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Fulltext Wireless displacement sensing of micromachined spiral-coil actuator using resonant frequency tracking

Ali MS, AbuZaiter A, Schlosser C, Bycraft B, Takahata K

Sensors (Basel), 2014 Jul 10;14(7):12399-409.
PMID: 25014100 DOI: 10.3390/s140712399

This paper reports a method that enables real-time displacement monitoring and control of micromachined resonant-type actuators using wireless radiofrequency (RF). The method is applied to an out-of-plane, spiral-coil microactuator based on shape-memory-alloy (SMA). The SMA spiral coil forms an inductor-capacitor resonant circuit that is excited using external RF magnetic fields to thermally actuate the coil. The actuation causes a shift in the circuit's resonance as the coil is displaced vertically, which is wirelessly monitored through an external antenna to track the displacements. Controlled actuation and displacement monitoring using the developed method is demonstrated with the microfabricated device. The device exhibits a frequency sensitivity to displacement of 10 kHz/µm or more for a full out-of-plane travel range of 466 µm and an average actuation velocity of up to 155 µm/s. The method described permits the actuator to have a self-sensing function that is passively operated, thereby eliminating the need for separate sensors and batteries on the device, thus realizing precise control while attaining a high level of miniaturization in the device.
Using walnut shells as low-cost adsorbent materials in an anaerobic filter medium of a De-centralized wastewater treatment system (DEWATS)

Zaheer M, Ali MS, Huang N, Ashraf MA

Chemosphere, 2023 Nov;341:140080.
PMID: 37678602 DOI: 10.1016/j.chemosphere.2023.140080

The flow of unprocessed sewage through municipal sewers is a great source of water contamination. This study aims to observe the pollutants removal efficiencies of walnut shells as an efficient low-cost adsorbent material compared to gravel materials as an anaerobic filter medium. Two models of the De-Centralized Wastewater Treatment System (DEWATS) were constructed. The wastewater flowing from toilets and handwashing places was connected to anaerobic filters filled with walnut shells and gravel. The efficiency of both filter media in the removal of biological oxygen demand (BOD), chemical oxygen demand (COD), total suspended solids (TSS), total dissolved solids (TDS), nitrate (NO3), and phosphate (PO43), pH and temperature were observed at the influent of the settler tank and then at the effluent of the collection tank (CT). Temperature and pH were within the acceptable limit of wastewater discharge. The results also indicated that the walnut shells filter media was more efficient at removing organic pollutants (TSS 94%, BOD5 88%, COD 85%, Nitrate 57%, phosphate 46%, and TDS 29%) than the gravel (TSS 81%, BOD5 82%, COD 84%, Nitrate 35%, phosphate 38%, and TDS 26%) at the successive stages. The average removal efficiency of the walnut shell was 88% while in the gravel case, it was 83%. The removal efficiency of walnut shell filters was extensively better over the complete experiment compared to gravel filters for the removal of pollutants, representing the high sorption capability of the walnut shell material. The results of this study show that the walnut shells may be a very useful substitute for other conventional fillers for anaerobic treatment in the anaerobic filter of DEWATS.
Unscrambling the effect of C-terminal tail deletion on the stability of a cold-adapted, organic solvent stable lipase from Staphylococcus epidermidis AT2

Kamarudin NH, Rahman RN, Ali MS, Leow TC, Basri M, Salleh AB

Mol Biotechnol, 2014 Aug;56(8):747-57.
PMID: 24771007 DOI: 10.1007/s12033-014-9753-1

Terminal moieties of most proteins are long known to be disordered and flexible. To unravel the functional role of these regions on the structural stability and biochemical properties of AT2 lipase, four C-terminal end residues, (Ile-Thr-Arg-Lys) which formed a flexible, short tail-like random-coil segment were targeted for mutation. Swapping of the tail-like region had resulted in an improved crystallizability and anti-aggregation property along with a slight shift of the thermostability profile. The lipolytic activity of mutant (M386) retained by 43 % compared to its wild-type with 18 % of the remaining activity at 45 °C. In silico analysis conducted at 25 and 45 °C was found to be in accordance to the experimental findings in which the RMSD values of M386 were more stable throughout the total trajectory in comparison to its wild-type. Terminal moieties were also observed to exhibit large movement and flexibility as denoted by high RMSF values at both dynamics. Variation in organic solvent stability property was detected in M386 where the lipolytic activity was stimulated in the presence of 25 % (v/v) of DMSO, isopropanol, and diethyl ether. This may be worth due to changes in the surface charge residues at the mutation point which probably involve in protein-solvent interaction.
Fulltext Trifolium pratense ethanolic extract alters the gut microbiota composition and regulates serum lipid profile in the ovariectomized rats

Quah Y, Park NH, Lee EB, Lee KJ, Yi-Le JC, Ali MS, et al.

