Abstract: 5-FU is a chemotherapeutic agent that has been used in colorectal cancer (CRC) treatment. However, it is usually associated with the acquired resistance, which decreases the therapeutic effects of 5-FU. miR-200c is involved in chemotherapeutic drug resistance, but its mechanism is not fully understood. In this study, the effect of inhibition of miR-200c in sensitivity of HCT-116 CRC cells to 5-FU was evaluated. HCT-116 cells were transfected with LNA-anti- miR-200c for 48 h. mRNA expression of miR-200c was evaluated using quantitative real- time PCR. The protein expression of phosphatase and tensin homolog (PTEN) and E-cadherin were analyzed by western blotting. Annexin V and propidium iodide staining assay were applied for apoptosis detection. The caspase-3 activation was evaluated by an enzymatic assay. The results showed LNA-anti-miR-200c inhibited the expression of PTEN and E-cadherin protein, apoptosis and activation of caspase 3 compared with control cells. In conclusion, these results suggest that miR-200c as a prognostic marker can overcome to 5-FU chemoresistance in CRC.
Abstract: This study was conducted to evaluate the effect of Echinacea purpurea on the expression of cyclooxygenase-2 (COX-2), interleukin-17F (IL-17F) in seven-day-old broiler chickens. Four groups were fed with concentration of 0 g/kg, 5 g/kg, 10 g/kg and 20 g/kg from the root of E. purpurea in the basal diet and two other groups were only fed with the basal diet for 21 days. At the 28th day, lipopolysaccharide (LPS, 2 mg/kg diet) was injected in four groups and the basal diet group was injected by saline as control. The chickens’ spleen RNA expression was measured for the COX-2 and IL-17F genes by Real-Time PCR. The results have shown that chickens which were fed E. purpurea had a lower COX-2 and IL-17F mRNA expression. The chickens who have received LPS only, lymphocyte was lower than other treatments. Vital organ weights were not significantly different, but body weight loss was recovered by dietary herbs inclusion. The results of this study have shown the positive effect of an anti-inflammatory herb to prevent the undesirable effect of inflammation.
Abstract: Gastric Cancer (GC) has high morbidity and fatality
rate in various countries. It is still one of the most frequent and
deadly diseases. Gastrokine1 (GKN1) and gastrokine2 (GKN2) genes
are highly expressed in the normal stomach epithelium and play
important roles in maintaining the integrity and homeostasis of
stomach mucosal epithelial cells. In this study, 47 paired samples that
were grouped according to the types of gastric cancer and the clinical
characteristics of the patients, including gender and average of age.
They were investigated with gene expression analysis and mutation
screening by monitoring RT-PCR, SSCP and nucleotide sequencing
techniques. Both GKN1 and GKN2 genes were observed significantly
reduced found by (Wilcoxon signed rank test; p
Abstract: Current research is targeting new molecular
mechanisms that underlie non-alcoholic fatty liver disease (NAFLD)
and associated metabolic disorders like non-alcoholic steatohepatitis
(NASH). Forty New Zealand White rabbits have been used and fed a
high protein (HP) and energy diet based on grains and containing
11.76 MJ/kg. Boron added to 3 experimental groups’ drinking waters
(30 mg boron/L) as boron compounds. Biochemical analysis
including boron levels, and nuclear magnetic resonance (NMR) based
metabolomics evaluation, and mRNA expression of peroxisome
proliferator-activated receptor (PPAR) family was performed. LDLcholesterol
concentrations alone were decreased in all the
experimental groups. Boron levels in serum and feces were increased.
Content of acetate was in about 2x higher for anhydrous borax group,
at least 3x higher for boric acid group. PPARα mRNA expression
was significantly decreased in boric acid group. Anhydrous borax
attenuated mRNA levels of PPARγ, which was further suppressed by
boric acid. Boron supplementation decreased the degenerative
alterations in hepatocytes. Except borax group other boron groups did
not have a pronounced change in tubular epithels of kidney. In
conclusion, high protein and energy diet leads hepatocytes’
degenerative changes which can be prevented by boron
supplementation. Boric acid seems to be more effective in this
situation.
