Abstract: We investigated oxidative DNA damage caused by
radio frequency radiation using 8-oxo-7, 8-dihydro-2'-
deoxyguanosine (8-oxodG) generated in mice tissues after exposure
to 900 MHz mobile phone radio frequency in three independent
experiments. The RF was generated by a Global System for Mobile
Communication (GSM) signal generator. The radio frequency field
was adjusted to 25 V/m. The whole body specific absorption rate
(SAR) was 1.0 W/kg. Animals were exposed to this field for 30 min
daily for 30 days. 24 h post-exposure, blood serum, brain and spleen
were removed and DNA was isolated. Enzyme-linked
immunosorbent assay (ELISA) was used to measure 8-oxodG
concentration. All animals survived the whole experimental period.
The body weight of animals did not change significantly at the end of
the experiment. No statistically significant differences observed in
the levels of oxidative stress. Our results are not in favor of the
hypothesis that 900 MHz RF induces oxidative damage.
Abstract: In recent years, there has been an increasing interest
toward the use of bovine genotyped embryos for commercial embryo
transfer programs. Biopsy of a few cells in morulla stage is essential
for preimplantation genetic diagnosis (PGD). Low amount of DNA
have limited performing the several molecular analyses within PGD
analyses. Whole genome amplification (WGA) promises to eliminate
this problem. We evaluated the possibility and performance of an
improved primer extension preamplification (I-PEP) method with a
range of starting bovine genomic DNA from 1-8 cells into the WGA
reaction. We optimized a short and simple I-PEP (ssI-PEP) procedure
(~3h). This optimized WGA method was assessed by 6 loci specific
polymerase chain reactions (PCRs), included restriction fragments
length polymorphism (RFLP). Optimized WGA procedure possesses
enough sensitivity for molecular genetic analyses through the few
input cells. This is a new era for generating characterized bovine
embryos in preimplantation stage.
Abstract: M. Kemal Ataturk was a great leader who was fond of art and he had displayed his being fond of art many times. In his speeches and writings you can see that he had showed his approval to art and the importance of artists and art for the society. During the foundation of republic, he also wanted renovation in art as in other fields and ordered many novelties both in art and society. One of the greatest steps in realizing this was to prepare a national Turkish opera. In this study, it was studied how a Turkish opera, Özsoy was prepared in the context of social and political conditions of that time and what kind of processes it passed. As a result, it is seen that there was two main aims for Ataturk with this opera. First, Ataturk wanted to abolish the sectarian conflict between Iran and Turkey going on for centuries. The second and maybe the most important is that he wanted to make a revolution in the field of art and aimed to reach the level of civilized countries.
Abstract: Rice seed expression (cDNA) library in the Lambda
Zap 11® phage constructed from the developing grain 10-20 days
after flowering was transformed into yeast for functional
complementation assays in three salt sensitive yeast mutants S.
cerevisiae strain CY162, G19 and Axt3K. Transformed cells of G19
and Axt3K with pYES vector with cDNA inserts showed enhance
tolerance than those with empty pYes vector. Sequencing of the
cDNA inserts revealed that they encode for the putative proteins with
the sequence homologous to rice putative protein PROLM24
(Os06g31070), a prolamin precursor. Expression of this cDNA did
not affect yeast growth in absence of salt. Axt3k and G19 strains
expressing the PROLM24 were able to grow upto 400 mM and 600
mM of NaCl respectively. Similarly, Axt3k mutant with PROLM24
expression showed comparatively higher growth rate in the medium
with excess LiCl (50 mM). The observation that expression of
PROLM24 rescued the salt sensitive phenotypes of G19 and Axt3k
indicates the existence of a regulatory system that ameliorates the
effect of salt stress in the transformed yeast mutants. However, the
exact function of the cDNA sequence, which shows partial sequence
homology to yeast UTR1 is not clear. Although UTR1 involved in
ferrous uptake and iron homeostasis in yeast cells, there is no
evidence to prove its role in Na+ homeostasis in yeast cells. Absence
of transmembrane regions in Os06g31070 protein indicates that salt
tolerance is achieved not through the direct functional
complementation of the mutant genes but through an alternative
mechanism.