BMC Complement Med Ther, 2022 Jan 04;22(1):5.
PMID: 34983484 DOI: 10.1186/s12906-021-03486-w

BACKGROUND: Trifolium pratense (red clover) ethanolic extract (TPEE) has been used as a popular over-the-counter remedy for the management of menopausal symptoms. Prolonged consumption of herbal extract has been shown to regulate the composition of gut microbiota. This study was designed to elucidate the influence of TPEE on the gut microbiota composition in the ovariectomized (OVX) rats.
METHODS: OVX rats were treated with TPEE at 125, 250, 500 mg/kg/day, or controls (pomegranate extract, 500 mg/kg/day; estradiol, 25 μg/kg/day) for 12 weeks. Gut microbiota analysis was conducted by extracting the microbial DNA from fecal samples and microbiome taxonomic profiling was carried out by using next-generation sequencing. The levels of serum biomarkers were analyzed using enzyme-linked immunosorbent assay (ELISA) kit. The prediction of functional biomarker of microbiota was performed using PICRUSt to investigate the potential pathways associated with gut health and serum lipid profile regulation. To study the correlation between gut microbiota composition and serum lipid levels, Spearman's correlation coefficients were defined and analyzed. Additionally, gas chromatography-mass spectrometry analysis was conducted to uncover additional physiologically active ingredients.
RESULTS: TPEE-treated OVX rats showed significant reduction in serum triglycerides (TG), total cholesterols (TCHOL), and LDL/VLDL levels but increase in HDL level. The alteration in the pathways involve in metabolism was the most common among the other KEGG categories. Particularly, TPEE also significantly reduced the relative abundance of sequences read associated with inflammatory bowel disease (IBD) and the peroxisome proliferator-activated receptor (PPAR) signalling pathway. TPEE intervention was seen to reduce the Firmicutes to Bacteroidetes (F/B) ratio in the OVX rats, denoting a reduction in microbial dysbiosis in the OVX rats. Correlation analysis at the phylum level revealed that Bacteriodetes and Proteobacteria were strongly correlated with serum TG, TCHOL and HDL levels. At the species level, Bifidobacterium pseudolongum group was seen to positively correlate with serum HDL level and negatively correlated with serum AST, ALT, LDL/VLDL, TCHOL, and TG levels.
CONCLUSIONS: TPEE treatment showed therapeutic benefits by improving the intestinal microbiota composition which strongly correlated with the serum lipid and cholesterol levels in the OVX rats.
Toluene promotes lid 2 interfacial activation of cold active solvent tolerant lipase from Pseudomonas fluorescens strain AMS8

Yaacob N, Mohamad Ali MS, Salleh AB, Rahman RNZRA, Leow ATC

J Mol Graph Model, 2016 07;68:224-235.
PMID: 27474867 DOI: 10.1016/j.jmgm.2016.07.003

The utilization of cold active lipases in organic solvents proves an excellent approach for chiral synthesis and modification of fats and oil due to the inherent flexibility of lipases under low water conditions. In order to verify whether this lipase can function as a valuable synthetic catalyst, the mechanism concerning activation of the lid and interacting solvent residues in the presence of organic solvent must be well understood. A new alkaline cold-adapted lipase, AMS8, from Pseudomonas fluorescens was studied for its structural adaptation and flexibility prior to its exposure to non-polar, polar aprotic and protic solvents. Solvents such as ethanol, toluene, DMSO and 2-propanol showed to have good interactions with active sites. Asparagine (Asn) and tyrosine (Tyr) were key residues attracted to solvents because they could form hydrogen bonds. Unlike in other solvents, Phe-18, Tyr-236 and Tyr-318 were predicted to have aromatic-aromatic side-chain interactions with toluene. Non-polar solvent also was found to possess highest energy binding compared to polar solvents. Due to this circumstance, the interaction of toluene and AMS8 lipase was primarily based on hydrophobicity and molecular recognition. The molecular dynamic simulation showed that lid 2 (residues 148-167) was very flexible in toluene and Ca(2+). As a result, lid 2 moves away from the catalytic areas, leaving an opening for better substrate accessibility which promotes protein activation. Only a single lid (lid 2) showed the movement following interactions with toluene, although AMS8 lipase displayed double lids. The secondary conformation of AMS8 lipase that was affected by toluene observed a reduction of helical strands and increased coil structure. Overall, this work shows that cold active lipase, AMS8 exhibits distinguish interfacial activation and stability in the presence of polar and non-polar solvents.
Fulltext The Role of Solvent-Accessible Leu-208 of Cold-Active Pseudomonas fluorescens Strain AMS8 Lipase in Interfacial Activation, Substrate Accessibility and Low-Molecular Weight Esterification in the Presence of Toluene

