Abstract: The Principal component regression (PCR) is a
combination of principal component analysis (PCA) and multiple linear regression (MLR). The objective of this paper is to revise the
use of PCR in shortwave near infrared (SWNIR) (750-1000nm) spectral analysis. The idea of PCR was explained mathematically and
implemented in the non-destructive assessment of the soluble solid
content (SSC) of pineapple based on SWNIR spectral data. PCR achieved satisfactory results in this application with root mean
squared error of calibration (RMSEC) of 0.7611 Brix°, coefficient of determination (R2) of 0.5865 and root mean squared error of crossvalidation
(RMSECV) of 0.8323 Brix° with principal components
(PCs) of 14.
Abstract: The Egyptian Bacillus thuringiensis isolate (M5) produce crystal proteins that is toxic against insects was irradiated with UV light to induce mutants. Upon testing 10 of the resulting mutants for their toxicity against cotton leafworm larvae, the three mutants 62, 64 and 85 proved to be the most toxic ones. Upon testing these mutants along with their parental isolate by SDS-PAGE analysis of spores-crystals proteins as well as vegetative cells proteins, new induced bands appeared in the three mutants by UV radiation and also they showed disappearance of some other bands as compared with the wild type isolate. Multiplex PCR technique, with five sets of specific primers, was used to detect the three types of cryI genes cryIAa, cryIAb and cryIAc. Results showed that these three genes exist, as distinctive bands, in the wild type isolate (M5) as well as in mutants 62 and 85, while the mutant 64 had two distinctive bands of cryIAb and cryIAc genes, and a faint band of cryI Aa gene. Finally, these results revealed that mutant 62 is considered as the promising mutant since it is UV resistant, highly toxic against Spodoptera littoralis and active against a wide range of Lepidopteran insects.
Abstract: Atherosclerosis was identified as a chronic inflammatory process resulting from interactions between plasma lipoproteins, cellular components (monocyte, macrophages, T lymphocytes, endothelial cells and smooth muscle cells) and the extracellular matrix of the arterial wall. Several types of genes were known to express during formation of atherosclerosis. This study is carried out to identify unknown differentially expressed gene (DEG) in atherogenesis. Rabbit’s aorta tissues were stained by H&E for histomorphology. GeneFishing™ PCR analysis was performed from total RNA extracted from the aorta tissues. The DNA fragment from DEG was cloned, sequenced and validated by Real-time PCR. Histomorphology showed intimal thickening in the aorta. DEG detected from ACP-41 was identified as cathepsin B gene and showed upregulation at week-8 and week-12 of atherogenesis. Therefore, ACP-based GeneFishing™ PCR facilitated identification of cathepsin B gene which was differentially expressed during development of atherosclerosis.
Abstract: This study describes a micro device integrated with
multi-chamber for polymerase chain reaction (PCR) with different
annealing temperatures. The device consists of the reaction
polydimethylsiloxane (PDMS) chip, a cover glass chip, and is
equipped with cartridge heaters, fans, and thermocouples for
temperature control. In this prototype, commercial software is utilized
to determine the geometric and operational parameters those are
responsible for creating the denaturation, annealing, and extension
temperatures within the chip. Two cartridge heaters are placed at two
sides of the chip and maintained at two different temperatures to
achieve a thermal gradient on the chip during the annealing step. The
temperatures on the chip surface are measured via an infrared imager.
Some thermocouples inserted into the reaction chambers are used to
obtain the transient temperature profiles of the reaction chambers
during several thermal cycles. The experimental temperatures
compared to the simulated results show a similar trend. This work
should be interesting to persons involved in the high-temperature
based reactions and genomics or cell analysis.