Abstract: Agriculture is the backbone of economy of Pakistan
and cotton is the major agricultural export and supreme source of raw
fiber for our textile industry. To combat severe problems of insect
and weed, combination of three genes namely Cry1Ac, Cry2A and
EPSPS genes was transferred in locally cultivated cotton variety
MNH-786 with the use of Agrobacterium mediated genetic
transformation. The present study focused on the molecular screening
of transgenic cotton plants at T3 generation in order to confirm
integration and expression of all three genes (Cry1Ac, Cry2A and
EPSP synthase) into the cotton genome. Initially, glyphosate spray
assay was used for screening of transgenic cotton plants containing
EPSP synthase gene at T3 generation. Transgenic cotton plants which
were healthy and showed no damage on leaves were selected after 07
days of spray. For molecular analysis of transgenic cotton plants in
the laboratory, the genomic DNA of these transgenic cotton plants
were isolated and subjected to amplification of the three genes. Thus,
seventeen out of twenty (Cry1Ac gene), ten out of twenty (Cry2A
gene) and all twenty (EPSP synthase gene) were produced positive
amplification. On the base of PCR amplification, ten transgenic plant
samples were subjected to protein expression analysis through
ELISA. The results showed that eight out of ten plants were actively
expressing the three transgenes. Real-time PCR was also done to
quantify the mRNA expression levels of Cry1Ac and EPSP synthase
gene. Finally, eight plants were confirmed for the presence and active
expression of all three genes at T3 generation.
Abstract: Aim of this work was to study the genetic basis for oil
accumulation in olive fruit via tracking DGAT2 (Diacylglycerol
acyltransferase type-2) gene in three Egyptian Origen Olive cultivars
namely Toffahi, Hamed and Maraki using molecular marker
techniques and bioinformatics tools. Results illustrate that, firstly:
specific genomic band of Maraki cultivars was identified as DGAT2
(Diacylglycerol acyltransferase type-2) and identical for this gene in
Olea europaea with 100% of similarity. Secondly, differential
genomic band of Maraki cultivars which produced from RAPD
fingerprinting technique reflected predicted distinguished sequence
which identified as DGAT2 (Diacylglycerol acyltransferase type-2)
in Fragaria vesca subsp. Vesca with 76% of sequential similarity.
Third and finally, specific genomic specific band of Hamed cultivars
was identified as two fragments, 1- Olea europaea cultivar Koroneiki
diacylglycerol acyltransferase type 2 mRNA, complete cds with two
matches regions with 99% or 2- Predicted: Fragaria vesca subsp.
vesca diacylglycerol O-acyltransferase 2-like (LOC101313050),
mRNA with 86 % of similarity.
Abstract: The MyD88 is an evolutionarily conserved host-expressed adaptor protein that is essential for proper TLR/ IL1R immune-response signaling. A previously identified complete cDNA (1626 bp) of OfMyD88 comprised an ORF of 867 bp encoding a protein of 288 amino acids (32.9 kDa). The gDNA (3761 bp) of OfMyD88 revealed a quinquepartite genome organization composed of 5 exons (with the sizes of 310, 132, 178, 92 and 155 bp) separated by 4 introns. All the introns displayed splice signals consistent with the consensus GT/AG rule. A bipartite domain structure with two domains namely death domain (24-103) coded by 1st exon, and TIR domain (151-288) coded by last 3 exons were identified through in silico analysis. Moreover, homology modeling of these two domains revealed a similar quaternary folding nature between human and rock bream homologs. A comprehensive comparison of vertebrate MyD88 genes showed that they possess a 5-exonic structure.In this structure, the last three exons were strongly conserved, and this suggests that a rigid structure has been maintained during vertebrate evolution.A cluster of TATA box-like sequences were found 0.25 kb upstream of cDNA starting position. In addition, putative 5'-flanking region of OfMyD88 was predicted to have TFBS implicated with TLR signaling, including copies of NFkB1, APRF/ STAT3, Sp1, IRF1 and 2 and Stat1/2. Using qPCR technique, a ubiquitous mRNA expression was detected in liver and blood. Furthermore, a significantly up-regulated transcriptional expression of OfMyD88 was detected in head kidney (12-24 h; >2-fold), spleen (6 h; 1.5-fold), liver (3 h; 1.9-fold) and intestine (24 h; ~2-fold) post-Fla challenge. These data suggest a crucial role for MyD88 in antibacterial immunity of teleosts.
