Abstract: Bacterial molecular chaperone DnaK plays an essential role in protein folding, stress response and transmembrane targeting of proteins. DnaKs from many bacterial species, including Escherichia coli, Salmonella typhimurium and Haemophilus infleunzae are the molecular targets for the insect-derived antimicrobial peptide pyrrhocoricin. Pyrrhocoricin-like peptides bind in the substrate recognition tunnel. Despite the high degree of crossspecies sequence conservation in the substrate-binding tunnel, some bacteria are not sensitive to pyrrhocoricin. This work addresses the molecular mechanism of resistance of Helicobacter pylori DnaK to pyrrhocoricin. Homology modelling, structural and sequence analysis identify a single aminoacid substitution at the interface between the lid and the β-sandwich subdomains of the DnaK substrate-binding domain as the major determinant for its resistance.
Abstract: This research project aims to investigate difference in
relative rates concerning phosphoryl transfer relevant to biological
catalysis of DNA and RNA in the pH-independent reactions.
Activated Models of DNA and RNA for alkyl-aryl phosphate diesters
(with 4-nitrophenyl as a good leaving group) have successfully been
prepared to gather kinetic parameters. Eyring plots for the pH–
independent hydrolysis of 1 and 2 were established at different
temperatures in the range 100–160 °C. These measurements have
been used to provide a better estimate for the difference in relative
rates between the reactivity of DNA and RNA cleavage. Eyring plot
gave an extrapolated rate of kH2O = 1 × 10-10 s -1 for 1 (RNA model)
and 2 (DNA model) at 25°C. Comparing the reactivity of RNA
model and DNA model shows that the difference in relative rates in
the pH-independent reactions is surprisingly very similar at 25°. This
allows us to obtain chemical insights into how biological catalysts
such as enzymes may have evolved to perform their current
functions.
Abstract: Tuberculosis (TB) is a bacterial infectious disease caused by the obligate human pathogen, Mycobacterium tuberculosis. Multidrug-resistant tuberculosis (MDR-TB) is a global reality that threatens tuberculosis control. Resistance to antibiotic Rifampicin, occurs in 95% of cases through nucleotide substitutions in an 81-bp core region of the rpoB i.e; beta subunit of DNA dependant RNA polymerase. In this paper, we studied the Rifampicin-rpoB receptor interactions In silico. First, homology modeling was performed to obtain the three dimensional structure of Mycobacterium rpoB. Sixty analogs of Rifampicin were prepared using Marvin sketch software. Both original Rifampicin and the analogs were docked with rpoB and energy values were obtained. Out of sixty analogs, 43 analogs had lesser energy values than conventional Rifampicin and hence are predicted to have greater binding affinity to rpoB. Thus, this study offers a route for the development of Rifampicin analogs against multi drug resistant Mycobacterium rpoB.
Abstract: Present study summarizes the control of Vibrio
alginolyticus infection in hatchery reared Clownfish, Amphiprion
sebae with the extract of the mangrove plant, Avicennia marina.
Fishes with visible symptoms of hemorrhagic spots were chosen and
the genomic DNA of the causative bacterium was isolated and
sequenced based on 16S rDNA gene. The in vitro assay revealed that
a fraction of A. marina leaf extract elucidated with ethyl acetate:
methanol (6:4) showed a high activity (28 mm) at 125 μg/ml
concentrations. About 4 % of the fraction fed along with live V.
alginolyticus was significantly decreased the cumulative mortality
(P
Abstract: The Partitioned Global Address Space (PGAS) programming
paradigm offers ease-of-use in expressing parallelism
through a global shared address space while emphasizing performance
by providing locality awareness through the partitioning of
this address space. Therefore, the interest in PGAS programming
languages is growing and many new languages have emerged and
are becoming ubiquitously available on nearly all modern parallel
architectures. Recently, new parallel machines with multiple cores
are designed for targeting high performance applications. Most of the
efforts have gone into benchmarking but there are a few examples of
real high performance applications running on multicore machines.
In this paper, we present and evaluate a parallelization technique
for implementing a local DNA sequence alignment algorithm using
a PGAS based language, UPC (Unified Parallel C) on a chip
multithreading architecture, the UltraSPARC T1.