Abstract: Simultaneous determination of multicomponents of phenol, resorcinol and catechol with a chemometric technique a PCranking artificial neural network (PCranking-ANN) algorithm is reported in this study. Based on the data correlation coefficient method, 3 representative PCs are selected from the scores of original UV spectral data (35 PCs) as the original input patterns for ANN to build a neural network model. The results obtained by iterating 8000 .The RMSEP for phenol, resorcinol and catechol with PCranking- ANN were 0.6680, 0.0766 and 0.1033, respectively. Calibration matrices were 0.50-21.0, 0.50-15.1 and 0.50-20.0 μg ml-1 for phenol, resorcinol and catechol, respectively. The proposed method was successfully applied for the determination of phenol, resorcinol and catechol in synthetic and water samples.
Abstract: Processing tabah bamboo shoot as fermented pickle is
one of the way to increase the shelf life of this bamboo shoot. The
advantage of this shoot is low concentration of hydro cyanic acid
(HCN) make it potential for functional food product. This study
aimed to determine the characteristic of tabah bamboo shoot pickle
such as total of lactic acid bacteria (LAB), pH, total acidity, and
hydro cyanic acid (HCN) content, and also find the LAB’s type
involved during fermentation, and organic acids’ profiles. The pickle
was made by natural fermentation with 6% salt concentration and
fermentation conducted for 13 days.
The result showed during the fermentation time, in the 4th day
LAB’s number was highest as much as 72 x 107 CFU/ml and the
lowest pH was 3.09. We also found decreasing in HCN from 37.8
ppm at the beginning to 20.52 ppm at the end of fermentation
process. The organic acids detected during the fermentation were
lactic acid with the highest concentration was 0.0546 g/100 g and
small amount of acetic acid. By using PCR method, the 18 of LABs
which had rod shape were detected as member of Lactobacillus spp.,
in which 17 strains detected as L. plantarum.
Abstract: The effects of irrigation with dairy factory wastewater
on soil properties were investigated at two sites that had received
irrigation for > 60 years. Two adjoining paired sites that had never
received DFE were also sampled as well as another seven fields from
a wider area around the factory. In comparison with paired sites that
had not received effluent, long-term wastewater irrigation resulted in
an increase in pH, EC, extractable P, exchangeable Na and K and
ESP. These changes were related to the use of phosphoric acid,
NaOH and KOH as cleaning agents in the factory. Soil organic C
content was unaffected by DFE irrigation but the size (microbial
biomass C and N) and activity (basal respiration) of the soil
microbial community were increased. These increases were
attributed to regular inputs of soluble C (e.g. lactose) present as milk
residues in the wastewater. Principal component analysis (PCA) of
the soils data from all 11sites confirmed that the main effects of DFE
irrigation were an increase in exchangeable Na, extractable P and
microbial biomass C, an accumulation of soluble salts and a liming
effect. PCA analysis of soil bacterial community structure, using
PCR-DGGE of 16S rDNA fragments, generally separated individual
sites from one another but did not group them according to irrigation
history. Thus, whilst the size and activity of the soil microbial
community were increased, the structure and diversity of the
bacterial community remained unaffected.
Abstract: Since polymerase chain reaction (PCR) has been
invented, it has emerged as a powerful tool in genetic analysis. The
PCR products are closely linked with thermal cycles. Therefore, to
reduce the reaction time and make temperature distribution uniform in
the reaction chamber, a novel oscillatory thermal cycler is designed.
The sample is placed in a fixed chamber, and three constant isothermal
zones are established and lined in the system. The sample is oscillated
and contacted with three different isothermal zones to complete
thermal cycles. This study presents the design of the geometric
characteristics of the chamber. The commercial software
CFD-ACE+TM is utilized to investigate the influences of various
materials, heating times, chamber volumes, and moving speed of the
chamber on the temperature distributions inside the chamber. The
chamber moves at a specific velocity and the boundary conditions
with time variations are related to the moving speed. Whereas the
chamber moves, the boundary is specified at the conditions of the
convection or the uniform temperature. The user subroutines compiled
by the FORTRAN language are used to make the numerical results
realistically. Results show that the reaction chamber with a rectangular
prism is heated on six faces; the effects of various moving speeds of
the chamber on the temperature distributions are examined. Regarding
to the temperature profiles and the standard deviation of the
temperature at the Y-cut cross section, the non-uniform temperature
inside chamber is found as the moving speed is larger than 0.01 m/s.
