Abstract: Retinoic acid is like a steroid hormone that plays a
role in embryo formation, proliferation of spermatogonia cells,
ephitelial cells differentiation and organogenesis. Retinoic acid can
influences seminiferous tubule formation during embryonic testis
development and also play a role in the regulation of ovarian function
and female reproductive tract by suppressing the hormones FSH
receptor expression. The excessive use of retinoic acid caused
abnormalities in the fetus. The result showed that there is the
influence of retinoic acid on the developmet of mice fetal testes, for
examples disruption of the formation of seminiferous tubules and
tubules seemed to be hollow, spermatogonia cells are relatively few
in number and caused Leydig cells count relatively more. While in
the female fetus does not caused the formation of primordial follicles
and disrupted the development of germinal ephitelial cells of fetal
ovaries of female mice (mus musculus) Swiss Webster.
Abstract: Microarrays have become the effective, broadly used tools in biological and medical research to address a wide range of problems, including classification of disease subtypes and tumors. Many statistical methods are available for analyzing and systematizing these complex data into meaningful information, and one of the main goals in analyzing gene expression data is the detection of samples or genes with similar expression patterns. In this paper, we express and compare the performance of several clustering methods based on data preprocessing including strategies of normalization or noise clearness. We also evaluate each of these clustering methods with validation measures for both simulated data and real gene expression data. Consequently, clustering methods which are common used in microarray data analysis are affected by normalization and degree of noise and clearness for datasets.
Abstract: Neem is a highly heterozygous and commercially
important perennial plant. Conventionally, it is propagated by seeds
which loose viability within two weeks. Strictly cross pollinating
nature of the plant causes serious barrier to the genetic improvement
by conventional methods. Alternative methods of tree improvement
such as somatic hybridization, mutagenesis and genetic
transformation require an efficient in vitro plant regeneration system.
In this regard, somatic embryogenesis particularly secondary somatic
embryogenesis may offer an effective system for large scale plant
propagation without affecting the clonal fidelity of the regenerants. It
can be used for synthetic seed production, which further bolsters
conservation of this tree species which is otherwise very difficult
The present report describes the culture conditions necessary to
induce and maintain repetitive somatic embryogenesis, for the first
time, in neem. Out of various treatments tested, the somatic embryos
were induced directly from immature zygotic embryos of neem on
MS + TDZ (0.1 μM) + ABA (4 μM), in more than 76 % cultures.
Direct secondary somatic embryogenesis occurred from primary
somatic embryos on MS + IAA (5 μM) + GA3 (5 μM) in 12.5 %
cultures. Embryogenic competence of the explant as well as of the
primary embryos was maintained for a long period by repeated
subcultures at frequent intervals. A maximum of 10 % of these
somatic embryos were converted into plantlets.
Abstract: The microbial production of ethanol from biodiesel¬derived crude glycerol by Enterobacter aerogenes TISTR1468, under micro-aerobic and anaerobic conditions, was investigated. The experimental results showed that micro-aerobic conditions were more favorable for cellular growth (4.0 g/L DCW), ethanol production (20.7 g/L) as well as the ethanol yield (0.47 g/g glycerol) than anaerobic conditions (1.2 g/L DCW, 6.3 g/L ethanol and 0.72 g/g glycerol, respectively). Crude glycerol (100 g/L) was consumed completely with the rate of 1.80 g/L/h. Two-stage fermentation (combination of micro-aerobic and anaerobic condition) exhibited higher ethanol production (24.5 g/L) than using one-stage fermentation (either micro-aerobic or anaerobic condition. The two- stage configuration, exhibited slightly higher crude glycerol consumption rate (1.81 g/L/h), as well as ethanol yield (0.56 g/g) than the one-stage configuration. Therefore, two-stage process was selected for ethanol production from E. aerogenes TISTR1468 in scale-up studies.
Abstract: Identifying protein coding regions in DNA sequences is a basic step in the location of genes. Several approaches based on signal processing tools have been applied to solve this problem, trying to achieve more accurate predictions. This paper presents a new predictor that improves the efficacy of three techniques that use the Fourier Transform to predict coding regions, and that could be computed using an algorithm that reduces the computation load. Some ideas about the combination of the predictor with other methods are discussed. ROC curves are used to demonstrate the efficacy of the proposed predictor, based on the computation of 25 DNA sequences from three different organisms.
