Abstract: The polyfunctional and highly reactive bio-polymer,
the chitosan was first regioselectively converted into dialkylated
chitosan using dimsyl anionic solution(NaH in DMSO) and
bromodecane after protecting amino groups by phthalic anhydride.
The dibenzo-18-crown-6-ether, on the other hand, was converted into
its carbonyl derivatives via Duff reaction prior to incorporate into
chitosan by Schiff base formation. Thus formed diformylated
dibenzo-18-crown-6-ether was condensed with lipophilic chitosan to
prepare the novel solvent extraction reagent. The products were
characterized mainly by IR and 1H-NMR. Hence, the multidentate
crown ether-embedded polyfunctional bio-material was tested for
extraction of Pd(II) and Pt(IV) in aqueous solution.
Abstract: Radiolabeled cyclic RGD peptides targeting integrin αvβ3 are reported as promising agents for the early diagnosis of metastatic tumors. With an aim to improve tumor uptake and retention of the peptide, cyclic RGD peptide dimer E[c (RGDfK)] 2 (E = Glutamic acid, f = phenyl alanine, K = lysine) coupled to the bifunctional chelator DOTA was custom synthesized and radiolabelled with 68Ga. Radiolabelling of cyclic RGD peptide dimer with 68Ga was carried out using HEPES buffer and biological evaluation of the complex was done in nude mice bearing HT29 tumors.
Abstract: Dredging activities inevitably cause sediment
dispersion. In certain locations, where there are important ecological
areas such as mangroves or coral reefs, carefully planning the
dredging can significantly reduce negative impacts. This article
utilizes the dredging at Phuket port, Thailand, as a case study to
demonstrate how computer simulations can be helpful to protect
existing coral reefs. A software package named MIKE21 was
applied. Necessary information required by the simulations was
gathered. After calibrating and verifying the model, various dredging
scenario were simulated to predict spoil movement. The simulation
results were used as guidance to setting up an environmental
measure. Finally, the recommendation to dredge during flood tide
with silt curtains installed was made.
Abstract: 16-Mercaptohexadecanoic acid (MHDA) and tripeptide glutathione conjugated with gold nanoparticles (Au-NPs) are characterized by Fourier Transform InfaRared (FTIR) spectroscopy combined with Surface-enhanced Raman scattering (SERS) spectroscopy. Surface Plasmon Resonance (SPR) technique based on FTIR spectroscopy has become an important tool in biophysics, which is perspective for the study of organic compounds. FTIR-spectra of MHDA shows the line at 2500 cm-1 attributed to thiol group which is modified by presence of Au-NPs, suggesting the formation of bond between thiol group and gold. We also can observe the peaks originate from characteristic chemical group. A Raman spectrum of the same sample is also promising. Our preliminary experiments confirm that SERS-effect takes place for MHDA connected with Au-NPs and enable us to detected small number (less than 106 cm-2) of MHDA molecules. Combination of spectroscopy methods: FTIR and SERS – enable to study optical properties of Au- NPs and immobilized bio-molecules in context of a bio-nano-sensors.
Abstract: The phylogenetic analysis using the most conservative
portions of 18S rRNA gene revealed the phylogenetic relationship
among the two populations where DNA divergence showed that the
nucleotides diversity value were -0.00838 for the Tanjung Dawai,
Kedah and -0.00708 for the Cherating, Pahang populations
respectively. The net nucleotide divergence among populations (Da)
was -0.0073 indicating a low polymorphism among the populations
studied. Total number of mutations in the Tanjung Dawai, Kedah
samples was higher than Cherating, Pahang samples, which are 73 and
59 respectively while shared mutations across the populations were 8,
and reveal the evolutionary in the genome of Malaysian T. gigas. The
tree topology of both populations inferred using Neigbour-joining
method by comparing 1791 bp of partial 18S rRNA sequence revealed
that T. gigas haplotypes were clustered into seven clades, suggesting
that they are genetically diverse among populations which derived
from a common ancestor.
Abstract: Dilated cardiomyopathy (DCM) is a severe
cardiovascular disorder characterized by progressive systolic
dysfunction due to cardiac chamber dilatation and inefficient
myocardial contractility often leading to chronic heart failure.