By reducing the heating faces to four, the standard deviation of the
temperature of the reaction chamber is under 1.4×10-3K with the range
of velocities between 0.0001 m/s and 1 m/s. The nature convective
boundary conditions are set at all boundaries while the chamber moves
between two heaters, the effects of various moving velocities of the
chamber on the temperature distributions are negligible at the assigned
time duration.
Abstract: A new target detection technique is presented in this
paper for the identification of small boats in coastal surveillance. The
proposed technique employs an adaptive progressive thresholding (APT) scheme to first process the given input scene to separate any
objects present in the scene from the background. The preprocessing
step results in an image having only the foreground objects, such as
boats, trees and other cluttered regions, and hence reduces the search
region for the correlation step significantly. The processed image is then fed to the shifted phase-encoded fringe-adjusted joint transform
correlator (SPFJTC) technique which produces single and delta-like
correlation peak for a potential target present in the input scene. A
post-processing step involves using a peak-to-clutter ratio (PCR) to determine whether the boat in the input scene is authorized or unauthorized. Simulation results are presented to show that the
proposed technique can successfully determine the presence of an authorized boat and identify any intruding boat present in the given input scene.
Abstract: Oxidative stress is considered to be the cause for onset
and the progression of type 2 diabetes mellitus (T2DM) and
complications including neuropathy. It is a deleterious process that
can be an important mediator of damage to cell structures: protein,
lipids and DNA. Data suggest that in patients with diabetes and
diabetic neuropathy DNA repair is impaired, which prevents effective
removal of lesions. Objective: The aim of our study was to evaluate
the association of the hOGG1 (326 Ser/Cys) and XRCC1 (194
Arg/Trp, 399 Arg/Gln) gene polymorphisms whose protein is
involved in the BER pathway with DNA repair efficiency in patients
with diabetes type 2 and diabetic neuropathy compared to the healthy
subjects. Genotypes were determined by PCR-RFLP analysis in 385
subjects, including 117 with type 2 diabetes, 56 with diabetic
neuropathy and 212 with normal glucose metabolism. The
polymorphisms studied include codon 326 of hOGG1 and 194, 399
of XRCC1 in the base excision repair (BER) genes. Comet assay was
carried out using peripheral blood lymphocytes from the patients and
controls. This test enabled the evaluation of DNA damage in cells
exposed to hydrogen peroxide alone and in the combination with the
endonuclease III (Nth). The results of the analysis of polymorphism
were statistically examination by calculating the odds ratio (OR) and
their 95% confidence intervals (95% CI) using the ¤ç2-tests. Our data
indicate that patients with diabetes mellitus type 2 (including those
with neuropathy) had higher frequencies of the XRCC1 399Arg/Gln
polymorphism in homozygote (GG) (OR: 1.85 [95% CI: 1.07-3.22],
P=0.3) and also increased frequency of 399Gln (G) allele (OR: 1.38
[95% CI: 1.03-1.83], P=0.3). No relation to other polymorphisms
with increased risk of diabetes or diabetic neuropathy. In T2DM
patients complicated by neuropathy, there was less efficient repair of
oxidative DNA damage induced by hydrogen peroxide in both the
presence and absence of the Nth enzyme. The results of our study
suggest that the XRCC1 399 Arg/Gln polymorphism is a significant
risk factor of T2DM in Polish population. Obtained data suggest a
decreased efficiency of DNA repair in cells from patients with
diabetes and neuropathy may be associated with oxidative stress.
Additionally, patients with neuropathy are characterized by even
greater sensitivity to oxidative damage than patients with diabetes,
which suggests participation of free radicals in the pathogenesis of
neuropathy.