Yaacob N, Ahmad Kamarudin NH, Leow ATC, Salleh AB, Raja Abd Rahman RNZ, Mohamad Ali MS

Molecules, 2017 Aug 12;22(8).
PMID: 28805665 DOI: 10.3390/molecules22081312

The alkaline cold-active lipase from Pseudomonas fluorescens AMS8 undergoes major structural changes when reacted with hydrophobic organic solvents. In toluene, the AMS8 lipase catalytic region is exposed by the moving hydrophobic lid 2 (Glu-148 to Gly-167). Solvent-accessible surface area analysis revealed that Leu-208, which is located next to the nucleophilic Ser-207 has a focal function in influencing substrate accessibility and flexibility of the catalytic pocket. Based on molecular dynamic simulations, it was found that Leu-208 strongly facilitates the lid 2 opening via its side-chain. The KM and Kcat/KM of L208A mutant were substrate dependent as it preferred a smaller-chain ester (pNP-caprylate) as compared to medium (pNP-laurate) or long-chain (pNP-palmitate) esters. In esterification of ethyl hexanoate, L208A promotes a higher ester conversion rate at 20 °C but not at 30 °C, as a 27% decline was observed. Interestingly, the wild-type (WT) lipase's conversion rate was found to increase with a higher temperature. WT lipase AMS8 esterification was higher in toluene as compared to L208A. Hence, the results showed that Leu-208 of AMS8 lipase plays an important role in steering a broad range of substrates into its active site region by regulating the flexibility of this region. Leu-208 is therefore predicted to be crucial for its role in interfacial activation and catalysis in toluene.
Fulltext The Effect of N-Terminal Domain Removal towards the Biochemical and Structural Features of a Thermotolerant Lipase from an Antarctic Pseudomonas sp. Strain AMS3

Latip W, Raja Abd Rahman RNZ, Leow ATC, Mohd Shariff F, Kamarudin NHA, Mohamad Ali MS

Int J Mol Sci, 2018 Feb 13;19(2).
PMID: 29438291 DOI: 10.3390/ijms19020560

Lipase plays an important role in industrial and biotechnological applications. Lipases have been subject to modification at the N and C terminals, allowing better understanding of lipase stability and the discovery of novel properties. A thermotolerant lipase has been isolated from Antarctic Pseudomonas sp. The purified Antarctic AMS3 lipase (native) was found to be stable across a broad range of temperatures and pH levels. The lipase has a partial Glutathione-S-transferase type C (GST-C) domain at the N-terminal not found in other lipases. To understand the influence of N-terminal GST-C domain on the biochemical and structural features of the native lipase, the deletion of the GST-C domain was carried out. The truncated protein was successfully expressed in E. coli BL21(DE3). The molecular weight of truncated AMS3 lipase was approximately ~45 kDa. The number of truncated AMS3 lipase purification folds was higher than native lipase. Various mono and divalent metal ions increased the activity of the AMS3 lipase. The truncated AMS3 lipase demonstrated a similarly broad temperature range, with the pH profile exhibiting higher activity under alkaline conditions. The purified lipase showed a substrate preference for a long carbon chain substrate. In addition, the enzyme activity in organic solvents was enhanced, especially for toluene, Dimethylsulfoxide (DMSO), chloroform and xylene. Molecular simulation revealed that the truncated lipase had increased structural compactness and rigidity as compared to native lipase. Removal of the N terminal GST-C generally improved the lipase biochemical characteristics. This enzyme may be utilized for industrial purposes.
Fulltext Structural adaptation of cold-active RTX lipase from Pseudomonas sp. strain AMS8 revealed via homology and molecular dynamics simulation approaches

