Abstract: Hyphal growth and the transcriptional regulation to the host environment are key issues during the pathogenesis of C. albicans. Tec1p is the C. albicans homolog of a TEA transcription factor family, which share a conserved DNA-binding TEA domain in their N-terminal. In order to define a structure-function relationship of the C. albicans Tec1p protein, we constructed several mutations on the N terminal, C terminal or in the TEA binding domain itself by homologous recombination technology. The modifications in the open reading frame of TEC1 were tested for reconstitution of the morphogenetic development of the tec1/tec1 mutant strain CaAS12. Mutation in the TEA consensus sequence did not confer transition to hyphae whereas the reconstitution of the full-length Tec1p has reconstituted hyphal development. A deletion in one of glutamine-rich regions either in the Tec1p N-terminal or the C-terminal in regions of 53-212 or 637–744 aa, respectively, did not restore morphological development in mutant CaAS12 strain. Whereas, the reconstitution with Tec1p mutants other than the glutamate-rich region has restored the morphogenetic switch. Additionally, the deletion of the glutamine-rich region has attenuated the invasive growth and the heat shock resistance of C. albicans. In conclusion, we show that a glutamine-rich region of Tec1p is essential for the hyphal development and mediating adaptation to the host environment of C. albicans.
Abstract: GRF, Growth regulating factor, genes encode a novel
class of plant-specific transcription factors. The GRF proteins play a
role in the regulation of cell numbers in young and growing tissues
and may act as transcription activations in growth and development
of plants. Identification of GRF genes and their expression are
important in plants to performance of the growth and development of
various organs. In this study, to better understanding the structural
and functional differences of GRFs family, 45 GRF proteins
sequences in A. thaliana, Z. mays, O. sativa, B. napus, B. rapa, H.
vulgare and S. bicolor, have been collected and analyzed through
bioinformatics data mining. As a result, in secondary structure of
GRFs, the number of alpha helices was more than beta sheets and in
all of them QLQ domains were completely in the biggest alpha helix.
In all GRFs, QLQ and WRC domains were completely protected
except in AtGRF9. These proteins have no trans-membrane domain
and due to have nuclear localization signals act in nuclear and they
are component of unstable proteins in the test tube.
Abstract: Various cis-regulatory module (CRM) predictors have been proposed in the last decade. Several well-established CRM predictors adopted different categories of prediction strategies, including window clustering, probabilistic modeling and phylogenetic footprinting. Appropriate integration of them has a potential to achieve high quality CRM prediction. This study analyzed four existing CRM predictors (ClusterBuster, MSCAN, CisModule and MultiModule) to seek a predictor combination that delivers a higher accuracy than individual CRM predictors. 465 CRMs across 140 Drosophila melanogaster genes from the RED fly database were used to evaluate the integrated CRM predictor proposed in this study. The results show that four predictor combinations achieved superior performance than the best individual CRM predictor.
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: Yeast cells live in a constantly changing environment that requires the continuous adaptation of their genomic program in order to sustain their homeostasis, survive and proliferate. Due to the advancement of high throughput technologies, there is currently a large amount of data such as gene expression, gene deletion and protein-protein interactions for S. Cerevisiae under various environmental conditions. Mining these datasets requires efficient computational methods capable of integrating different types of data, identifying inter-relations between different components and inferring functional groups or 'modules' that shape intracellular processes. This study uses computational methods to delineate some of the mechanisms used by yeast cells to respond to environmental changes. The GRAM algorithm is first used to integrate gene expression data and ChIP-chip data in order to find modules of coexpressed and co-regulated genes as well as the transcription factors (TFs) that regulate these modules. Since transcription factors are themselves transcriptionally regulated, a three-layer regulatory cascade consisting of the TF-regulators, the TFs and the regulated modules is subsequently considered. This three-layer cascade is then modeled quantitatively using artificial neural networks (ANNs) where the input layer corresponds to the expression of the up-stream transcription factors (TF-regulators) and the output layer corresponds to the expression of genes within each module. This work shows that (a) the expression of at least 33 genes over time and for different stress conditions is well predicted by the expression of the top layer transcription factors, including cases in which the effect of up-stream regulators is shifted in time and (b) identifies at least 6 novel regulatory interactions that were not previously associated with stress-induced changes in gene expression. These findings suggest that the combination of gene expression and protein-DNA interaction data with artificial neural networks can successfully model biological pathways and capture quantitative dependencies between distant regulators and downstream genes.
