Abstract: Polymerase chain reaction (PCR) assays targeting genomic DNA segments have been established for the detection of Helicobacter pylori in clinical specimens. However, the data on comparative evaluations of various targets in detection of H. pylori are limited. Furthermore, the frequencies of vacA (s1 and s2) and cagA genotypes, which are suggested to be involved in the pathogenesis of H. pylori in other parts of the world, are not well studied in Kuwait. The aim of this study was to evaluate PCR assays for the detection and genotyping of H. pylori by targeting the amplification of DNA targets from four genomic segments. The genomic DNA were isolated from 72 clinical isolates of H. pylori and tested in PCR with four pairs of oligonucleotides primers, i.e. ECH-U/ECH-L, ET-5U/ET-5L, CagAF/CagAR and Vac1F/Vac1XR, which were expected to amplify targets of various sizes (471 bp, 230 bp, 183 bp and 176/203 bp, respectively) from the genomic DNA of H. pylori. The PCR-amplified DNA were analyzed by agarose gel electrophoresis. PCR products of expected size were obtained with all primer pairs by using genomic DNA isolated from H. pylori. DNA dilution experiments showed that the most sensitive PCR target was 471 bp DNA amplified by the primers ECH-U/ECH-L, followed by the targets of Vac1F/Vac1XR (176 bp/203 DNA), CagAF/CagAR (183 bp DNA) and ET-5U/ET-5L (230 bp DNA). However, when tested with undiluted genomic DNA isolated from single colonies of all isolates, the Vac1F/Vac1XR target provided the maximum positive results (71/72 (99% positives)), followed by ECH-U/ECH-L (69/72 (93% positives)), ET-5U/ET-5L (51/72 (71% positives)) and CagAF/CagAR (26/72 (46% positives)). The results of genotyping experiments showed that vacA s1 (46% positive) and vacA s2 (54% positive) genotypes were almost equally associated with VaCA+/CagA- isolates (P > 0.05), but with VacA+/CagA+ isolates, S1 genotype (92% positive) was more frequently detected than S2 genotype (8% positive) (P< 0.0001). In conclusion, among the primer pairs tested, Vac1F/Vac1XR provided the best results for detection of H. pylori. The genotyping experiments showed that vacA s1 and vacA s2 genotypes were almost equally associated with vaCA+/cagA- isolates, but vacA s1 genotype had a significantly increased association with vacA+/cagA+ isolates.
Abstract: Fuel cell grade gas-diffusion layer carbon paper (CP) electrodes are subjected to electrophoresis in N,N’-dimethylformamide (DMF) consisting of reduced graphene oxide (rGO). The rGO modified electrodes are compared with CP in a single asymmetric all-vanadium redox battery system (employing a double serpentine flow channel for each half-cell). Peak power densities improved by 4% when the rGO deposits were facing the ion-exchange membrane (cell performance was poorer when the rGO was facing the flow field). Cycling of the cells showed least degradation of the CP electrodes that were coated with rGO in comparison to pristine samples.
Abstract: Migration of a core-shell soft particle under the
influence of an external electric field in an electrolyte solution is
studied numerically. The soft particle is coated with a positively
charged polyelectrolyte layer (PEL) and the rigid core is having
a uniform surface charge density. The Darcy-Brinkman extended
Navier-Stokes equations are solved for the motion of the ionized
fluid, the non-linear Nernst-Planck equations for the ion transport and
the Poisson equation for the electric potential. A pressure correction
based iterative algorithm is adopted for numerical computations. The
effects of convection on double layer polarization (DLP) and diffusion
dominated counter ions penetration are investigated for a wide range
of Debye layer thickness, PEL fixed surface charge density, and
permeability of the PEL. Our results show that when the Debye
layer is in order of the particle size, the DLP effect is significant
and produces a reduction in electrophoretic mobility. However, the
double layer polarization effect is negligible for a thin Debye layer
or low permeable cases. The point of zero mobility and the existence
of mobility reversal depending on the electrolyte concentration are
also presented.
Abstract: In this study, encapsulation of agarwood oil with non-ionic surfactant, Tween 80 was prepared at critical micelle concentration of 0.0167 % v/v to produce the most stable nano-emulsion in aqueous. The encapsulation has minimized the bioactive compounds degradation in various pH conditions thus prolong their shelf life and maintained its initial oil grade. The oil grading of the prepared samples were conducted using the gel electrophoresis instead of using common analytical industrial grading such as gas chromatography- mass spectrometry (GC- MS). The grading method was chosen due to their unique zeta potential value after the encapsulation process. This paper demonstrates the feasibility of applying the electrophoresis principles to separate the encapsulated agarwood oil or grading of the emulsified agarwood oil. The results indicated that the grading process are potential to be further investigate based on their droplet size and zeta potential value at various pH condition when the droplet were migrate through polyacrylamide gel.