Abstract: Abstract–The objectives of the current study are to determine the
prevalence, etiological agents, drug susceptibility pattern and plasmid
profile of Acinetobacter baumannii isolates from Hospital-Acquired
Infections (HAI) at Community Hospital, Al Jouf Province, Saudi
Arabia. A total of 1890 patients had developed infection during
hospital admission and were included in the study. Among those who
developed nosocomial infections, 15(9.4), 10(2.7) and 118 (12.7) had
respiratory tract infection (RTI), blood stream infections (BSI) and
urinary tract (UTI) respectively. A total of 268 bacterial isolates were
isolated from nosocomial infection. S. aureus was reported in 23.5%
for of the total isolates followed by Klebsiella pneumoniae (17.5%), E.
coli (17.2%), P. aeruginosa (11.9%), coagulase negative
staphylococcus (9%), A. baumannii (7.1%), Enterobacter spp.
(3.4%), Citrobacter freundii (3%), Proteus mirabilis (2.6%), and
Proteus vulgaris and Enterococcous faecalis (0.7%). Isolated
organisms are multi-drug resistant, predominantly Gram-positive
pathogens with a high incidence of methicillin-resistant S. aureus,
extended spectrum beta lactamase and vancomycin resistant
enterococci organisms. The RFLP (Fragment Length Polymorphisms)
patterns of plasmid preparations from isolated A. baumannii isolates
had altered RFLP patterns, possibly due to the presence of plasmid(s).
Five A. baumannii isolates harbored plasmids all of which were not
less than 2.71kbp in molecular weight. Hence, it showed that the gene
coding for the isolates were located on the plasmid DNA while the
remaining isolates which have no plasmid might showed gene coding
for antibiotic resistance being located on chromosomal DNA.
Nosocomial infections represent a current problem in Community
Hospital, Al Jouf Province, Saudi Arabia. Problems associated with
SSI include infection with multidrug resistant pathogens which are
difficult to treat and are associated with increased mortality.
Abstract: Before performing polymerase chain reactions (PCR), a feasible primer set is required. Many primer design methods have been proposed for design a feasible primer set. However, the majority of these methods require a relatively long time to obtain an optimal solution since large quantities of template DNA need to be analyzed. Furthermore, the designed primer sets usually do not provide a specific PCR product. In recent years, evolutionary computation has been applied to PCR primer design and yielded promising results. In this paper, a particle swarm optimization (PSO) algorithm is proposed to solve primer design problems associated with providing a specific product for PCR experiments. A test set of the gene CYP1A1, associated with a heightened lung cancer risk was analyzed and the comparison of accuracy and running time with the genetic algorithm (GA) and memetic algorithm (MA) was performed. A comparison of results indicated that the proposed PSO method for primer design finds optimal or near-optimal primer sets and effective PCR products in a relatively short time.
Abstract: EcoDam is an adenine-N6 DNA methyltransferase
that methylates the GATC sites in the Escherichia coli genome.
DNA-adenine methylation is not present in higher eukaryotes
including humans. These observations raise the possibility that dam
inhibitors may be used as anti-microbial agents. Polyphosphate
(Poly(P)) is an important metabolite and signaling molecule in
prokaryotes and eukaryotes. Here, by using gel retardation
experiments to investigate the competition of DNA binding by
EcoDam in the presence of polyphosphate, we found that Poly (P)
strongly interferes with DNA binding by EcoDam, while same
concentration of monophosphate does not. In addition, we
demonstrated that Poly (P) binding inhibits the activity of EcoDam
and our results suggest that Poly (P) led to strong inhibition of the
EcoDam catalytic activity, while monophosphate had only moderate
effect.
Abstract: Breast carcinoma is the most common form of cancer
in women. Multicolour fluorescent in-situ hybridisation (m-FISH) is
a common method for staging breast carcinoma. The interpretation
of m-FISH images is complicated due to two effects: (i) Spectral
overlap in the emission spectra of fluorochrome marked DNA probes
and (ii) tissue autofluorescence. In this paper hyper-spectral images of
m-FISH samples are used and spectral unmixing is applied to produce
false colour images with higher contrast and better information
content than standard RGB images. The spectral unmixing is realised
by combinations of: Orthogonal Projection Analysis (OPA), Alterating
Least Squares (ALS), Simple-to-use Interactive Self-Modeling
Mixture Analysis (SIMPLISMA) and VARIMAX. These are applied
on the data to reduce tissue autofluorescence and resolve the spectral
overlap in the emission spectra. The results show that spectral unmixing
methods reduce the intensity caused by tissue autofluorescence by
up to 78% and enhance image contrast by algorithmically reducing
the overlap of the emission spectra.
