designed with the .com website builder. Create your website today. Start Now energy drink. Cerebellar S100 expression was evaluated immunohistochemically. Against the background of CED oral administration during two and four weeks, the density of granule cell layer becomes lower indicating neuronal loss. S100 protein was upregulated in group 1 in the entire cerebellar cortex. Thus, CED oral exposure resulted in the development of cerebellar astrogliosis. Four-week-long CED consumption resulted in S100 downregulation in the molecular and granular layers. Our findings demonstrate the damage to the cerebellum in rats exposed to CEDs with overexpression of S100, followed by a decrease in its expression.
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Page 43 - 47 Ayah Rebhi Hilles, Syed Mahmood, Mohd Arifin Kaderi & Ridzwan Hashim
IDENTIFICATION OF THE BIOACTIVE COMPOUNDS OF SKIN MUCUS FROM ASIAN SWAMP EEL (Monopterus albus) USING LIQUID CHROMATOGRAPHY QUADRUPOLE-TIME-OF-FLIGHT MASS SPECTROMETRY
Abstract Asian swamp eels have been widely accepted as sources of food, especially among various Asian cultures. However, their potential values as novel sources of therapeutic agents have not been widely appreciated. Like most other tropical fishes and amphibians, the outer integumentary system of Monopterus albus is covered with mucus layers, which may act as a mechanical and biochemical barrier for their skin. The biochemical components of these mucus layers may have certain compounds that may be medically beneficial to human. The current study was interested to screen the bioactive compounds of skin mucus from the tropical Asian swamp eel (Monopterus albus) using Liquid Chromatography Quadrupole-Time-Of-Flight Mass Spectrometry (LC-QTOF-MS), for this purpose, eel skin mucus extract was used for LC-QTOF-MS analysis. The screening results for the bioactive compounds revealed different bioactive compounds which possess multiple biological properties mainly anticancer, antimicrobial, anti-inflammatory and antioxidant activities. In conclusion, the current study illustrated that eel skin mucus contain different bioactive compounds which might be consider as therapeutic-promising agents.
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Page 48 - 54
Edmund Ui-Hang Sim and Keh-Li Yew
PUTATIVE TARGET PROTEINS OF THE RIBOSOMAL PROTEIN, RPeL27 IN NASOPHARYNGEAL CARCINOMA CELLS
Abstract The pathogenesis of nasopharyngeal carcinoma (NPC) is multifactorial and multigenic. Despite the identification of several NPC-associated ribosomal proteins (RPs), the roles of these factors and their interacting partners in NPC tumourigenesis are poorly understood. To date, NPC- associated RP genes are either up or down-regulated in diseased/tumour situation compared to normal condition. The ribosomal protein eL27 (RPeL27) has been known to be over-expressed at both transcript and protein levels in NPC cell lines. This hypothesis was reinforced by our study herein. More importantly, using gene knockdown (RNA interference technique) followed by 2D gel electrophoresis (2D GE) and in silico analysis; we revealed 15 proteins that are likely to interact with RPeL27 during situation of NPC tumourigenesis. These include COTL1, MAGOHB, UBE2N, NDPKA, TMED10, PSMB6, CA2, PGAM1, RPeL14, RPeS8, TPI1, PSMA2, RPeL19, GSTP1, and TPM1. Their association with RPeL27 could attribute to gene expression alteration, cell migration disruption and invasion, promotion of cancer cell survival, immune evasion, and genomic instability. Our findings provide new theoretical insights into the mechanism and involvement of RPeL27 in NPC pathogenesis. This is pertinent in understanding the molecular pathogenesis mediated by ribosomal proteins in the malignancy of the nasopharyngeal tissues.
