Abstract: Application of pesticides in the paddy fields has
deleterious effects on non-target organisms including cyanobacteria
which are photosynthesizing and nitrogen fixing micro-organisms
contributing significantly towards soil fertility and crop yield.
Pesticide contamination in the paddy fields has manifested into a
serious global environmental concern. To study the effect of one such
pesticide, three cyanobacterial strains; Anabaena fertilissima,
Aulosira fertilissima and Westiellopsis prolifica were selected for
their stress responses to an Organochlorine insecticide - 6, 7, 8, 9, 10,
10-hexachloro-1, 5, 5a, 6, 9, 9a-hexahydro-6, 9-methano-2, 4, 3-
benzodioxathiepine-3-oxide, with reference to their photosynthesic
pigments-chlorophyll-a and carotenoids as well as accessory
pigments-phycobiliproteins (phycocyanin, allophycocyanin and
phycoerythrin), stress induced biochemical metabolites like
carbohydrates, proteins, amino acids, phenols and enzymes-nitrate
reductase, glutamine synthetase and succinate dehydrogenase. All
the three cyanobacterial strains were adversely affected by the
insecticide doses and inhibition was dose dependent. Reduction in
photosynthetic and accessory pigments, metabolites, nitrogen fixing
and respiratory enzymes of the test organisms were accompanied
with an initial increase in their total protein at lower Organochlorine
doses. On the other hand, increased amount of phenols in all the
insecticide treated concentrations was indicative of stressed activities
of the organisms.
Abstract: One of the major problems in genomic field is to perform sequence comparison on DNA and protein sequences. Executing sequence comparison on the DNA and protein data is a computationally intensive task. Sequence comparison is the basic step for all algorithms in protein sequences similarity. Parallel computing is an attractive solution to provide the computational power needed to speedup the lengthy process of the sequence comparison. Our main research is to enhance the protein sequence algorithm using dynamic programming method. In our approach, we parallelize the dynamic programming algorithm using multithreaded program to perform the sequence comparison and also developed a distributed protein database among many PCs using Remote Method Interface (RMI). As a result, we showed how different sizes of protein sequences data and computation of scoring matrix of these protein sequence on different number of processors affected the processing time and speed, as oppose to sequential processing.
Abstract: Three batches of yogurts were made with soy protein
isolate (SPI) supplemented with 2% (S2), 4% (S4) or 6% (S6) of
skim milk powder (SMP). The fourth batch (control; S0) was
prepared from SPI without SMP supplementation. Lactobacillus
delbrueckii ssp. bulgaricus ATCC 11842 (Lb 11842) and
Streptococcus thermophilus ST 1342 (ST 1342) were used as the
starter culture. Biotransformation of the inactive forms, isoflavone
glycosides (IG) to biologically active forms, isoflavone aglycones
(IA), was determined during 28 d storage. The viability of both
microorganisms was significantly higher (P < 0.05) in S2, S4, and S6
than that in S0. The ratio of lactic acid/acetic acid in S0 was in the
range of 15.53 – 22.31 compared to 7.24 – 12.81 in S2, S4 and S6.
The biotransformation of IG to IA in S2, S4 and S6 was also
enhanced by 9.9 -13.3% compared to S0.
Abstract: Carbon tetrachloride (CCl4) is a well-known
hepatotoxin and exposure to this chemical is known to induce
oxidative stress and causes liver injury by the formation of free
radicals. Flacourtia indica commonly known as 'Baichi' has been
reported as an effective remedy for the treatment of a variety of
diseases. The objective of this study was to investigate the
hepatoprotective activity of aqueous extract of leaves of Flacourtia
indica against CCl4 induced hepatotoxicity. Animals were pretreated
with the aqueous extract of Flacourtia indica (250 & 500 mg/kg
body weight) for one week and then challenged with CCl4 (1.5 ml/kg
bw) in olive oil (1:1, v/v) on 7th day. Serum marker enzymes (ALP,
AST, ALT, Total Protein & Total Bilirubin) and TBARS level
(Marker for oxidative stress) were estimated in all the study groups.
