Aliphatic glucosinolate is an important secondary metabolite responsible in plant defense mechanism and carcinogenic
activity. It plays a crucial role in plant adaptation towards changes in the environment such as salinity and drought.
However, in many plant genomes, there are thousands of genes encoding proteins still with putative functions and
incomplete annotations. Therefore, the genome of Arabidopsis thaliana was selected to be investigated further to identify
any putative genes that are potentially involved in the aliphatic glucosinolate biosynthesis pathway, most of its gene are
with incomplete annotation. Known genes for aliphatic glucosinolates were retrieved from KEGG and AraCyc databases.
Three co-expression databases i.e., ATTED-II, GeneMANIA and STRING were used to perform the co-expression network
analysis. The integrated co-expression network was then being clustered, annotated and visualized using Cytoscape plugin,
MCODE and ClueGO. Then, the regulatory network of A. thaliana from AtRegNet was mapped onto the co-expression
network to build the transcriptional regulatory network. This study showed that a total of 506 genes were co-expressed
with the 61 aliphatic glucosinolate biosynthesis genes. Five transcription factors have been predicted to be involved
in the biosynthetic pathway of aliphatic glucosinolate, namely SEPALLATA 3 (SEP3), PHYTOCHROME INTERACTING FACTOR
3-like 5 (AtbHLH15/PIL5), ELONGATED HYPOCOTYL 5 (HY5), AGAMOUS-like 15 (AGL15) and GLABRA 3 (GL3). Meanwhile,
three other genes with high potential to be involved in the aliphatic glucosinolates biosynthetic pathway were identified,
i.e., methylthioalkylmalate-like synthase 4 (MAML-4) and aspartate aminotransferase (ASP1 and ASP4). These findings
can be used to complete the aliphatic glucosinolate biosynthetic pathway in A. thaliana and to update the information
on the glucosinolate-related pathways in public metabolic databases.
The use of photoplethysmography (PPG) as one of cardiovascular disease (CVD) marker has got more attention due to
its simplicity, noninvasive and portable characteristics. Two new markers had been developed from PPG namely PPG
fitness index (PPGF) and vascular risk prediction index (VPRI). The aim of the present study was to compare PPGF level
between young women with and without CVD risk factors, to investigate the relationship between PPGF with other CVD
markers and to assess the sensitivity of VRPI in classifying young women that have CVD risk factors. A total of 148 young
women aged 20-40 years old with and without CVD risk factors were involved in this study. CVD risk factors comprised of
abdominal obesity, hypertension, dyslipidemia, smoking and family history of premature CVD. Subjects were categorized
into healthy or having CVD risk factor. Measurements taken were anthropometric data, blood pressure, lipid profile,
pulse wave velocity (PWV), augmentation index (AIx), high sensitivity C-Reactive Protein (hs-CRP), PPGF and VRPI. SPSS
version 20 was used for data analysis with p<0.05 as significant value. The mean subjects’ age was 29.97±5.27 years
old. There was no difference in PPGF level between groups (p>0.05). PPGF was independently determined by PWV (β=-
0.31, p<0.001) and height (β=0.16, p=0.04). VRPI had 77.9% sensitivity in identifying subjects with CVD risk factor. In
conclusion, PPGF correlates with PWV and has potential to be an indicator of aortic stiffness while VRPI is sensitive to
classify those with CVD risk factor.
Curcuma aeruginosa or temu hitam is herbaceous plant with high therapeutic values in its rhizome that is widely used in
traditional medicine. However, molecular studies on the secondary metabolite biosynthetic pathway of C. aeruginosa is
still limited. Hence, the aim of this study was to explore and reconstruct the secondary metabolite biosynthetic pathway
of C. aeruginosa rhizome by integrating the metabolite profiling and transcriptomic data. A total of 81 metabolites were
identified in the rhizome of C. aeruginosa; amongst others are curzerene and β-Cubebene which are potent antioxidants.
A total of 28,225 unigene were obtained from the transcriptomic sequencing of C. aeruginosa rhizome and analysed
to identify potential genes associated with the biosynthesis of its metabolites. Of these, 43 unigenes were identified and
mapped onto five sub-pathways; i.e. carotenoid biosynthetic pathway, diterpenoid biosynthetic pathway, monoterpenoid
biosynthetic pathway, terpenoid and steroid biosynthetic pathway, and sesquiterpenoid and triterpenoid biosynthetic
pathway. This study demonstrated a systematic bioinformatic approach to reconstruct a metabolic pathway in the rhizome
of C. aeruginosa using bioinformatic approach.
