Malaysian Journal of Biochemistry
& Molecular Biology
(E-ISSN: 2600-9005)
The Official Publication of the Malaysian Society for Biochemistry & Molecular Biology (MSBMB)
Indexed by SCOPUS and Malaysian Citation Index (MYCITE)
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December 2025
Malay. J. Biochem. Mol. Biol. (2025) 28 (3)
TABLE OF CONTENTS
Page 1- 9
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Rafidah Saaduna, Chia Suet Lin, Heera Rajandas, Muhammad Asyraf Md Hatta and Tan Geok Hun*
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CLONING, EXPRESSION AND CHARACTERIZATION OF RECOMBINANT ENDOLYSIN FROM XANTHOMONAS PHAGE N1
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Abstract
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The evolving resistance of Xanthomonas oryzae pv. oryzae (Xoo) causing Bacterial Leaf Blight (BLB) in Malaysian rice crops, demands innovative biological solutions. In addressing the Xoo evolution, this study explores the prospects of phage-encoded endolysin, produced as a recombinant protein. The endolysin gene was isolated from phage N1 targeting Xoo that showed lytic activity through plaque formation on double-layer agar (DLA) plate. The phage lysate was purified using PEG 8000/NaCl precipitation and genomic DNA was obtained from cetyltrimethylammonium bromide (CTAB) extraction at a concentration of 170.4 ng/μL and purity of 1.8. The 558 bp of phage-encoded endolysin gene, namely EN1, was amplified by PCR and cloned into the T7 expression vector pETite to form the recombinant plasmid pETite-EN1. The nucleotide sequencing of the positive clones revealed a high similarity to the endolysin gene of Xanthomonas phage N1 (Accession No: MZ666966). Transformation into E. coli BL21 (DE3) cell enabled the expression of the recombinant endolysin protein LysEN1 with a molecular weight of approximately 19.5 kDa. Optimal expression of LysEN1 protein was observed at 25°C after 3 hrs of induction with 0.5 mM IPTG, as revealed by SDS-PAGE. Rapid growth inhibition of host cells was observed in all tested conditions but slower decline at 25 °C. The solubility analysis showed that LysEN1 protein was present in soluble and insoluble fractions. While the expression of LysEN1 recombinant protein poses challenges and holds potential for improvement, the LysEN1 can be a prospect for managing BLB disease in rice, thereby supporting food security.
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Page 10-19
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Nur Shadrina Mohd Shahrel, Noor Hydayaty Md Yusuf and Vijay Subbiah Kumar*
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IDENTIFICATION OF MICRORNA-DIRECTED CLEAVAGE OF TARGETS IN PINEAPPLE (ANANAS COMOSUS) FRUIT DEVELOPMENT USING DEGRADOME SEQUENCING
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Abstract
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A large number of microRNAs (miRNA) have been previously discovered in pineapple (Ananas comosus), which is a model organism for tropical non-climacteric fruits. These miRNAs are believed to be involved in the regulation of many endogenous genes. In silico computational analysis can provide predictive identification of microRNAs (miRNAs) and their putative target genes. However, the main criterion used to distinguish between regulated and non-regulated genes in pineapple is that the targeted transcripts (mRNA) will undergo degradation. Therefore, by using degradome sequencing we aim to provide first hand empirical data to identify gene targets that are regulated by miRNA in MD2 pineapple by identifying mRNA transcripts that have been expressed and subsequently degraded by these small RNA molecules. We first performed degradome sequencing, which is likened to a modified 5'-rapid amplification of cDNA ends (RACE) with next generation sequencing (NGS) which allows the identification of over-represented 5'-ends (miRNA cleavage sites) within mRNAs. Subsequently, we discovered 144 targets which were mapped to at least 21 miRNA families and were consistently expressed in all three biological replicates. Among them, seven miRNAs associated with plant development along with eight target mRNAs (including auxin response factor, squamosa promoter-binding-like protein, transport inhibitor response 1 protein, growth-regulating factor 5 and transcription factor GAMYB were detected in MD2 pineapple using RT-qPCR. Furthermore, to confirm and validate the cleavage sites of the target genes cleaved by miR159, miR160 and miR408, a modified 5’ RACE PCR was conducted followed by DNA sequencing. The results showed that the predominant cleavage site in the miRNA target genes were at position 11 from the 5’ end of the miRNA complementary region. The findings here provided validation of miRNA targets through clear empirical data. Our findings shows that miRNA play a key role in regulating the expression of target genes and will assist towards understanding the mechanisms of MD2 pineapple fruit development.
