Abstract: MicroRNAs are small non-coding RNA found in
many different species. They play crucial roles in cancer such as
biological processes of apoptosis and proliferation. The identification
of microRNA-target genes can be an essential first step towards to
reveal the role of microRNA in various cancer types. In this paper,
we predict miRNA-target genes for lung cancer by integrating
prediction scores from miRanda and PITA algorithms used as a
feature vector of miRNA-target interaction. Then, machine-learning
algorithms were implemented for making a final prediction. The
approach developed in this study should be of value for future studies
into understanding the role of miRNAs in molecular mechanisms
enabling lung cancer formation.
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: Cancer is still one of the serious diseases threatening
the lives of human beings. How to have an early diagnosis and
effective treatment for tumors is a very important issue. The animal
carcinoma model can provide a simulation tool for the studies of
pathogenesis, biological characteristics, and therapeutic effects.
Recently, drug delivery systems have been rapidly developed to
effectively improve the therapeutic effects. Liposome plays an
increasingly important role in clinical diagnosis and therapy for
delivering a pharmaceutic or contrast agent to the targeted sites.
Liposome can be absorbed and excreted by the human body, and is
well known that no harm to the human body. This study aimed to
compare the therapeutic effects between encapsulated (doxorubicin
liposomal, Lipodox) and un-encapsulated (doxorubicin, Dox)
anti-tumor drugs using magnetic resonance imaging (MRI).
Twenty-four New Zealand rabbits implanted with VX2 carcinoma at
left thighs were classified into three groups: control group (untreated),
Dox-treated group, and LipoDox-treated group, 8 rabbits for each
group. MRI scans were performed three days after tumor implantation.
A 1.5T GE Signa HDxt whole body MRI scanner with a high
resolution knee coil was used in this study. After a 3-plane localizer
scan was performed, three-dimensional (3D) fast spin echo (FSE)
T2-weighted Images (T2WI) was used for tumor volumetric
quantification. Afterwards, two-dimensional (2D) spoiled gradient
recalled echo (SPGR) dynamic contrast-enhanced (DCE) MRI was
used for tumor perfusion evaluation. DCE-MRI was designed to
acquire four baseline images, followed by contrast agent Gd-DOTA
injection through the ear vein of rabbit. A series of 32 images were
acquired to observe the signals change over time in the tumor and
muscle. The MRI scanning was scheduled on a weekly basis for a
period of four weeks to observe the tumor progression longitudinally.
The Dox and LipoDox treatments were prescribed 3 times in the first
week immediately after the first MRI scan; i.e. 3 days after VX2 tumor
implantation. ImageJ was used to quantitate tumor volume and time
course signal enhancement on DCE images. The changes of tumor size
showed that the growth of VX2 tumors was effectively inhibited for
both LipoDox-treated and Dox-treated groups. Furthermore, the tumor
volume of LipoDox-treated group was significantly lower than that of
Dox-treated group, which implies that LipoDox has better therapeutic effect than Dox. The signal intensity of LipoDox-treated group is
significantly lower than that of the other two groups, which implies
that targeted therapeutic drug remained in the tumor tissue. This study
provides a radiation-free and non-invasive MRI method for
therapeutic monitoring of targeted liposome on an animal tumor
model.
Abstract: Wheat is the first and the most important grain of the
world and its bakery property is due to glutenin and gliadin qualities.
Wheat seed proteins were divided into four groups according to
solubility including albumin, globulin, glutenin and prolamin or
gliadin. Gliadins are major components of the storage proteins in
wheat endosperm. It seems that little information is available about
gliadin genes in Iranian wild relatives of wheat. Thus, the aim of this
study was the evaluation of the wheat wild relatives collected from
different origins of Zagros Mountains in Iran, in terms of coding
gliadin genes using specific primers. For this, forty accessions of
Triticum boeoticum and Triticum urartu were selected for this study.
For each accession, genomic DNA was extracted and PCRs were
performed in total volumes of 15 μl. The amplification products were
separated on 1.5% agarose gels. In results, for Gli-2A locus three
allelic variants were detected by Gli-2As primer pairs. The sizes of
PCR products for these alleles were 210, 490 and 700 bp. Only five
(13%) and two accessions (5%) produced 700 and 490 bp fragments
when their DNA was amplified with the Gli.As.2 primer pairs.