Abstract: Identifying protein coding regions in DNA sequences is a basic step in the location of genes. Several approaches based on signal processing tools have been applied to solve this problem, trying to achieve more accurate predictions. This paper presents a new predictor that improves the efficacy of three techniques that use the Fourier Transform to predict coding regions, and that could be computed using an algorithm that reduces the computation load. Some ideas about the combination of the predictor with other methods are discussed. ROC curves are used to demonstrate the efficacy of the proposed predictor, based on the computation of 25 DNA sequences from three different organisms.
Abstract: P16/INK4A is tumor suppressor protein that plays a critical role in cell cycle regulation. Loss of P16 protein expression has been implicated in pathogenesis of many cancers, including lymphoma. Therefore, we sought to investigate if loss of P16 protein expression is associated with lymphoma and/or any specific lymphoma subtypes (Hodgkin-s lymphoma (HL) and nonHodgkin-s lymphoma (NHL)). Fifty-five lymphoma cases consisted of 30 cases of HL and 25 cases of NHL, with an age range of 3 to 78 years, were examined for loss of P16 by immunohistochemical technique using a specific antibody reacting against P16. In total, P16 loss was seen in 33% of all lymphoma cases. P16 loss was identified in 47.7% of HL cases. In contrast, only 16% of NHL showed loss of P16. Loss of P16 was seen in 67% of HL patients with 50 years of age or older, whereas P16 loss was found in only 42% of HL patients with less than 50 years of age. P16 loss in HL is somewhat higher in male (55%) than in female (30%). In subtypes of HL, P16 loss was found exclusively in all cases of lymphocyte depletion, lymphocyte predominance and unclassified cases, whereas P16 loss was seen in 39% of mixed cellularity and 29% of nodular sclerosis cases. In low grade NHL patients, P16 loss was seen in approximately one-third of cases, whereas no or very rare of P16 loss was found in intermediate and high grade cases. P16 loss did not show any correlation with age or gender of NHL patients. In conclusion, the high rate of P16 loss seen in our study suggests that loss of P16 expression plays a critical role in the pathogenesis of lymphoma, particularly with HL.
Abstract: Atherosclerosis was identified as a chronic inflammatory process resulting from interactions between plasma lipoproteins, cellular components (monocyte, macrophages, T lymphocytes, endothelial cells and smooth muscle cells) and the extracellular matrix of the arterial wall. Several types of genes were known to express during formation of atherosclerosis. This study is carried out to identify unknown differentially expressed gene (DEG) in atherogenesis. Rabbit’s aorta tissues were stained by H&E for histomorphology. GeneFishing™ PCR analysis was performed from total RNA extracted from the aorta tissues. The DNA fragment from DEG was cloned, sequenced and validated by Real-time PCR. Histomorphology showed intimal thickening in the aorta. DEG detected from ACP-41 was identified as cathepsin B gene and showed upregulation at week-8 and week-12 of atherogenesis. Therefore, ACP-based GeneFishing™ PCR facilitated identification of cathepsin B gene which was differentially expressed during development of atherosclerosis.
Abstract: Phytases (myo-inositol hexakisphosphate
phosphohydrolases; EC 3.1.3.8) catalyze the hydrolysis of phytic acid
(myoinositol hexakisphosphate) to the mono-, di-, tri-, tetra-, and
pentaphosphates of myo-inositol and inorganic phosphate.
Therrmophilic bacteria isolated from water sampled from hot spring.
About 120 isolates of bacteria were successfully isolated form hot
spring water sample and tested for extracellular phytase producing.
After 5 passages of the screening on the PSM media, 4 isolates were
found stable in producing phytase enzyme. The 16s RDNA
sequencing for identification of bacteria using molecular technique
revealed that all isolates those positive in phytase producing are
belong to Geobacillus spp. And Anoxybacillus spp. Anoxybacillus
rupiensis UniSZA-7 were identified for their carbon source utilization
using Phenotype Microarray Plate of Biolog and found they utilize
several kind of carbon source provided.
Abstract: Complex assemblies of interacting proteins carry out
most of the interesting jobs in a cell, such as metabolism, DNA
synthesis, mitosis and cell division. These physiological properties
play out as a subtle molecular dance, choreographed by underlying
regulatory networks that control the activities of cyclin-dependent
kinases (CDK). The network can be modeled by a set of nonlinear
differential equations and its behavior predicted by numerical
simulation. In this paper, an innovative approach has been proposed
that uses genetic algorithms to mine a set of behavior data output by
a biological system in order to determine the kinetic parameters of
the system. In our approach, the machine learning method is
integrated with the framework of existent biological information in a
wiring diagram so that its findings are expressed in a form of system
dynamic behavior. By numerical simulations it has been illustrated
that the model is consistent with experiments and successfully shown
that such application of genetic algorithms will highly improve the
performance of mathematical model of the cell division cycle to
simulate such a complicated bio-system.