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Page 20-28
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Fatin Fathiah Safiudin, Chee Fah Wong*, Zatty Syamimi Adura Mat Said, Nurniwalis Abdul Wahab*
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LIPASE: THE BIOLOGICAL FUNCTION AND INDUSTRIAL APPLICATION
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Abstract
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Over the years, lipase has been acknowledged as an important enzyme and one of the most widely employed globally due to its versatility and variety. They are recognised by the presence of an α/β hydrolase fold, a catalytic triad, and a lid domain in their structure. Lipase exists in almost all hierarchies of life which further highlights its significance. Lipase is commonly known solely for its role in lipid metabolism to produce energy, though its functionality extends beyond this. In plants, animals and fungi, some lipases are responsible for stress management and pathogenicity as well. The display of unique and distinctive performance by lipase in their biological body has intrigued its implementation as a biocatalyst in various oleochemical, body care and food industrial applications. This review explores the diverse sources, biological roles, and industrial applications of plant, animal and fungi lipases, by focusing on their importance in natural and commercial contexts.
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Page 29-41
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Norul Amalina Sabri, Fairolniza Mohd Shariff, Siti Azma Jusoh and Nazahiyah Ahmad Rodzli
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​STRUCTURAL INSIGHTS INTO THE ALPHAFOLD2-GENERATED MODEL OF LEPTOSPIRAL LIPOPROTEIN SIGNAL PEPTIDASE (LspLep) USING MOLECULAR DYNAMICS SIMULATIONS
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Abstract
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Leptospirosis, primarily caused by Leptospira interrogans, is a neglected zoonotic disease endemic to tropical regions. As the third deadliest infectious disease after malaria and dengue, leptospirosis highlights the pressing need for novel therapeutic strategies, as existing broad-spectrum antibiotic regimens are frequently ineffective in severe cases. This study focused on leptospiral lipoprotein signal peptidase (LspLep), a critical enzyme involved in the maturation of lipoproteins essential for bacterial survival, presenting it as a potential therapeutic target. Due to the limitations of experimental structure determination, computational approaches were implemented to elucidate the structure and dynamic properties of LspLep. The AlphaFold2-predicted structure of LspLep exhibited strong homology to its orthologs LspPae (Pseudomonas aeruginosa) and LspMrs (Staphylococcus aureus), while distinctively featuring an additional periplasmic loop (PL2). Molecular dynamics (MD) simulations conducted for 500 ns demonstrated significant structural stability of LspLep in a lipid bilayer. Further analyses revealed the correlation between the dynamics in the unique PL2 and that of β-cradle. In addition, the simulation trajectories revealed the conformational transitions of LspLep from open to intermediate and closed states, alongside the persistent occupancy of a lipid molecule in the active site. In conclusion, these findings offer detailed structural and dynamic profiles of LspLep, guiding the development of structure-based therapeutic drugs against leptospirosis.