Induced pluripotent stem cells (iPSC) is a novel technology useful for therapeutic and research applications. To date, iPSCs
is produced through genetic modification that can promote mutation; making it harmful for therapeutic use. Therefore,
application of non-genetic modification through direct delivery of recombinant proteins aided by protein transduction
domain (PTD) enable a safer production of iPSC. This study is aimed to establish a stable production of secretable
recombinant protein via recombination of green fluorescence protein (GFP) and a novel PTD peptide, namely TATκ-GFP.
293Tcell line was transfected with 20 µg/ml of TATκ-GFP plasmid and the stably transfected 293T cells were then cultured
for 54 days to determine the stability of expression and secretion of TATκ-GFP recombinant protein in prolonged culture.
Methylation at the CMV promoter of the TATκ-GFP plasmid was investigated following treatment of transfected cells with
3 µM/mL of demethylation agent, namely 5-Azacytidine for 72 h in three cycles. Flow cytometry analysis demonstrated
a transfection efficiency of 9.33% and successful secretion of TATκ-GFP proteins into the culture medium as analysed by
Western blot at 72 h post-transfection. However, the transfected cells exhibited a decreasing level of GFP expression and
secretion following prolonged culture with notable stability that only sustained for two weeks. 5-Azacytidine-treated cells
showed a slight increase of GFP expression compared to non-treated control, suggesting possible promoter methylation
which could cause instability of TATκ-GFP expression. Conclusively, promoter methylation should be considered for future
establishment of iPSCs as it could inhibit stable expression and secretion of recombinant proteins.
Plutella xylostella (L.) (Lepidoptera: Plutellidae), the major insect pest of cruciferous crops worldwide shows significant
resistance to almost all classes of insecticides. In order to effectively prevent and manage the insecticidal resistance,
it is crucial to understand the physiological adaptation of insects against insecticides. Identification of insect protein
that interacting with insecticides and characterization of their modification in resistant strains can be done by using
differential proteomics approach. This study focuses on optimizing a sensitive and rapid method for the extraction of
high quality protein of both larva and adult tissues of P. xylostella to be used in two-dimensional gel electrophoresis.
Five extraction methods were evaluated for protein concentration, yields and resolving patterns of one-dimensional
and two-dimensional electrophoresis. The results showed that trichloroacetic acid/acetone extraction methods with
two different concentrations of 2-mercaptoethanol produced the highest protein concentration and yield for both adult
and larva tissues, respectively. Meanwhile, trichloroacetic acid/acetone with dithiothreitol extraction method gave
better separation of spots and intensity for both larva and adult tissues compared to other methods tested. As such, we
concluded that trichloroacetic acid/acetone with dithiothreitol successfully yielded high total protein concentration and
good separation of two-dimensional electrophoresis gel spots in both adult and larva P. xylostella.
Skin wound healing is a complex physiological event, involving many cellular and molecular components. The event of
wound healing is the coordinated overlap of a number of distinct phases, namely haemostasis, inflammatory, proliferative
and remodelling. The molecular events surrounding wound healing, particularly the reepithelialisation, has been reported
to be similar to the epithelial to mesenchymal transition (EMT). In this review, the mechanism between epithelialisation
and EMT were compared. Both are characterised by the loss of epithelial integrity and increased motility. In terms of
the signalling kinases, Smad and mitogen-activated protein kinase (MAPK) has been reported to be involved in both
reepithelialisation and EMT. At the transcriptional level, SLUG transcription factor has been reported to be important for
both reepithelialisation and EMT. Extracellular matrix proteins that have been associated with both events are collagen
and laminin. Lastly, both events required the interplay between matrix metalloproteinases (MMPs) and its inhibitor. As a
conclusion, both reepithelialisation and EMT shares similar signaling cascade and transcriptional regulation to exhibit
decreased epithelial traits and increased motility in keratinocytes.