Mohamad Ali MS, Mohd Fuzi SF, Ganasen M, Abdul Rahman RN, Basri M, Salleh AB

Biomed Res Int, 2013;2013:925373.
PMID: 23738333 DOI: 10.1155/2013/925373

The psychrophilic enzyme is an interesting subject to study due to its special ability to adapt to extreme temperatures, unlike typical enzymes. Utilizing computer-aided software, the predicted structure and function of the enzyme lipase AMS8 (LipAMS8) (isolated from the psychrophilic Pseudomonas sp., obtained from the Antarctic soil) are studied. The enzyme shows significant sequence similarities with lipases from Pseudomonas sp. MIS38 and Serratia marcescens. These similarities aid in the prediction of the 3D molecular structure of the enzyme. In this study, 12 ns MD simulation is performed at different temperatures for structural flexibility and stability analysis. The results show that the enzyme is most stable at 0°C and 5°C. In terms of stability and flexibility, the catalytic domain (N-terminus) maintained its stability more than the noncatalytic domain (C-terminus), but the non-catalytic domain showed higher flexibility than the catalytic domain. The analysis of the structure and function of LipAMS8 provides new insights into the structural adaptation of this protein at low temperatures. The information obtained could be a useful tool for low temperature industrial applications and molecular engineering purposes, in the near future.
Fulltext Status of Serum Calcium, Vitamin D and Parathyroid Hormone and Hematological Indices Among Lead Exposed Jewelry Workers in Dhaka, Bangladesh

Mazumdar I, Goswami K, Ali MS

Indian J Clin Biochem, 2017 Mar;32(1):110-116.
PMID: 28149023 DOI: 10.1007/s12291-016-0582-9

Jewelry utilizes lead either directly or as a base metal. Costume jewelry requires lead before molding and plating the product with valuable metals. Therefore, such ornaments have a great potential to release heavy metals having health hazards. Also, jewelry makers engaged in preparing German silver, an alloy, apply lead in smelting, alloying, rolling and milling silver wires and pieces. The metal is taken up by blood, soft tissues and bone. The biological effects of lead are dependent upon the level and duration of exposure. Lead inhibits three enzymes of heme biosynthesis- δ-amino-levulinic-acid dehydratase (ALAD), coproporphyrin oxidase, and ferrochelatase, impairing heme synthesis and depressing serum level of erythropoietin resulting in decreased hemoglobin synthesis. Lead exposure also affects calcium metabolism and impair the synthesis of Calcitriol. In the present study, jewelry makers from Dhaka, Bangladesh, were shown to have significantly high levels of lead, protein, albumin, and parathormone in their blood, and significantly high amount of zinc-protoporphyrin and δ-amino-levulinic-acid in their urine. The control group, on the other hand showed significantly higher amounts of calcium (both total and ionized form) Vitamin D3and non-activated erythrocyte ALAD in their blood, along with hemoglobin. It might be due to inhibition of 1-α-hydroxylase enzyme in renal tubules. Lead causes nephro-toxicity and inhibits 1-α- hydroxylase enzyme leading to decreased calcitriol synthesis resulting in impaired calcium absorption across gastro-intestinal tract and renal tubules. Low Vitamin D3and significantly increased Parathyroid hormone (PTH) in study group has been found.
Fulltext Spray-dried immobilized lipase from Geobacillus sp. strain ARM in sago

Mohtar NS, Abdul Rahman MB, Mustafa S, Mohamad Ali MS, Raja Abd Rahman RNZ

PeerJ, 2019;7:e6880.
PMID: 31183251 DOI: 10.7717/peerj.6880

Sago starch is traditionally used as food especially in Southeast Asia. Generally, sago is safe for consumption, biodegradable, easily available and inexpensive. Therefore, this research was done to expand the potential of sago by using it as a support for enzyme immobilization. In this study, ARM lipase, which was isolated from Geobacillus sp. strain ARM, was overexpressed in Escherichia coli system and then purified using affinity chromatography. The specific activity of the pure enzyme was 650 U/mg, increased 7 folds from the cell lysate. The purified enzyme was immobilized in gelatinized sago and spray-dried by entrapment technique in order to enhance the enzyme operational stability for handling at high temperature and also for storage. The morphology of the gelatinized sago and immobilized enzyme was studied by scanning electron microscopy. The results showed that the spray-dried gelatinized sago was shrunken and became irregular in structure as compared to untreated sago powder. The surface areas and porosities of spray-dried gelatinized sago with and without the enzyme were analyzed using BET and BJH method and have shown an increase in surface area and decrease in pore size. The immobilized ARM lipase showed good performance at 60-80 °C, with a half-life of 4 h and in a pH range 6-9. The immobilized enzyme could be stored at 10 °C with the half-life for 9 months. Collectively, the spray-dried immobilized lipase shows promising capability for industrial uses, especially in food processing.
Fulltext Short-term Gini coefficient estimation using nonlinear autoregressive multilayer perceptron model

Amin Megat Ali MS, Zabidi A, Md Tahir N, Mohd Yassin I, Eskandari F, Saadon A, et al.

