Abstract: D-erythro-cyclohexylserine (D
chiral unnatural β-hydroxy amino acid expected for the synthesis of drug for AIDS treatment. To develop a continuous bioconversion
system with whole cell biocatalyst of D-threonine aldolase (D genes for the D-erythro-CHS production, D-threonine aldolase gene
was amplified from Ensifer arboris 100383 by direct PCR amplication using two degenerated oligonucleotide primers designed based on
genomic sequence of Shinorhizobium meliloti
Sequence analysis of the cloned DNA fragment revealed one
open-reading frame of 1059 bp and 386 amino acids. This putative
D-TA gene was cloned into NdeI and EcoRI (pEnsi
His-tag sequence or BamHI (pEnsi-DTA[2])
sequence of the pET21(a) vector. The expression level of the cloned gene was extremely overexpressed by E. coli BL21(DE3) transformed with pEnsi-DTA[1] compared to E. coli BL21(DE3) transformed with
pEnsi-DTA[2]. When the cells expressing the wild
used for D-TA enzyme activity, 12 mM glycine was successfully
detected in HPLC analysis. Moreover, the whole cells harbouring the
recombinant D-TA was able to synthesize D-erythro
of 0.6 mg/ml in a batch reaction.
Abstract: Prediction of bacterial virulent protein sequences can
give assistance to identification and characterization of novel
virulence-associated factors and discover drug/vaccine targets against
proteins indispensable to pathogenicity. Gene Ontology (GO)
annotation which describes functions of genes and gene products as a
controlled vocabulary of terms has been shown effectively for a
variety of tasks such as gene expression study, GO annotation
prediction, protein subcellular localization, etc. In this study, we
propose a sequence-based method Virulent-GO by mining informative
GO terms as features for predicting bacterial virulent proteins.
Each protein in the datasets used by the existing method
VirulentPred is annotated by using BLAST to obtain its homologies
with known accession numbers for retrieving GO terms. After
investigating various popular classifiers using the same five-fold
cross-validation scheme, Virulent-GO using the single kind of GO
term features with an accuracy of 82.5% is slightly better than
VirulentPred with 81.8% using five kinds of sequence-based features.
For the evaluation of independent test, Virulent-GO also yields better
results (82.0%) than VirulentPred (80.7%). When evaluating single
kind of feature with SVM, the GO term feature performs much well,
compared with each of the five kinds of features.
Abstract: Bio-chips are used for experiments on genes and
contain various information such as genes, samples and so on. The
two-dimensional bio-chips, in which one axis represent genes and the
other represent samples, are widely being used these days. Instead of
experimenting with real genes which cost lots of money and much
time to get the results, bio-chips are being used for biological
experiments. And extracting data from the bio-chips with high
accuracy and finding out the patterns or useful information from such
data is very important. Bio-chip analysis systems extract data from
various kinds of bio-chips and mine the data in order to get useful
information. One of the commonly used methods to mine the data is
classification. The algorithm that is used to classify the data can be
various depending on the data types or number characteristics and so
on. Considering that bio-chip data is extremely large, an algorithm that
imitates the ecosystem such as the ant algorithm is suitable to use as an
algorithm for classification. This paper focuses on finding the
classification rules from the bio-chip data using the Ant Colony
algorithm which imitates the ecosystem. The developed system takes
in consideration the accuracy of the discovered rules when it applies it
to the bio-chip data in order to predict the classes.
Abstract: It has been established that microRNAs (miRNAs) play
an important role in gene expression by post-transcriptional regulation
of messengerRNAs (mRNAs). However, the precise relationships
between microRNAs and their target genes in sense of numbers,
types and biological relevance remain largely unclear. Dissecting the
miRNA-target relationships will render more insights for miRNA
targets identification and validation therefore promote the understanding
of miRNA function. In miRBase, miRanda is the key
algorithm used for target prediction for Zebrafish. This algorithm
is high-throughput but brings lots of false positives (noise). Since
validation of a large scale of targets through laboratory experiments
is very time consuming, several computational methods for miRNA
targets validation should be developed. In this paper, we present an
integrative method to investigate several aspects of the relationships
between miRNAs and their targets with the final purpose of extracting
high confident targets from miRanda predicted targets pool. This is
achieved by using the techniques ranging from statistical tests to
clustering and association rules. Our research focuses on Zebrafish.