MeSH terms: Collagen; Hemostasis; Laminin; Transcription Factors; Wound Healing; Signal Transduction; Keratinocytes; Extracellular Matrix Proteins; Matrix Metalloproteinases; Mitogen-Activated Protein Kinases; Epithelial-Mesenchymal Transition; Re-Epithelialization; Snail Family Transcription Factors
Microbial production of natural products using metabolic engineering and synthetic biology approaches often involves
the assembly of multiple gene fragments including regulatory elements, especially when using eukaryotes as hosts.
Traditional cloning strategy using restriction enzyme digestion and ligation are laborious and inflexible owing to the
high number of sequential cloning steps, limited cutting sites and generation of undesired ‘scar’ sequences. In this study,
a homology-based isothermal DNA assembly method was carried out for one-step simultaneous assembly of multiple DNA
fragments to engineer plant phenylpropanoid biosynthesis in Saccharomyces cerevisiae. Rapid construction of yeast
plasmid harboring dual gene expression cassettes was achieved via isothermal assembly of four DNA fragments designed
with 20 bp overlapping sequences. The rate-limiting enzyme of phenylpropanoid pathway, cinnamate 4-hydroxylase
encoded by C4H gene from Polygonum minus was cloned in tandem with yeast promoter and terminator elements of S.
cerevisiae for efficient construction of phenylpropanoid biosynthetic pathway in recombinant yeast. The assembled pAGCAT (C4H-ADH1t-TEF1p) shuttle plasmid and transformation of S. cerevisiae with the plant C4H gene were confirmed
via PCR analysis. Based on these findings, the yeast shuttle plasmid harboring P. minus phenylpropanoid biosynthesis
gene was efficiently constructed to be the starting platform for the production of plant natural products in geneticallyengineered S. cerevisiae.
Protein degradation can occur through Ubiquitin 26S-Proteosome System (UPS). The degradation can be mediated by
the SCF E3 ubiquitin ligase complex consisting of Skp1, Cullin, and F-box protein as the main components. The F-box
protein at the C-terminal domain functions to recognize the targeted protein to be ubiquitinated and degraded via UPS.
A stress-responsive F-box gene, PmF-box1 from Persicaria minor was categorized in the F-box containing kelch repeat
(FBK) family; a family that specific to plant kingdom. To identify the targeted protein of PmF-box1, yeast-two hybrid system
(Y2H) was used. In the Y2H screening process, mating efficiency is very important to fish out the interacting proteins.
Therefore, one modification was conducted to increase the mating efficiency. In this screening, PmF-box1 was used as a
bait to screen for the Y2H library which was constructed using RNA from plant samples treated with abscisic acid (ABA)
and polyethylene glycol (PEG)-8000 and control sample. Autoactivation and toxicity tests of bait were performed before
the Y2H screening. Tests on PmF-box1 showed that it is not toxic to the yeast and cannot autoactivate the yeast reporter
genes. Mating efficiency was improved from 2.07% to 9.15% after addition of PEG-4000 in the mating culture compared
to the original protocol, which it also increased the colony number in the screening step afterward. Additionally, bands
of gene with different sizes were observed on electrophoresis gel after colony PCR analysis from the improved technique.
Those genes may code for potential interacting proteins that needs further identification and confirmation.
The purpose of the present study was to assess quality of life (QOL) in n-AMD patients seen in a Malaysian public hospital
and to further identify visual and demographic factors that may contribute to QOL scores of these patients. Patients
with any form of n-AMD in at least one eye were recruited from hospital’s ophthalmology department. Bahasa Malaysia
version of National Eye Institute Visual function questionnaire-25 (NEI-VFQ-25) was administered to all participants.
Demographics, visual functions (VF) including best corrected distance visual acuity (BCDVA), contrast sensitivity (CS),
near visual acuity (NVA) and reading speed (RS) were recorded. Eighty-six patients (Malay=26, Indian=23, Chinese=37)
aged 52 to 85 years, diagnosed with n-AMD were chosen to participate. Their mean NEI-VFQ composite score (NEI-VFQ
CS) was 66.91 ± 13.07. However, no significant difference in NEI-VFQ CS between gender, races and between the two sub
groups of n-AMD were observed (p>0.05). NEI-VFQ CS showed a significant association with RS (correlation coefficient
(ρ) =0.627), NVA (ρ = -.660), BCDVA (ρ = -.586), CS (ρ =.0.515). A linear model showed that a combination of BCDVA,
NVA, CS is accounted for a significant 38 % variability of NEI-VFQ CS (R2
=0.382, p<0.001). In conclusion, the QOL of
Malaysian n-AMD patients were found to be low. Thus, the study results indicated the need of developing necessary
management strategies to address this QOL issues in n-AMD patients in Malaysia. Furthermore, the present study suggested
incorporating appropriate VF such as near acuity, contrast sensitivity, reading speed in clinical settings while assessing
n-AMD patients as these VF explain the patient’s perception about the impact of this disease.