Heliyon, 2024 Feb 29;10(4):e26438.
PMID: 38420485 DOI: 10.1016/j.heliyon.2024.e26438

Poverty, an intricate global challenge influenced by economic, political, and social elements, is characterized by a deficiency in crucial resources, necessitating collective efforts towards its mitigation as embodied in the United Nations' Sustainable Development Goals. The Gini coefficient is a statistical instrument used by nations to measure income inequality, economic status, and social disparity, as escalated income inequality often parallels high poverty rates. Despite its standard annual computation, impeded by logistical hurdles and the gradual transformation of income inequality, we suggest that short-term forecasting of the Gini coefficient could offer instantaneous comprehension of shifts in income inequality during swift transitions, such as variances due to seasonal employment patterns in the expanding gig economy. System Identification (SI), a methodology utilized in domains like engineering and mathematical modeling to construct or refine dynamic system models from captured data, relies significantly on the Nonlinear Auto-Regressive (NAR) model due to its reliability and capability of integrating nonlinear functions, complemented by contemporary machine learning strategies and computational algorithms to approximate complex system dynamics to address these limitations. In this study, we introduce a NAR Multi-Layer Perceptron (MLP) approach for brief term estimation of the Gini coefficient. Several parameters were tested to discover the optimal model for Malaysia's Gini coefficient within 1987-2015, namely the output lag space, hidden units, and initial random seeds. The One-Step-Ahead (OSA), residual correlation, and residual histograms were used to test the validity of the model. The results demonstrate the model's efficacy over a 28-year period with superior model fit (MSE: 1.14 × 10-7) and uncorrelated residuals, thereby substantiating the model's validity and usefulness for predicting short-term variations in much smaller time steps compared to traditional manual approaches.
Fulltext Quantification of Berberine in Berberis vulgaris L. Root Extract and Its Curative and Prophylactic Role in Cisplatin-Induced In Vivo Toxicity and In Vitro Cytotoxicity

Ahmad S, Hussain A, Hussain A, Abdullah I, Ali MS, Froeyen M, et al.

Antioxidants (Basel), 2019 Jun 19;8(6).
PMID: 31248160 DOI: 10.3390/antiox8060185

Cisplatin is amongst the most potent chemotherapeutic drugs with applications in more than 50% of cancer treatments, but dose-dependent side effects limit its usefulness. Berberis vulgaris L. (B. vulgaris) has a proven role in several therapeutic applications in the traditional medicinal system. High-performance liquid chromatography was used to quantify berberine, a potent alkaloid in the methanolic root extract of B. vulgaris (BvRE). Berberine chloride in BvRE was found to be 10.29% w/w. To assess the prophylactic and curative protective effects of BvRE on cisplatin-induced nephrotoxicity, hepatotoxicity, and hyperlipidemia, in vivo toxicity trials were carried out on 25 healthy male albino Wistar rats (130-180 g). Both prophylactic and curative trials included a single dose of cisplatin (4 mg/kg, i.p.) and nine doses of BvRE (500 mg/kg/day, orally). An array of marked toxicity effects appeared in response to cisplatin dosage evident by morphological condition, biochemical analysis of serum (urea, creatinine, total protein, alanine transaminase, aspartate transaminase, total cholesterol, and triglyceride), and organ tissue homogenates (malondialdehyde and catalase). Statistically-significant (p < 0.05) variations were observed in various parameters. Moreover, histological studies of liver and kidney tissues revealed that the protective effect of BvRE effectively minimized and reversed nephrotoxic, hepatotoxic, and hyperlipidemic effects caused by cisplatin in both prophylactic and curative groups with relatively promising ameliorative effects in the prophylactic regimen. The in vitro cell viability effect of cisplatin, BvRE, and their combination was determined on HeLa cells using the tetrazolium (MTT) assay. MTT clearly corroborated that HeLa cells appeared to be less sensitive to cisplatin and berberine individually, while the combination of both at the same concentrations resulted in growth inhibition of HeLa cells in a remarkable synergistic way. The present study validated the use of BvRE as a protective agent in combination therapy with cisplatin.
Purification and characterisation of an F16L mutant of a thermostable lipase