Abstract: DNA microarrays allow the measurement of expression levels for a large number of genes, perhaps all genes of an organism, within a number of different experimental samples. It is very much important to extract biologically meaningful information from this huge amount of expression data to know the current state of the cell because most cellular processes are regulated by changes in gene expression. Association rule mining techniques are helpful to find association relationship between genes. Numerous association rule mining algorithms have been developed to analyze and associate this huge amount of gene expression data. This paper focuses on some of the popular association rule mining algorithms developed to analyze gene expression data.
Abstract: The cDNA encoding the 326 amino acids of a Class I
basic chitinase gene from Leucaena leucocephala de Wit (KB3,
Genbank accession: AAM49597) was cloned under the control of
CaMV35S promoter in pCAMBIA 1300 and transferred to
Koshihikari. Calli of Koshihikari rice was transformed with
agrobacterium with this construct expressing the chitinase and β-
glucouronidase (GUS). The frequencies of calli 90 % has been
obtained from rice seedlings cultured on NB medium. The high
regeneration frequencies, 74% was obtained from calli cultured on
regeneration medium containing 4 mg/l BAP, and 7 g/l phytagel at
25°C. Various factors were studied in order to establish a procedure
for the transformation of Koshihikari Agrobacterium tumefaciens.
Supplementation of 50 mM acetosyringone to the medium during
coculivation was important to enhance the frequency to transient
transformation. The 4 week-old scutellum-derived calli were
excellent starting materials. Selection medium based on NB medium
supplement with 40 mg/l hygromycin and 400 mg/l cefotaxime were
an optimized medium for selection of transformed rice calli. The
percentage of transformation 70 was obtained. Recombinant calli and
regenerated rice plants were checked the expression of chitinase and
gus by PCR, northern blot gel, southern blot gel, and gus assay.
Chitinase and gus were expressed in all parts of recombinant rice.
The rice line expressing the KB3 chiitnase was more resistant to the
blast fungus Fusarium monoliforme than control line.
Abstract: Above Elbow Prosthesis is one of the most commonly
amputated or missing limbs. The research is done for modelling
techniques of upper limb prosthesis and design of high torque, light
weight and compact in size elbow actuator. The purposed actuator
consists of a DC motor, planetary gear set and a harmonic drive. The
calculations show that the actuator is good enough to be used in real
life powered prosthetic upper limb or rehabilitation exoskeleton.
Abstract: This paper presents a new steganography approach suitable for Arabic texts. It can be classified under steganography feature coding methods. The approach hides secret information bits within the letters benefiting from their inherited points. To note the specific letters holding secret bits, the scheme considers the two features, the existence of the points in the letters and the redundant Arabic extension character. We use the pointed letters with extension to hold the secret bit 'one' and the un-pointed letters with extension to hold 'zero'. This steganography technique is found attractive to other languages having similar texts to Arabic such as Persian and Urdu.
Abstract: research goal was to determine the expression levels cDNA of brain embrio at gestation days 10 (GD-10). The Electroforesis DNA results showed that GAPDH, Fibronectin1, Ncam1, Tenascin, Vimentin, Neurofilament heavy, Neurofilament medium and Neurofilament low were 447 bp, 462 bp, 293 bp. 416 bp, 327 bp, 301 bp, 398 bp and 289 bp. Result of real-time RT-PCR on brain Embryo at gestation days 10 showed that the expression of copy gen Fibronectin 36 copies, Ncam 21,708 copies; Tenascin 24,505 copies; Vimentin 538,554 copies; Neurofilament heavy 2,419 copies; Neurofilament medium 92,928 copies; Neurofilament low 125,809 copies. Vimentin expressed gene copies is very high compared with other gene copies. This condition are caused by Vimentin, that contribute to proliferate of brain development. The vimentin role to cell proliferation of brain.