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Page 42-50
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Mohammed A. Hami
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THE ACCURACY ANALYSIS AND ASSOCIATION OF VITAMIN B 12, URIC ACID AND SOME TRACE ELEMENTS IN PRE-DIABETES AND DIABETES MELLITUS
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Abstract
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Background: Diabetes is a major global health issue that is associated with severe complications. Trace elements and vitamins play a key role in the metabolism of glucose and synthesis and secretion of insulin. There are also significant number of undiagnosed pre-diabetic and diabetic individual. Hence, effective and reliable biomarkers are needed for the diagnosis and screening of pre-diabetes and diabetes patients. Objectives: The aim of this study is to assess the levels of vitamin B12, uric acid and some trace elements in diabetes and pre-diabetic patients and also studying the correlations among these variables. Materials and methods: The study involved 120 individuals that were divided into three groups (control, diabetic and pre-diabetic groups). HbA1c was measured by fully automated analyzer (Bio-Rad, Montreal, Canada). The elements serum calcium, phosphorus and magnesium were measured by Cobas 6000 c501 autoanalyzer system (Roche Diagnostics, Mannheim, Germany). Serum vitamin B12 and uric acid were measured by Roche Cobas e 411 immunoassay analyzer (Roche Diagnostics, Mannheim, Germany). Results: What stands out from the results of this research is the significant difference in the level of P/Mg in both males and females, in which this ratio is significantly higher in both diabetic and pre-diabetic groups. The ratio of Ca/Mg is significantly lower in diabetic groups compared to the control group. Regarding the partial correlation between the elements and vitamin B12 and uric acid, there is a significant negative correlation between vitamin B12 and serum Ca. In addition, serum uric acid correlated significantly and positively with serum Ca and phosphorus in female individuals. Regarding the ROC, none of the measured parameters can be used to detect diabetes or pre-diabetes in males and females except the ratio P/Mg. Conclusion: The ratio P/Mg can be used to screen or diagnose diabetes and pre-diabetes. Ca level has an important effect on the level of vitamin B12 in male individuals and uric acid in female individuals.
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August 2025
Malay. J. Biochem. Mol. Biol. (2025) 28 (2)
TABLE OF CONTENTS
Page 1- 13
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Md Shaekh Forid, Amit Dubey, Miah Roney, Aisha Tufail, A. K. M. Moyeenul Huq , Mohd Hamzah Bin Mohd Nasir, Mohd Fadhlizil Fasihi Mohd Aluwi , Muhammad Saupi Azuri , Wan Maznah Binti Wan Ishak*
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INSIGHTS FROM COMPUTATIONAL EXPLORATION OF BIOACTIVE COMPOUNDS OF COMBRETUM INDICUM TARGETING TGF-β1 TO TREAT WOUND HEALING: MOLECULAR DOCKING AND DFT APPROACHES
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Abstract
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Transforming growth factor-beta type-1 (TGF-β1), a protein that is a druggable target for inflammation, has been identified to be associated with wound healing. Dysregulation of the wound-healing process can result in the development of chronic ulcers or excessive inflammation. Despite the availability of the TGF-β1 inhibitor drug, there is an urgent requirement for additional therapeutic treatment options to effectively manage wound healing in the expanding global population. In this study, the molecular docking and Density-Functional Theory (DFT) approach were used to discover wound healing agents that can target TGF-β1. Seventeen compounds detected via UPLC-Q-TOF/MS analysis of Combretum indicum were selected from our previous report to obtain the hit compound(s) that exhibit inhibition of TGF-β1. The molecular docking findings revealed that actinidioionoside (-56.2999 kcal/ mol) binding affinity is stronger than the studied compound as well as the co-crystal ligand (-43.016 kcal/ mol), indicating a potentially more substantial interaction with the target. Moreover, actinidioionoside interacted with four amino acid residues, namely, Ly337, Lys232, Asp351, and Leu278, while a co-crystal ligand interacted with His283, which formed a hydrogen bond. Furthermore, DFT and Molecular Electrostatic Potential (MESP) findings emerged as the most promising hit with all the above favorable properties of actinidioionoside. Based on the results, it can be concluded that actinidioionoside is a promising prospective agent against TGF-β1 for regulating wound healing. However, further in vitro and in vivo research on C.indicum are needed.