Farah Fadwa Benbelgacem, Oualid Abdelkader Bellag, Adibah Parman, Ibrahim Ali Noorbatcha, Mohd Noor Mat Isa, Muhammad Alfatih Muddathir Abdelrahim, et al.
Metagenomic DNA library from palm oil mill effluent (POME) was constructed and subjected to high-throughput screening
to find genes encoding cellulose- and xylan-degrading enzymes. DNA of 30 positive fosmid clones were sequenced with next
generation sequencing technology and the raw data (short insert-paired) was analyzed with bioinformatic tools. First,
the quality of 64,821,599 reverse and forward sequences of 101 bp length raw data was tested using Fastqc and SOLEXA.
Then, raw data filtering was carried out by trimming low quality values and short reads and the vector sequences were
removed and again the output was checked and the trimming was repeated until a high quality read sets was obtained.
The second step was the de novo assembly of sequences to reconstruct 2900 contigs following de Bruijn graph algorithm.
Pre-assembled contigs were arranged in order, the distances between contigs were identified and oriented with SSPACE,
where 2139 scaffolds have been reconstructed. 16,386 genes have been identified after gene prediction using Prodigal
and putative ID assignment with Blastp vs NR protein. The acceptable strategy to handle metagenomic NGS-data in order
to detect known and potentially unknown genes is presented and we showed the computational efficiency of de Bruijn
graph algorithm of de novo assembly to 21 bioprospect genes encoding cellulose-degrading enzymes and 6 genes
encoding xylan-degrading enzymes of 30.3% to 100% identity percentage.
Porphyromonas gingivalis is the bacterium responsible for chronic periodontitis, a severe periodontal disease. Virulence
factors produced by this bacterium are secreted by the Type IX Secretion System (T9SS). The specific functions for
each protein component of the T9SS have yet to be characterized thus limiting our understanding of the mechanisms
associated with the translocation and modification processes of the T9SS. This study aims to identify the sequence motifs
for each T9SS component and predict the functions associated with each discovered motif using motif comparisons. We
extracted the sequences of 20 T9SS components from the P. gingivalis proteome that were experimentally identified to
be important for T9SS function and used them for homology searching against fully sequenced bacterial proteomes.
We developed a rigorous pipeline for the identification of seed sequences for each protein family of T9SS components.
We verified that each selected seed sequence are true members of the protein family hence sharing conserved sequence
motifs using profile Hidden Markov Models. The motifs for each T9SS component are identified and compared to motifs
in the Pfam database. The discovered motifs for 11 components with known functions matched the motifs associated
with the reported functions. We also suggested the putative functions for four components. PorM and PorW might form
the putative energy transduction complex. PorP and PorT might be the putative O-deacylases. The identified motifs for
five components matched the motifs associated with functions that related/unrelated to the T9SS.
A structured weight management programme at a workplace may help in reducing the prevalence of overweight and obesity.
Therefore, this intervention study was to determine the effectiveness of weight loss programmes including face-to-face,
online and control group at workplace among employees who are overweight and obese. A total of 108 overweight and
obese adults were recruited and randomly divided into three groups (face-to-face group (FT), n=38; online group (OG),
n=31; control group (CG), n=39). In the FT group, the participants took part in health talks, interactive activities and
counselling; the OG group was given access to an online weight management program and the CG group was provided
with educational booklets on weight loss. All information given was related to nutrition, physical activity and motivation
to reduce weight. Body weight, body mass index (BMI), waist circumference (WC), body fat percentage, dietary intake,
fasting lipid profile and glucose levels were assessed at baseline and 4 months. The FT group showed greater reduction
in body weight (-5.80 kg) compared to OG (-1.12 kg) and CG (-1.82 kg). Significant interaction effects were found for BMI,
WC, fasting serum triglycerides, HDL-cholesterol and total cholesterol/HDL-cholesterol ratio (all p<0.05), with the FT
group showing the biggest improvements, compared to the other groups. The face-to-face weight management program
offered in the workplace showed to be the most effective at improving anthropometric profile, fasting serum triglycerides,
HDL-C, total cholesterol/HDL-C ratio, and dietary intake among overweight and obese employees.