Abstract: P16/INK4A is tumor suppressor protein that plays a critical role in cell cycle regulation. Loss of P16 protein expression has been implicated in pathogenesis of many cancers, including lymphoma. Therefore, we sought to investigate if loss of P16 protein expression is associated with lymphoma and/or any specific lymphoma subtypes (Hodgkin-s lymphoma (HL) and nonHodgkin-s lymphoma (NHL)). Fifty-five lymphoma cases consisted of 30 cases of HL and 25 cases of NHL, with an age range of 3 to 78 years, were examined for loss of P16 by immunohistochemical technique using a specific antibody reacting against P16. In total, P16 loss was seen in 33% of all lymphoma cases. P16 loss was identified in 47.7% of HL cases. In contrast, only 16% of NHL showed loss of P16. Loss of P16 was seen in 67% of HL patients with 50 years of age or older, whereas P16 loss was found in only 42% of HL patients with less than 50 years of age. P16 loss in HL is somewhat higher in male (55%) than in female (30%). In subtypes of HL, P16 loss was found exclusively in all cases of lymphocyte depletion, lymphocyte predominance and unclassified cases, whereas P16 loss was seen in 39% of mixed cellularity and 29% of nodular sclerosis cases. In low grade NHL patients, P16 loss was seen in approximately one-third of cases, whereas no or very rare of P16 loss was found in intermediate and high grade cases. P16 loss did not show any correlation with age or gender of NHL patients. In conclusion, the high rate of P16 loss seen in our study suggests that loss of P16 expression plays a critical role in the pathogenesis of lymphoma, particularly with HL.
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: The article analyses historical aspects of the formation
of the Kazakh nation in the conditions of the multicultural society.
The authors underline cultural integration as a significant stage of the
cultural advancement of the Kazakh nation. The transition to the
modern-style houses, the adoption and development of the secular
education gave a rise to the development of the society and culture
on the whole.
Abstract: Anti-allergic effects of royal jelly were evaluated in a human-like mouse model of atopic dermatitis. NC/Nga mice were cutaneously applied with royal jelly for 6 weeks. Royal jelly-treated mice exhibited lower levels of serum total immunoglobulin E in comparison with controls. We found that the treatment decreased (11% to the control) expression of mRNA for aquaporin-3, which is involved in the modulation of epidermal hydration. Microarray analysis revealed more than 10-fold changes in the expression of several genes, such as transglutaminase 2, repetin, and keratins. In normal human epidermal keratinocytes, royal jelly extract suppressed interleukin-8 elevation induced by TNF-α and interferon-γ, suggesting direct anti-inflammatory activity in keratinocytes. Collectively, topical application of royal jelly may be useful for amelioration of lesions and inflammation in atopic dermatitis.
Abstract: We report a novel fusion tag for expressing
recombinant proteins in E. coli. The fusion tag is the C-terminus part
of the human GMCSF gene comprising 45 amino acids, which aid in
over expression of otherwise non expressible genes. Expression of
hIFN a2b with this fusion tag also escapes the requirement of rare
codons for expression. This is also a first report of a small fusion tag
of human origin having affinity to heparin sepharose column
facilitating the purification of fusion protein.
Abstract: Our results showed that for the growth of qualitative
seedling and vegetative raw material of ðó. marschallianus Willd. and
T. serphyllum L. it is more profitable to use the in vitro and
hydroponics combined method. In in vitro culture it is possible to do
micro-propagation whole year with 98-99% rhizogenesis. 30000
micro-plants were obtained from one explant during 9 months.
Hydroponic conditions provide the necessary microclimate for
microplants where the survival rate without acclimatization was
93.3%. The essential oil content in hydroponic dry herb of both
species in vegetative and blossom phase was 1.3% whereas in wild
plants it was 1.2%, the content of extractive substances and vitamin
C also exceeded wild plants. Our biochemical and radiochemical
investigations indicated that the medicinal raw materials obtained
from hydroponic and wild plants of Thymus species correspond to
the demands of SPh XI, and the content of artificial radionuclides
does not exceed the MACL.
