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: 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.
Abstract: In recent years, there has been an increasing interest
toward the use of bovine genotyped embryos for commercial embryo
transfer programs. Biopsy of a few cells in morulla stage is essential
for preimplantation genetic diagnosis (PGD). Low amount of DNA
have limited performing the several molecular analyses within PGD
analyses. Whole genome amplification (WGA) promises to eliminate
this problem. We evaluated the possibility and performance of an
improved primer extension preamplification (I-PEP) method with a
range of starting bovine genomic DNA from 1-8 cells into the WGA
reaction. We optimized a short and simple I-PEP (ssI-PEP) procedure
(~3h). This optimized WGA method was assessed by 6 loci specific
polymerase chain reactions (PCRs), included restriction fragments
length polymorphism (RFLP). Optimized WGA procedure possesses
enough sensitivity for molecular genetic analyses through the few
input cells. This is a new era for generating characterized bovine
embryos in preimplantation stage.
Abstract: Before performing polymerase chain reactions (PCR), a feasible primer set is required. Many primer design methods have been proposed for design a feasible primer set. However, the majority of these methods require a relatively long time to obtain an optimal solution since large quantities of template DNA need to be analyzed. Furthermore, the designed primer sets usually do not provide a specific PCR product. In recent years, evolutionary computation has been applied to PCR primer design and yielded promising results. In this paper, a particle swarm optimization (PSO) algorithm is proposed to solve primer design problems associated with providing a specific product for PCR experiments. A test set of the gene CYP1A1, associated with a heightened lung cancer risk was analyzed and the comparison of accuracy and running time with the genetic algorithm (GA) and memetic algorithm (MA) was performed. A comparison of results indicated that the proposed PSO method for primer design finds optimal or near-optimal primer sets and effective PCR products in a relatively short time.
Abstract: As part of national epidemiological survey on bovine
viral diarrhea virus (BVDV), a total of 274 dejecta samples were
collected from 14 cattle farms in 8 areas of Xinjiang Uygur
Autonomous Region in northwestern China. Total RNA was extracted
from each sample, and 5--untranslated region (UTR) of BVDV
genome was amplified by using two-step reverse
transcriptase-polymerase chain reaction (RT-PCR). The PCR products
were subsequently sequenced to study the genetic variations of BVDV
in these areas. Among the 274 samples, 33 samples were found
virus-positive. According to sequence analysis of the PCR products,
the 33 samples could be arranged into 16 groups. All the sequences,
however, were highly conserved with BVDV Osloss strains. The virus
possessed theses sequences belonged to BVDV-1b subtype by
phylogenetic analysis. Based on these data, we established a typing
tree for BVDV in these areas. Our results suggested that BVDV-1b
was a predominant subgenotype in northwestern China and no
correlation between the genetic and geographical distances could be
observed above the farm level.
Abstract: Many high-risk pathogens that cause disease in
humans are transmitted through various food items. Food-borne
disease constitutes a major public health problem. Assessment of the
quality and safety of foods is important in human health. Rapid and
easy detection of pathogenic organisms will facilitate precautionary
measures to maintain healthy food. The Polymerase Chain Reaction
(PCR) is a handy tool for rapid detection of low numbers of bacteria.
We have designed gene specific primers for most common food
borne pathogens such as Staphylococci, Salmonella and E.coli.
Bacteria were isolated from food samples of various food outlets and
identified using gene specific PCRs. We identified Staphylococci,
Salmonella and E.coli O157 using gene specific primers by rapid and
direct PCR technique in various food samples. This study helps us in
getting a complete picture of the various pathogens that threaten to
cause and spread food borne diseases and it would also enable
establishment of a routine procedure and methodology for rapid
identification of food borne bacteria using the rapid technique of
direct PCR. This study will also enable us to judge the efficiency of
present food safety steps taken by food manufacturers and exporters.