Abstract: Although, arsenic trioxide has been the subject of
toxicological research, in vitro cytotoxicity and genotoxicity studies
using relevant cell models and uniform methodology are not well
elucidated. Hence, the aim of the present study was to evaluate the
cytotoxicity and genotoxicity induced by arsenic trioxide in human
keratinocytes (HaCaT) using the MTT [3-(4, 5-dimethylthiazol-2-yl)-
2,5-diphenyltetrazolium bromide] and alkaline single cell gel
electrophoresis (Comet) assays, respectively. Human keratinocytes
were treated with different doses of arsenic trioxide for 4 h prior to
cytogenetic assessment. Data obtained from the MTT assay indicated
that arsenic trioxide significantly reduced the viability of HaCaT cells
in a dose-dependent manner, showing an IC50 value of 34.18 ± 0.6
μM. Data generated from the comet assay also indicated a significant
dose-dependent increase in DNA damage in HaCaT cells associated
with arsenic trioxide exposure. We observed a significant increase in
comet tail length and tail moment, showing an evidence of arsenic
trioxide -induced genotoxic damage in HaCaT cells. This study
confirms that the comet assay is a sensitive and effective method to
detect DNA damage caused by arsenic.
Abstract: The extracellular proteins secreted by bacteria may be increased in stressful surroundings, such as in the presence of antibiotics. It appears that many antibiotics, when used at low concentrations, have in common the ability to activate or repress gene transcription, which is distinct from their inhibitory effect. There have been comparatively few studies on the potential of antibiotics as a specific chemical signal that can trigger a variety of biological functions. Therefore, this study was carried out to determine the effect of Streptomycin Sulfate in regulating extracellular proteins secreted by Bacillus subtilis ATCC21332. Results of Microdilution assay showed that the Minimum Inhibition Concentration (MIC) of Streptomycin Sulfate on B. subtilis ATCC21332 was 2.5 mg/ml. The bacteria cells were then exposed to Streptomycin Sulfate at concentration of 0.01 MIC before being further incubated for 48h to 72 h. The extracellular proteins secreted were then isolated and analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Proteins profile revealed that three additional bands with approximate sizes of 30 kDa, 22 kDa and 23 kDa were appeared for the treated bacteria with Streptomycin Sulfate. Thus, B. subtilis ATCC21332 in stressful condition with the presence of Streptomycin Sulfate at low concentration could induce the extracellular proteins secretion.
Abstract: Collagen was isolated from chicken feet by using papain and pepsin enzymes in acetic acid solution at 4°C for 24h with a yield of 18.16% and 22.94% by dry weight, respectively. Chemical composition and characteristics of chicken feet collagen such as amino acid composition, SDS-PAGE patterns, FTIR spectra and thermal properties were evaluated. The chicken feet collagen is rich in the amino acids glycine, glutamic acid, proline and hydroxyproline. Electrophoresis pattern demonstrated two distinct α-chains (α1 and α2) and β chain, indicating that type I collagen is a major component of chicken feet collagen. The thermal stability of collagen isolated by papain and pepsin revealed stable denaturation temperatures of 48.40 and 53.35°C, respectively. The FTIR spectra of both collagens were similar with amide regions in A, B, I, II and III. The study demonstrated that chicken feet collagen using papain isolation method is possible as commercial alternative ingredient.
Abstract: Deoxyribonucleic Acid or DNA computing has
emerged as an interdisciplinary field that draws together chemistry,
molecular biology, computer science and mathematics. Thus, in this
paper, the possibility of DNA-based computing to solve an absolute
1-center problem by molecular manipulations is presented. This is
truly the first attempt to solve such a problem by DNA-based
computing approach. Since, part of the procedures involve with
shortest path computation, research works on DNA computing for
shortest path Traveling Salesman Problem, in short, TSP are reviewed.
These approaches are studied and only the appropriate one is adapted
in designing the computation procedures. This DNA-based
computation is designed in such a way that every path is encoded by
oligonucleotides and the path-s length is directly proportional to the
length of oligonucleotides. Using these properties, gel electrophoresis
is performed in order to separate the respective DNA molecules
according to their length. One expectation arise from this paper is that
it is possible to verify the instance absolute 1-center problem using
DNA computing by laboratory experiments.
Abstract: Lighvan cheese is basically made from sheep milk in
the area of Sahand mountainside which is located in the North West
of Iran. The main objective of this study was to investigate the effect
of enterococci isolated from traditional Lighvan cheese on the quality
of Iranian UF white during ripening. The experimental design was
split plot based on randomized complete blocks, main plots were four
types of starters and subplots were different ripening durations.