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Page 14 - 24
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Nur Hanisah Azmi,*, Mohamad Norisham Mohamad Rosdi, Zainul Amiruddin Zakaria, Norsharina Ismail, Mustapha Umar Imam and Ramlah Mohamad Ibrahim
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MULTIFACETED NEUROPROTECTIVE PROPERTIES OF GERMINATED BROWN RICE: A REVIEW
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Abstract
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Germinated brown rice (GBR) has garnered attention for its potential neuroprotective effects, especially concerning neurodegenerative diseases like Alzheimer's disease (AD). The bioactive compounds in GBR have shown promise in reducing oxidative stress and enhancing neuronal survival. Studies indicate that GBR extracts, rich in antioxidants, can mitigate oxidative damage in neuronal cells. This review highlights on the neuroprotective properties of GBR are attributed to its modulation of signalling pathways such as Nuclear factor kappa B (NF-κB), c-Jun N-terminal kinase (JNK), and Mitogen-activated protein kinases (MAPK), in addition to modulation of antioxidant enzymes and amyloid processing pathways. Compounds like γ-aminobutyric acid (GABA) and phenolics contribute to GBR's neuroprotective effects, and improvements in cognitive function and memory have also been associated with GBR consumption. Furthermore, this review demonstrated that GBR offers various health benefits, including antihyperlipidaemia, antihypertension, and a reduced risk of chronic diseases such as cancer, diabetes, and cardiovascular diseases. Future research should explore multi-omics approaches, including metabolomics, proteomics, and microbiome research, to provide deeper mechanistic insights into GBR’s neuroprotective properties. . In conclusion, GBR emerges as a promising natural product with potential to safeguard neuronal health and combat neurodegenerative diseases. Continued research efforts are essential to fully unlock the therapeutic potential of GBR and translate its neuroprotective properties into clinical applications for improved brain health and disease management.
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April 2025
Malay. J. Biochem. Mol. Biol. (2025) 28 (1)
TABLE OF CONTENTS
Page 1- 7
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Noor Jannah Yob, Anas Nazreen Nasir, Izzati Fatini Zainal Abidin and Rosnani Hasham
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EFFICIENCY OF SOLVENTS ON TOTAL YIELDS, PHENOLS FLAVONOIDS AND ANTIMICROBIAL ACTIVITY OF Acalypha indica LINN.
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Abstract
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New innovative bioactive chemicals are needed to solve the serious side effects and the increasing problem of antimicrobial resistance. For this reason, scientists are seeking new sources for which to develop antimicrobial agents, such as plant extract. Acalypha indica is has been studied for its potential as a source of antimicrobial agents, as it contains phytochemicals such as phenols and flavonoids. Extraction was carried out of a range of solvents of increasing polarity (n-hexane, chloroform, acetone, methanol and water) using sequential extraction. The results showed that the methanolic extract had the highest extraction yield (4.35% w/w), followed by water (4.13% w/w). The n-hexane extract had the highest phenolic and flavonoids content 19.51 mg GAE /g and 812.55 mg QE /g of extract, respectively. The antimicrobial activity of the A. indica extracts was tested against Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli and Candida albicans by diffusion method. Only the n-hexane, chloroform, acetone and methanol extracts showed active inhibition of both P. aeruginosa between (31% to 35%) and S. aureus between (35% to 42%), while E. coli was not inhibited. Acetone extracts showed the highest inhibition zone against P. aeruginosa (9.50 mm) and S. aureus (9.00 mm), followed by methanol, n-hexane and chloroform. In addition, n-hexane and water extracts showed strong antifungal activity against C. albicans, with 48% (20 mm) and 43% (18 mm), respectively. In conclusion, these results underline the potential of A. indica as a valuable source of bioactive compounds with promising antimicrobial properties.