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Harika Vemugadda, Prajna P Shetty, Monalisa Biswas, Revathi P Shenoy, Nalini K Page 33 - 37 ERYTHROCYTE ARGINASE ACTIVITY AND SERUM NITRIC OXIDE IN DIABETES MELLITUS
Abstract The study is to estimate and correlate the erythrocyte arginase activity and serum nitric oxide levels in normal, prediabetes and type 2 diabetes mellitus. This is a case control study with total 124 samples which were grouped as normal, pre-diabetes and diabetes based on HbA1C values. Blood samples were collected from Clinical Biochemistry laboratory, Kasturba Hospital, Manipal, after the completion of HbA1C analysis. Erythrocyte Arginase activity is https://msbmb2010.wixsite.com/mjbmb/december-2019 3/5 11/29/2020 December 2019 | mjbmb laboratory, Kasturba Hospital, Manipal, after the completion of HbA1C analysis. Erythrocyte Arginase activity is estimated by measuring the ornithine formed by Chinard reaction and Arginase activity is expressed as ornithine This sreleasedite was d peresig minutened wit hper th egr am hemoglobin.com webs iunderte buil dassaer. Cyr econditions.ate your w eNitricbsite otxideoday .is estimatedStart No bwy reducing the serum
nitrate to nitrite by using Griess reaction method. The increase in arginase activity was seen in both prediabetes and diabetes compared to normals. Compared to normal group, there was significant decrease in nitric oxide level in pre diabetes (P=0.013) however decrease is not significant in type 2 diabetes. Significant positive correlation between the arginase and nitric oxide levels is seen in normals and type 2 diabetes whereas negative correlation in prediabetes. Increase in arginase activity is indirectly affecting the nitric oxide levels and causing the macrovascular (atherosclerosis, hypertension, gangrene of foot, diabetic neuropathy) and microvascular (diabetic nephropathy, diabetic retinopathy) complications in type 2 diabetic patients.
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Page 55 - 57 Norshidah Harun, Khairul Anwar Azmi, Fazrin Adhwa Shaifulbahri & Gouri Kumar Dash
ANTIBACTERIAL SUSCEPTIBILITY TEST OF Channa striatus FILLETS AND MUCUS AGAINST Staphylococcus aureus AND Pseudomonas aeruginosa
Abstract Channa striatus is an indigenous fresh water carnivorous air breathing fish species and widely distributed in Malaysia. This white boneless meaty and tender taste edible fish is both a popular food of choice and a natural remedy in traditional medicine due to its pharmacological activities such antimicrobial, anti-inflammatory, cell proliferation and many more. Due to these salutary values of this natural product, Channa striatus often being studied in countless times in order to determine valuable information which researcher may gain. Therefore, the determination of effect exerted from both extracts particular in antibacterial activity was conducted to provide antibacterial effectivity for future formulation development. In this study, we followed the method of Wei et al.
(2015) for the collection of Channa striatus mucus. Whilst for the fillets, the extraction method of Morachis-Valdez et al. (2017) and Susakate, S. et al. (2019) were referred. As both products were strongly claimed to have beneficial towards wound healing, the antibacterial investigation was carried out against two important pathogens causing wound infection. Comparing the two, Channa striatus has shown a better inhibition zone against Pseudomonas aeruginosa compared to Staphylococcus aureus. As conclusion, the potential values of Channa striatus fillets and mucus extracts need to be studied in greater detail covers the aspects of raw materials, extraction standardization to the formulation development in order to create a new natural sources product that potentially could act as alternative agent to fight bacterial infection and heal wound much quicker than natural healing process.
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Page 58 - 65 Yiing Jye Yap, Khuen Yen Ng, Rhun Yian Koh & Soi Moi Chye3
THE PRO-APOPTOTIC MECHANISMS OF MELATONIN IN CANCER
Abstract Cancer is a leading cause of morbidity and mortality worldwide. Various therapies including chemotherapy, radiation therapy, surgery and hormone therapy have been used in the past decades to treat cancers. However, most treatments are associated with unwanted side effects; therefore a better anticancer approach that has less severe side effects and better efficacy is needed. Melatonin is an endogenous indolamine hormone that is mainly produced and secreted by pineal gland. It has oncostatic properties and induces apoptosis in cancer cells. This review describes the pro-apoptotic mechanisms of melatonin on a variety of tumor cells.