Abstract: We study the molecular evolution of insulin from metric geometry point of view. In mathematics, and in particular in geometry, distances and metrics between objects are of fundamental importance.
Using a weaker notion than the classical distance, namely the weighted quasi-metrics, one can study the geometry of biological
sequences (DNA, mRNA, or proteins) space.
We analyze from geometrical point of view a family of 60 insulin homologous sequences ranging on a large variety of living organisms from human to the nematode C. elegans. We show that the distances between sequences provide important information about the evolution and function of insulin.
Abstract: An expressed sequence tag (EST) analysis provideus portions of expressed genes. We have constructed cDNA library and determined randomly sequences from cDNA library clones of T. molitor injected with acholeplasma lysate. We identified the homologous to a galectin gene. As the result of cloning and characterization of novel, we found that the protein has an open reading frame (ORF) of 495 bp, with 164 amino acid residues and molecular weight of 18.5 kDa. To characterize the role of novel Tm-galectin in immune system, we quantified the mRNA level of galectin at different times after treatment with immune elicitors. The galectin mRNA was up-regulated about 7-folds within 18 hrs. This suggests that Tm-galectin is a novel member of animal lectins, and has a role in the process of pathogen recognition. Our study would be helpful for the study on immune defense system and signaling cascade.
Abstract: Inferring the network structure from time series data
is a hard problem, especially if the time series is short and noisy.
DNA microarray is a technology allowing to monitor the mRNA
concentration of thousands of genes simultaneously that produces
data of these characteristics. In this study we try to investigate the
influence of the experimental design on the quality of the result.
More precisely, we investigate the influence of two different types of
random single gene perturbations on the inference of genetic networks
from time series data. To obtain an objective quality measure for
this influence we simulate gene expression values with a biologically
plausible model of a known network structure. Within this framework
we study the influence of single gene knock-outs in opposite to
linearly controlled expression for single genes on the quality of the
infered network structure.
Abstract: Among all microRNAs (miRNAs) in 12 plant species investigated in this study, only miR398 targeted the copper chaperone for superoxide dismutase (CCS). The nucleotide sequences of miRNA binding sites were located in the mRNA protein-coding sequence (CDS) and were highly homologous. These binding sites in CCS mRNA encoded a conservative GDLGTL hexapeptide. The binding sites for miR398 in the CDS of superoxide dismutase 1 mRNA encoded GDLGN pentapeptide. The conservative miR398 binding site located in the CDS of superoxide dismutase 2 mRNA encoded the GDLGNI hexapeptide. The miR398 binding site in the CDS of superoxide dismutase 3 mRNA encoded the GDLGNI or GDLGNV hexapeptide. Gene expression of the entire superoxide dismutase family in the studied plant species was regulated only by miR398. All members of the miR398 family, i.e. miR398a,b,c were connected to one site for each CuZnSOD and chaperone mRNA.
Abstract: MiRNAs participate in gene regulation of translation.
Some studies have investigated the interactions between genes and
intragenic miRNAs. It is important to study the miRNA binding sites
of genes involved in carcinogenesis. RNAHybrid 2.1 and ERNAhybrid
programmes were used to compute the hybridization free
energy of miRNA binding sites. Of these 54 mRNAs, 22.6%, 37.7%,
and 39.7% of miRNA binding sites were present in the 5'UTRs,
CDSs, and 3'UTRs, respectively. The density of the binding sites for
miRNAs in the 5'UTR ranged from 1.6 to 43.2 times and from 1.8 to
8.0 times greater than in the CDS and 3'UTR, respectively. Three
types of miRNA interactions with mRNAs have been revealed: 5'-
dominant canonical, 3'-compensatory, and complementary binding
sites. MiRNAs regulate gene expression, and information on the
interactions between miRNAs and mRNAs could be useful in
molecular medicine. We recommend that newly described sites
undergo validation by experimental investigation.