Ali MS, Yun CC, Chor AL, Rahman RN, Basri M, Salleh AB

Protein J, 2012 Mar;31(3):229-37.
PMID: 22350313 DOI: 10.1007/s10930-012-9395-8

A mutant of the lipase from Geobacillus sp. strain T1 with a phenylalanine to leucine substitution at position 16 was overexpressed in Escherichia coli strain BL21(De3)pLysS. The crude enzyme was purified by two-step affinity chromatography with a final recovery and specific activity of 47.4 and 6,315.8 U/mg, respectively. The molecular weight of the purified F16L lipase was approximately 43 kDa by 12% SDS-PAGE analysis. The F16L lipase was demonstrated to be a thermophilic enzyme due its optimum temperature at 70 °C and showed stability over a temperature range of 40-60 °C. The enzyme exhibited an optimum pH 7 in phosphate buffer and was relatively stable at an alkaline pH 8-9. Metal ions such as Ca(2+), Mn(2+), Na(+), and K(+) enhanced the lipase activity, but Mg(2+), Zn(2+), and Fe(2+) inhibited the lipase. All surfactants tested, including Tween 20, 40, 60, 80, Triton X-100, and SDS, significantly inhibited the lipolytic action of the lipase. A high hydrolytic rate was observed on long-chain natural oils and triglycerides, with a notable preference for olive oil (C18:1; natural oil) and triolein (C18:1; triglyceride). The F16L lipase was deduced to be a metalloenzyme because it was strongly inhibited by 5 mM EDTA. Moderate inhibition was observed in the presence of PMSF at a similar concentration, indicating that serine residues are involved in its catalytic action. Further, the activity was not impaired by water-miscible solvents, including methanol, ethanol, and acetone.
Fulltext Optimized artificial neural network to improve the accuracy of estimated fault impedances and distances for underground distribution system

Naidu K, Ali MS, Abu Bakar AH, Tan CK, Arof H, Mokhlis H

PLoS One, 2020;15(1):e0227494.
PMID: 31999711 DOI: 10.1371/journal.pone.0227494

This paper proposes an approach to accurately estimate the impedance value of a high impedance fault (HIF) and the distance from its fault location for a distribution system. Based on the three-phase voltage and current waveforms which are monitored through a single measurement in the network, several features are extracted using discrete wavelet transform (DWT). The extracted features are then fed into the optimized artificial neural network (ANN) to estimate the HIF impedance and its distance. The particle swarm optimization (PSO) technique is employed to optimize the parameters of the ANN to enhance the performance of fault impedance and distance estimations. Based on the simulation results, the proposed method records encouraging results compared to other methods of similar complexity for both HIF impedance values and estimated distances.
Opportunistic yeast pathogen Candida spp.: Secreted and membrane-bound virulence factors

Lim SJ, Mohamad Ali MS, Sabri S, Muhd Noor ND, Salleh AB, Oslan SN

Med Mycol, 2021 Dec 03;59(12):1127-1144.
PMID: 34506621 DOI: 10.1093/mmy/myab053

Candidiasis is a fungal infection caused by Candida spp. especially Candida albicans, C. glabrata, C. parapsilosis and C. tropicalis. Although the medicinal therapeutic strategies have rapidly improved, the mortality rate as candidiasis has continuously increased. The secreted and membrane-bound virulence factors (VFs) are responsible for fungal invasion, damage and translocation through the host enterocytes besides the evasion from host immune system. VFs such as agglutinin-like sequences (Als), heat shock protein 70, phospholipases, secreted aspartyl proteinases (Sap), lipases, enolases and phytases are mostly hydrolases which degrade or interact with the enterocyte membrane components. Candidalysin, however, acts as a peptide toxin to induce necrotic cell lysis. To date, structural studies of the VFs remain underexplored, hindering their functional analyses. Among the VFs, only Sap and Als have their structures deposited in Protein Data Bank (PDB). Therefore, this review scrutinizes the mechanisms of these VFs by discussing the VF-deficient studies of several Candida spp. and their abilities to produce these VFs. Nonetheless, their latest reported sequential and structural analyses are discussed to impart a wider perception of the host-pathogen interactions and potential vaccine or antifungal drug targets. This review signifies that more VFs structural investigations and mining in the emerging Candida spp. are required to decipher their pathogenicity and virulence mechanisms compared to the prominent C. albicans.
LAY SUMMARY: Candida virulence factors (VFs) including mainly enzymes and proteins play vital roles in breaching the human intestinal barrier and causing deadly invasive candidiasis. Limited VFs' structural studies hinder deeper comprehension of their mechanisms and thus the design of vaccines and antifungal drugs against fungal infections.
Night eating and its relationship with BMI, stress, sleep quality and duration of study among university students

