Abstract: The prediction of transmembrane helical segments
(TMHs) in membrane proteins is an important field in the
bioinformatics research. In this paper, a new method based on discrete
wavelet transform (DWT) has been developed to predict the number
and location of TMHs in membrane proteins. PDB coded as 1KQG
was chosen as an example to describe the prediction of the number and
location of TMHs in membrane proteins by using this method. To
access the effect of the method, 80 proteins with known 3D-structure
from Mptopo database are chosen at random as the test objects
(including 325 TMHs), 308 of which can be predicted accurately, the
average predicted accuracy is 96.3%. In addition, the above 80
membrane proteins are divided into 13 groups according to their
function and type. In particular, the results of the prediction of TMHs
of the 13 groups are satisfying.
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: In vitro gastro-duodenal digestion model was used to investigate the changes of emulsions under digestion conditions. Oil in water emulsions stabilized by whey proteins (2%) and stabilized by whey proteins (2%) with addition of carboxymethyl cellulose (0.75%) as gelling agent of continuous phase were prepared at pH7. Both emulsions were destabilized under gastric conditions; however the protective role of carboxymethyl cellulose was indicated by recording delay of fat digestibility of this emulsion. In the presence of carboxymethyl cellulose whey proteins on the interfacial surface of droplets were more resistant to gastric degradation causing limited hydrolysis of fat due to the poor acceptability of lipids for the enzymes. Studies of emulsions using in vivo model supported results from in vitro studies. Lower content of triglycerides in blood serum and higher amount of fecal fat of rats were determined when rats were fed by diet containing emulsion made with whey proteins and carboxymethyl cellulose.
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: The effects of commercial or bovine yeasts on the
performance and blood variables of broiler chickens intoxicated with
aflatoxin were investigated in broilers. Four hundred eighty broilers
(Arbor Acres; 3-wk-old) were randomly assigned to 4 groups. Each
group (120 broiler chickens) was further randomly divided into 6
replicates of 20 chickens. The treatments were control diet without
additives (treatment 1), 250 ppb AFB1 (treatment 2), commercial
yeast, Saccharomyces cerevisiae, (CY 2.5 x 107 CFU/g) + 250 ppb
AFB1 (treatment 3) and bovine yeast, Saccharomyces cerevisiae,
(BY 2.5 x 107 CFU/g + 250 ppb AFB1 (treatment 4). Complete
randomized design (CRD) was used in the experiment. Feed
consumption and body weight were recorded at every five-day
period. On day 42, carcass compositions were determined from 30
birds per treatment. While chicks were sacrificed, 3-4 ml blood
sample was taken and stored frozen at (-20°C) for serum chemical
analysis to determine effects of consumption of diets on blood
chemistry (total protein, albumin, glucose, urea, cholesterol and
triglycerides). There were no significant differences in ADFI among
the treatments(P>0.05). However, BWG, FCR and mortality were
highly significantly different (P
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: An attempt was made to study of nitrogen
components response of corn (Zea mays L.) to drought stress. A farm
research was done in RCBD as split-plot with four replications in
Khorramabad, west Iran. Drought stress levels as irrigation regimes
after 75 (control), 100, and 120 (stress) mm cumulative evaporation
were in main plots, and four seed corn varieties include 500 (medium
maturity), 647, 700, and 704 (long maturity) were as subplots.
Soluble protein, nitrate and proline amino acid were measured in
shoot and root at flowering stage, and grain yield was measured in
harvesting stage. As the drought progressed, the amount of nitrate
and proline followed an increasing trend, but soluble protein
decreased in shoot and root. The highest amount of nitrate and
proline was observed in longer maturity varieties than shorter ones,
but decrease yield of long maturity varieties was higher than medium
maturity varieties in drought condition, because of long duration of
stress.