Abstract: Microarrays technique allows the simultaneous measurements of the expression levels of thousands of mRNAs. By mining this data one can identify the dynamics of the gene expression time series. By recourse of principal component analysis, we uncover the circadian rhythmic patterns underlying the gene expression profiles from Cyanobacterium Synechocystis. We applied PCA to reduce the dimensionality of the data set. Examination of the components also provides insight into the underlying factors measured in the experiments. Our results suggest that all rhythmic content of data can be reduced to three main components.
Abstract: Human genome is not only the evolutionary
summation of all advantageous events, but also houses lesions of
deleterious foot prints. A single gene mutation sometimes may
express multiple consequences in numerous tissues and a linear
relationship of the genotype and the phenotype may often be obscure.
ß Thalassemia minor, a transfusion independent mild anaemia,
coupled with environment among other factors may articulate into
phenotypic pleotropy with Hypocholesterolemia, Vitamin D
deficiency, Tissue hypoxia, Hyper-parathyroidism and Psychological
alterations. Occurrence of Pancreatic insufficiency, resultant
steatorrhoea, Vitamin-D (25-OH) deficiency (13.86 ngm/ml) with
Hypocholesterolemia (85mg/dl) in a 30 years old male ß Thal-minor
patient (Hemoglobin 11mg/dl with Fetal Hemoglobin 2.10%, Hb A2
4.60% and Hb Adult 84.80% and altered Hemogram) with increased
Para thyroid hormone (62 pg/ml) & moderate Serum Ca+2
(9.5mg/ml) indicate towards a cascade of phenotypic pleotropy
where the ß Thalassemia mutation ,be it in the 5’ cap site of the
mRNA , differential splicing etc in heterozygous state is effecting
several metabolic pathways. Compensatory extramedulary
hematopoiesis may not coped up well with the stressful life style of
the young individual and increased erythropoietic stress with high
demand for cholesterol for RBC membrane synthesis may have
resulted in Hypocholesterolemia.Oxidative stress and tissue hypoxia
may have caused the pancreatic insufficiency, leading to Vitamin D
deficiency. This may in turn have caused the secondary
hyperparathyroidism to sustain serum Calcium level. Irritability and
stress intolerance of the patient was a cumulative effect of the vicious
cycle of metabolic compromises. From these findings we propose
that the metabolic deficiencies in the ß Thalassemia mutations may
be considered as the phenotypic display of the pleotropy to explain
the genetic epidemiology.
According to the recommendations from the NIH Workshop on
Gene-Environment Interplay in Common Complex Diseases: Forging
an Integrative Model, study design of observations should be
informed by gene-environment hypotheses and results of a study
(genetic diseases) should be published to inform future hypotheses.
Variety of approaches is needed to capture data on all possible
aspects, each of which is likely to contribute to the etiology of
disease. Speakers also agreed that there is a need for development of
new statistical methods and measurement tools to appraise
information that may be missed out by conventional method where
large sample size is needed to segregate considerable effect.
A meta analytic cohort study in future may bring about significant
insight on to the title comment.