Emmy HKI, Boleh NC, Ali MS, Jakiwa J, Mardiyati NL, Ahmad MF

Med J Malaysia, 2024 Mar;79(Suppl 1):134-139.
PMID: 38555898

INTRODUCTION: Night eating is a very common dietary behaviour among university students. This study aims to investigate the relationship between night eating and BMI, stress, sleep quality and duration of study among university students.
MATERIALS AND METHODS: A total of 385 university students including foundation and undergraduate students took part in this study. Self-administered online surveys were used to obtain sociodemographic data, and anthropometry measurements including weight and height, night eating during studying, duration of the study, opinion on eating and academic performance, sleep quality, level of depression, anxiety, and stress of the respondents. Questionnaires were validated and IBM SPSS Statistics Software version 26.0 was used to analyse categorical and continuous variables.
RESULTS: The findings showed that there was an association between night eaters and coffee consumption with BMI (p<0.001) and sleep quality (p<0.05). However, there was no association (p>0.05) found between the types of food eaten during night studying and the mean duration of the study. The results showed drinking coffee had an association with depression, anxiety, and stress (p<0.05) among Malaysian university students.
CONCLUSION: Coffee consumption was common among undergraduate students during studying. Awareness of the risk of overconsumption of caffeine intake should be implemented in the future. However, this study did not include all types of food choices and drinks. Thus, frequency of eating energy dense food during night studying among students should be conducted in the future.
Fulltext New Recombinant Cold-Adapted and Organic Solvent Tolerant Lipase from Psychrophilic Pseudomonas sp. LSK25, Isolated from Signy Island Antarctica

Salwoom L, Raja Abd Rahman RNZ, Salleh AB, Mohd Shariff F, Convey P, Mohamad Ali MS

Int J Mol Sci, 2019 Mar 13;20(6).
PMID: 30871178 DOI: 10.3390/ijms20061264

In recent years, studies on psychrophilic lipases have become an emerging area of research in the field of enzymology. The study described here focuses on the cold-adapted organic solvent tolerant lipase strain Pseudomonas sp. LSK25 isolated from Signy Station, South Orkney Islands, maritime Antarctic. Strain LSK25 lipase was successfully cloned, sequenced, and over-expressed in an Escherichia coli system. Sequence analysis revealed that the lipase gene of Pseudomonas sp. LSK25 consists of 1432 bp, lacks an N-terminal signal peptide and encodes a mature protein consisting of 476 amino acids. The recombinant LSK25 lipase was purified by single-step purification using Ni-Sepharose affinity chromatography and had a molecular mass of approximately 65 kDa. The final recovery and purification fold were 44% and 1.3, respectively. The LSK25 lipase was optimally active at 30 °C and at pH 6. Stable lipolytic activity was reported between temperatures of 5⁻30 °C and at pH 6⁻8. A significant enhancement of lipolytic activity was observed in the presence of Ca2+ ions, the organic lipids of rice bran oil and coconut oil, a synthetic C12 ester and a wide range of water immiscible organic solvents. Overall, lipase strain LSK25 is a potentially desirable candidate for biotechnological application, due to its stability at low temperatures, across a range of pH and in organic solvents.
Fulltext Molecular Cloning and Functional Expression of a Δ9- Fatty Acid Desaturase from an Antarctic Pseudomonas sp. A3

Garba L, Mohamad Ali MS, Oslan SN, Rahman RN

PLoS One, 2016;11(8):e0160681.
PMID: 27494717 DOI: 10.1371/journal.pone.0160681

Fatty acid desaturase enzymes play an essential role in the synthesis of unsaturated fatty acids. Pseudomonas sp. A3 was found to produce a large amount of palmitoleic and oleic acids after incubation at low temperatures. Using polymerase Chain Reaction (PCR), a novel Δ9- fatty acid desaturase gene was isolated, cloned, and successfully expressed in Escherichia coli. The gene was designated as PA3FAD9 and has an open reading frame of 1,185 bp which codes for 394 amino acids with a predicted molecular weight of 45 kDa. The activity of the gene product was confirmed via GCMS, which showed a functional putative Δ9-fatty acid desaturase capable of increasing the total amount of cellular unsaturated fatty acids of the E. coli cells expressing the gene. The results demonstrate that the cellular palmitoleic acids have increased two-fold upon expression at 15°C using only 0.1 mM IPTG. Therefore, PA3FAD9 from Pseudomonas sp.A3 codes for a Δ9-fatty acid desaturase-like protein which was actively expressed in E. coli.
Fulltext Mechanistic Studies of the Antiallergic Activity of Phyllanthus amarus Schum. & Thonn. and Its Compounds