Abstract: The aim of this study was to screen for
microorganism that able to utilize 3-N-trimethylamino-1-propanol
(homocholine) as a sole source of carbon and nitrogen. The aerobic
degradation of homocholine has been found by a gram-positive
Rhodococcus sp. bacterium isolated from soil. The isolate was
identified as Rhodococcus sp. strain A4 based on the phenotypic
features, physiologic and biochemical characteristics, and
phylogenetic analysis. The cells of the isolated strain grown on both
basal-TMAP and nutrient agar medium displayed elementary
branching mycelia fragmented into irregular rod and coccoid
elements. Comparative 16S rDNA sequencing studies indicated that
the strain A4 falls into the Rhodococcus erythropolis subclade and
forms a monophyletic group with the type-strains of R. opacus, and
R. wratislaviensis. Metabolites analysis by capillary electrophoresis,
fast atom bombardment-mass spectrometry, and gas
chromatography- mass spectrometry, showed trimethylamine (TMA)
as the major metabolite beside β-alanine betaine and
trimethylaminopropionaldehyde. Therefore, the possible degradation
pathway of trimethylamino propanol in the isolated strain is through
consequence oxidation of alcohol group (-OH) to aldehyde (-CHO)
and acid (-COOH), and thereafter the cleavage of β-alanine betaine
C-N bonds yielded trimethylamine and alkyl chain.
Abstract: Very Large and/or computationally complex optimization problems sometimes require parallel or highperformance computing for achieving a reasonable time for computation. One of the most popular and most complicate problems of this family is “Traveling Salesman Problem". In this paper we have introduced a Branch & Bound based algorithm for the solution of such complicated problems. The main focus of the algorithm is to solve the “symmetric traveling salesman problem". We reviewed some of already available algorithms and felt that there is need of new algorithm which should give optimal solution or near to the optimal solution. On the basis of the use of logarithmic sampling, it was found that the proposed algorithm produced a relatively optimal solution for the problem and results excellent performance as compared with the traditional algorithms of this series.
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: Fractional-order controller was proven to perform better than the integer-order controller. However, the absence of a pole at origin produced marginal error in fractional-order control system. This study demonstrated the enhancement of the fractionalorder PI over the integer-order PI in a steam temperature control. The fractional-order controller was cascaded with an error compensator comprised of a very small zero and a pole at origin to produce a zero steady-state error for the closed-loop system. Some modification on the error compensator was suggested for different order fractional integrator that can improve the overall phase margin.
Abstract: The major objective of this study is to understand the
potential of a newly fabricated equipment to study the thermal
properties of nonwoven textile fabrics treated with aerogel at subzero
temperatures. Thermal conductivity was calculated by using the
empirical relation Fourier’s law, The relationship between the
thermal conductivity and thermal resistance of the samples were
studied at various environmental temperatures (which was set in the
clima temperature system between +25oC to -25oC). The newly
fabricated equipment was found to be a suitable for measuring at
subzero temperatures. This field of measurements is being developed
and will be the subject of further research which will be more suitable
for measurement of the various thermal characteristics.
Abstract: Background: Dialign is a DNA/Protein alignment tool
for performing pairwise and multiple pairwise alignments through the
comparison of gap-free segments (fragments) between sequence
pairs. An alignment of two sequences is a chain of fragments, i.e
local gap-free pairwise alignments, with the highest total score.
METHOD: A new approach is defined in this article which relies on
the concept of using three-dimensional fragments – i.e. local threeway
alignments -- in the alignment process instead of twodimensional
ones. These three-dimensional fragments are gap-free
alignments constituting of equal-length segments belonging to three
distinct sequences. RESULTS: The obtained results showed good
improvments over the performance of DIALIGN.
Abstract: The major objective of this paper is to introduce a new method to select genes from DNA microarray data. As criterion to select genes we suggest to measure the local changes in the correlation graph of each gene and to select those genes whose local changes are largest. More precisely, we calculate the correlation networks from DNA microarray data of cervical cancer whereas each network represents a tissue of a certain tumor stage and each node in the network represents a gene. From these networks we extract one tree for each gene by a local decomposition of the correlation network. The interpretation of a tree is that it represents the n-nearest neighbor genes on the n-th level of a tree, measured by the Dijkstra distance, and, hence, gives the local embedding of a gene within the correlation network. For the obtained trees we measure the pairwise similarity between trees rooted by the same gene from normal to cancerous tissues. This evaluates the modification of the tree topology due to tumor progression. Finally, we rank the obtained similarity values from all tissue comparisons and select the top ranked genes. For these genes the local neighborhood in the correlation networks changes most between normal and cancerous tissues. As a result we find that the top ranked genes are candidates suspected to be involved in tumor growth. This indicates that our method captures essential information from the underlying DNA microarray data of cervical cancer.