Recently, a genome-wide association studies (GWASs) on DCM
indicate that the ZBTB17 gene rs10927875 single nucleotide
polymorphism is associated with DCM. The aim of the study was to
identify the distribution of ZBTB17 gene rs10927875 polymorphism
in 50 Slovak patients with DCM and 80 healthy control subjects
using the Custom Taqman®SNP Genotyping assays. Risk factors
detected at baseline in each group included age, sex, body mass
index, smoking status, diabetes and blood pressure. The mean age of
patients with DCM was 52.9±6.3 years; the mean age of individuals
in control group was 50.3±8.9 years. The distribution of investigated
genotypes of rs10927875 polymorphism within ZBTB17 gene in the
cohort of Slovak patients with DCM was as follows: CC (38.8%), CT
(55.1%), TT (6.1%), in controls: CC (43.8%), CT (51.2%), TT
(5.0%). The risk allele T was more common among the patients with
dilated cardiomyopathy than in normal controls (33.7% versus
30.6%). The differences in genotype or allele frequencies of ZBTB17
gene rs10927875 polymorphism were not statistically significant
(p=0.6908; p=0.6098). The results of this study suggest that ZBTB17
gene rs10927875 polymorphism may be a risk factor for
susceptibility to DCM in Slovak patients with DCM. Studies of
numerous files and additional functional investigations are needed to
fully understand the roles of genetic associations.
Abstract: SeqWord Gene Island Sniffer, a new program for
the identification of mobile genetic elements in sequences of bacterial chromosomes is presented. This program is based on the
analysis of oligonucleotide usage variations in DNA sequences. 3,518 mobile genetic elements were identified in 637 bacterial
genomes and further analyzed by sequence similarity and the
functionality of encoded proteins. The results of this study are stored in an open database http://anjie.bi.up.ac.za/geidb/geidbhome.
php). The developed computer program and the database provide the information valuable for further investigation of the
distribution of mobile genetic elements and virulence factors among bacteria. The program is available for download at www.bi.up.ac.za/SeqWord/sniffer/index.html.
Abstract: A nucleotide sequence can be expressed as a numerical sequence when each nucleotide is assigned its proton number. A resulting gene numerical sequence can be investigated for its fractal dimension in terms of evolution and chemical properties for comparative studies. We have investigated such nucleotide fluctuation in the 16S rRNA gene of archaea thermophiles. The studied archaea thermophiles were archaeoglobus fulgidus, methanothermobacter thermautotrophicus, methanocaldococcus jannaschii, pyrococcus horikoshii, and thermoplasma acidophilum. The studied five archaea-euryarchaeota thermophiles have fractal dimension values ranging from 1.93 to 1.97. Computer simulation shows that random sequences would have an average of about 2 with a standard deviation about 0.015. The fractal dimension was found to correlate (negative correlation) with the thermophile-s optimal growth temperature with R2 value of 0.90 (N =5). The inclusion of two aracheae-crenarchaeota thermophiles reduces the R2 value to 0.66 (N = 7). Further inclusion of two bacterial thermophiles reduces the R2 value to 0.50 (N =9). The fractal dimension is correlated (positive) to the sequence GC content with an R2 value of 0.89 for the five archaea-euryarchaeota thermophiles (and 0.74 for the entire set of N = 9), although computer simulation shows little correlation. The highest correlation (positive) was found to be between the fractal dimension and di-nucleotide Shannon entropy. However Shannon entropy and sequence GC content were observed to correlate with optimal growth temperature having an R2 of 0.8 (negative), and 0.88 (positive), respectively, for the entire set of 9 thermophiles; thus the correlation lacks species specificity. Together with another correlation study of bacterial radiation dosage with RecA repair gene sequence fractal dimension, it is postulated that fractal dimension analysis is a sensitive tool for studying the relationship between genotype and phenotype among closely related sequences.
Abstract: Tandem mass spectrometry (MS/MS) is the engine
driving high-throughput protein identification. Protein mixtures possibly
representing thousands of proteins from multiple species are
treated with proteolytic enzymes, cutting the proteins into smaller
peptides that are then analyzed generating MS/MS spectra. The
task of determining the identity of the peptide from its spectrum
is currently the weak point in the process. Current approaches to de
novo sequencing are able to compute candidate peptides efficiently.
The problem lies in the limitations of current scoring functions. In this
paper we introduce the concept of proteome signature. By examining
proteins and compiling proteome signatures (amino acid usage) it is
possible to characterize likely combinations of amino acids and better
distinguish between candidate peptides. Our results strongly support
the hypothesis that a scoring function that considers amino acid usage
patterns is better able to distinguish between candidate peptides. This
in turn leads to higher accuracy in peptide prediction.
Abstract: The capturing of gel electrophoresis image represents
the output of a DNA computing algorithm. Before this image is being
captured, DNA computing involves parallel overlap assembly (POA)
and polymerase chain reaction (PCR) that is the main of this
computing algorithm. However, the design of the DNA
oligonucleotides to represent a problem is quite complicated and is
prone to errors. In order to reduce these errors during the design stage
before the actual in-vitro experiment is carried out; a simulation
software capable of simulating the POA and PCR processes is
developed. This simulation software capability is unlimited where
problem of any size and complexity can be simulated, thus saving
cost due to possible errors during the design process. Information
regarding the DNA sequence during the computing process as well as
the computing output can be extracted at the same time using the
simulation software.