Abstract: NFκB is a transcription factor regulating many
function of the vessel wall. In the normal condition , NFκB is
revealed diffuse cytoplasmic expressionsuggesting that the system is
inactive. The presence of activation NFκB provide a potential
pathway for the rapid transcriptional of a variety of genes encoding
cytokines, growth factors, adhesion molecules and procoagulatory
factors. It is likely to play an important role in chronic inflamatory
disease involved atherosclerosis. There are many stimuli with the
potential to active NFκB, including hyperlipidemia. We used 24 mice
which was divided in 6 groups. The HFD given by et libitum
procedure during 2, 4, and 6 months. The parameters in this study
were the amount of NFKB activation ,H2O2 as ROS and VCAM-1 as
a product of NFKB activation. H2O2 colorimetryc assay performed
directly using Anti Rat H2O2 ELISA Kit. The NFKB and VCAM-1
detection obtained from aorta mice, measured by ELISA kit and
imunohistochemistry. There was a significant difference activation of
H2O2, NFKB and VCAM-1 level at induce HFD after 2, 4 and 6
months. It suggest that HFD induce ROS formation and increase the
activation of NFKB as one of atherosclerosis marker that caused by
hyperlipidemia as classical atheroschlerosis risk factor.
Abstract: Transcription factor p53 has a powerful tumor
suppressing function that is associated with many cancers. However,
p53 of the molecular weight was higher make the limitation across to
skin or cell membrane. Thymidine dinucleotide (pTT), an
oligonucleotide, can activate the p53 transcription factor. pTT is a
hydrophilic and negative charge oligonucleotide, which delivery in to
cell membrane need an appropriate carrier. The aim of this study was
to improve the bioavailability of the nucleotide fragment, thymidine
dinucleotide (pTT), using elasic liposome carriers to deliver the drug
into the skin. The study demonstrate that dioleoylphosphocholine
(DOPC) incorporated with sodium cholate at molar ratio 1:1 can
archived the particle size about 220 nm. This elastic liposome could
penetration through skin from stratum corneum to whole epidermis by
confocal laser scanning microscopy (CLSM). Moreover, we observed
the the slight increase in generation of p53 by western blot.
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: MicroRNAs (miRNAs) are small, non-coding and
regulatory RNAs about 20 to 24 nucleotides long. Their conserved
nature among the various organisms makes them a good source of
new miRNAs discovery by comparative genomics approach. The
study resulted in 21 miRNAs of 20 pre-miRNAs belonging to 16
families (miR156, 157, 158, 164, 165, 168, 169, 172, 319, 390, 393,
394, 395, 400, 472 and 861) in evergreen spruce tree (Picea). The
miRNA families; miR 157, 158, 164, 165, 168, 169, 319, 390, 393,
394, 400, 472 and 861 are reported for the first time in the Picea. All
20 miRNA precursors form stable minimum free energy stem-loop
structure as their orthologues form in Arabidopsis and the mature
miRNA reside in the stem portion of the stem loop structure. Sixteen
(16) miRNAs are from Picea glauca and five (5) belong to Picea
sitchensis. Their targets consist of transcription factors, growth
related, stressed related and hypothetical proteins.
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: Bones are dynamic and responsive organs, they
regulate their strength and mass according to the loads which they are subjected. Because, the Wnt/β-catenin pathway has profound
effects on the regulation of bone mass, we hypothesized that mechanical loading of bone cells stimulates Wnt/β-catenin signaling, which results in the generation of new bone mass.
Mechanical loading triggers the secretion of the Wnt molecule, which after binding to transmembrane proteins, causes GSK-3β (Glycogen synthase kinase 3 beta) to cease the phosphorylation of β-catenin. β-catenin accumulation in the cytoplasm, followed by its
transport into the nucleus, binding to transcription factors (TCF/LEF)
that initiate transcription of genes related to bone formation. To test this hypothesis, we used TOPGAL (Tcf Optimal Promoter
β-galactosidase) mice in an experiment in which cyclic loads were
applied to the forearm. TOPGAL mice are reporters for cells effected
by the Wnt/β-catenin signaling pathway. TOPGAL mice are genetically engineered mice in which transcriptional activation of β-
catenin, results in the production of an enzyme, β-galactosidase. The
presence of this enzyme allows us to localize transcriptional
activation of β-catenin to individual cells, thereby, allowing us to quantify the effects that mechanical loading has on the Wnt/β-catenin pathway and new bone formation. The ulnae of loaded TOPGAL
mice were excised and transverse slices along different parts of the
ulnar shaft were assayed for the presence of β-galactosidase.
Our results indicate that loading increases β-catenin transcriptional
activity in regions where this pathway is already primed (i.e. where basal activity is already higher) in a load magnitude dependent
manner. Further experiments are needed to determine the temporal and spatial activation of this signaling in relation to bone formation.
Abstract: Candida albicans ATCC 10231 had low endogenous activity of the alternative oxidase compared with that of C. albicans ATCC 10261. In C. albicans ATCC 10231 the endogenous activity declined as the cultures aged. Alternative oxidase activity could be induced in C. albicans ATCC 10231 by treatment with cyanide, but the induction of this activity required the presence of oxygen which could be replaced, at least in part, with high concentrations of potassium ferricyanide. We infer from this that the expression of the gene encoding the alternative oxidase is under the control of a redoxsensitive transcription factor.