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: COPD is characterized by loss of elastic fibers from
small airways and alveolar walls, with the decrease in elastin
increasing with disease severity. It is unclear why there is a lack of
repair of elastic fibers. We have examined fibroblasts cultured from
lung tissue from normal and COPD subjects to determine if the
secretory profile explains lack of tissue repair. In this study,
fibroblasts were cultured from lung parenchyma of bronchial
carcinoma patients with varying degrees of COPD; controls
(non-COPD, n=5), mild COPD (GOLD 1, n=5) and moderate-severe
COPD (GOLD 2-3, n=12). Measurements were made of proliferation,
senescence-associated beta-galactosidase-1, mRNA expression of
IL-6, IL-8, MMP-1, tropoelastin and versican, and protein levels for
IL-6, IL-8, PGE2, tropoelastin, insoluble elastin, and versican. It was
found that GOLD 2-3 fibroblasts proliferated more slowly (p
Abstract: The small interfering RNA (siRNA) alters the
regulatory role of mRNA during gene expression by translational
inhibition. Recent studies show that upregulation of mRNA because
serious diseases like cancer. So designing effective siRNA with good
knockdown effects plays an important role in gene silencing. Various
siRNA design tools had been developed earlier. In this work, we are
trying to analyze the existing good scoring second generation siRNA
predicting tools and to optimize the efficiency of siRNA prediction
by designing a computational model using Artificial Neural Network
and whole stacking energy (%G), which may help in gene silencing
and drug design in cancer therapy. Our model is trained and tested
against a large data set of siRNA sequences. Validation of our results
is done by finding correlation coefficient of experimental versus
observed inhibition efficacy of siRNA. We achieved a correlation
coefficient of 0.727 in our previous computational model and we
could improve the correlation coefficient up to 0.753 when the
threshold of whole tacking energy is greater than or equal to -32.5
kcal/mol.
Abstract: In this paper we investigate the influence of external
noise on the inference of network structures. The purpose of our
simulations is to gain insights in the experimental design of microarray
experiments to infer, e.g., transcription regulatory networks
from microarray experiments. Here external noise means, that the
dynamics of the system under investigation, e.g., temporal changes of
mRNA concentration, is affected by measurement errors. Additionally
to external noise another problem occurs in the context of microarray
experiments. Practically, it is not possible to monitor the mRNA
concentration over an arbitrary long time period as demanded by the
statistical methods used to learn the underlying network structure. For
this reason, we use only short time series to make our simulations
more biologically plausible.
Abstract: Bone marrow-derived stem cells have been widely
studied as an alternative source of stem cells. Mesenchymal stem
cells (MSCs) were mostly investigated and studies showed MSCs can
promote neurogenesis. Little is known about the non-mesenchymal
mononuclear cell fraction, which contains both hematopoietic and
nonhematopoietic cells, including monocytes and endothelial
progenitor cells. This study focused on unfractionated bone marrow
mononuclear cells (BMMCs), which remained 72 h after MSCs were
adhered to the culture plates. We showed that BMMC-conditioned
medium promoted morphological changes of human SH-SY5Y
neuroblastoma cells from an epithelial-like phenotype towards a
neuron-like phenotype as indicated by an increase in neurite
outgrowth, like those observed in retinoic acid (RA)-treated cells.
The result could be explained by the effects of trophic factors
released from BMMCs, as shown in the RT-PCR results that
BMMCs expressed nerve growth factor (NGF), brain-derived
neurotrophic factor (BDNF), and ciliary neurotrophic factor (CNTF).
Similar results on the cell proliferation rate were also observed
between RA-treated cells and cells cultured in BMMC-conditioned
medium, suggesting that cells creased proliferating and differentiated
into a neuronal phenotype. Using real-time RT-PCR, a significantly
increased expression of tyrosine hydroxylase (TH) mRNA in SHSY5Y
cells indicated that BMMC-conditioned medium induced
catecholaminergic identities in differentiated SH-SY5Y cells.
Abstract: Tumour suppressors are key participants in the
prevention of cancer. Regulation of their expression through
miRNAs is important for comprehensive translation inhibition of
tumour suppressors and elucidation of carcinogenesis mechanisms.
We studies the possibility of 1521 miRNAs to bind with 873 mRNAs
of human tumour suppressors using RNAHybrid 2.1 and ERNAhybrid
programmes. Only 978 miRNAs were found to be
translational regulators of 812 mRNAs, and 61 mRNAs did not have
any miRNA binding sites. Additionally, 45.9% of all miRNA binding
sites were located in coding sequences (CDSs), 33.8% were located
in 3' untranslated region (UTR), and 20.3% were located in the
5'UTR. MiRNAs binding with more than 50 target mRNAs and
mRNAs binding with several miRNAs were selected. Hsa-miR-5096
had 15 perfectly complementary binding sites with mRNAs of 14
tumour suppressors. These newly indentified miRNA binding sites
can be used in the development of medicines (anti-sense therapies)
for cancer treatment.