Abstract: The main aim is to perform mutational analysis of CTLA4 gene Exon 1 in SLE patients. A total of 61 SLE patients fulfilling “American College of Rheumatology (ACR) criteria" and 61 controls were enrolled in this study. The region of CTLA4 gene exon 1 was amplified by using Step-down PCR technique. Extracted DNA of band 354 bp was sequenced to analyze mutations in the exon-1 of CTLA-4 gene. Further, protein sequences were identified from nucleotide sequences of CTLA4 Exon 1 by using Expasy software and through Blast P software it was found that CTLA4 protein sequences of Pakistani SLE patients were similar to that of Chinese SLE population. No variations were found after patients sequences were compared with that of the control sequence. Furthermore it was found that CTLA4 protein sequences of Pakistani SLE patients were similar to that of Chinese SLE population. Thus CTLA4 gene may not be responsible for an autoimmune disease SLE.
Abstract: Bean common mosaic necrosis virus (BCMNV) is a
potyvirus with a worldwide distribution. This virus causes serious
economic losses in Iran in many leguminoses. During 20008,
samples were collected from soybeans fields in Tehran Province.
Four isolates (S1, S2 and S3) were inoculated on 15 species of
Cucurbitaceae, Chenopodiaceae, Solanacae and Leguminosae.
Chenopodium quinoa and C. amaranticolor.
Did not developed any symptoms.all isolates caused mosaic
symptoms on Phaseolus vulgaris cv. Red Kidney and P. vulgaris cv.
Bountiful. The molecular weights of coat protein using SDS-PAGE
and western blotting were estimated at 33 kDa. Reverse transcription
polymerase chain reaction (RT-PCR) was performed using one
primer pairs designed by L. XU et al. An approximately 920 bp
fragment was amplified with a specific primer.
Abstract: Atrazine, a herbicide widely used in sugarcane and corn production, is a frequently detected groundwater contaminant. An atrazine-degrading bacterium, strain KB02, was obtained from long-term atrazine-treated sugarcane field soils in Kanchanaburi province of Thailand. Strain KB02 had a rod-to-coccus morphological cycle during growth. Sequence analysis of the PCR product indicated that the 16S rRNA gene in strain KB02 was ranging from 97-98% identical to the same region in Klebsiella sp. Based on biochemical, physiological analysis and 16S rDNA sequence analysis of one representative isolate, strain KB02, the isolates belong to the genus Klebsiella in the family Enterobacteriaceae. Interestingly that the various primers for atzA, B and C failed to amplify genomic DNA of strain KB02. Whereas the expected PCR product of atzA, B and C were obtained from the reference strain, Arthrobacter sp. strain KU001.
Abstract: Expression and secretion of inflammation markers are
disturbed in obesity. Interleukin-6 reduces body fat mass. The
common G-174C polymorphism in the promoter of IL-6 gene has
been reported that effects on transcriptional regulation. The objective
was to investigate association of the common polymorphism G-174C
with obesity in Iranian population. The present study is cross
sectional association study that included 242 individuals (110 men
and 132 women). Serum IL-6 levels, C-reactive protein, fasting
blood glucose and blood lipids profile were measured .BMI and
WHR were calculated. Genotyping is carried out by PCR and RFLP.
The frequencies of G and C allele were 64.5% and 35.5%,
respectively. The G-174C polymorphism was not associated with
BMI and WHR. However in obese individual, fasting blood glucose
was significantly higher in carrier of C allele compared with the noncarrier.
The IL-6 G-174C polymorphism is not a risk factor for
obesity in Iranian population.
Abstract: Legionella pneumophila is involved in more than 95%
cases of severe atypical pneumonia. Infection is mainly by
inhalation the indoor aerosols through the water-coolant systems.
Because some Legionella strains may be viable but not culturable,
therefore, Taq polymerase, DNA amplification and semi-nested-PCR
were carried out to detect Legionella-specific 16S-rDNA sequence.
For this purpose, 1.5 litter of water samples from 77 water-coolant
system were collected from four different hospitals, two nursing
homes and one student hostel in Kerman city of Iran, each in a brand
new plastic bottle during summer season of 2006 (from April to
August). The samples were filtered in the sterile condition through
the Millipore Membrane Filter. DNA was extracted from membrane
and used for PCR to detect Legionella spp. The PCR product was
then subjected to semi-nested PCR for detection of L. pneumophila.
