Abstract: Microbial oil was produced by soil isolated
oleaginous yeast YU5/2 in flask-batch fermentation. The yeast was
identified by molecular genetics technique based on sequence
analysis of the variable D1/D2 domain of the large subunit (26S)
ribosomal DNA and it was identified as Torulaspora globosa. T.
globosa YU5/2 supported maximum values of 0.520 g/L/d, 0.472 g
lipid/g cells, 4.16 g/L, and 0.156 g/L/d for volumetric lipid
production rate, and specific yield of lipid, lipid concentration, and
specific rate of lipid production respectively, when culture was
performed in nitrogen-limiting medium supplemented with 80g/L
glucose. Among the carbon sources tested, maximum cell yield
coefficient (YX/S, g/L), maximum specific yield of lipid (YP/X, g
lipid/g cells) and volumetric lipid production rate (QP, g/L/d) were
found of 0.728, 0.237, and 0.619, respectively, using sweet potato
tubers hydrolysates as carbon source.
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: The aim of this work was to detect genetic variability among the set of 40 castor genotypes using 8 RAPD markers. Amplification of genomic DNA of 40 genotypes, using RAPD analysis, yielded in 66 fragments, with an average of 8.25 polymorphic fragments per primer. Number of amplified fragments ranged from 3 to 13, with the size of amplicons ranging from 100 to 1200 bp. Values of the polymorphic information content (PIC) value ranged from 0.556 to 0.895 with an average of 0.784 and diversity index (DI) value ranged from 0.621 to 0.896 with an average of 0.798. The dendrogram based on hierarchical cluster analysis using UPGMA algorithm was prepared and analyzed genotypes were grouped into two main clusters and only two genotypes could not be distinguished. Knowledge on the genetic diversity of castor can be used for future breeding programs for increased oil production for industrial uses.
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: In this study, Li4SiO4 powder was successfully
synthesized via sol gel method followed by drying at 150oC. Lithium
oxide, Li2O and silicon oxide, SiO2 were used as the starting
materials with citric acid as the chelating agent. The obtained powder
was then sintered at various temperatures. Crystallographic phase
analysis, morphology and ionic conductivity were investigated
systematically employing X-ray diffraction, Fourier Transform
Infrared, Scanning Electron Microscopy and AC impedance
spectroscopy. XRD result showed the formation of pure monoclinic
Li4SiO4 crystal structure with lattice parameters a = 5.140 Å, b =
6.094 Å, c = 5.293 Å, β = 90o in the sample sintered at 750oC. This
observation was confirmed by FTIR analysis. The bulk conductivity
of this sample at room temperature was 3.35 × 10-6 S cm-1 and the
highest bulk conductivity of 1.16 × 10-4 S cm-1 was obtained at
100°C. The results indicated that, the Li4SiO4 compound has
potential to be used as host for LISICON structured solid electrolyte
for low temperature application.
Abstract: The present work analyses different parameters of pressure die casting to minimize the casting defects. Pressure diecasting is usually applied for casting of aluminium alloys. Good surface finish with required tolerances and dimensional accuracy can be achieved by optimization of controllable process parameters such as solidification time, molten temperature, filling time, injection pressure and plunger velocity. Moreover, by selection of optimum process parameters the pressure die casting defects such as porosity, insufficient spread of molten material, flash etc. are also minimized. Therefore, a pressure die casting component, carburetor housing of aluminium alloy (Al2Si2O5) has been considered. The effects of selected process parameters on casting defects and subsequent setting of parameters with the levels have been accomplished by Taguchi-s parameter design approach. The experiments have been performed as per the combination of levels of different process parameters suggested by L18 orthogonal array. Analyses of variance have been performed for mean and signal-to-noise ratio to estimate the percent contribution of different process parameters. Confidence interval has also been estimated for 95% consistency level and three conformational experiments have been performed to validate the optimum level of different parameters. Overall 2.352% reduction in defects has been observed with the help of suggested optimum process parameters.