However, 93% of the accessions carried allele 210 bp, and only 8%
did not any product for this marker. Therefore, these germplasm
could be used as rich gene pool to broaden the genetic base of bread
wheat.
Abstract: Tannins are a unique category of plant phytochemicals
especially in terms of their vast potential health-benefiting properties.
Researchers have described the capacity of tannins to enhance
glucose uptake and inhibit adipogenesis, thus being potential drugs
for the treatment of non-insulin dependent diabetes mellitus. Thus,
the present research was conducted to find out tannin content of food
products. The percentage of tannin in various analyzed sources
ranged from 0.0 to 108.53%; highest in kathaa and lowest in ker and
mango bark. The percentage of tannins present in the plants,
however, varies. Numerous studies have confirmed that the naturally
occurring polyphenols are key factor for the beneficial effects of the
herbal medicines. Isolation and identification of active constituents
from plants, preparation of standardized dose & dosage regimen can
play a significant role in improving the hypoglycaemic action.
Abstract: Massive rock avalanches formed some of the largest landslide deposits on Earth and they represent one of the major geohazards in high-relief mountains. This paper interprets a very large sedimentary fan (the Sernio fan, Valtellina, Northern Italy), located 20 Km SW from Val Pola Rock avalanche (1987), as the deposit of a partial collapse of a Deep Seated Gravitational Slope Deformation (DSGSD), afterwards eroded and buried by debris flows. The proposed emplacement sequence has been reconstructed based on geomorphological, structural and mechanical evidences. The Sernio fan is actually considered anomalous with reference to the very high ratio between the fan area (≈ 4.5km2) and the basin area (≈ 3km2). The morphology of the fan area is characterised by steep slopes (dip ≈ 20%) and the fan apex is extended for 1.8 km inside the small catchment basin. This sedimentary fan was originated by a landslide that interested a part of a large deep-seated gravitational slope deformation, involving a wide area of about 55 km². The main controlling factor is tectonic and it is related to the proximity to regional fault systems and the consequent occurrence of fault weak rocks (GSI locally lower than 10 with compressive stress lower than 20MPa). Moreover, the fan deposit shows sedimentary evidences of recent debris flow events. The best current explanation of the Sernio fan involves an initial failure of some hundreds of Mm3. The run-out was quite limited because of the morphology of Valtellina’s valley floor, and the deposit filled the main valley forming a landslide dam, as confirmed by the lacustrine deposits detected upstream the fan. Nowadays the debris flow events represent the main hazard in the study area.
Abstract: Several embryonic cellular mechanism including cell
cycle, growth and apoptosis are regulated by phosphatidylinositol-3-
kinase (PI3K)/Akt signaling pathway. The goal of present study is to
determine the effects of annatto (Bixa orellana)-derived δ-tocotrienol
(δ-TCT) on the regulations of PI3K/Akt genes in murine morula.
Twenty four 6-8 week old (23-25g) female balb/c mice were
randomly divided into four groups (G1-G4; n=6). Those groups were
subjected to the following treatments for 7 consecutive days: G1
(control) received tocopherol stripped corn oil, G2 was given 60
mg/kg/day of δ-TCT mixture (contains 90% delta & 10% gamma
isomers), G3 was given 60 mg/kg/day of pure δ-TCT (>98% purity)
and G4 received 60 mg/kg/day α-TOC. On Day 8, females were
superovulated with 5 IU Pregnant Mare’s Serum Gonadotropin
(PMSG) for 48 hours followed with 5 IU human Chorionic
Gonadotropin (hCG) before mated with males at the ratio of 1:1.
Females were sacrificed by cervical dislocation for embryo collection
48 hours post-coitum. About fifty morulas from each group were
used in the gene expression analyses using Affymetrix QuantiGene
Plex 2.0 Assay. Present data showed a significant increase (p
Abstract: In this study, lipid-deprived residuals of microalgae
were hydrolyzed for the production of reducing sugars by using the
recombinant Bacillus cellulosome, carrying eight genes from the
Clostridium thermocellum ATCC27405. The obtained cellulosome
was found to exist mostly in the broth supernatant with a cellulosome
activity of 2.4 U/mL. Furthermore, the Michaelis-Menten constant
(Km) and Vmax of cellulosome were found to be 14.832 g/L and 3.522
U/mL. The activation energy of the cellulosome to hydrolyze
microalgae LDRs was calculated as 32.804 kJ/mol.
