Abstract: Array-based gene expression analysis is a powerful
tool to profile expression of genes and to generate information on
therapeutic effects of new anti-cancer compounds. Anti-apoptotic
effect of thymoquinone was studied in MCF7 breast cancer cell line
using gene expression profiling with cDNA microarray. The purity
and yield of RNA samples were determined using RNeasyPlus Mini
kit. The Agilent RNA 6000 NanoLabChip kit evaluated the quantity
of the RNA samples. AffinityScript RT oligo-dT promoter primer
was used to generate cDNA strands. T7 RNA polymerase was used to
convert cDNA to cRNA. The cRNA samples and human universal
reference RNA were labelled with Cy-3-CTP and Cy-5-CTP,
respectively. Feature Extraction and GeneSpring softwares analysed
the data. The single experiment analysis revealed involvement of 64
pathways with up-regulated genes and 78 pathways with downregulated
genes. The MAPK and p38-MAPK pathways were
inhibited due to the up-regulation of PTPRR gene. The inhibition of
p38-MAPK suggested up-regulation of TGF-ß pathway. Inhibition of
p38-MAPK caused up-regulation of TP53 and down-regulation of
Bcl2 genes indicating involvement of intrinsic apoptotic pathway.
Down-regulation of CARD16 gene as an adaptor molecule regulated
CASP1 and suggested necrosis-like programmed cell death and
involvement of caspase in apoptosis. Furthermore, down-regulation
of GPCR, EGF-EGFR signalling pathways suggested reduction of
ER. Involvement of AhR pathway which control cytochrome P450
and glucuronidation pathways showed metabolism of Thymoquinone.
The findings showed differential expression of several genes in
apoptosis pathways with thymoquinone treatment in estrogen
receptor-positive breast cancer cells.
Abstract: A simple, rapid and non-invasive electromagnetic sensor (C-FAST device) was- patented; for diagnosis of HCV RNA. Aim: To test the validity of the device compared to standard HCV PCR. Subjects and Methods: The first phase was done as pilot in Egypt on 79 participants; the second phase was done in five centers: one center from Egypt, two centers from Pakistan and two centers from India (800, 92 and 113 subjects respectively). The third phase was done nationally as multicenter study on (1600) participants for ensuring its representativeness. Results: When compared to PCR technique, C-FAST device revealed sensitivity 95% to 100%, specificity 95.5% to 100%, PPV 89.5% to 100%, NPV 95% to 100% and positive likelihood ratios 21.8% to 38.5%. Conclusion: It is practical evidence that HCV nucleotides emit electromagnetic signals that can be used for its identification. As compared to PCR, C-FAST is an accurate, valid and non-invasive device.
Abstract: The purpose of this study was to evaluate the use of
mucus production as a biomarker. This was done by exposing the
mussel Perna perna to various sublethal concentrations of Cu.
Mussels are effective as a bioindicator species as they accumulate Cu
in their tissues. Differences in mucus production rates were evaluated
at different Cu concentrations. The findings of this study indicate that
increasing Cu concentrations had a significant effect on the mucus
production rates over a 24 hour exposure. There were also significant
differences between the mucus production rates at different Cu
concentrations (p < 0.05). Thus, mucus is an essential detoxification
mechanism.
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: Protein structure determination and prediction has
been a focal research subject in the field of bioinformatics due to the
importance of protein structure in understanding the biological and
chemical activities of organisms. The experimental methods used by
biotechnologists to determine the structures of proteins demand
sophisticated equipment and time. A host of computational methods
are developed to predict the location of secondary structure elements
in proteins for complementing or creating insights into experimental
results. However, prediction accuracies of these methods rarely
exceed 70%.
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: The full length mitochondrial small subunit ribosomal
(mt-rns) gene has been characterized for Ophiostoma novo-ulmi
subspecies americana. The gene was also characterized for
Ophiostoma ulmi and a group II intron was noted in the mt-rns gene
of O. ulmi. The insertion in the mt-rns gene is at position S952 and it
is a group IIB1 intron that encodes a double motif LAGLIDADG
homing endonuclease from an open reading frame located within a
loop of domain III. Secondary structure models for the mt-rns RNA
of O. novo-ulmi subsp. americana and O. ulmi were generated to
place the intron within the context of the ribosomal RNA. The in vivo
splicing of the O.ul-mS952 group II intron was confirmed with
reverse transcription-PCR. A survey of 182 strains of Dutch Elm
Diseases causing agents showed that the mS952 intron was absent in
what is considered to be the more aggressive species O. novo-ulmi
but present in strains of the less aggressive O. ulmi. This observation
suggests that the O.ul-mS952 intron can be used as a PCR-based
molecular marker to discriminate between O. ulmi and O. novo-ulmi
subsp. americana.
Abstract: Non-viral gene carriers composed of biodegradable
polymers or lipids have been considered as a safer alternative for gene
carriers over viral vectors. We have developed multi-functional
nano-micelles for both drug and gene delivery application.
Polyethyleneimine (PEI) was modified by grafting stearic acid (SA)
and formulated to polymeric micelles (PEI-SA) with positive surface
charge for gene and drug delivery. Our results showed that PEI-SA
micelles provided high siRNA binding efficiency. In addition, siRNA
delivered by PEI-SA carriers also demonstrated significantly high
cellular uptake even in the presence of serum proteins. The
post-transcriptional gene silencing efficiency was greatly improved by
the polyplex formulated by 10k PEI-SA/siRNA. The amphiphilic
structure of PEI-SA micelles provided advantages for multifunctional
tasks; where the hydrophilic shell modified with cationic charges can
electrostatically interact with DNA or siRNA, and the hydrophobic
core can serve as payloads for hydrophobic drugs, making it a
promising multifunctional vehicle for both genetic and chemotherapy
application.