It was found that validated targets do not necessarily associate with
the highest sequence matching. Besides, for some miRNA families,
the frequency of their predicted targets is significantly higher in the
genomic region nearby their own physical location. Finally, in a case
study of dre-miR-10 and dre-miR-196, it was found that the predicted
target genes hoxd13a, hoxd11a, hoxd10a and hoxc4a of dre-miR-
10 while hoxa9a, hoxc8a and hoxa13a of dre-miR-196 have similar
characteristics as validated target genes and therefore represent high
confidence target candidates.
Abstract: MicroRNAs (miRNAs) are a class of non-coding
RNAs that hybridize to mRNAs and induce either translation
repression or mRNA cleavage. Recently, it has been reported that
miRNAs could possibly play an important role in human diseases. By
integrating miRNA target genes, cancer genes, miRNA and mRNA
expression profiles information, a database is developed to link
miRNAs to cancer target genes. The database provides experimentally
verified human miRNA target genes information, including oncogenes
and tumor suppressor genes. In addition, fragile sites information for
miRNAs, and the strength of the correlation of miRNA and its target
mRNA expression level for nine tissue types are computed, which
serve as an indicator for suggesting miRNAs could play a role in
human cancer. The database is freely accessible at
http://ppi.bioinfo.asia.edu.tw/mirna_target/index.html.
Abstract: Direct and indirect somatic embryogenesis (SE) from
petiole and leaf explants of Scaevola aemula R. Br. cv. 'Purple
Fanfare' was achieved. High frequency of somatic embryos was
obtained directly from petiole and leaf explants using an inductive
plant growth regulator signal thidiazuron (TDZ). Petiole explants
were more responsive to SE than leaves. Plants derived from somatic
embryos of petiole explants germinated more readily into plants. SE
occurred more efficiently in half-strength Murashige and Skoog
(MS) medium than in full-strength MS medium. Non-embryogenic
callus induced by 2, 4-dichlorophenoxyacetic acid was used to
investigate the feasibility of obtaining SE with TDZ as a secondary
inductive plant growth regulator (PGR) signal. Non-embryogenic
callus of S. aemula was able to convert into an “embryogenic
competent mode" with PGR signal. Protocol developed for induction
of direct and indirect somatic embryogenesis in S. aemula can
improve the large scale propagation system of the plant in future.
Abstract: Sense-antisense gene pair (SAGP) is a pair of two oppositely transcribed genes sharing a common region on a chromosome. In the mammalian genomes, SAGPs can be organized in more complex sense-antisense gene architectures (CSAGA) in which at least one gene could share loci with two or more antisense partners. Many dozens of CSAGAs can be found in the human genome. However, CSAGAs have not been systematically identified and characterized in context of their role in human diseases including cancers. In this work we characterize the structural-functional properties of a cluster of 5 genes –TMEM97, IFT20, TNFAIP1, POLDIP2 and TMEM199, termed TNFAIP1 / POLDIP2 module. This cluster is organized as CSAGA in cytoband 17q11.2. Affymetrix U133A&B expression data of two large cohorts (410 atients, in total) of breast cancer patients and patient survival data were used. For the both studied cohorts, we demonstrate (i) strong and reproducible transcriptional co-regulatory patterns of genes of TNFAIP1/POLDIP2 module in breast cancer cell subtypes and (ii) significant associations of TNFAIP1/POLDIP2 CSAGA with amplification of the CSAGA region in breast cancer, (ii) cancer aggressiveness (e.g. genetic grades) and (iv) disease free patient-s survival. Moreover, gene pairs of this module demonstrate strong synergetic effect in the prognosis of time of breast cancer relapse. We suggest that TNFAIP1/ POLDIP2 cluster can be considered as a novel type of structural-functional gene modules in the human genome.