Abstract: Mutations of the telomeric copy of the survival motor neuron 1 (SMN1) gene cause spinal muscular atrophy. A deletion of the Eef1a2 gene leads to lower motor neuron degeneration in wasted mice. Indirect evidences have been shown that the eEF1A protein family may interact with SMN, and our previous study showed that abnormalities of neuromuscular junctions in wasted mice were similar to those of Smn mutant mice. To determine potential colocalization between SMN and tissue-specific translation elongation factor 1A2 (eEF1A2), an immunochemical analysis of HeLa cells transfected with the plasmid pcDNA3.1(+)C-hEEF1A2- myc and a new quantitative test of colocalization by intensity correlation analysis (ICA) was used to explore the association of SMN and eEF1A2. Here the results showed that eEF1A2 redistributed from the cytoplasm to the nucleus in response to serum and epidermal growth factor. In the cytoplasm, compelling evidence showed that staining for myc-tagged eEF1A2 varied in synchrony with that for SMN, consistent with the formation of a SMN-eEF1A2 complex in the cytoplasm of HeLa cells. These findings suggest that eEF1A2 may colocalize with SMN in the cytoplasm and may be a component of the SMN complex. However, the limitation of the ICA method is an inability to resolve colocalization in components of small organelles such as the nucleus.
Abstract: User-Centered Design (UCD), Usability Engineering (UE) and Participatory Design (PD) are the common Human- Computer Interaction (HCI) approaches that are practiced in the software development process, focusing towards issues and matters concerning user involvement. It overlooks the organizational perspective of HCI integration within the software development organization. The Management Information Systems (MIS) perspective of HCI takes a managerial and organizational context to view the effectiveness of integrating HCI in the software development process. The Human-Centered Design (HCD) which encompasses all of the human aspects including aesthetic and ergonomic, is claimed as to provide a better approach in strengthening the HCI approaches to strengthen the software development process. In determining the effectiveness of HCD in the software development process, this paper presents the findings of a content analysis of HCI approaches by viewing those approaches as a technology which integrates user requirements, ranging from the top management to other stake holder in the software development process. The findings obtained show that HCD approach is a technology that emphasizes on human, tools and knowledge in strengthening the HCI approaches to strengthen the software development process in the quest to produce a sustainable, usable and useful software product.
Abstract: Increasing use of cell phone as a medium of human interaction is playing a vital role in solving riddles of crime as well. A young girl went missing from her home late in the evening in the month of August, 2008 when her enraged relatives and villagers physically assaulted and chased her fiancée who often frequented her home. Two years later, her mother lodged a complaint against the relatives and the villagers alleging that after abduction her daughter was either sold or killed as she had failed to trace her. On investigation, a rusted cell phone with partial visible IMEI number, clothes, bangles, human skeleton etc. recovered from abandoned well in the month of May, 2011 were examined in the lab. All hopes pinned on identity of cell phone, for only linking evidence to fix the scene of occurrence supported by call detail record (CDR) and to dispel doubts about mode of sudden disappearance or death as DNA technology did not help in establishing identity of the deceased. The conventional scientific methods were used without success and international mobile equipment identification number of the cell phone could be generated by using statistical analysis followed by online verification.
Abstract: Biochemical and molecular analysis of some
antioxidant enzyme genes revealed different level of gene expression
on oilseed (Brassica napus). For molecular and biochemical
analysis, leaf tissues were harvested from plants at eight different
developmental stages, from young to senescence. The levels of total
protein and chlorophyll were increased during maturity stages of
plant, while these were decreased during the last stages of plant
growth. Structural analysis (nucleotide and deduced amino acid
sequence, and phylogenic tree) of a complementary DNA revealed a
high level of similarity for a family of Catalase genes. The
expression of the gene encoded by different Catalase isoforms was
assessed during different plant growth phase. No significant
difference between samples was observed, when Catalase activity
was statistically analyzed at different developmental stages. EST
analysis exhibited different transcripts levels for a number of other
relevant antioxidant genes (different isoforms of SOD and
glutathione). The high level of transcription of these genes at
senescence stages was indicated that these genes are senescenceinduced
genes.