Addition of Enterococcus spp. did not significantly (P
Abstract: Genome profiling (GP), a genotype based technology, which exploits random PCR and temperature gradient gel electrophoresis, has been successful in identification/classification of organisms. In this technology, spiddos (Species identification dots) and PaSS (Pattern similarity score) were employed for measuring the closeness (or distance) between genomes. Based on the closeness (PaSS), we can buildup phylogenetic trees of the organisms. We noticed that the topology of the tree is rather robust against the experimental fluctuation conveyed by spiddos. This fact was confirmed quantitatively in this study by computer-simulation, providing the limit of the reliability of this highly powerful methodology. As a result, we could demonstrate the effectiveness of the GP approach for identification/classification of organisms.
Abstract: Tumor cells have an invasive and metastatic phenotype
that is the main cause of death for cancer patients. Tumor
establishment and penetration consists of a series of complex
processes involving multiple changes in gene expression. In this study,
intraperitoneal administration of a high concentration of ascorbic acid
inhibited tumor establishment and decreased tumor mass in BALB/C
mice implanted with S-180 sarcoma cancer cells. To identify proteins
involved in the ascorbic acid-mediated inhibition of tumor
progression, changes in the tumor proteome associated with ascorbic
acid treatment of BALB/C mice implanted with S-180 were
investigated using two-dimensional gel electrophoresis and mass
spectrometry. Twenty protein spots were identified whose expression
was different between control and ascorbic acid treatment groups.
Abstract: We have studied the migration of a charged permeable aggregate in electrolyte under the influence of an axial electric field and pressure gradient. The migration of the positively charged aggregate leads to a deformation of the anionic cloud around it. The hydrodynamics of the aggregate is governed by the interaction of electroosmotic flow in and around the particle, hydrodynamic friction and electric force experienced by the aggregate. We have computed the non-linear Nernest-Planck equations coupled with the Dracy- Brinkman extended Navier-Stokes equations and Poisson equation for electric field through a finite volume method. The permeability of the aggregate enable the counterion penetration. The penetration of counterions depends on the volume charge density of the aggregate and ionic concentration of electrolytes at a fixed field strength. The retardation effect due to the double layer polarization increases the drag force compared to an uncharged aggregate. Increase in migration sped from the electrophretic velocity of the aggregate produces further asymmetry in charge cloud and reduces the electric body force exerted on the particle. The permeability of the particle have relatively little influence on the electric body force when Double layer is relatively thin. The impact of the key parameters of electrokinetics on the hydrodynamics of the aggregate is analyzed.
Abstract: Sickle cell anemia is a recessive genetic disease
caused by the presence in the red blood cell, of abnormal hemoglobin
called hemoglobin S. It results from the replacement in the beta chain
of the acid glutamic acid by valin at position 6. Topics may be
homozygous (SS) or heterozygous (AS) most often
asymptomatic. Other mutations result in compound heterozygous:
- Synthesis of hemoglobin C mutation in the sixth leucin codon
(heterozygous SC);
- ß-thalassemia (heterozygous S-ß thalassemia).
SS homozygous, heterozygous SC and S- ß -thalassemia are grouped
under the major sickle cell syndromes.
To make a laboratory diagnosis of hemoglobinopathies in a
portion of the population in region of Batna, our study was
conducted on 115 patients with suspected sickle cell anemia, all cases
have benefited from hematological tests as blood count (count RBC,
calculated erythrocyte indices, MCV and MCHC, measuring the
hemoglobin concentration) and a biochemical test in this case
electrophoresis CAPILLARYS HEMOGLOBIN (E).
The results showed:
27 cases of sickle cell anemia were found on 115 suspected cases,
73,03% homozygous sickle cell disease and 59,25% sickle cell trait.
Finally, the double heterozygous S/C, represent the incidence rate of
3, 70%.
Abstract: In order to characterize the soy protein hydrolysate obtained in this study, gel chromatography on Sephadex G-25 was used to perform the separation of the peptide mixture and electrophoresis in SDS-polyacrylamide gel has been employed. Protein hydrolysate gave high antioxidant activities, but didn't give any antimicrobial activities. The antioxidant activities of protein hydrolysate was in the same trend of peptide content which gave high antioxidant activities and high peptide content between fractions 15 to 50. With increasing peptide concentrations, the scavenging effect on DPPH radical increased until about 70%, thereafter reaching a plateau. In compare to different concentrations of BHA, which exhibited higher activity (90%), soybean protein hydrolysate exhibited high antioxidant activities (70%) at a concentration of 1.45 mg/ml at fraction 25. Electrophoresis analysis indicated that, low- MW hydrolysate fractions (F1) appeared, on average, to have higher DPPH scavenging activities than high-MW fractions. These results revealed that soybean peptides probably contain substances that were proton donors and could react with free radicals to convert them to stable diamagnetic molecules.