MeSH terms: Adipose Tissue; Adult; Anthropometry; Body Weight; Counseling; Fasting; Glucose; Humans; Cholesterol, HDL; Motivation; Obesity; Pamphlets; Triglycerides; Weight Loss; Exercise; Body Mass Index; Prevalence; Workplace; Control Groups; Overweight; Waist Circumference; Weight Reduction Programs
Laryngeal cancer is the most common head and neck cancer in the world and its incidence is on the rise. However, the
molecular mechanism underlying laryngeal cancer pathogenesis is poorly understood. The goal of this study was to
develop a protein-protein interaction (PPI) network for laryngeal cancer to predict the biological pathways that underlie
the molecular complexes in the network. Genes involved in laryngeal cancer were extracted from the OMIM database
and their interaction partners were identified via text and data mining using Agilent Literature Search, STRING and
GeneMANIA. PPI network was then integrated and visualised using Cytoscape ver3.6.0. Molecular complexes in the
network were predicted by MCODE plugin and functional enrichment analyses of the molecular complexes were performed
using BiNGO. 28 laryngeal cancer-related genes were present in the OMIM database. The PPI network associated with
laryngeal cancer contained 161 nodes, 661 edges and five molecular complexes. Some of the complexes were related to
the biological behaviour of cancer, providing the foundation for further understanding of the mechanism of laryngeal
cancer development and progression.
MeSH terms: Goals; Laryngeal Neoplasms; Oncogenes; Incidence; Databases, Genetic; Data Mining; Protein Interaction Maps
In this paper, we study the effects of symmetrization by the implicit midpoint rule (IMR) and the implicit trapezoidal rule
(ITR) on the numerical solution of ordinary differential equations. We extend the study of the well-known formula of Gragg
to a two-step symmetrizer and compare the efficiency of their use with the IMR and ITR. We present the experimental results
on nonlinear problem using variable stepsize setting and the results show greater efficiency of the two-step symmetrizers
over the one-step symmetrizers of IMR and ITR.
Ruta angustifolia (L.) Pers. is a Rutaceous species which contains various anthranilic acid derived alkaloids including
the bioactive quinolones. This study is aimed at identifying the antimicrobial active alkaloids of R. angustifolia and
evaluating their potential as synergistic enhancers in alkaloid-antibiotic combinations. Antimicrobial bioautographyguided isolation of alkaloidal fractions of R. angustifolia leaves has led to the identification of 2,3-dimethoxy-1-hydroxy10-methylacridone [arborinine]; and 4,7,8-trimethoxyfuro[2,3-b]quinoline [skimmianine]; together with the major
active alkaloid, 1-methyl-2-[3’,4’-methylenedioxyphenyl]-4-quinolone [graveoline]. Graveoline showed Minimum
Inhibitory Concentration (MIC) values ranging from 500 to 1000 µg/mL against Staphylococcus aureus ATCC 25923,
Enterococcus faecalis ATCC 29212 and Escherichia coli ATCC 25922. Checkerboard assay for antimicrobial combination
effects between graveoline with either erythromycin or vancomycin showed enhancement of the antimicrobial activity
of both antibiotics with Fractional Inhibitory Concentration Indices (FICI) ranged from 0.37 to 1.50. Synergistic effect
with FICI of 0.37 was observed for graveoline-erythromycin combination against S. aureus compared to FICI of 1.00 for
ciprofloxacin-erythromycin additive effect. Graveoline was a potential candidate for antimicrobial combination agent
especially against S. aureus. The result supports the idea of using plant metabolites as antimicrobial synergistic agents.
The problem of stagnation point flow over a stretching/shrinking sheet immersed in a micropolar fluid is analyzed
numerically. The governing partial differential equations are transformed into a system of ordinary (similarity) differential
equation and are then solved numerically using the boundary value problem solver (bvp4c) in Matlab software. The
effects of various parameters on the velocity and the angular velocity as well as the skin friction coefficient and the couple
stress are shown in tables and graphs. The noticeable results are found that the micropolar and the slip parameters
decrease the skin friction coefficient and the couple stress in the existence of magnetic field. Dual solutions appear for
certain range of the shrinking strength. A stability analysis is performed to determine which one of the solutions is stable.