Abd Rani NZ, Lam KW, Jalil J, Mohamad HF, Mat Ali MS, Husain K

Molecules, 2021 Jan 28;26(3).
PMID: 33525733 DOI: 10.3390/molecules26030695

Phyllanthus amarus Schum. & Thonn. (Phyllanthaceae) is a medicinal plant that is commonly used to treat diseases such as asthma, diabetes, and anemia. This study aimed to examine the antiallergic activity of P. amarus extract and its compounds. The antiallergic activity was determined by measuring the concentration of allergy markers release from rat basophilic leukemia (RBL-2H3) cells with ketotifen fumarate as the positive control. As a result, P. amarus did not stabilize mast cell degranulation but exhibited antihistamine activity. The antihistamine activity was evaluated by conducting a competition radioligand binding assay on the histamine 1 receptor (H1R). Four compounds were identified from the high performance liquid chromatography (HPLC) analysis which were phyllanthin (1), hypophyllanthin (2), niranthin (3), and corilagin (4). To gain insights into the binding interactions of the most active compound hypophyllanthin (2), molecular docking was conducted and found that hypophyllanthin (2) exhibited favorable binding in the H1R binding site. In conclusion, P. amarus and hypophyllanthin (2) could potentially exhibit antiallergic activity by preventing the activation of the H1 receptor.
Fulltext Lid opening and conformational stability of T1 Lipase is mediated by increasing chain length polar solvents

Maiangwa J, Mohamad Ali MS, Salleh AB, Rahman RNZRA, Normi YM, Mohd Shariff F, et al.

PeerJ, 2017;5:e3341.
PMID: 28533982 DOI: 10.7717/peerj.3341

The dynamics and conformational landscape of proteins in organic solvents are events of potential interest in nonaqueous process catalysis. Conformational changes, folding transitions, and stability often correspond to structural rearrangements that alter contacts between solvent molecules and amino acid residues. However, in nonaqueous enzymology, organic solvents limit stability and further application of proteins. In the present study, molecular dynamics (MD) of a thermostable Geobacillus zalihae T1 lipase was performed in different chain length polar organic solvents (methanol, ethanol, propanol, butanol, and pentanol) and water mixture systems to a concentration of 50%. On the basis of the MD results, the structural deviations of the backbone atoms elucidated the dynamic effects of water/organic solvent mixtures on the equilibrium state of the protein simulations in decreasing solvent polarity. The results show that the solvent mixture gives rise to deviations in enzyme structure from the native one simulated in water. The drop in the flexibility in H2O, MtOH, EtOH and PrOH simulation mixtures shows that greater motions of residues were influenced in BtOH and PtOH simulation mixtures. Comparing the root mean square fluctuations value with the accessible solvent area (SASA) for every residue showed an almost correspondingly high SASA value of residues to high flexibility and low SASA value to low flexibility. The study further revealed that the organic solvents influenced the formation of more hydrogen bonds in MtOH, EtOH and PrOH and thus, it is assumed that increased intraprotein hydrogen bonding is ultimately correlated to the stability of the protein. However, the solvent accessibility analysis showed that in all solvent systems, hydrophobic residues were exposed and polar residues tended to be buried away from the solvent. Distance variation of the tetrahedral intermediate packing of the active pocket was not conserved in organic solvent systems, which could lead to weaknesses in the catalytic H-bond network and most likely a drop in catalytic activity. The conformational variation of the lid domain caused by the solvent molecules influenced its gradual opening. Formation of additional hydrogen bonds and hydrophobic interactions indicates that the contribution of the cooperative network of interactions could retain the stability of the protein in some solvent systems. Time-correlated atomic motions were used to characterize the correlations between the motions of the atoms from atomic coordinates. The resulting cross-correlation map revealed that the organic solvent mixtures performed functional, concerted, correlated motions in regions of residues of the lid domain to other residues. These observations suggest that varying lengths of polar organic solvents play a significant role in introducing dynamic conformational diversity in proteins in a decreasing order of polarity.

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