Abstract: We develop new nonlinear methods of
immunofluorescence analysis for a sensitive technology of
respiratory burst reaction of DNA fluorescence due to oxidative
activity in the peripheral blood neutrophils. Histograms in flow
cytometry experiments represent a fluorescence flashes frequency as
functions of fluorescence intensity. We used the Shannon-Weaver
index for definition of neutrophils- biodiversity and Hurst index for
definition of fractal-s correlations in immunofluorescence for
different donors, as the basic quantitative criteria for medical
diagnostics of health status. We analyze frequencies of flashes,
information, Shannon entropies and their fractals in
immunofluorescence networks due to reduction of histogram range.
We found the number of simplest universal correlations for
biodiversity, information and Hurst index in diagnostics and
classification of pathologies for wide spectra of diseases. In addition
is determined the clear criterion of a common immunity and human
health status in a form of yes/no answers type. These answers based
on peculiarities of information in immunofluorescence networks and
biodiversity of neutrophils. Experimental data analysis has shown the
existence of homeostasis for information entropy in oxidative activity
of DNA in neutrophil nuclei for all donors.
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: Gamboge disorder (GD) or fruit damage by the yellow sap is a major problem in mangosteen. Mangosteen plants varied in the level of GD, from very low or non GD to low, moderate and high GD. However it was difficult to differentiate between GD and non GD plants because evaluation of the disorder is strongly influenced by environment. In this study we investigated the usefulness of primer designed from bioinformatics related to cell wall strength, termed as MCWS, to predict GD. Plant materials used were 28 mangosteen plants selected based on percentage of GD categorized as high, moderate, low and very low or non GD. The result showed that the specific DNA fragments were absent in the high GD accessions. The MCWS marker suggests as a novel polymorphic marker for GD in mangosteen as well as a marker for detect variability in mangosteen as apomictic plant.
Abstract: To study on effect of PEG and NaCl stress on
germination and early seedling stages on two cultivar of corn, two
separated experiment were laid out at physiology laboratory, faculty
of Agriculture, Razi University, Kermanshah, Iran in 2009. This
investigation was performed as factorial experiment under Complete
Randomized Design (CRD) with three replications. Cultivar factor
contains of two varieties (sweet corn SC403 and Flint corn SC704)
and five levels of stress (0, -2, -4, -6 and -8 bar). The principal aim of
current study was to compare the two varieties of maize in relative to
the stress conditions. Results indicated that significant decrease was
observed in percentage of germination, germination rate, length of
radicle and plumule and radicle and plumule dry matter. On the basis
of the results, NaCl as compared with PEG had more effect on
germination and early seedling stage and sweet corn had more
resistant than flint corn in both stress conditions.
Abstract: Biological data has several characteristics that strongly differentiate it from typical business data. It is much more complex, usually large in size, and continuously changes. Until recently business data has been the main target for discovering trends, patterns or future expectations. However, with the recent rise in biotechnology, the powerful technology that was used for analyzing business data is now being applied to biological data. With the advanced technology at hand, the main trend in biological research is rapidly changing from structural DNA analysis to understanding cellular functions of the DNA sequences. DNA chips are now being used to perform experiments and DNA analysis processes are being used by researchers. Clustering is one of the important processes used for grouping together similar entities. There are many clustering algorithms such as hierarchical clustering, self-organizing maps, K-means clustering and so on. In this paper, we propose a clustering algorithm that imitates the ecosystem taking into account the features of biological data. We implemented the system using an Ant-Colony clustering algorithm. The system decides the number of clusters automatically. The system processes the input biological data, runs the Ant-Colony algorithm, draws the Topic Map, assigns clusters to the genes and displays the output. We tested the algorithm with a test data of 100 to1000 genes and 24 samples and show promising results for applying this algorithm to clustering DNA chip data.
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: A new code for spectral-amplitude coding optical
code-division multiple-access system is proposed called Random
diagonal (RD) code. This code is constructed using code segment and
data segment. One of the important properties of this code is that the
cross correlation at data segment is always zero, which means that
Phase Intensity Induced Noise (PIIN) is reduced. For the performance
analysis, the effects of phase-induced intensity noise, shot noise, and
thermal noise are considered simultaneously. Bit-error rate (BER)
performance is compared with Hadamard and Modified Frequency
Hopping (MFH) codes. It is shown that the system using this new
code matrices not only suppress PIIN, but also allows larger number
of active users compare with other codes. Simulation results shown
that using point to point transmission with three encoded channels,
RD code has better BER performance than other codes, also its found
that at 0 dbm PIIN noise are 10-10 and 10-11 for RD and MFH
respectively.