Abstract: In the immunologic sense, clinical infection is a state
of failure of the immune system to combat the pathogenic weapon of
the bacteria invading the host. A motile gram negative vibroid
organism associated with marked mono and poly nuclear cell
responses was traced during the examination of a clinical material
from an infected common carp Cyprinus carpio. On primary plate
culture, growth was shown to be pure, dense population of an
Aeromonas-like colony morphotype. The pure isolate was found to
be; Aerobic, facultatively anaerobic, non-halophilic, grew at 0C, and
37C, oxidase positive utilizes glucose through fermentative pathway,
resist 0/129 and novobiocin, produces alanine and lysine
decarboxylases but non-producing ornithine dehydrolases. Tests for
the in vitro determinants of pathogenicity has shown to be; Betahaemolytic
onto blood agar, gelatinase, casienase and amylase
producer. Three in vivo determinants of pathogenicity were tested as,
the lethal dose fifty, the pathogenesis and pathogenicity. It was
evident that 0.1 milliliter of the causal bacterial cell suspension of a
density 1 x 107 CFU/ml injected intramuscularly into an average of
100gms fish toke five days incubation period, then at the day six
morbidity and mortality were initiated. LD50 was recorded at the day
12 post-infection. Use of an LD50 doses to study the pathogenicity,
reveals mononuclear and polynuclear cell responses, on examining
the stained direct films of the clinical materials from the
experimentally infected fish. Re-isolation tests confirm that the reisolant
is same. The course of the infection in natural case was shown
manifestation of; skin ulceration, haemorrhage and descaling. On
evisceration, the internal organs were shown; congestion in the
intestines, spleen and, air sacs. The induced infection showed a
milder form of these manifestations. The grading of the virulence of
this organism was virulent causing chronic course of infections as
indicated from the pathogenesis and pathogenicity studies. Thus the
infectious bacteria were consistent with Aeromonas hydrophila, and
the infection was chronic.
Abstract: Methicillin/multiple-resistant Staphylococcus aureus
(MRSA) are infectious bacteria that are resistant to common
antibiotics. A previous in silico study in our group has identified a
hypothetical protein SAV1226 as one of the potential drug targets. In
this study, we reported the bioinformatics characterization, as well as
cloning, expression, purification and kinetic assays of hypothetical
protein SAV1226 from methicillin/vancomycin-resistant
Staphylococcus aureus Mu50 strain. MALDI-TOF/MS analysis
revealed a low degree of structural similarity with known proteins.
Kinetic assays demonstrated that hypothetical protein SAV1226 is
neither a domain of an ATP dependent dihydroxyacetone kinase nor
of a phosphotransferase system (PTS) dihydroxyacetone kinase,
suggesting that the function of hypothetical protein SAV1226 might
be misannotated on public databases such as UniProt and
InterProScan 5.
Abstract: For the music composer Myriam Marbe the musical
time and memory represent 2 (complementary) phenomena with
conclusive impact on the settlement of new musical ontologies.
Summarizing the most important achievements of the contemporary
techniques of composition, her vision on the microform presented in
The Concert for Daniel Kientzy, saxophone and orchestra transcends
the linear and unidirectional time in favour of a flexible, multivectorial
speech with spiral developments, where the sound substance
is auto(re)generated by analogy with the fundamental processes of
the memory. The conceptual model is of an archetypal essence, the
music composer being concerned with identifying the mechanisms of
the creation process, especially of those specific to the collective
creation (of oral tradition). Hence the spontaneity of expression,
improvisation tint, free rhythm, micro-interval intonation, coloristictimbral
universe dominated by multiphonics and unique sound
effects, hence the atmosphere of ritual, however purged by the
primary connotations and reprojected into a wonderful spectacular
space. The Concert is a work of artistic maturity and enforces respect,
among others, by the timbral diversity of the three species of
saxophone required by the music composer (baritone, sopranino and
alt), in Part III Daniel Kientzy shows the performance of playing two
saxophones concomitantly. The score of the music composer Myriam
Marbe contains a deeply spiritualized music, full or archetypal
symbols, a music whose drama suggests a real cinematographic
movement.