Abstract: The whole-cell protein-profiling technique was
evaluated for studying differences in banding pattern of three
different species of Cyanobacteria i.e. Anabaena fertilissima,
Aulosira fertilissima and Westiellopsis prolifica under the influence
of four different pesticides-2,4-D (Ethyl Ester of 2,4-Dichloro
Phenoxy Acetic Acid), Pencycuron (N-[(4-chlorophenyl)methyl]-Ncyclopentyl-
N'–phenylurea), Endosulfan (6,7,8,9,10,10hexachloro-
1,5,5a,6,9,9a-hexahydro-6,9-methano-2,4,3-benzodioxathiepine-3-
oxide) and Tebuconazole (1-(4-Chlorophenyl)-4,4-dimethyl-3-(1,2,4-
triazol-1-ylmethyl)pentan-3-ol). Whole-cell extracts were obtained by
sonication treatment (Sonifier cell disruptor -Branson Digital Sonifier
S-450D, USA) and were analyzed by sodium dodecyl sulfate
polyacrylamide gel electrophoresis (SDS-PAGE). SDS-PAGE
analyses of the total protein profile of Anabaena fertilissima,
Aulosira fertilissima and Westiellopsis prolifica showed a linear
decrease in the protein content with increasing pesticide stress when
administered to different concentrations of 2, 4-D, Pencycuron,
Endosulfan and Tebuconazole. The results indicate that different
stressors exert specific effects on cyanobacterial protein synthesis.
Abstract: Cry j 1 is a causative substance of Japanese cedar
pollinosis, and it may deteriorate by Cry j 1 invasion to a lower
respiratory tract. We observed airborne particles containing Cry j 1 by
an immunofluorescence technique using a fluorescence microscope,
and we clarified that Cry j 1 exist as aggregates of airborne fine
particles (< 1.1 μm) in the urban atmosphere. Airborne Cry j 1 may
react with air pollutants and be denature to a substance deteriorated
Japanese cedar pollinosis. Therefore, we applied a sodium dodecyl
sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to evaluate a
Cry j 1 reacted with various air pollutants by liquid phase reaction,
and calculated kinetics constants of Cry j 1 extracted from pollens
collected in various sites and airborne fine particles containing Cry j
1 by using a surface plasmon resonance (SPR) method. As a result, it
is suggested that Cry j 1 may be denatured by air pollutants during
the transportation to the urban atmosphere.
Abstract: Supplementation of palm vitamin E has been reported
to prevent loss of bone density in ovariectomised female rats. The
mechanism by which palm vitamin E exerts these effects is still
unknown. We hypothesized that palm vitamin E may act by
preventing the protein expression changes. Two dimensional poly
acyrilamide gel electrophoresis (2-D PAGE) and PD Quest software
genomic solutions Investigator (proteomics) was used to analyze the
differential protein expression profile in femoral and humeri bones
harvested from three groups of rats; sham-operated rats (SO),
ovariectomised rats (Ovx) and ovariectomised rats supplemented for
2 months with palm vitamin E. The results showed that there were
over 300 valued spot on each of the groups PVE and OVX as
compared to about 200 in SO. Comparison between the differential
protein expression between OVX and PVE groups showed that ten
spots were down –regulated in OVX but up-regulated in PVE. The
ten differential spots were separately named P1-P10. The
identification and understanding of the pathway of the differential
protein expression among the groups is ongoing and may account for
the molecular mechanism through which palm vitamin E exert its
anti-osteoporotic effect.
Abstract: The two-dimensional gel electrophoresis method
(2-DE) is widely used in Proteomics to separate thousands of proteins
in a sample. By comparing the protein expression levels of proteins in
a normal sample with those in a diseased one, it is possible to identify
a meaningful set of marker proteins for the targeted disease. The major
shortcomings of this approach involve inherent noises and irregular
geometric distortions of spots observed in 2-DE images. Various
experimental conditions can be the major causes of these problems. In
the protein analysis of samples, these problems eventually lead to
incorrect conclusions. In order to minimize the influence of these
problems, this paper proposes a partition based pair extension method
that performs spot-matching on a set of gel images multiple times and
segregates more reliable mapping results which can improve the
accuracy of gel image analysis. The improved accuracy of the
proposed method is analyzed through various experiments on real
2-DE images of human liver tissues.
Abstract: Von Willebrand-s disease is the most common
inherited bleeding disorder in humans, it
caused by qualitative abnormalities of the von Willebrand factor
(vWF). Our objective is to determine the prevalence of this disease at
part of the Algerian population in the East and the South by a
biological diagnosis based on specific biological tests (automated
platelet count, the bleeding time (TS), the time of cephalin + activator
(TCA), measure of the prothrombin rate (TP), vWF rate and factor
VIII rate, Molecular electrophoresis of vWF multimers in agarose gel
in the presence of SDS). Four patients of type III or severe
Willebrand-s disease were found on 200 suspect cases. All cases are
showed a deficit in vWF rate (< 5%), and factor VIII (P
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.