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Page 66 - 71 Talal Sabhan Salih, Muhammad Abdul-Ghani Muhammad and Mohammed Abdul-Razaq Ibraheem
MOLECULAR PHYLOGENETIC ANALYSIS USING 16S RIBOSOMAL RNA AND MULTIPLE HOUSEKEEPING GENES OF A BIOACTIVE Streptomyces sp. ISOLATED FROM MOSUL, IRAQ
Abstract https://msbmb2010.wixsite.com/mjbmb/december-2019 4/5 11/29/2020 December 2019 | mjbmb bst act The genus of Streptomyces is the most well known candidate producer of antibiotics and many pharmaceutically Thimportantis site was secondary designed wmetabolites.ith the Multilocus.com web ssequenceite builde ranalysis. Create y(MLSour wA)e bhassite shown today. to beS ata promisingrt Now method for streptomycetes taxonomy. In this study, a new bioactive Streptomyces sp. designated TMM19 was isolated from Mosul city, Iraq. The isolate grown strong on all International Streptomyces Project (ISP) media and exhibited different colours of aerial mycelia. S. sp. TMM19 strain displayed bioactivity against Staphylococcus aureus (ATCC 43300), Enterococcus faecalis (ATCC 51299) and Bacillus subtilis (ATCC 23857) pathogens. The results of phylogenetic analyses showed that S. sp. TMM19 was most related to Streptomyces sp. ZFG47 (accession no. CP030073.1) and S. actuosus (accession no. CP029788.1) based on the 16S rRNA genes tree, and to S. sp. Z022 (accession no. CP033073.1) and S. puniciscabiei (accession no. CP017248.1) based on MLSA of three protein-coding genes (atpD, recA and rpoB). The merged 16S rRNA and the three housekeeping genes phylogenetic tree showed that S. sp. TMM19 was again most related to sp. ZFG47 and S. actuosus, this might be explained by the highly conserved of 16S rRNA gene among Streptomyces strains. The 16S rRNA gene of Streptomyces sp. TMM19 strain was deposited in the GenBank database (NCBI) under the accession no. MN062265.1.
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Page 72 - 75 Umar A. A1*., Fakai, I. M & Bagudo, A. I
EXPRESSION OF RECOMBINANT HUMAN EXONUCLEASE1 (HEXO1) FROM BACTERIA
Abstract Human exonuclease1 (hExo1) directly involves in many events of DNA processing such as replication, mismatch repair (MMR), and double strand break repair (DSBR), and can also act as a sensor to lesion and inducer of apoptosis in the event of DNA lesion. Human Exo1 protein was functionally expressed in E. coli strain BL21- CodonPlus (DE3)-RIL. Expression of hEXo1 in E. coli under the transcriptional regulation of the T7 promoter yielded a soluble cytosolic monomeric protein with an apparent molecular mass of 110 kDa, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Recombinant hExo1 was purified to near homogeneity using a two-step purification procedure that involves affinity chromatography using heparin column and size-exclusion chromatography. A yield of about 100 μg of the hExo1 protein could be purified from 500 mL of E. coli strain BL21- CodonPlus (DE3)-RIL cells. The purified protein was analysed by LC-ESI-tandem MS on a Q-TOF2 mass spectrometer fitted with a nanoflow ESI (electrospray ionization) source and confirmed to be hExo1.
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MALAYSIAN JOURNAL OF BIOCHEMISTRY & MOLECULAR BIOLOGY
The Official Publication of The Malaysian Society for Biochemistry & Molecular Biology (MSBMB) http://mjbmb.org
DNA HOMOLOGICAL ANALYSIS OF THE GELOINA SHELL IN REULEUNG LEUPUNG MANGROVE ECOSYSTEM, ACEH BESAR DISTRICT, ACEH PROVINCE, INDONESIA M. Ali Sarong 1*, S. Supriyatno 1, Asiah M.D. 1, Mimie Saputri 1, S. Safika 2, Asri Mursawal3, Wenni Novita Sari 4 & Agung S. Batubara 4,5
1Department of Biology Education, Faculty of Education and Teaching Training, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia 2Department of Veterinary Medicine, Faculty of Veterinary Medicine, IPB University, Bogor, Indonesia 3Graduate Program in Marine Sciences, IPB University, Bogor, Indonesia 4Doctoral Program in Mathematics and Sciences Application (DMAS), Graduate Program, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia 5Faculty of Marine and Fisheries, Syiah Kuala University, Banda Aceh 23111, Indonesia
*Corresponding Author: [email protected]
History Abstract Received: 16th July 2019 Three species of Geloina shells were found in the Reuleung Leupung mangrove ecosystem Accepted: 22nd December 2019 area, Aceh Besar District, Indonesia which consists of Geloina erosa, G. expansa, and G. coaxana. The phylogenetic relationship of the three closely related species is currently not Keywords: established. In this study, we analyze the DNA sequence homology of the three Geloina species and compare them with other mangrove shells species stored at NCBI GenBank. The research Mangrove shells, Geloina shell, activities were conducted from July to September 2017, in the area of the Reuleng Leupung phylogeny, Polymesoda carolina mangrove ecosystem where Geloina shells were obtained using destructive sampling method. The results showed that the three Geloina shells have a high similarity with Polymesoda carolina Voucher, Cyrenoida floridana Partial, Cyrenoida floridana Voucher, Glauconome rugosa Voucher, Corbicula fluminea, Glauconome viren Partial, where a very close level of phylogenetic relationship was shown at Polymesoda carolina Voucher sequence homology of 99%. We conclude that due to 99% DNA homology between G. erosa, G. expansa, and G. coaxan and Polymesoda carolina, they are of the same species.