Abstract: Tumor classification is a key area of research in the
field of bioinformatics. Microarray technology is commonly used in
the study of disease diagnosis using gene expression levels. The
main drawback of gene expression data is that it contains thousands
of genes and a very few samples. Feature selection methods are used
to select the informative genes from the microarray. These methods
considerably improve the classification accuracy. In the proposed
method, Genetic Algorithm (GA) is used for effective feature
selection. Informative genes are identified based on the T-Statistics,
Signal-to-Noise Ratio (SNR) and F-Test values. The initial candidate
solutions of GA are obtained from top-m informative genes. The
classification accuracy of k-Nearest Neighbor (kNN) method is used
as the fitness function for GA. In this work, kNN and Support Vector
Machine (SVM) are used as the classifiers. The experimental results
show that the proposed work is suitable for effective feature
selection. With the help of the selected genes, GA-kNN method
achieves 100% accuracy in 4 datasets and GA-SVM method
achieves in 5 out of 10 datasets. The GA with kNN and SVM
methods are demonstrated to be an accurate method for microarray
based tumor classification.
Abstract: Biochemical and molecular analysis of some
antioxidant enzyme genes revealed different level of gene expression
on oilseed (Brassica napus). For molecular and biochemical
analysis, leaf tissues were harvested from plants at eight different
developmental stages, from young to senescence. The levels of total
protein and chlorophyll were increased during maturity stages of
plant, while these were decreased during the last stages of plant
growth. Structural analysis (nucleotide and deduced amino acid
sequence, and phylogenic tree) of a complementary DNA revealed a
high level of similarity for a family of Catalase genes. The
expression of the gene encoded by different Catalase isoforms was
assessed during different plant growth phase. No significant
difference between samples was observed, when Catalase activity
was statistically analyzed at different developmental stages. EST
analysis exhibited different transcripts levels for a number of other
relevant antioxidant genes (different isoforms of SOD and
glutathione). The high level of transcription of these genes at
senescence stages was indicated that these genes are senescenceinduced
genes.
Abstract: Environmental micro-organisms include a large number of taxa and some species that are generally considered nonpathogenic, but can represent a risk in certain conditions, especially for elderly people and immunocompromised individuals. Chemotaxonomic identification techniques are powerful tools for environmental micro-organisms, and cellular fatty acid methyl esters (FAME) content is a powerful fingerprinting identification technique. A system based on an unsupervised artificial neural network (ANN) was set up using the fatty acid profiles of standard bacterial strains, obtained by gas-chromatography, used as learning data. We analysed 45 certified strains belonging to Acinetobacter, Aeromonas, Alcaligenes, Aquaspirillum, Arthrobacter, Bacillus, Brevundimonas, Enterobacter, Flavobacterium, Micrococcus, Pseudomonas, Serratia, Shewanella and Vibrio genera. A set of 79 bacteria isolated from a drinking water line (AMGA, the major water supply system in Genoa) were used as an example for identification compared to standard MIDI method. The resulting ANN output map was found to be a very powerful tool to identify these fresh isolates.
Abstract: Brassinosteroids (BRs) regulate cell elongation,
vascular differentiation, senescence, and stress responses. BRs signal
through the BES1/BZR1 family of transcription factors, which
regulate hundreds of target genes involved in this pathway. In this
research a comprehensive genome-wide analysis was carried out in
BES1/BZR1 gene family in Arabidopsis thaliana, Cucumis sativus,
Vitis vinifera, Glycin max and Brachypodium distachyon.
Specifications of the desired sequences, dot plot and hydropathy plot
were analyzed in the protein and genome sequences of five plant
species. The maximum amino acid length was attributed to protein
sequence Brdic3g with 374aa and the minimum amino acid length
was attributed to protein sequence Gm7g with 163aa. The maximum
Instability index was attributed to protein sequence AT1G19350
equal with 79.99 and the minimum Instability index was attributed to
protein sequence Gm5g equal with 33.22. Aliphatic index of these
protein sequences ranged from 47.82 to 78.79 in Arabidopsis
thaliana, 49.91 to 57.50 in Vitis vinifera, 55.09 to 82.43 in Glycin
max, 54.09 to 54.28 in Brachypodium distachyon 55.36 to 56.83 in
Cucumis sativus. Overall, data obtained from our investigation
contributes a better understanding of the complexity of the
BES1/BZR1 gene family and provides the first step towards directing
future experimental designs to perform systematic analysis of the
functions of the BES1/BZR1 gene family.
Abstract: Visfatin and apelin are two new adipokines that recently gained a special interest in diabetes research. This study was conducted to study the interplay between these two adipokines and their correlation with other inflammatory and biochemical parameters in type 2 diabetic (T2D) postmenopausal women with CAD. Visfatin and apelin were measured by enzyme-linked immunoassay (ELISA). Visfatin was found to be significantly higher in the following groups: T2D patients without CAD, non-obese and obese T2D patients with CAD when compared to control group. Apelin was found to be significantly lower in non-obese and obese T2D patients with CAD when compared to control group. Visfatin and apelin were found to be significantly associated with each other and with other biochemical parameters. The current study provides evidence for the interplay between visfatin and apelin through the inflammatory milieu characteristic of T2D and their possible role in the pathogenesis of CAD complication of T2D.