Alteration in the levels of biochemical markers of hepatic damage
like AST, ALT, ALP, Total Protein, Total Bilirubin and lipid
peroxides (TBARS) were tested in both CCl4 treated and extract
treated groups. CCl4 has enhanced the AST, ALT, ALP and the
Lipid peroxides (TBARS) in liver. Treatment of aqueous extract of
Flacourtia indica leaves (250 & 500 mg/kg) exhibited a significant
protective effect by altering the serum levels of AST, ALT, ALP,
Total Protein, Total Bilirubin and liver TBARS. These biochemical
observations were supported by histopathological study of liver
sections. From this preliminary study it has been concluded that the
aqueous extract of the leaves of Flacourtia indica protects liver
against oxidative damages and could be used as an effective protector
against CCl4 induced hepatic damage. Our findings suggested that
Flacourtia indica possessed good hepatoprotective activity
Abstract: In this study, The physico-chemical and nutritional
properties of `Musmula` Medlar (Mespilus germanica L.) fruit and
seed grown in Northeast Anatolia was investigated. In the fruit,
length, width, thickness, weight, total soluble solids, colour (1),
colour (2) [L, a, b values], protein, crude ash, crude fiber, crude oil,
texture and pH were determinated as 4.34 cm, 4.22 cm, 3.67 cm,
38.36 g, 23.97 %, S60O60Y41,, [53.85, 17.15, 33.75], 1.06 %, 0.79 %,
4.24 %, 0.005 %, 1.21 kg/cm2 and 4.26 respectively. Also, pulp ratio,
seed ratio and pulp/seed ratio were found to be 92.88 %, 7.11 % and
14.07 %, respectively. In addition, the mineral composition of medlar
fruit in Northeast Anatolia was studied. In the fruit, 23 minerals were
analyzed and 19 minerals were present at detectable levels. The
medlar fruit was richest in potassium (6962 ppm), calcium (1186.378
ppm), magnesium (1070.08 ppm) and phosphor (763.425 ppm).
Abstract: The ability to distinguish missense nucleotide
substitutions that contribute to harmful effect from those that do not
is a difficult problem usually accomplished through functional in
vivo analyses. In this study, instead current biochemical methods, the
effects of missense mutations upon protein structure and function
were assayed by means of computational methods and information
from the databases. For this order, the effects of new missense
mutations in exon 5 of PTEN gene upon protein structure and
function were examined. The gene coding for PTEN was identified
and localized on chromosome region 10q23.3 as the tumor
suppressor gene. The utilization of these methods were shown that
c.319G>A and c.341T>G missense mutations that were recognized in
patients with breast cancer and Cowden disease, could be pathogenic.
This method could be use for analysis of missense mutation in others
genes.
Abstract: Cancer becomes one of the leading cause of death in
many countries over the world. Fourier-transform infrared (FTIR)
spectra of human lung cancer cells (A549) treated with PMF (natural
product extracted from PM 701) for different time intervals were
examined. Second derivative and difference method were taken in
comparison studies. Cesium (Cs) and Rubidium (Rb) nanoparticles in
PMF were detected by Energy Dispersive X-ray attached to Scanning
Electron Microscope SEM-EDX. Characteristic changes in protein
secondary structure, lipid profile and changes in the intensities of
DNA bands were identified in treated A549 cells spectra. A
characteristic internucleosomal ladder of DNA fragmentation was
also observed after 30 min of treatment. Moreover, the pH values
were significantly increases upon treatment due to the presence of Cs
and Rb nanoparticles in the PMF fraction. These results support the
previous findings that PMF is selective anticancer agent and can
produce apoptosis to A549 cells.
Abstract: Bones are dynamic and responsive organs, they
regulate their strength and mass according to the loads which they are subjected. Because, the Wnt/β-catenin pathway has profound
effects on the regulation of bone mass, we hypothesized that mechanical loading of bone cells stimulates Wnt/β-catenin signaling, which results in the generation of new bone mass.