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Page 8 - 20
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Tran Thi Phuong Nhung and Le Pham Tan Quoc
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ACUTE TOXICITY EVALUATION OF ETHANOL LEAF EXTRACT OF BEAD TREE (MELIA AZEDARACH LINNE) ON WHITE-SPOTTED FRESHWATER CATFISH (CLARIAS FUSCUS)
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Abstract
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The acute toxicity assessment is a commonly employed procedure in evaluating the biological safety of herbal extracts in sustainable aquaculture. A biological test was conducted to investigate the effects of acute toxicity (96 h, LD50) of the ethanol leaf extract of Melia azedarach L. on the behavior, hematological and biochemical parameters, tissue histology of the liver and gill in the white-spotted freshwater catfish (Clarias fuscus). Fresh leaves of M. azedarach were harvested, dried, soaked, and extracted with ethanol solvent (EEMA), containing chemical compounds such as tannins, flavonoids, alkaloids, saponins, and steroids, to be used as a test material for acute toxicity assessment on the catfish. One hundred and eighty (180) C. fuscus weighing between 50 - 52g were randomly divided into eight (8) treatment groups/concentrations for acute toxicity testing. Agitation, increased respiration rate, erratic swimming, loss of balance, rough skin, and excessive mucous secretion were observed as behavioral changes in the groups exposed to higher concentrations of 280 and 320 mg/L. The average LD50 over 96 h was 319.81 mg/L, with the safety threshold value (safe value) of EEMA being 240 mg/L. Significant differences (p < 0.05) in red blood cell (RBC) and white blood cell (WBC) counts (7.33 ± 0.14 × 106 cells/mm3 and 8.25 ± 0.16 × 103 cells/mm3, respectively) were noted in the treatment groups compared to the control group (7.83 ± 0.25 × 106 cells/mm3, 7.35 ± 0.14 × 106 cells/mm3) after exposure to EEMA for 96 h. Urea and creatinine levels (38.52 ± 0.11 mg/dL, 1.49 ± 0.09 U/L) also showed a significant increase in the group treated with 320 mg/L EEMA compared to the control (38.29 ± 0.09 mg/dL, 1.22 ± 0.08 U/L) (p < 0.05). Histological effects on the liver and gill revealed hepatocyte hypertrophy, abnormally shaped nuclei, fatty degeneration, and congestion, with the epithelial lining of the gill raised and partly fused in the secondary epithelial layer. These changes indicate that EEMA is toxic to the test fish at high concentrations (280 and 320 mg/L). However, there were no significant changes in water quality among the test groups compared to the control group (p > 0.05), except for conductivity in the test groups at concentrations of 280 and 320 mg/L (p < 0.05). This study establishes safe limits for the ethanol leaf extract of M. azedarach (40-200 mg/L) before its therapeutic values can be considered for practical use.
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Page 21 - 28
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Akrimi Najihah Mohd Khamil, Teck Wei Lim, Deron R. Herr, Jualang Azlan Gansau, Siew-Eng How
and Lucky Poh Wah Goh
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PHYTOCHEMICAL CONTENTS AND BIOACTIVITY OF Nephelium lappaceum L. (RAMBUTAN) AND Nephelium ramboutan-ake (PULASAN)
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Abstract
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Fruits are the natural sources of antioxidants. In this study, we determined the total phenolic content (TPC), total flavonoid content (TFC), and antioxidant activities of various parts (peels, seeds, and pulps) of Nephelium lappaceum L. (rambutan merah and rambutan kuning) and Nephelium ramboutan-ake (pulasan). The fruit extracts were obtained by maceration with ethanol (70%) as the solvent. The TPC, TFC, and antioxidant activities were determined by Folin-Ciocalteu reagent, aluminum chloride colorimetric method, and 2, 2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging method, respectively. The results were statistically analyzed by ANOVA and Tukey’s Honest Significant Difference (HSD) post hoc test. Overall, the fruits peel yielded the highest TPC (9.63 mg gallic acid equivalents, GAE/g on average) and TFC (740.83 mg quercetin equivalent, QE/g on average). Furthermore, the fruit peels showed the highest antioxidant activity (1.483 antioxidant activity index, AAI on average). Meanwhile, by comparing the edible pulps, Nephelium ramboutan-ake showed the highest TPC (4.33 mg GAE/g), TFC (94.31 mg QE/g), and antioxidant activity (1.17 AAI) among the fruits. In conclusion, the results suggest that the byproducts (peels and seeds) of the fruits could be potentially processed as functional foods and alternative sources of antioxidants.