expansa, G. coaxan, Scylla serrata and Macrobranchium INTRODUCTION rosenbergi [1]. Geloina erosa, G. expansa and G. coaxan are common Mangrove ecosystems are brackish water forest areas with shells found in the water of the RLME [1]. These three shells biodiverse flora and fauna. Specific flora that makes up the belong to the Genus Geloina, Family Corbiculidae, Order mangrove ecosystem included Rhizophora apiculata, R. Corbicula and Class Bivalvia which have a morphological Mucronata, Sonneratia alba, S. caseolaris, Nypa fruticans, appearance of shells with various shapes. G. erosa has the same Acrosticum auretum, Bruguera sp., and Acanthus sp. [1]. The shell length on both sides, G. expansa has asymmetrical shell fauna inhabited in the mangrove ecosystem consists of terrestrial length, and G. coaxan has a thick shell so that the body thickness fauna and aquatic fauna [2]. Terrestrial fauna found in the is more dominant when compared to its length and width. mangrove ecosystem, include Egretta media, E. alba and Varanus Although different in morphology, the three species that sp. The benthic fauna in the mangrove ecosystem includes Scylla live in the RLME are thought to have a high DNA sequence serrata, Geloina erosa, G. expansa, G. coaxan, Faunus ater, similarity. Here, we analyze the DNA sequence homology of the Pyramidella sulcata, Crassostrea sp. [3]. The coastal area of three Geloina species and compare them with other mangrove Reuleung Leupung in Aceh Besar District, Aceh Province, shells species stored at NCBI GenBank. Specifically, we study of Indonesia includes a major mangrove ecosystem. The aquatic the DNA homology of the three Geloina species with six other fauna found in the Reuleung Leupung mangrove ecosystem species of mangrove shells found in various mangrove ecosystems (RLME) include Alcedo attis, Amourornis phenicurus, Varanus in the world. sp., Macaca fascicularis, and Sus crofa. The terrestrial fauna inhabited in this area were Faunus ater, Geloina erosa, G.
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MATERIALS AND METHODS three Geloina shells and Polymesoda caroliniana means that all isolates can be grouped as one species. Site and time The sampling of G. erosa, G. expansa, and G. coaxan was Table 1. Homology level of Geloina shells from the mangrove ecosystem conducted in the RLME, Aceh Besar District, Aceh Province, of Reuleung Leupung, Aceh Besar District, Indonesia Indonesia in July 2017. The DNA analysis was conducted at the Species The homologous species Identity Homology Research Laboratory of the Faculty of Veterinary Medicine, name in GenBank
Universitas Syiah Kuala, Banda Aceh, Indonesia. G. erosa Polymesoda caroliniana voucher 99% 1. The nucleotide base G. expansa BivAToL- 281 18S ribosomal arrangement has a homology Tissue sample collection G. Coaxan RNA gene, partial sequence level of 99%
The Geloina shells were obtained by scraping the bottom of the 2. The shells has two plates, waters with small knife in the RLME. After the Geloina shells so the homology level is were identified, they were cleaned from the mud attached to the 100% shell and then collected in sample bag. Geloina shells that have 3. Equally included in the been collected are then separated by species before proceeding to Class Bivalvia, Order the DNA analysis. Corbicula and Family Corbiculidae, with a level of DNA extraction similarity of 100% The principle of DNA isolation is to lyse, precipitate, and extract DNA from solid materials such as cellulose and protein [4, 5]. In this study, we isolate 16S rDNA. rDNA isolation from each The results of the phylogenetic tree analysis showed a high species was conducted by taking ± 1 mm of tissue which is then phylogenetic relationship among the three shells species (G. erosa, ground using mortar by adding 10 ml of aquadest. The ground G. expansa, and G. coaxan) that lived in the RLME in Aceh Besar materials were then transferred to 1.5 ml microtube to separate the District (Figure 1). These results showed from the branch of the rDNA from debris such as carbohydrates, fats, and proteins. The phylogeny in one monophyletic cluster. This is consistent with the amplification process was conducted using PCR and then run statement of Combosch et al. [13], monophyletic species from the through electrophoresis using agarose gel. The nucleotide Bivalve family have very close phylogenetic relationship levels sequences of each shell were then used for phylogenetic and relatively similar DNA structures. construction to see the phylogenetic relationship with other mangrove shells recorded in the GenBank.