Mechanical loading triggers the secretion of the Wnt molecule, which after binding to transmembrane proteins, causes GSK-3β (Glycogen synthase kinase 3 beta) to cease the phosphorylation of β-catenin. β-catenin accumulation in the cytoplasm, followed by its
transport into the nucleus, binding to transcription factors (TCF/LEF)
that initiate transcription of genes related to bone formation. To test this hypothesis, we used TOPGAL (Tcf Optimal Promoter
β-galactosidase) mice in an experiment in which cyclic loads were
applied to the forearm. TOPGAL mice are reporters for cells effected
by the Wnt/β-catenin signaling pathway. TOPGAL mice are genetically engineered mice in which transcriptional activation of β-
catenin, results in the production of an enzyme, β-galactosidase. The
presence of this enzyme allows us to localize transcriptional
activation of β-catenin to individual cells, thereby, allowing us to quantify the effects that mechanical loading has on the Wnt/β-catenin pathway and new bone formation. The ulnae of loaded TOPGAL
mice were excised and transverse slices along different parts of the
ulnar shaft were assayed for the presence of β-galactosidase.
Our results indicate that loading increases β-catenin transcriptional
activity in regions where this pathway is already primed (i.e. where basal activity is already higher) in a load magnitude dependent
manner. Further experiments are needed to determine the temporal and spatial activation of this signaling in relation to bone formation.
Abstract: With the rapid development in the field of life
sciences and the flooding of genomic information, the need for faster
and scalable searching methods has become urgent. One of the
approaches that were investigated is indexing. The indexing methods
have been categorized into three categories which are the lengthbased
index algorithms, transformation-based algorithms and mixed
techniques-based algorithms. In this research, we focused on the
transformation based methods. We embedded the N-gram method
into the transformation-based method to build an inverted index
table. We then applied the parallel methods to speed up the index
building time and to reduce the overall retrieval time when querying
the genomic database. Our experiments show that the use of N-Gram
transformation algorithm is an economical solution; it saves time and
space too. The result shows that the size of the index is smaller than
the size of the dataset when the size of N-Gram is 5 and 6. The
parallel N-Gram transformation algorithm-s results indicate that the
uses of parallel programming with large dataset are promising which
can be improved further.
Abstract: In order to evaluation the effects of soil organic
matter and biofertilizer on chickpea quality and biological
nitrogen fixation, field experiments were carried out in 2007
and 2008 growing seasons. In this research the effects of
different strategies for soil fertilization were investigated on
grain yield and yield component, minerals, organic compounds
and cooking time of chickpea. Experimental units were
arranged in split-split plots based on randomized complete
blocks with three replications. Main plots consisted of (G1):
establishing a mixed vegetation of Vicia panunica and
Hordeum vulgare and (G2): control, as green manure levels.
Also, five strategies for obtaining the base fertilizer
requirement including (N1): 20 t.ha-1 farmyard manure; (N2):
10 t.ha-1 compost; (N3): 75 kg.ha-1 triple super phosphate;
(N4): 10 t.ha-1 farmyard manure + 5 t.ha-1 compost and (N5):
10 t.ha-1 farmyard manure + 5 t.ha-1 compost + 50 kg.ha-1
triple super phosphate were considered in sub plots.
Furthermoree four levels of biofertilizers consisted of (B1):
Bacillus lentus + Pseudomonas putida; (B2): Trichoderma
harzianum; (B3): Bacillus lentus + Pseudomonas putida +
Trichoderma harzianum; and (B4): control (without
biofertilizers) were arranged in sub-sub plots. Results showed
that integrating biofertilizers (B3) and green manure (G1)
produced the highest grain yield. The highest amounts of yield
were obtained in G1×N5 interaction. Comparison of all 2-way
and 3-way interactions showed that G1N5B3 was determined
as the superior treatment. Significant increasing of N, P2O5,
K2O, Fe and Mg content in leaves and grains emphasized on
superiority of mentioned treatment because each one of these
nutrients has an approved role in chlorophyll synthesis and
photosynthesis abilities of the crops. The combined application
of compost, farmyard manure and chemical phosphorus (N5)
in addition to having the highest yield, had the best grain
quality due to high protein, starch and total sugar contents, low
crude fiber and reduced cooking time.
Abstract: The size, complexity and number of databases used
for protein information have caused bioinformatics to lag behind in
adapting to the need to handle this distributed information.
Integrating all the information from different databases into one
database is a challenging problem. Our main research is to develop a
tool which can be used to access and manipulate protein information
from difference databases. In our approach, we have integrated
difference databases such as Swiss-prot, PDB, Interpro, and EMBL
and transformed these databases in flat file format into relational
form using XML and Bioperl. As a result, we showed this tool can
search different sizes of protein information stored in relational
database and the result can be retrieved faster compared to flat file
database. A web based user interface is provided to allow user to
access or search for protein information in the local database.