Abstract: Kidney cancer is the most lethal urological cancer
accounting for 3% of adult malignancies. VHL, a tumor-suppressor
gene, is best known to be associated with renal cell carcinoma
(RCC). The VHL functions as negative regulator of hypoxia inducible
factors. Recent sequencing efforts have identified several novel
frequent mutations of histone modifying and chromatin remodeling
genes in ccRCC (clear cell RCC) including PBRM1 and SETD2. The
PBRM1 gene encodes the BAF180 protein, which involved in
transcriptional activation and repression of selected genes. SETD2
encodes a histone methyltransferase, which may play a role in
suppressing tumor development. In this study, RNAs of 30 paired
tumor and normal samples that were grouped according to the types
of kidney cancer and clinical characteristics of patients, including
gender and average age were examined by RT-PCR, SSCP and
sequencing techniques. VHL, PBRM1 and SETD2 expressions were
relatively down-regulated. However, statistically no significance was
found (Wilcoxon signed rank test, p>0.05). Interestingly, no mutation
was observed on the contrary of previous studies. Understanding the
molecular mechanisms involved in the pathogenesis of RCC has
aided the development of molecular-targeted drugs for kidney cancer.
Further analysis is required to identify the responsible genes rather
than VHL, PBRM1 and SETD2 in kidney cancer.
Abstract: The mechanisms underlying the association between
obesity and asthma may be related to a decreased immunological
tolerance induced by a defective function of regulatory T cells
(Tregs). The aim of this study is to establish the potential link
between these diseases and CD4+, CD25+ FoxP3+ Tregs as well as T
helper cells (Ths) in children. This is a prospective case control
study. Obese (n:40), asthmatic (n:40), asthmatic obese (n:40) and
healthy children (n:40), who don't have any acute or chronic diseases,
were included in this study. Obese children were evaluated according
to WHO criteria. Asthmatic patients were chosen based on GINA
criteria. Parents were asked to fill up the questionnaire. Informed
consent forms were taken. Blood samples were marked with CD4+,
CD25+ and FoxP3+ in order to determine Tregs and Ths by flow
cytometric method. Statistical analyses were performed. p≤0.05 was
chosen as meaningful threshold. Tregs exhibiting anti-inflammatory
nature were significantly lower in obese (0,16%; p≤0,001), asthmatic
(0,25%; p≤0,01) and asthmatic obese (0,29%; p≤0,05) groups than
the control group (0,38%). Ths were counted higher in asthma group
than the control (p≤0,01) and obese (p≤0,001) groups. T cell
immunity plays important roles in obesity and asthma pathogeneses.
Decreased numbers of Tregs found in obese, asthmatic and asthmatic
obese children may help to elucidate some questions in
pathophysiology of these diseases. For HOMA-IR levels, any
significant difference was not noted between control and obese
groups, but statistically higher values were found for obese
asthmatics. The values obtained in all groups were found to be below
the critical cut off points. This finding has made the statistically
significant difference observed between Tregs of obese, asthmatic,
obese asthmatic and control groups much more valuable. These
findings will be useful in diagnosis and treatment of these disorders
and future studies are needed. The production and propagation of
Tregs may be promising in alternative asthma and obesity treatments.
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: The influences of cell-free solutions (CFSs) of lactic
acid bacteria (LAB) on cadaverine and other biogenic amines
production by Listeria monocytogenes and Staphylococcus aureus
were investigated in lysine decarboxylase broth (LDB) using HPLC.
Cell free solutions were prepared from Lactococcus lactis subsp.
lactis, Leuconostoc mesenteroides subsp. cremoris, Pediococcus
acidilactici and Streptococcus thermophiles. Two different
concentrations that were 50% and 25% CFS and the control without
CFSs were prepared. Significant variations on biogenic amine
production were observed in the presence of L. monocytogenes and S.
aureus (P < 0.05). The function of CFS on biogenic amine production
by foodborne pathogens varied depending on strains and specific
amine. Cadaverine formation by L. monocytogenes and S. aureus in
control were 500.9 and 948.1 mg/L, respectively while the CFSs of
LAB induced 4-fold lower cadaverine production by L.
monocytogenes and 7-fold lower cadaverine production by S. aureus.