Abstract: The study describes chitosan membrane platform
modified with nanostructure pattern which using nanotechnology to
fabricate. The cell-substrate interaction between neuro-2a neuroblasts
cell lines and chitosan membrane (flat, nanostructure and
nanostructure pattern types) was investigated. The adhered
morphology of neuro-2a cells depends on the topography of chitosan
surface. We have found that neuro-2a showed different morphogenesis
when cells adhered on flat and nanostructure chitosan membrane. The
cell projected area of neuro-2a on flat chitosan membrane is larger
than on nanostructure chitosan membrane. In addition, neuro-2a cells
preferred to adhere on flat chitosan surface region than on
nanostructure chitosan membrane to immobilize and differentiation.
The experiment suggests surface topography can be used as a critical
mechanism to isolate group of neuro-2a to a particular rectangle area
on chitosan membrane. Our finding will provide a platform to take
patch clamp to record electrophysiological behavior about neurons in
vitro in the future.
Abstract: In vitro plant regeneration has been successfully obtained from basal shoot explant of Vetiveria zizanioides through indirect organogenesis. The explant was cultured in Murashige & Skoog’s (MS) media supplemented with 2,4-D, IAA, and kinetin in various concentrations. Callus was well induced in media supplemented with 2 ppm 2,4-D, 1 ppm IAA, and 1 ppm kinetin. This callus was then transferred to MS media supplemented with 1 - 5 ppm of BAP for shoot regeneration. The media supplemented with 3 ppm BAP was a suitable medium for shoot induction, as well as for shoot multiplication. Rooting was well developed in shoot following transferred to half MS media containing 0.2 ppm IBA. Plantlet was then transferred to husk charcoal for acclimatization, and almost all (90%) of plantlets were survived during acclimatization.
Abstract: In this study, we investigated the effects of ginger and
L-carnitine on the reproductive performance of male rats with respect
to semen parameters, male sex hormones and the testicular
antioxidant system. A total of sixty mature male albino rats were
divided into four groups of fifteen rats. The control group received
saline, whereas the other three groups received ginger (100 mg kg-1 d-
1.), L-carnitine (150 mg kg-1 d-1.) or a combination of both ginger
(100 mg kg-1 d-1.) and L-carnitine (150 mg kg-1 d-1.) via a stomach
tube daily for one month. At the end of the treatment period, the rats
were sacrificed, and their sperm characteristics (count, motility and
viability), antioxidant enzyme factors levels (reduced glutathione,
catalase, superoxide dismutase and total antioxidant capacity) and sex
hormone levels (testosterone, Follicle stimulating hormone(FSH) and
luteinizing hormone (LH) were analysed. Our results showed that the
three experimental treatments improved sperm parameters,
antioxidant enzyme activity and testosterone hormone levels; the
most pronounced positive effects were observed in the group that
received a combination of both ginger and L-carnitine. Therefore, the
administration of a combination of ginger and L-carnitine may be
beneficial for improving male sexual performance.
Abstract: It is believed that DNA damaging toxic metabolites contributes to the development of different pathological conditions. To prevent harmful influence of toxic agents, cells developed number of protecting mechanisms, such as enzymatic reaction of detoxification of reactive metabolites and repair of DNA damage. The aim of the study was to examine the association between polymorphism of GSTT1/GSTM1 and XRCC1/3 genes and coronary artery disease (CAD) incidence. To examine a polymorphism of these genes in CAD susceptibility in patients and controls, PCR based genotyping assay was performed. For GST genes, frequency of GSTM1 null genotype among CAD affected group was significantly increased than in control group (P0.1). We found that neither XRCC1 Arg399Gln nor XRCC3 Thr241Met were associated with CAD risk. Obtained data suggests that GSTM1 null genotype carriers are more susceptible to CAD development.