Abstract: The classification of the protein structure is commonly
not performed for the whole protein but for structural domains, i.e.,
compact functional units preserved during evolution. Hence, a first
step to a protein structure classification is the separation of the
protein into its domains. We approach the problem of protein domain
identification by proposing a novel graph theoretical algorithm. We
represent the protein structure as an undirected, unweighted and
unlabeled graph which nodes correspond the secondary structure
elements of the protein. This graph is call the protein graph. The
domains are then identified as partitions of the graph corresponding
to vertices sets obtained by the maximization of an objective function,
which mutually maximizes the cycle distributions found in the
partitions of the graph. Our algorithm does not utilize any other kind
of information besides the cycle-distribution to find the partitions. If
a partition is found, the algorithm is iteratively applied to each of
the resulting subgraphs. As stop criterion, we calculate numerically
a significance level which indicates the stability of the predicted
partition against a random rewiring of the protein graph. Hence,
our algorithm terminates automatically its iterative application. We
present results for one and two domain proteins and compare our
results with the manually assigned domains by the SCOP database
and differences are discussed.
Abstract: Proteomics is one of the largest areas of research for
bioinformatics and medical science. An ambitious goal of proteomics
is to elucidate the structure, interactions and functions of all proteins
within cells and organisms. Predicting Protein-Protein Interaction
(PPI) is one of the crucial and decisive problems in current research.
Genomic data offer a great opportunity and at the same time a lot of
challenges for the identification of these interactions. Many methods
have already been proposed in this regard. In case of in-silico
identification, most of the methods require both positive and negative
examples of protein interaction and the perfection of these examples
are very much crucial for the final prediction accuracy. Positive
examples are relatively easy to obtain from well known databases. But
the generation of negative examples is not a trivial task. Current PPI
identification methods generate negative examples based on some
assumptions, which are likely to affect their prediction accuracy.
Hence, if more reliable negative examples are used, the PPI prediction
methods may achieve even more accuracy. Focusing on this issue, a
graph based negative example generation method is proposed, which
is simple and more accurate than the existing approaches. An
interaction graph of the protein sequences is created. The basic
assumption is that the longer the shortest path between two
protein-sequences in the interaction graph, the less is the possibility of
their interaction. A well established PPI detection algorithm is
employed with our negative examples and in most cases it increases
the accuracy more than 10% in comparison with the negative pair
selection method in that paper.
Abstract: Dried soy protein hydrolysate powder was added to
the burger in order to enhance the oxidative stability as well as
decreases the microbial spoilage. The soybean bioactive compounds
(soy protein hydrolysate) as antioxidant and antimicrobial were added
at level of 1, 2 and 3 %.Chemical analysis and physical properties
were affected by protein hydrolysate addition. The TBA values were
significantly affected (P < 0.05) by the storage period and the level of
soy protein hydrolysate. All the tested soybean protein hydrolysate
additives showed strong antioxidant properties. Samples of soybean
protein hydrolysate showed the lowest (P < 0.05) TBA values at each
time of storage.
The counts of all determined microbiological indicators were
significantly (P < 0.05) affected by the addition of the soybean
protein hydrolysate. Decreasing trends of different extent were also
observed in samples of the treatments for total viable counts,
Coliform, Staphylococcus aureus, yeast and molds. Storage period
was being significantly (P < 0.05) affected on microbial counts in all
samples Staphylococcus aureus were the most sensitive microbe
followed by Coliform group of the sample containing protein
hydrolysate, while molds and yeast count showed a decreasing trend
but not significant (P < 0.05) until the end of the storage period
compared with control sample. Sensory attributes were also
performed, added protein hydrolysate exhibits beany flavor which
was clear about samples of 3% protein hydrolysate.