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Page 29 - 35
Roslina Mat Yazid, Che Radziah Che Mohd Zain, Mohd Fareed Mohd Sairi, Ismanizan Ismail, Mohd Fahmi Abu Bakar and Nik Marzuki Sidik
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THE EFFECTS OF LEAD STRESS ON PHOTOSYNTHESIS, STOMATAL CONDUCTANCE, TRANSPIRATION, AND CHLOROPHYLL CONTENT OF Cayratia trifolia
Abstract
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Lead (Pb), a widespread heavy metal pollutant in our environment, can affect plant physiology and productivity worldwide. Cayratia trifolia is a terrestrial plant found in a former sludge farm treatment area that is highly contaminated with petroleum hydrocarbon and high salinity. This study examines the effect of Pb on photosynthesis rate, transpiration rate, stomatal conductance, and chlorophyll content of Cayratia trifolia. The plant specimens were treated with different concentrations, including 10, 300, and 600 mg/kg of Pb, for 48 hours. The photosynthesis, transpiration, and stomatal conductance were observed through an infrared gas analyzer (IRGA) and a LICOR 6400 portable photosynthesis system (Lincoln, Nebraska, USA). Meanwhile, the chlorophyll content was determined by extraction method. The finding shows that the photosynthesis rate, transpiration rate, stomatal conductance, and chlorophyll content were reduced at 300 and 600 mg/kg of Pb-treated plants. However, at low concentrations of Pb (10 mg/kg), photosynthesis rate, transpiration rate, stomatal conductance, and chlorophyll content increased. Pearson’s correlation shows that photosynthesis rate was positively correlated with stomatal conductance, transpiration rate, and chlorophyll content. In addition, the Inductively Coupled Plasma Mass Spectrometry (ICP-MS) analysis showed that Pb accumulated more in the plant roots compared to the leaves. Thus, this study concludes that Pb accumulation has a negative effect on plant physiology, including photosynthesis rate, transpiration rate, stomatal conductance, and chlorophyll content of Cayratia trifolia.
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Page 36 - 43
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Siti Norazura Jamala, Dhilia Udie Lamasudin, Belal J. Muhialdin, Noor Baity Saidi, Kok Song Lai and Mohd Termizi Yusof
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PEPTIDE PROFILING AND ANTIMICROBIAL ACTIVITY CORRELATION IN Bactronophorus thoracites FERMENTED PROTEIN USING LC-MS/MS ANALYSIS
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Abstract
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The study examines the antimicrobial properties of proteins found in Bactronophorus thoracites, a wood-boring shipworm, which could help combat leaf blight disease in rice in Malaysia. Using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS), 18 cationic peptides were identified in the shipworm's fermented protein. These peptides vary in size (1015.13 to 4071.501 Da) and are rich in Arginine (Arg) and Serine (Ser), amino acids known for their antimicrobial abilities. Most of these peptides are hydrophilic and water-soluble, with a GRAVY index indicating their solubility in water. The study found that peptides with a neutral GRAVY index were more effective due to their balanced water-loving and water-repelling properties. The peptides' structures are mainly α-helix and random coil, with the former penetrating microbial cell membranes and the latter adapting to different microbial surfaces. This structural diversity enhances their antimicrobial effectiveness. This research is significant for its identification of antimicrobial peptides (AMPs) in the shipworm protein. These AMPs are short, positively charged, and have a mix of coiled and α-helical structures. The findings lay a foundation for further exploration of these peptides in treating infectious diseases.
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Page 44 - 52
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Suk Jiun Ling, Ewen Se Thoe, Yi Yuen Chia, Wai Keat Yam and Yoke Yin Chia
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A GENETIC FUNCTION APPROXIMATION 2 DIMENSIONAL-QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP PREDICTIVE MODEL FOR PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR-γ AGONISTIC ACTIVITY
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Abstract
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Peroxisome proliferator-activated receptor (PPAR) - γ agonists modulate metabolic events including lipid and glucose haemostasis, displaying potential for treatment against metabolic diseases. Glycyrrhizic acid (GA) is a natural ligand that has anti-diabetic effects and could likely be a PPAR-γ agonist. In this study, a 2 dimensional-quantitative structure-activity relationship (2D-QSAR) predictive model was developed using known PPAR-γ agonists and subsequently used to evaluate PPAR-γ binding properties of GA and its derivatives. Molecular docking was then employed as a validation step. A set of 152 known agonists for PPAR-γ was used to create the 2D-QSAR model using the genetic function approximation (GFA) approach. The 2D-QSAR model developed showed R2 value of 0.766 in the training set and an R2 value of 0.720 in the test set. The 2D-QSAR model created was used to predict the biological activities of 114 GA derivatives and 4 of them were identified to be potential PPAR-γ agonists. In conclusion, the 2D-QSAR model of PPAR-γ agonists showed good predictive power within applicability domain and predicted 4 potential GA derivatives to be PPAR-γ agonist.
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