Abstract: Aptamers are useful tools in microorganism
researches, diagnoses, and treatment. Aptamers are specific target
molecules formed by oligonucleic acid molecules, and are not
decomposed by alcohol. Aptamers used to detect Mycobacterium
tuberculosis (MTB) have been proved to have specific affinity to the
outer membrane proteins of MTB. This article presents a biosensor
chip set with aptamers for early detection of MTB with high specificity
and sensitivity, even in very low concentration. Meanwhile, we have
already made a modified hydrophobic facial mask module with
internal rendering hydrophobic for effectively collecting M.
tuberculosis.
Abstract: The present models and simulation algorithms of intracellular stochastic kinetics are usually based on the premise that diffusion is so fast that the concentrations of all the involved species are homogeneous in space. However, recents experimental measurements of intracellular diffusion constants indicate that the assumption of a homogeneous well-stirred cytosol is not necessarily valid even for small prokaryotic cells. In this work a mathematical treatment of diffusion that can be incorporated in a stochastic algorithm simulating the dynamics of a reaction-diffusion system is presented. The movement of a molecule A from a region i to a region j of the space is represented as a first order reaction Ai k- ! Aj , where the rate constant k depends on the diffusion coefficient. The diffusion coefficients are modeled as function of the local concentration of the solutes, their intrinsic viscosities, their frictional coefficients and the temperature of the system. The stochastic time evolution of the system is given by the occurrence of diffusion events and chemical reaction events. At each time step an event (reaction or diffusion) is selected from a probability distribution of waiting times determined by the intrinsic reaction kinetics and diffusion dynamics. To demonstrate the method the simulation results of the reaction-diffusion system of chaperoneassisted protein folding in cytoplasm are shown.
Abstract: An alarming emergence of multidrug-resistant strains
of the tuberculosis pathogen Mycobacterium tuberculosis and
continuing high worldwide incidence of tuberculosis has invigorated
the search for novel drug targets. The enzyme glutamate racemase
(MurI) in bacteria catalyzes the stereoconversion of L-glutamate to
D-glutamate which is a component of the peptidoglycan cell wall of
the bacterium. The inhibitors targeted against MurI from several
bacterial species have been patented and are advocated as promising
antibacterial agents. However there are none available against MurI
from Mycobacterium tuberculosis, due to the lack of its threedimensional
structure. This work accomplished two major objectives.
First, the tertiary structure of MtMurI was deduced computationally
through homology modeling using the templates from bacterial
homologues. It is speculated that like in other Gram-positive bacteria,
MtMurI exists as a dimer and many of the protein interactions at the
dimer interface are also conserved. Second, potent candidate
inhibitors against MtMurI were identified through docking against
already known inhibitors in other organisms.
Abstract: Uterine and oviducal fluids are necessary for
capacitation of the spermatozoa and early embryonic development.
The aim of the present study was to determine the effects of estrous
cycle phases (follicular and luteal) on some biological parameters
(enzymes, electrolytes and total proteins) in uterine and oviducal
secretions of ewes. Oviducal and uterine fluids were collected,
diluted and centrifuged. According to our results, concentrations of
GPT, G6PDH, total proteins, K and Na were significantly (P
Abstract: Bone remodeling occurs by the balanced action of
bone resorbing osteoclasts (OC) and bone-building osteoblasts.
Increased bone resorption by excessive OC activity contributes
to malignant and non-malignant diseases including osteoporosis.
To study OC differentiation and function, OC formed in
in vitro cultures are currently counted manually, a tedious
procedure which is prone to inter-observer differences. Aiming
for an automated OC-quantification system, classification of
OC and precursor cells was done on fluorescence microscope
images based on the distinct appearance of fluorescent nuclei.
Following ellipse fitting to nuclei, a combination of eight
features enabled clustering of OC and precursor cell nuclei.
After evaluating different machine-learning techniques, LOGREG
achieved 74% correctly classified OC and precursor cell
nuclei, outperforming human experts (best expert: 55%). In
combination with the automated detection of total cell areas,
this system allows to measure various cell parameters and most
importantly to quantify proteins involved in osteoclastogenesis.