Abstract: Cow milk, is a product of the mammary gland and
soymilk is a beverage made from soybeans; it is the liquid that
remains after soybeans are soaked. In this research effort, we
compared nutritional parameters of this two kind milk such as total
fat, fiber, protein, minerals (Ca, Fe and P), fatty acids, carbohydrate,
lactose, water, total solids, ash, pH, acidity and calories content in
one cup (245 g). Results showed soymilk contains 4.67 grams of fat,
0.52 of fatty acids, 3.18 of fiber, 6.73 of protein, 4.43 of
carbohydrate, 0.00 of lactose, 228.51 of water, 10.40 of total solids
and 0.66 of ash, also 9.80 milligrams of Ca, 1.42 of Fe, and 120.05 of
P, 79 Kcal of calories, pH=6.74 and acidity was 0.24%. Cow milk
contains 8.15 grams of fat, 5.07 of fatty acids, 0.00 of fiber, 8.02 of
protein, 11.37 of carbohydrate, ´Çá4.27 of lactose, 214.69 of water,
12.90 of total solids, 1.75 of ash, 290.36 milligrams of Ca, 0.12 of
Fe, and 226.92 of P, 150 Kcal of calories, pH=6.90 and acidity was
0.21% . Soy milk is one of plant-based complete proteins and cow
milk is a rich source of nutrients as well. Cow milk is containing near
twice as much fat as and ten times more fatty acids do soymilk. Cow
milk contains greater amounts of mineral (except Fe) it contain more
than three hundred times the amount of Ca and nearly twice the
amount of P as does soymilk but soymilk contains more Fe (ten time
more) than does cow milk. Cow milk and soy milk contain nearly
identical amounts of protein and water and fiber is a big plus, dairy
has none. Although what we choose to drink is really a mater of
personal preference and our health objectives but looking at the
comparison, soy looks like healthier choices.
Abstract: Brassinosteroids (BRs) regulate cell elongation,
vascular differentiation, senescence, and stress responses. BRs signal
through the BES1/BZR1 family of transcription factors, which
regulate hundreds of target genes involved in this pathway. In this
research a comprehensive genome-wide analysis was carried out in
BES1/BZR1 gene family in Arabidopsis thaliana, Cucumis sativus,
Vitis vinifera, Glycin max and Brachypodium distachyon.
Specifications of the desired sequences, dot plot and hydropathy plot
were analyzed in the protein and genome sequences of five plant
species. The maximum amino acid length was attributed to protein
sequence Brdic3g with 374aa and the minimum amino acid length
was attributed to protein sequence Gm7g with 163aa. The maximum
Instability index was attributed to protein sequence AT1G19350
equal with 79.99 and the minimum Instability index was attributed to
protein sequence Gm5g equal with 33.22. Aliphatic index of these
protein sequences ranged from 47.82 to 78.79 in Arabidopsis
thaliana, 49.91 to 57.50 in Vitis vinifera, 55.09 to 82.43 in Glycin
max, 54.09 to 54.28 in Brachypodium distachyon 55.36 to 56.83 in
Cucumis sativus. Overall, data obtained from our investigation
contributes a better understanding of the complexity of the
BES1/BZR1 gene family and provides the first step towards directing
future experimental designs to perform systematic analysis of the
functions of the BES1/BZR1 gene family.
Abstract: The understanding of the system level of biological behavior and phenomenon variously needs some elements such as gene sequence, protein structure, gene functions and metabolic pathways. Challenging problems are representing, learning and reasoning about these biochemical reactions, gene and protein structure, genotype and relation between the phenotype, and expression system on those interactions. The goal of our work is to understand the behaviors of the interactions networks and to model their evolution in time and in space. We propose in this study an ontological meta-model for the knowledge representation of the genetic regulatory networks. Ontology in artificial intelligence means the fundamental categories and relations that provide a framework for knowledge models. Domain ontology's are now commonly used to enable heterogeneous information resources, such as knowledge-based systems, to communicate with each other. The interest of our model is to represent the spatial, temporal and spatio-temporal knowledge. We validated our propositions in the genetic regulatory network of the Aarbidosis thaliana flower
Abstract: In this study, a high accuracy protein-protein interaction
prediction method is developed. The importance of the proposed
method is that it only uses sequence information of proteins while
predicting interaction. The method extracts phylogenetic profiles of
proteins by using their sequence information. Combining the phylogenetic
profiles of two proteins by checking existence of homologs
in different species and fitting this combined profile into a statistical
model, it is possible to make predictions about the interaction status
of two proteins.