Abstract: Aurein 1.2 is a 13-residue amphipathic peptide with antibacterial and anticancer activity. Aurein1.2 and its retro analog were synthesized to study the activity of the peptides in relation to their structure. The antibacterial test result showed the retro-analog is inactive. The secondary structural analysis by CD spectra indicated that both of the peptides at TFE/Water adopt alpha-helical conformation. MD simulation was performed on aurein 1.2 and retro-analog in water and TFE in order to analyse the factors that are involved in the activity difference between retro and the native peptide. The simulation results are discussed and validated in the light of experimental data from the CD experiment. Both of the peptides showed a relatively similar pattern for their hydrophobicity, hydrophilicity, solvent accessible surfaces, and solvent accessible hydrophobic surfaces. However, they showed different in directions of dipole moment of peptides. Also, Our results further indicate that the reversion of the amino acid sequence affects flexibility .The data also showed that factors causing structural rigidity may decrease the activity. Consequently, our finding suggests that in the case of sequence-reversed peptide strategy, one has to pay attention to the role of amino acid sequence order in making flexibility and role of dipole moment direction in peptide activity. KeywordsAntimicrobial peptides, retro, molecular dynamic, circular dichroism.
Abstract: Transcription factor p53 has a powerful tumor
suppressing function that is associated with many cancers. However,
p53 of the molecular weight was higher make the limitation across to
skin or cell membrane. Thymidine dinucleotide (pTT), an
oligonucleotide, can activate the p53 transcription factor. pTT is a
hydrophilic and negative charge oligonucleotide, which delivery in to
cell membrane need an appropriate carrier. The aim of this study was
to improve the bioavailability of the nucleotide fragment, thymidine
dinucleotide (pTT), using elasic liposome carriers to deliver the drug
into the skin. The study demonstrate that dioleoylphosphocholine
(DOPC) incorporated with sodium cholate at molar ratio 1:1 can
archived the particle size about 220 nm. This elastic liposome could
penetration through skin from stratum corneum to whole epidermis by
confocal laser scanning microscopy (CLSM). Moreover, we observed
the the slight increase in generation of p53 by western blot.
Abstract: Gene, principal unit of inheritance, is an ordered
sequence of nucleotides. The genes of eukaryotic organisms include
alternating segments of exons and introns. The region of
Deoxyribonucleic acid (DNA) within a gene containing instructions
for coding a protein is called exon. On the other hand, non-coding
regions called introns are another part of DNA that regulates gene
expression by removing from the messenger Ribonucleic acid (RNA)
in a splicing process. This paper proposes to determine splice
junctions that are exon-intron boundaries by analyzing DNA
sequences. A splice junction can be either exon-intron (EI) or intron
exon (IE). Because of the popularity and compatibility of the
artificial neural network (ANN) in genetic fields; various ANN
models are applied in this research. Multi-layer Perceptron (MLP),
Radial Basis Function (RBF) and Generalized Regression Neural
Networks (GRNN) are used to analyze and detect the splice junctions
of gene sequences. 10-fold cross validation is used to demonstrate
the accuracy of networks. The real performances of these networks
are found by applying Receiver Operating Characteristic (ROC)
analysis.
Abstract: The multidelays linear control systems described by
difference differential equations are often studied in modern control
theory. In this paper, the delay-independent stabilization algebraic
criteria and the theorem of delay-independent stabilization for linear
systems with multiple time-delays are established by using the
Lyapunov functional and the Riccati algebra matrix equation in the
matrix theory. An illustrative example and the simulation result, show
that the approach to linear systems with multiple time-delays is
effective.
Abstract: Life is beautiful. But, it is decided by genes, environment and the individual and shattered by the natural and / or the invited problems. Most of the global rural helpless masses are struggling for their survival since; they are neglected in all aspects of life including health. Amidst a countless number of miserable diseases in man, diabetes is becoming a dreaded killer and ramifying the entire globe in a jet speed. Diabetes control continues as a Herculean task to the scientific community and the modern society in the 21st century also. T2DM is not pertaining to any age and it can develop even during the childhood. This multifactorial disease abruptly changes the activities of certain vital biomarkers in the present rural T2DM cases. A remarkable variation in the levels of biomarkers like AST, ALT, GGT, ALP, LDH, HbA1C, C- peptide, fasting sugar, post-prandial sugar, sodium, potassium, BUN, creatinine and insulin show the rampant nature of T2DM in this physically active rural agrarian community.
Abstract: This study has investigated the antidiabetic and
antioxidant potential of Pseudovaria macrophylla bark extract on
streptozotocin–nicotinamide induced type 2 diabetic rats. LCMSQTOF
and NMR experiments were done to determine the chemical
composition in the methanolic bark extract. For in vivo experiments,
the STZ (60 mg/kg/b.w, 15 min after 120 mg/kg/1 nicotinamide, i.p.)
induced diabetic rats were treated with methanolic extract of
Pseuduvaria macrophylla (200 and 400 mg/kg·bw) and
glibenclamide (2.5 mg/kg) as positive control respectively.