Abstract: Image synthesis is an important area in image processing.
To synthesize images various systems are proposed in
the literature. In this paper, we propose a bio-inspired system to
synthesize image and to study the generating power of the system, we
define the class of languages generated by our system. We call image
as array in this paper. We use a primitive called iso-array to synthesize
image/array. The operation is double splicing on iso-arrays. The
double splicing operation is used in DNA computing and we use
this to synthesize image. A comparison of the family of languages
generated by the proposed self restricted double splicing systems on
iso-arrays with the existing family of local iso-picture languages is
made. Certain closure properties such as union, concatenation and
rotation are studied for the family of languages generated by the
proposed model.
Abstract: Gene expression profiling is rapidly evolving into a
powerful technique for investigating tumor malignancies. The
researchers are overwhelmed with the microarray-based platforms
and methods that confer them the freedom to conduct large-scale
gene expression profiling measurements. Simultaneously,
investigations into cross-platform integration methods have started
gaining momentum due to their underlying potential to help
comprehend a myriad of broad biological issues in tumor diagnosis,
prognosis, and therapy. However, comparing results from different
platforms remains to be a challenging task as various inherent
technical differences exist between the microarray platforms. In this
paper, we explain a simple ratio-transformation method, which can
provide some common ground for cDNA and Affymetrix platform
towards cross-platform integration. The method is based on the
characteristic data attributes of Affymetrix- and cDNA- platform. In
the work, we considered seven childhood leukemia patients and their
gene expression levels in either platform. With a dataset of 822
differentially expressed genes from both these platforms, we carried
out a specific ratio-treatment to Affymetrix data, which subsequently
showed an improvement in the relationship with the cDNA data.
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: Transcription factors are a group of proteins that
helps for interpreting the genetic information in DNA.
Protein-protein interactions play a major role in the execution
of key biological functions of a cell. These interactions are
represented in the form of a graph with nodes and edges.
Studies have showed that some nodes have high degree of
connectivity and such nodes, known as hub nodes, are the
inevitable parts of the network. In the present paper a method
is proposed to identify hub transcription factor proteins using
sequence information. On a complete data set of transcription
factor proteins available from the APID database, the
proposed method showed an accuracy of 77%, sensitivity of
79% and specificity of 76%.
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 P-Bigram method is a string comparison methods
base on an internal two characters-based similarity measure. The edit
distance between two strings is the minimal number of elementary
editing operations required to transform one string into the other. The
elementary editing operations include deletion, insertion, substitution
two characters. In this paper, we address the P-Bigram method to
sole the similarity problem in DNA sequence. This method provided
an efficient algorithm that locates all minimum operation in a string.
We have been implemented algorithm and found that our program
calculated that smaller distance than one string. We develop PBigram
edit distance and show that edit distance or the similarity and
implementation using dynamic programming. The performance of
the proposed approach is evaluated using number edit and percentage
similarity measures.
Abstract: Bovine viral diarrhea virus (BVDV) can cause lifelong
persistent infection. One reason for the phenomena is attributed to
BVDV infection to placenta tissue. However the mechanisms that
BVDV invades into placenta tissue remain unclear. To clarify the
molecular mechanisms, we investigated the possible means that
BVDV entered into bovine trophoblast cells (TPC). Yeast two-hybrid
system was used to identify proteins extracted from TPC, which
interact with BVDV envelope glycoprotein E2. A PGbkt7-E2 yeast
expression vector and TPC cDNA library were constructed. Through
two rounds of screening, three positive clones were identified.
Sequencing analysis indicated that all the three positive clones
encoded the same protein clathrin. Physical interaction between
clathrin and BVDV E2 protein was further confirmed by
coimmunoprecipitation experiments. This result suggested that the
clathrin might play a critical role in the process of BVDV entry into
placenta tissue and might be a novel antiviral target for preventing
BVDV infection.