Homologous analysis of DNA of Geloina with shells in GenBank DNA homology analysis was conducted using the BLASTN program. The similarity or homology of the DNA sequences of three species of mangrove shells found in the RLME with six species of shells deposited in GenBank, can be seen through the alignment of sample DNA sequences with nucleotide data at the National Center for Biotechnology Information (NCBI) via the http: //www.ncbi.nlm.nih.gov. [6, 7].
Figure 1. Research map in the Reuleung Leupung mangrove ecosystem in Phylogenetic analysis Aceh Besar District, Indonesia The phylogenetic relationship between the three shells species found in the RLME and the mangrove shells species recorded in The G. erosa, G. expansa, and G. coaxan that live in the RLME in the GenBank was conducted descriptively using the MEGA 7.0 Aceh Besar District, have close phylogenetic relationship with program [8]. Polymesoda caroliniana, which recorded in GenBank. This is indicated by the presence of three species of G. erosa, G. expansa, RESULTS AND DISCUSSION and G. coaxan shells in one phylogenetic branch and directly related to Polymesoda caroliniana in one phylogenetic branch. The results of DNA homology analysis showed that G. erosa, G. The level of similarity that occurs is based on a sequence of expansa, and G. Coaxan (GenBank accession no: MG946720, nucleotide bases that have a very close degree of similarity MG946718 and MG763131) found in the RLME in Aceh Besar between each of these species. Notredame [14] state that District had a similarity value 99% with Polymesoda caroliniana phylogenetics is a phylogeny that compares genes that are (GenBank accession no: KX713338.1) (Table 1). According to equivalent to various species to reconstruct the tree of life and find Puillandre et al. [9] and Armani et al. [10], DNA sequences that out which species are most dean related to others, so that life have similarities value > 98%, are considered members of the history can be reconstructed and can explain the level of diversity species mentioned in GenBank. However, if the percentage of of living things. According to Livi et al. [15], species positioned homology value is less than 97%, it is considered to be of a in one quadrant within a phylogenetic tree have close different species [11]. According to Hebert et al. [12], a species is phylogenetic relationship [16]. This phylogenetic relationship is said to be different if the DNA variation reaches 3% (DNA indicated by the DNA base arrangement that composes the DNA identity <97%). Thus, 99% DNA homology value between the bands in each of these shells species, which have the same pair structure of DNA bases.
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AM774558.1 Corbicula fluminea
LT614689.1 Cyrenoida sp. NHMUK 20160352
KC429368.1 Cyrenoida floridana
KX713326.1 Corbula tunicate
JF899202.1 Bankia australis
JF899205.1 Bankia setacea JF899210.1 Kuphus polythalamia
BA G erosa
BG G expansa
BL G Eloina
KX713338.1 Polymesoda caroliniana
KC429392.1 Glauconome rugosa
KC429377.1 Arctica islandica
AM774557.1 Trapezium sublaevigatum
AM774564.1 Calyptogena pacifica
KT345536.1 Phreagena soyoae
KT345535.1 Vesicomya gigas
KT345540.1 Calyptogena extenta
EF426294.1 Saxidomus purpuratus
JN996709.1 Callista brevisiphonata
JN807349.1 Ruditapes variegatus
EU660733.1 Tapes rhomboides
KX713340.1 Ruditapes decussatus
EU660729.1 Tapes pullastra
EU660731.1 Tapes decussate
JN996722.1 Paphia undulata isolate TaPun
JQ277784.1 Paphia undulata
JN996721.1 Paphia textile
EF613236.1 Paphia undulata
AJ007613.1 Callista chione
AJ007614.1 Venus verrucosa
Figure 2. The dendogram of phylogenetic tree of three species (blue, red and green colour) of Reuleung Leupung Mangrove Ecosystem, Aceh
Besar District and the level of homology with other bivalve families
Previous research conducted by Carter [17] mentions that G. erosa, G. expansa, G. coaxan is the synonym name of Polymesoda erosa, this conclusion is based on several marine Biodiversity Information Facilities (SeaLifeBase and Catalog of Life, WoRMS and OBIS). Furthermore, other studies also mention that Geloina is a synonym for Polymesoda taxa [18- 21].