Abstract: The rheological properties, structure and potential synergistic interactions of whey proteins (1-6%) and inulin (20%) in mixed gels in the presence of CaCl2 was the aim of this study. Whey proteins have a strong influence on inulin gel formation. At low concentrations (2%) whey proteins did not impair in inulin gel formation. At higher concentration (4%) whey proteins impaired inulin gelation and inulin impaired the formation of a Ca2+-induced whey protein network. The presence of whey proteins at a level allowing for protein gel network formation (6%) significantly increased the rheological parameters values of the gels. SEM micrographs showed that whey protein structure was coated by inulin moieties which could make the mixed gels firmer. The protein surface hydrophobicity measurements did not exclude synergistic interactions between inulin and whey proteins, however. The use of an electrophoretic technique did not show any stable inulin-whey protein complexes.
Abstract: Knowledge of patterns of genetic diversity enhances
the efficiency of germplasm conservation and improvement. In this
study 96 Iranian landraces of Triticum turgidum originating from
different geographical areas of Iran, along with 18 durum cultivars
from ten countries were evaluated for variation in morphological and
high molecular weight glutenin subunit (HMW-GS) composition.
The first two principal components clearly separated the Iranian
landraces from cultivars. Three alleles were present at the Glu-A1
locus and 11 alleles at Glu-B1. In both cultivars and landraces of
durum wheat, the null allele (Glu-A1c) was observed more
frequently than the Glu-A1a and Glu-A1b alleles. Two alleles,
namely Glu-B1a (subunit 7) and Glu-B1e (subunit 20) represented
the more frequent alleles at Glu-B1 locus. The results showed that
the evaluated Iranian landraces formed an interesting source of
favourable glutenin subunits that might be very desirable in breeding
activities for improving pasta-making quality.
Abstract: The paper makes part from a complex research project
on Romanian Grey Steppe, a unique breed in terms of biological and
cultural-historical importance, on the verge of extinction and which
has been included in a preservation programme of genetic resources
from Romania. The study of genetic polymorphism of protean
fractions, especially kappa-casein, and the genotype relations of
these lactoproteins with some quantitative and qualitative features of
milk yield represents a current theme and a novelty for this breed. In
the estimation of the genetic parameters we used R.E.M.L.
(Restricted Maximum Likelihood) method.
The main lactoprotein from milk, kappa - casein (K-cz),
characterized in the specialized literature as a feature having a high
degree of hereditary transmission, behaves as such in the nucleus under
study, a value also confirmed by the heritability coefficient (h2 = 0.57
%). We must mention the medium values for milk and fat quantity
(h2=0.26, 0.29 %) and the fat and protein percentage from milk
having a high hereditary influence h2 = 0.71 - 0.63 %.
Correlations between kappa-casein and the milk quantity are
negative and strong. Between kappa-casein and other qualitative
features of milk (fat content 0.58-0.67 % and protein content 0.77-
0.87%), there are positive and very strong correlations. At the same
time, between kappa-casein and β casein (β-cz), β lactoglobulin (β-
lg) respectively, correlations are positive having high values (0.37 –
0.45 %), indicating the same causes and determining factors for the
two groups of features.
Abstract: Biologically active peptides are of particular interest
in food science and human nutrition because they have been shown to play several physiological roles. In vitro gastrointestinal digestion of lentil and whey proteins in this study produced high angiotensin-I converting enzyme inhibitory activity with 75.5±1.9 and 91.4±2.3%
inhibition, respectively. High ACE inhibitory activity was observed in lentil after 5 days of germination (84.3±1.2%). Fractionation by
reverse phase chromatography gave inhibitory activities as high as
86.3±2.0 for lentil, 94.8±1.8% for whey and 93.7±1.7% at 5th day of germination. Further purification by HPLC resulted in several
inhibitory peptides with IC50 values ranging from 0.064 to 0.164
mg/ml. These results demonstrate that lentil proteins are a good
source of peptides with ACE inhibitory activity that can be released by germination or gastrointestinal digestion. Despite the lower bioactivity in comparison with whey proteins, incorporation of lentil proteins in functional food formulations and natural drugs look promising.