For this purpose, we apply a collection of pattern recognition
techniques on the dataset of combined phylogenetic profiles of protein
pairs. Support Vector Machines, Feature Extraction using ReliefF,
Naive Bayes Classification, K-Nearest Neighborhood Classification,
Decision Trees, and Random Forest Classification are the methods
we applied for finding the classification method that best predicts
the interaction status of protein pairs. Random Forest Classification
outperformed all other methods with a prediction accuracy of 76.93%
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: A rare phenomenon of SDS-induced activation of a latent protease activity associated with the purified silkworm excretory red fluorescent protein (SE-RFP) was noticed. SE-RFP aliquots incubated with SDS for different time intervals indicated that the protein undergoes an obligatory breakdown into a number of subunits which exhibit autoproteolytic (acting upon themselves) and/or heteroproteolytic (acting on other proteins) activities. A strong serine protease activity of SE-RFP subunits on Bombyx mori nucleopolyhedrovirus (BmNPV) polyhedral protein was detected by zymography technique. A complete inhibition of BmNPV infection to silkworms was observed by the oral administration assay of the SE-RFP. Here, it is proposed that the SE-RFP prevents the initial infection of BmNPV to silkworms by obliterating the polyhedral protein. This is the first report on a silkworm red fluorescent protein that exhibits a protease activity on exposure to SDS. The present studies would help in understanding the antiviral mechanism of silkworm red fluorescent proteins.
Abstract: Matrix metalloproteinases (MMP) are a class of
structural and functional related enzymes involved in altering the
natural elements of the extracellular matrix. Most of the MMP
structures are cristalographycally determined and published in
WorldWide ProteinDataBank, isolated, in full structure or bound to
natural or synthetic inhibitors. This study proposes an algorithm to
replace missing crystallographic structures in PDB database. We
have compared the results of a chosen docking algorithm with a
known crystallographic structure in order to validate enzyme sites
reconstruction there where crystallographic data are missing.
Abstract: the obligatory step during immunoglobulin and lysozyme concentration process is thermal treatment. The combination of temperature and time used in processing can affect the structure of the proteins and involve unfolding and aggregation. The aim of the present study was to evaluate the heat stability of total Igs, the particular immunoglobulin classes and lysozyme in milk. Milk samples were obtained from conventional dairy herd in Latvia. Raw milk samples were pasteurized in different regimes: 63 °C 30 min, 72 °C 15-20 s, 78 °C 15-20 s, 85 °C 15-20 s, 95 °C 15-20 s. The concentrations of Igs (IgA, IgG, IgM) and lysozyme were determined by turbodimetric method. During research was established, that activity of antimicrobial proteins decreases differently. Less concentration reduce was established in a case of lysozyme.
Abstract: Phaseolus coccineus L. is the third most important
cultivated Phaseolus species in the world. It is widely grown in
Latvia due to its earliness, good taste and uniform and qualitative
yield. Experiments were carried out in the laboratories of Department
of Food Technology and Agronomical Analysis Scientific Laboratory
at Latvia Universityof Agriculture. Beans (Phaseolus coccineus L.)
crude protein, crude ash content as well as colour measurements were
analyzed. Results show, that brown coloured beans have less crude
protein content than others, and ash content have significant
differences.
Abstract: Kwashiorkor is one of nutritional problem in
Indonesia, which lead to decrease immune system. This condition
causes susceptibility to infectious disease, especially tuberculosis.
Development of new tuberculosis vaccine will be an important
strategy to eliminate tuberculosis in kwashiorkor. Previous research
showed that 38-kDa Mycobacterium tuberculosis protein is one of the
potent immunogen. However, the role of oral immunization with 38-
kDa Mycobacterium tuberculosis protein to the number of
lymphocytes in the rat model of kwashiorkor is still unknown. We
used kwashiorkor rat model groups with 4% and 2% low protein diet.
Oral immunization with 38-kDa Mycobacterium tuberculosis protein
given with 2 booster every week. The lymphocytes number were
measured by flowcytometry. There was no significant difference
between the number of lymphocytes in the normal rat group and the
kwashiorkor rat groups. It may reveal the role of 38-kDa
Mycobacterium tuberculosis protein as a potent immunogen that can
increase the lymphocytes number from kwashiorkor rat model same
as normal rat.