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Therefore, G. erosa, G. expansa, and G. coaxan were identified as laboratory: pulses, perils, and pitfalls. J. Clinic. Microbiol. Polymesoda taxa, thus forming a monophyletic cluster with 45(9), 2761-2764. Polymesoda caroliniana in the phylogenetic tree (Figure 2). 12 Hebert, P.D.N., Cywinska, A., Ball, S.L. and deWaard, J.R. (2003) Biological identifications through DNA barcodes. Proc. Royal Soc. London Ser. B-Biol. Sci. 270, 313–321. CONCLUSIONS 13 Combosch, D.J., Collins, T.M., Glover, E.A., Graf, D.L., Harper, E.M., Healy, J.M., Kawauchi, G.Y., Lemer, S., In the Reuleung Leupung mangrove ecosystem in Aceh Besar McIntyre, E., Strong, E.E. and Taylor, J.D. (2017) A family- District based on morphological identification, there are three level tree of life for bivalves based on a Sanger-sequencing species of shells, namely G. erosa, G. expansa, and G. coaxan. approach. Mol. Phylogen. Evol. 107, 191-208. The results of 16S rDNA genomic DNA analysis showed G. erosa, 14 Notredame, C. (2007) Recent evolutions of multiple sequence G. expansa, and G. coaxan formed a monophyletic in the alignment algorithms. PLoS computational biol. 3(8), e123. phylogenetic tree with Polymesoda carolina species. Furthermore, 15 Livi, S., Cordisco, C., Damiani, C., Romanelli, M. and Crosetti, D. (2006) Identification of bivalve species at an early blast results show G. erosa, G. expansa, and G. coaxan have high developmental stage through PCR-SSCP and sequence analysis similarity with Polymesoda carolina (99% DNA identity). of partial 18S rDNA. Mar. Biol. 149(5), 1149-1161. Therefore, it is concluded that G. erosa, G. expansa, and G. 16 Giribet, G. and Wheeler, W. (2002) On bivalve phylogeny: A coaxan found in the RLME in Aceh Besar District are high‐ level analysis of the Bivalvia (Mollusca) based on Polymesoda carolina species. combined morphology and DNA sequence data. Invertebr. Biol. 121(4), 271-324. CONFLICT OF INTEREST 17 Carter, M. (2014) Subsistence shell fishing in NW Santa Isabel, Solomon Islands: Ethnoarchaeology and the identification of two Polymedia (Solander 1786) species. Ethnoarchaeol. 6(1), The authors declare that there is no conflict of interests regarding 40-60. the publication of this manuscript. 18 Schalie, H.V. (1933) Notes on the brackish water bivalve, Polymesoda caroliniana (Bosc.) (The University of Michigan REFERENCES Press) Ann Arbor, Michigan. 19 Morton, B. (1976) The biology and functional morphology of 1 Widhowati, I., Suprianto, J., Hartati, R. and Dwiono, S.A.P. the Southeast Asian mangrove bivalve, Polymesoda (Geloina) (2005) Hubungan dimensi cangkang dengan berat kerang totk erosa (Solander, 1786) (Bivalvia: Corbiculidae). Canadian J. Polymesoda erosa (Bivalvia: Corbiculidae) dari segara anakan Zool. 54(4), 482-500. Cilacap. Prosiding Seminar Nasional Biologi dan Akukultur 20 Morton, B. 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