Biochemical parameters were assayed in the blood samples of all
groups of rats. The pro-inflammatory cytokines, antioxidant status
and plasma transforming growth factor βeta-1 (TGF-β1) were
evaluated. The histological study of the pancreas was examined and
its expression level of insulin was observed by
immunohistochemistry. In addition, the expression of glucose
transporters (GLUT 1, 2 and 4) were assessed in pancreas tissue by
western blot analysis. The outcomes of the study displayed that the
bark methanol extract of Pseuduvaria macrophylla has potentially
normalized the elevated blood glucose levels and improved serum
insulin and C-peptide levels with significant increase in the
antioxidant enzyme, reduced glutathione (GSH) and decrease in the
level of lipid peroxidation (LPO). Additionally, the extract has
markedly decreased the levels of serum pro-inflammatory cytokines
and transforming growth factor beta-1 (TGF-β1). Histopathology
analysis demonstrated that Pseuduvaria macrophylla has the
potential to protect the pancreas of diabetic rats against peroxidation
damage by downregulating oxidative stress and elevated
hyperglycaemia. Furthermore, the expression of insulin protein,
GLUT-1, GLUT-2 and GLUT-4 in pancreatic cells was enhanced.
The findings of this study support the anti-diabetic claims of
Pseudovaria macrophylla bark.
Abstract: The mathematical modeling of storm surge in sea and
coastal regions such as the South China Sea (SCS) and the Gulf of
Thailand (GoT) are important to study the typhoon characteristics.
The storm surge causes an inundation at a lateral boundary exhibiting
in the coastal zones particularly in the GoT and some part of the SCS.
The model simulations in the three dimensional primitive equations
with a high resolution model are important to protect local properties
and human life from the typhoon surges. In the present study, the
mathematical modeling is used to simulate the typhoon–induced
surges in three case studies of Typhoon Linda 1997. The results
of model simulations at the tide gauge stations can describe the
characteristics of storm surges at the coastal zones.
Abstract: The White Kwao (Pueraria mirifica), a potent phytoestrogenic medicinal plant, has long been use in Thailand as a traditional folkmedicine. However, no scientific information of the direct effect of White Kwao on the development of mammalian embryo was available. Therefore, the purpose of this study was to investigate the effect of White Kwao extract on the in vitro development and implantation rate of mouse embryos. This study was designed into two experiments. In the first experiment, the two-cell stage mouse embryos were collected from the oviduct of superovulated mature female mice, and randomly cultured in three different media, the M16, M16 supplemented with 0.52μg esthinylestradiol-17β, and M16 supplemented with 10 mg/ml White Kwao extract. The culture was incubated in CO2 incubator at 37 oC . After the embryos were cultivated, the developments of embryos were observed every 24 hours for 5 days. The development rate of embryos from the two-cell stage to blastocyst stage in the media was with White Kwao was significantly higher (p
Abstract: This study aims to demonstrate the quantification of
peptides based on isotope dilution surface enhanced Raman
scattering (IDSERS). SERS spectra of phenylalanine (Phe), leucine
(Leu) and two peptide sequences TGQIFK (T13) and
YSFLQNPQTSLCFSESIPTPSNR (T6) as part of the 22-kDa
human growth hormone (hGH) were obtained on Ag-nanoparticle
covered substrates. On the basis of the dominant Phe and Leu
vibrational modes, precise partial least squares (PLS) prediction
models were built enabling the determination of unknown T13 and
T6 concentrations. Detection of hGH in its physiological
concentration in order to investigate the possibility of protein
quantification has been achieved.
Abstract: β-Glucosidase is an important enzyme for production
of ethanol from lignocellulose. With hydrolytic activity on
cellooligosaccharides, especially cellobiose, β-glucosidase removes
product inhibitory effect on cellulases and forms fermentable sugars.
In this study, β-glucosidase encoding gene (BGL1) from traditional
starter yeast Saccharomycosis fibuligera BMQ908 was cloned and
expressed in Pichia pastoris. BGL1 of S. fibuligera BMQ 908 shared
98% nucleotide homology with the closest GenBank sequence
(M22475) but identity in amino-acid sequences of catalytic domains.
Recombinant plasmid pPICZαA/BGL1 containing the sequence
encoding BGL1 mature protein and α-factor secretion signal was
constructed and transformed into methylotrophic yeast P. pastoris by
electroporation. The recombinant strain produced single extracellular
protein with molecular weight of 120 kDa and cellobiase activity of
60 IU/ml. The optimum pH of the recombinant β-glucosidase was 5.0
and the optimum temperature was 50°C.