Abstract: The PAX6, a transcription factor, is essential for the morphogenesis of the eyes, brain, pituitary and pancreatic islets. In rodents, the loss of Pax6 function leads to central nervous system defects, anophthalmia, and nasal hypoplasia. The haplo-insufficiency of Pax6 causes microphthalmia, aggression and other behavioral abnormalities. It is also required in brain patterning and neuronal plasticity. In human, heterozygous mutation of Pax6 causes loss of iris [aniridia], mental retardation and glucose intolerance. The 3- deletion in Pax6 leads to autism and aniridia. The phenotypes are variable in peneterance and expressivity. However, mechanism of function and interaction of PAX6 with other proteins during development and associated disease are not clear. It is intended to explore interactors of PAX6 to elucidated biology of PAX6 function in the tissues where it is expressed and also in the central regulatory pathway. This report describes In-silico approaches to explore interacting proteins of PAX6. The models show several possible proteins interacting with PAX6 like MITF, SIX3, SOX2, SOX3, IPO13, TRIM, and OGT. Since the Pax6 is a critical transcriptional regulator and master control gene of eye and brain development it might be interacting with other protein involved in morphogenesis [TGIF, TGF, Ras etc]. It is also presumed that matricelluar proteins [SPARC, thrombospondin-1 and osteonectin etc] are likely to interact during transport and processing of PAX6 and are somewhere its cascade. The proteins involved in cell survival and cell proliferation can also not be ignored.
Abstract: MATCH project [1] entitle the development of an
automatic diagnosis system that aims to support treatment of colon
cancer diseases by discovering mutations that occurs to tumour
suppressor genes (TSGs) and contributes to the development of
cancerous tumours. The constitution of the system is based on a)
colon cancer clinical data and b) biological information that will be
derived by data mining techniques from genomic and proteomic
sources The core mining module will consist of the popular, well
tested hybrid feature extraction methods, and new combined
algorithms, designed especially for the project. Elements of rough
sets, evolutionary computing, cluster analysis, self-organization maps
and association rules will be used to discover the annotations
between genes, and their influence on tumours [2]-[11].
The methods used to process the data have to address their high
complexity, potential inconsistency and problems of dealing with the
missing values. They must integrate all the useful information
necessary to solve the expert's question. For this purpose, the system
has to learn from data, or be able to interactively specify by a domain
specialist, the part of the knowledge structure it needs to answer a
given query. The program should also take into account the
importance/rank of the particular parts of data it analyses, and adjusts
the used algorithms accordingly.
Abstract: The purpose of this paper is to demonstrate the ability
of a genetic programming (GP) algorithm to evolve a team of data
classification models. The GP algorithm used in this work is
“multigene" in nature, i.e. there are multiple tree structures (genes)
that are used to represent team members. Each team member assigns
a data sample to one of a fixed set of output classes. A majority vote,
determined using the mode (highest occurrence) of classes predicted
by the individual genes, is used to determine the final class
prediction. The algorithm is tested on a binary classification problem.
For the case study investigated, compact classification models are
obtained with comparable accuracy to alternative approaches.
Abstract: A scaffold is necessary for tooth regeneration because of its three-dimensional geometry. For restoration of defect, it is necessary for the scaffold to be prepared in the shape of the defect. Sponges made from polyvinyl alcohol with formalin cross-linking (PVF sponge) have been used for scaffolds for bone formation in vivo. To induce osteogenesis within the sponge, methods of growing rat bone marrow cells (rBMCs) among the fiber structures in the sponge might be considered. Storage of rBMCs among the fibers in the sponge coated with dextran (10 kDa) was tried. After seeding of rBMCs to PVF sponge immersed in dextran solution at 2 g/dl concentration, osteogenesis was recognized in subcutaneously implanted PVF sponge as a scaffold in vivo. The level of osteocalcin was 25.28±5.71 ng/scaffold and that of Ca was 129.20±19.69 µg/scaffold. These values were significantly higher than those in sponges without dextran coating (p
Abstract: In April 2009, a new variant of Influenza A virus
subtype H1N1 emerged in Mexico and spread all over the world. The
influenza has three subtypes in human (H1N1, H1N2 and H3N2)
Types B and C influenza tend to be associated with local or regional
epidemics. Preliminary genetic characterization of the influenza
viruses has identified them as swine influenza A (H1N1) viruses.