The CFSs resulted in strong decreases in cadaverine and putrescine
production by L. monocytogenes and S. aureus, although remarkable
increases were observed for histamine, spermidine, spermine,
serotonin, dopamine, tyramine and agmatine in the presence of LAB
in lysine decarboxylase broth.
Abstract: Development of a method to estimate gene functions is
an important task in bioinformatics. One of the approaches for the
annotation is the identification of the metabolic pathway that genes are
involved in. Since gene expression data reflect various intracellular
phenomena, those data are considered to be related with genes’
functions. However, it has been difficult to estimate the gene function
with high accuracy. It is considered that the low accuracy of the
estimation is caused by the difficulty of accurately measuring a gene
expression. Even though they are measured under the same condition,
the gene expressions will vary usually. In this study, we proposed a
feature extraction method focusing on the variability of gene
expressions to estimate the genes' metabolic pathway accurately. First,
we estimated the distribution of each gene expression from replicate
data. Next, we calculated the similarity between all gene pairs by KL
divergence, which is a method for calculating the similarity between
distributions. Finally, we utilized the similarity vectors as feature
vectors and trained the multiclass SVM for identifying the genes'
metabolic pathway. To evaluate our developed method, we applied the
method to budding yeast and trained the multiclass SVM for
identifying the seven metabolic pathways. As a result, the accuracy
that calculated by our developed method was higher than the one that
calculated from the raw gene expression data. Thus, our developed
method combined with KL divergence is useful for identifying the
genes' metabolic pathway.
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: Analyzing DNA microarray data sets is a great
challenge, which faces the bioinformaticians due to the complication
of using statistical and machine learning techniques. The challenge
will be doubled if the microarray data sets contain missing data,
which happens regularly because these techniques cannot deal with
missing data. One of the most important data analysis process on
the microarray data set is feature selection. This process finds the
most important genes that affect certain disease. In this paper, we
introduce a technique for imputing the missing data in microarray
data sets while performing feature selection.
Abstract: The present study was done to evaluate the presence
of tetracycline resistance genes in Lactococcus garvieae isolated
from cultured rainbow trout, West Iran. The isolates were examined
for antimicrobial resistance using disc diffusion method. Of the 49
strains tested, 19 were resistant to tetracycline (38.7%), 32 to
enrofloxacin (65.3%), 21 to erythromycin (42.8%), 20 to
chloramphenicol and trimetoprim-sulfamethoxazole (40.8%). The
strains were then characterized for their genotypic resistance profiles.
The results revealed that all 49 isolates contained at least one of the
tetracycline resistance genes. Tet (A) was found in 89.4% of
tetracycline resistant isolates and the frequency of other gene were as
follows: tet (E) 42.1%, tet (B) 47.3%, tet (D) 15.7%, tet (L) 26.3%,
tet (K) 52.6%, tet (G) 36.8%, tet (34) 21%, tet (S) 63.1%, tet (C)
57.8%, tet (M) 73.6%, tet (O) 42.1%. The results revealed high levels
of antibiotic resistance in L. garvieae strains which is a potential
danger for trout culture as well as for public health.
Abstract: The Roma (Gypsies) is a transnational minority with a
high degree of consanguineous marriages. Similar to other
genetically isolated founder populations, the Roma harbor a number
of unique or rare genetic disorders. This paper discusses about a rare
form of Charcot-Marie-Tooth disease – type 4G (CMT4G), also
called Hereditary Motor and Sensory Neuropathy type Russe, an
autosomal recessive disease caused by mutation private to Roma
characterized by abnormally increased density of non-myelinated
axons. CMT4G was originally found in Bulgarian Roma and in 2009
two putative causative mutations in the HK1 gene were identified.
Since then, several cases were reported in Roma families mainly
from Bulgaria and Spain. Here we present a Slovak Roma family in
which CMT4G was diagnosed on the basis of clinical examination
and genetic testing. This case is a further proof of the role of the HK1
gene in pathogenesis of the disease. It confirms that mutation in the
HK1 gene is a common cause of autosomal recessive CMT disease in
Roma and should be considered as a common part of a diagnostic
procedure.