Abstract: Mendelian Disease Genes represent a collection of single points of failure for the various systems they constitute. Such genes have been shown, on average, to encode longer proteins than 'non-disease' proteins. Existing models suggest that this results from the increased likeli-hood of longer genes undergoing mutations. Here, we show that in saturated mutagenesis experiments performed on model organisms, where the likelihood of each gene mutating is one, a similar relationship between length and the probability of a gene being lethal was observed. We thus suggest an extended model demonstrating that the likelihood of a mutated gene to produce a severe phenotype is length-dependent. Using the occurrence of conserved domains, we bring evidence that this dependency results from a correlation between protein length and the number of functions it performs. We propose that protein length thus serves as a proxy for protein cardinality in different networks required for the organism's survival and well-being. We use this example to argue that the collection of Mendelian Disease Genes can, and should, be used to study the rules governing systems vulnerability in living organisms.
Abstract: Serial Analysis of Gene Expression is a powerful
quantification technique for generating cell or tissue gene expression
data. The profile of the gene expression of cell or tissue in several
different states is difficult for biologists to analyze because of the large
number of genes typically involved. However, feature selection in
machine learning can successfully reduce this problem. The method
allows reducing the features (genes) in specific SAGE data, and
determines only relevant genes. In this study, we used a genetic
algorithm to implement feature selection, and evaluate the
classification accuracy of the selected features with the K-nearest
neighbor method. In order to validate the proposed method, we used
two SAGE data sets for testing. The results of this study conclusively
prove that the number of features of the original SAGE data set can be
significantly reduced and higher classification accuracy can be
achieved.
Abstract: Acute disseminated encephalomyelitis (ADEM) has
been reported to develop after a hymenoptera sting, but its
pathogenesis is not known in detail. Myelin basic protein (MBP)-
specific T cells have been detected in the blood of patients with
ADEM, and a proportion of these patients develop multiple sclerosis
(MS). In an attempt to understand the mechanisms underlying
ADEM, molecular mimicry between hymenoptera venom peptides
and the human immunodominant MBP peptide was scrutinized,
based on the sequence and structural similarities, whether it was the
root of the disease. The results suggest that the three wasp venom
peptides have low sequence homology with the human
immunodominant MBP residues 85-99. Structural similarity analysis
among the three venom peptides and the MS-related HLA-DR2b
(DRA, DRB1*1501)-associated immunodominant MHC
binding/TCR contact residues 88-93, VVHFFK showed that
hyaluronidase residues 7-12, phospholipase A1 residues 98-103, and
antigen 5 residues 109-114 showed a high degree of similarity
83.3%, 100%, and 83.3% respectively. In conclusion, some wasp
venom peptides, particularly phospholipase A1, may potentially act
as the molecular motifs of the human 3HLA-DR2b-associated
immunodominant MBP88-93, and possibly present a mechanism for
induction of wasp sting-associated ADEM.
Abstract: The neurogenic potential of many herbal extracts used
in Indian medicine is hitherto unknown. Extracts derived from
Clitoria ternatea Linn have been used in Indian Ayurvedic system of
medicine as an ingredient of “Medhya rasayana", consumed for
improving memory and longevity in humans and also in treatment of
various neurological disorders. Our earlier experimental studies with
oral intubation of Clitoria ternatea aqueous root extract (CTR) had
shown significant enhancement of learning and memory in postnatal
and young adult Wistar rats. The present study was designed to
elucidate the in vitro effects of 200ng/ml of CTR on proliferation,
differentiation and growth of anterior subventricular zone neural
stem cells (aSVZ NSC-s) derived from prenatal and postnatal rat
pups. Results show significant increase in proliferation and growth of
neurospheres and increase in the yield of differentiated neurons of
aSVZ neural precursor cells (aSVZNPC-s) at 7 days in vitro when
treated with 200ng/ml of CTR as compared to age matched control.
Results indicate that CTR has growth promoting neurogenic effect on
aSVZ neural stem cells and their survival similar to neurotrophic
factors like Survivin, Neuregulin 1, FGF-2, BDNF possibly the basis
for enhanced learning and memory.