Abstract: The aim of this paper is to provide a better
understanding of the implementation of Project Management
practices by UiTM contractors to ensure project success. A
questionnaire survey was administered to 120 UiTM contractors in
Malaysia. The purpose of this method was to gather information on
the contractors- project background and project management skills. It
was found that all of the contractors had basic knowledge and
understanding of project management skills. It is suggested that a
reasonable project plan and an appropriate organizational structure
are influential factors for project success. It is recommended that the
contractors need to have an effective program of work and up to date
information system are emphasized.
Abstract: An important task in solving second order linear ordinary differential equations by the finite difference is to choose a suitable stepsize h. In this paper, by using the stochastic arithmetic, the CESTAC method and the CADNA library we present a procedure to estimate the optimal stepsize hopt, the stepsize which minimizes the global error consisting of truncation and round-off error.
Abstract: In this study, three strains of Vibrio parahaemolyticus
(690, BCRC 13023 and BCRC 13025) were subjected to acid
adaptation at pH 5.5 for 90 min. The survival of acid-adapted and
non-adapted V. parahaemolyticus strains under simulated gastric
condition and their protein expression profiles were investigated.
Results showed that acid adaptation increased the survival of the test
V. parahaemolyticus strains after exposure to simulated gastric juice
(pH 3). Additionally, acid adaptation also affected the protein
expression in these V. parahaemolyticus strains. Nine proteins,
identified as atpA, atpB, DnaK, GroEL, OmpU, enolase,
fructose-bisphosphate aldolase, phosphoglycerate kinase and
triosephosphate isomerase, were induced by acid adaptation in two or
three of the test strains. These acid-adaptive proteins may play
important regulatory roles in the acid tolerance response (ATR) of V.
parahaemolyticus.
Abstract: In this paper, we propose an efficient hierarchical DNA
sequence search method to improve the search speed while the
accuracy is being kept constant. For a given query DNA sequence,
firstly, a fast local search method using histogram features is used as a
filtering mechanism before scanning the sequences in the database.
An overlapping processing is newly added to improve the robustness
of the algorithm. A large number of DNA sequences with low
similarity will be excluded for latter searching. The Smith-Waterman
algorithm is then applied to each remainder sequences. Experimental
results using GenBank sequence data show the proposed method
combining histogram information and Smith-Waterman algorithm is
more efficient for DNA sequence search.
Abstract: The effects of irrigation with dairy factory wastewater
on soil properties were investigated at two sites that had received
irrigation for > 60 years. Two adjoining paired sites that had never
received DFE were also sampled as well as another seven fields from
a wider area around the factory. In comparison with paired sites that
had not received effluent, long-term wastewater irrigation resulted in
an increase in pH, EC, extractable P, exchangeable Na and K and
ESP. These changes were related to the use of phosphoric acid,
NaOH and KOH as cleaning agents in the factory. Soil organic C
content was unaffected by DFE irrigation but the size (microbial
biomass C and N) and activity (basal respiration) of the soil
microbial community were increased. These increases were
attributed to regular inputs of soluble C (e.g. lactose) present as milk
residues in the wastewater. Principal component analysis (PCA) of
the soils data from all 11sites confirmed that the main effects of DFE
irrigation were an increase in exchangeable Na, extractable P and
microbial biomass C, an accumulation of soluble salts and a liming
effect. PCA analysis of soil bacterial community structure, using
PCR-DGGE of 16S rDNA fragments, generally separated individual
sites from one another but did not group them according to irrigation
history. Thus, whilst the size and activity of the soil microbial
community were increased, the structure and diversity of the
bacterial community remained unaffected.
Abstract: Com Poisson distribution is capable of modeling the count responses irrespective of their mean variance relation and the parameters of this distribution when fitted to a simple cross sectional data can be efficiently estimated using maximum likelihood (ML) method. In the regression setup, however, ML estimation of the parameters of the Com Poisson based generalized linear model is computationally intensive. In this paper, we propose to use quasilikelihood (QL) approach to estimate the effect of the covariates on the Com Poisson counts and investigate the performance of this method with respect to the ML method. QL estimates are consistent and almost as efficient as ML estimates. The simulation studies show that the efficiency loss in the estimation of all the parameters using QL approach as compared to ML approach is quite negligible, whereas QL approach is lesser involving than ML approach.