Out of 77 water samples that were tested by PCR, 30 (39%) were
positive for most species of Legionella. However, L. pneumophila
was detected from 14 (18.2%) water samples by semi-nested PCR.
From the above results it can be concluded that water coolant
systems of different hospitals and nursing homes in Kerman city of
Iran are highly contaminated with L. pneumophila spp. and pose
serious concern. So, we recommend avoiding such type of coolant
system in the hospitals and nursing homes.
Abstract: Quantitative Structure-Activity Relationship (QSAR)
approach for discovering novel more active Calanone derivative as
anti-leukemia compound has been conducted. There are 6
experimental activities of Calanone compounds against leukemia cell
L1210 that are used as material of the research. Calculation of
theoretical predictors (independent variables) was performed by
AM1 semiempirical method. The QSAR equation is determined by
Principle Component Regression (PCR) analysis, with Log IC50 as
dependent variable and the independent variables are atomic net
charges, dipole moment (μ), and coefficient partition of noctanol/
water (Log P). Three novel Calanone derivatives that
obtained by this research have higher activity against leukemia cell
L1210 than pure Calanone.
Abstract: This study describes a capillary-based device
integrated with the heating and cooling modules for polymerase chain
reaction (PCR). The device consists of the reaction
polytetrafluoroethylene (PTFE) capillary, the aluminum blocks, and is
equipped with two cartridge heaters, a thermoelectric (TE) cooler, a
fan, and some thermocouples for temperature control. The cartridge
heaters are placed into the heating blocks and maintained at two
different temperatures to achieve the denaturation and the extension
step. Some thermocouples inserted into the capillary are used to obtain
the transient temperature profiles of the reaction sample during
thermal cycles. A 483-bp DNA template is amplified successfully in
the designed system and the traditional thermal cycler. This work
should be interesting to persons involved in the high-temperature
based reactions and genomics or cell analysis.
Abstract: Tasks of the work were study the possible E.coli
contamination in red deer meat, identify pathogenic strains from
isolated E.coli, determine their incidence in red deer meat and
determine the presence of VT1, VT2 and eaeA genes for the
pathogenic E.coli. 8 (10%) samples were randomly selected from 80
analysed isolates of E.coli and PCR reaction was performed on them.
PCR was done both on initial materials – samples of red deer meat -
and for already isolated liqueurs. Two of analysed venison samples
contain verotoxin-producing strains of E. coli. It means that this meat
is not safe to consumer. It was proven by the sequestration reaction of
E. coli and by comparison of the obtained results with the database of
microorganism genome available on the internet that the isolated
culture corresponds to region 16S rDNS of E. coli thus presenting
correctness of the microbiological methods.
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: Matrix metalloproteinase-3 (MMP3) is key member
of the MMP family, and is known to be present in coronary
atherosclerotic. Several studies have demonstrated that MMP-3
5A/6A polymorphism modify each transcriptional activity in allele
specific manner. We hypothesized that this polymorphism may play
a role as risk factor for development of coronary stenosis. The aim of
our study was to estimate MMP-3 (5A/6A) gene polymorphism on
interindividual variability in risk for coronary stenosis in an Iranian
population.DNA was extracted from white blood cells and genotypes
were obtained from coronary stenosis cases (n=95) and controls
(n=100) by PCR (polymerase chain reaction) and restriction
fragment length polymorphism techniques. Significant differences
between cases and controls were observed for MMP3 genotype
frequencies (X2=199.305, p< 0.001); the 6A allele was less
frequently seen in the control group, compared to the disease group
(85.79 vs. 78%, 6A/6A+5A/6A vs. 5A/5A, P≤0.001). These data
imply the involvement of -1612 5A/6A polymorphism in coronary
stenosis, and suggest that probably the 6A/6A MMP-3 genotype is a
genetic susceptibility factor for coronary stenosis.