Practical applications include polymer extrusion, where one deals with stretching of plastic sheets and in metallurgy
that involves the cooling of continuous strips.
In this paper, the homotopy decomposition method with a modified definition of beta fractional derivative is adopted
to find approximate solutions of higher-dimensional time-fractional diffusion equations. To apply this method, we find
the modified beta integral for both sides of a fractional differential equation first, then using homotopy decomposition
method we can obtain the solution of the integral equation in a series form. We compare the solutions obtained by the
proposed method with the exact solutions obtained using fractional variational homotopy perturbation iteration method
via modified Riemann-Liouville derivative. The comparison shows that the results are in a good agreement.
MeSH terms: Diffusion; Numerical Analysis, Computer-Assisted; Paper
Hypertension is one of the risk factors for cardiovascular diseases and has been associated with about 13% of global deaths
worldwide. Oxidative stress and reduced nitric oxide (NO) bioavailability contribute to the development of endothelial
dysfunction and subsequently hypertension. Nɷ-nitro-L-arginine methyl ester hydrochloride (L-NAME) inhibits NO synthesis;
leading to hypertension. Piper sarmentosum (PS) is an herb with antioxidant, antiatherosclerosis and antiinflammation
properties. PS also stimulated NO production by endothelial cells. The aim of this study was to determine the effects of
aqueous extract of Piper sarmentosum (AEPS) on blood pressure, oxidative stress and the level of nitric oxide in L-NAMEinduced hypertensive rats. Hypertension was induced by oral administration of L-NAME (100 mg/L) in drinking water for
four weeks. The rats were concurrently treated with AEPS by oral gavage in serial doses (125, 250 and 500 mg/kg/day).
Blood pressure was measured using non-invasive tail-cuff method at baseline and fortnightly thereafter. Serum level of
NO and an oxidative stress marker, malondialdehyde (MDA) were measured at baseline and at the end of treatment. The
results showed that treatment with three different doses of AEPS successfully reduced systolic blood pressure (p<0.001),
diastolic blood pressure (p<0.05) and mean arterial pressure (p<0.05) in L-NAME-induced hypertensive rats. Treatment
with AEPS also reduced MDA level (p<0.001) and increased serum NO (p<0.001) in L-NAME-induced hypertensive rats.
The findings showed that AEPS decreased blood pressure by protecting against oxidative stress and increasing NO in
L-NAME-induced hypertensive rats.
The El-Nino phenomenon in early 2014 contributed to the lack of water supply in most Southeast Asian countries.
Suggestions have since been made to ensure the continuity of water supply, one of which involves membrane technology
to treat mine water so that it is compatible for citizens’ use. Accordingly, the objective of this research was to study the
efficiency of membrane technology in treating mine water. Our elucidation of all the parameters has showed that the
best attainable classification is at Class IV. Although it was still regarded as polluted, the treated mine water can be
used as water supply reservoir. For the membranes tested such as ultrafiltration 10 kDa, 5 kDa and reverse osmosis,
the percentage of rejection for chemical oxygen demand is 21-72%, 40-96% for total suspended solids and 21-72% for
ammonia nitrogen. The pH also gradually shifted to almost neutral after the filtration.
The first visibility of the dawn occurs at a definite angle of the sun depression, Do
which is used to calculate the fajr
(dawn) prayer time. Dawn observations were carried out using Digital Single-lens Reflex (DSLR) camera in the period
from February to December 2017 at several locations in both Malaysia and Indonesia (Lat. between 2.0° - 7.0° N,
Long. 95.0°-106.0°E). Within the observational period, 64 days of the dawn luminance at horizon were recorded with
backgrounds of both sea and land. The purpose of these observations was to determine the sun depression angle Do
at the first moment when the dawn is seen using a DSLR camera. The results indicated that Do
can be determined using
a DSLR camera. The value of Do
is between -14.5° and -18.5° with a mean value of -16.67° and standard deviation of
0.9992. This suggests that the new sun depression angle Do
for dawn prayer is -17.0°.