Nucleotide sequence analysis of the Haemagglutinin (HA) and
Neuraminidase (NA) are similar to each other and the majority of
their genes of swine influenza viruses, two genes coding for the
neuraminidase (NA) and matrix (M) proteins are similar to
corresponding genes of swine influenza. Sequence similarity between
the 2009 A (H1N1) virus and its nearest relatives indicates that its
gene segments have been circulating undetected for an extended
period. Nucleic acid sequence Maximum Likelihood (MCL) and
DNA Empirical base frequencies, Phylogenetic relationship amongst
the HA genes of H1N1 virus isolated in Genbank having high
nucleotide sequence homology.
In this paper we used 16 HA nucleotide sequences from NCBI for
computing sequence relationships similarity of swine influenza A
virus using the following method MCL the result is 28%, 36.64% for
Optimal tree with the sum of branch length, 35.62% for Interior
branch phylogeny Neighber – Join Tree, 1.85% for the overall
transition/transversion, and 8.28% for Overall mean distance.
Abstract: Certain tRNA synthetases have developed highly accurate molecular machinery to discriminate their cognate amino acids. Those aaRSs achieve their goal via editing reaction in the Connective Polypeptide 1 (CP1). Recently mutagenesis studies have revealed the critical importance of residues in the CP1 domain for editing activity and X-ray structures have shown binding mode of noncognate amino acids in the editing domain. To pursue molecular mechanism for amino acid discrimination, molecular modeling studies were performed. Our results suggest that aaRS bind the noncognate amino acid more tightly than the cognate one. Finally, by comparing binding conformations of the amino acids in three systems, the amino acid binding mode was elucidated and a discrimination mechanism proposed. The results strongly reveal that the conserved threonines are responsible for amino acid discrimination. This is achieved through side chain interactions between T252 and T247/T248 as well as between those threonines and the incoming amino acids.
Abstract: Tofurther advance research on immune-related genes
from T. molitor, we constructed acDNA library and analyzed
expressed sequence taq (EST) sequences from 1,056 clones. After
removing vector sequence and quality checkingthrough thePhred
program (trim_alt 0.05 (P-score>20), 1039 sequences were generated.
The average length of insert was 792 bp. In addition, we identified 162
clusters, 167 contigs and 391 contigs after clustering and assembling
process using a TGICL package. EST sequences were searchedagainst
NCBI nr database by local BLAST (blastx, E
Abstract: The objective of current issue was to develop a model
of testicular herpes simplex virus (HSV) type I infection for
assessment of viral effect on fertility. 56 male mice were inoculated
intraperitoneally with different concentrations of HSV on 8 day post
partum. It was revealed that the optimal dose was 100 plaque
forming units per mice as it provided testicular infection in 100% of
survivors. HSV proteins were detected both in somatic and germ
cells (spermatogonia, spermatocytes, spermatides). Although DNA
load in testis was descending from 3 to 28 days post infection only
12.5% of infected males had offspring after mating with uninfected
females comparing to 87.5% in control (p=0.012). These results are
the first direct evidence for HSV impact in male sterility. Prepuberal
mice appeared to be a suitable model for investigation of
pathogenesis of virus-associated fertility disorders.
Abstract: Using DNA microarrays the comparative analysis of a
gene expression profiles is carried out in a liver and kidneys of pigs.
The hypothesis of a cross hybridization of one probe with different
cDNA sites of the same gene or different genes is checked up, and it
is shown, that cross hybridization can be a source of essential errors
at revealing of a key genes in organ-specific transcriptome. It is
reveald that distinctions in profiles of a gene expression are well coordinated
with function, morphology, biochemistry and histology of
these organs.