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: 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: 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: 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: Globin superfamily proteins including myoglobin and
hemoglobin, have welcome new members recently, namely,
cytoglobin, neuroglobin and globin X, though their physiological
functions are still to be addressed. Fish are the excellent models for the
study of these globins, but their characteristics have not yet been
discussed to date. In the present study, attempts have been made to
characterize their structural uniqueness by making use of proteomics
approach. This is the first comparative study on the characterization of
globin superfamily proteins from fish.
Abstract: The paper is included within the framework of a
complex research program, which was initiated from the hypothesis
arguing on the existence of a correlation between pineal indolic and
peptide hormones and the somatic development rhythm, including
thus the epithalamium-epiphysis complex involvement. At birds,
pineal gland contains a circadian oscillator, playing a main role in the
temporal organization of the cerebral functions. The secretion of
pineal indolic hormones is characterized by a high endogenous
rhythmic alternation, modulated by the light/darkness (L/D)
succession and by temperature as well. The research has been carried
out using 100 chicken broilers - “Ross" commercial hybrid,
randomly allocated in two experimental batches: Lc batch, reared
under a 12L/12D lighting schedule and Lexp batch, which was photic
pinealectomised through continuous exposition to light (150 lux, 24
hours, 56 days). Chemical and physical features of the meat issued
from breast fillet and thighs muscles have been studied, determining
the dry matter, proteins, fat, collagen, salt content and pH value, as
well. Besides the variations of meat chemical composition in relation
with lighting schedule, other parameters have been studied: live
weight dynamics, feed intake and somatic development degree. The
achieved results became significant since chickens have 7 days of
age, some variations of the studied parameters being registered,
revealing that the pineal gland physiologic activity, in relation with
the lighting schedule, could be interpreted through the monitoring of
the somatic development technological parameters, usually studied
within the chicken broilers rearing aviculture practice.
Abstract: Mendelian Disease Genes represent a collection of single points of failure for the various systems they constitute. Such genes have been shown, on average, to encode longer proteins than 'non-disease' proteins. Existing models suggest that this results from the increased likeli-hood of longer genes undergoing mutations. Here, we show that in saturated mutagenesis experiments performed on model organisms, where the likelihood of each gene mutating is one, a similar relationship between length and the probability of a gene being lethal was observed. We thus suggest an extended model demonstrating that the likelihood of a mutated gene to produce a severe phenotype is length-dependent. Using the occurrence of conserved domains, we bring evidence that this dependency results from a correlation between protein length and the number of functions it performs. We propose that protein length thus serves as a proxy for protein cardinality in different networks required for the organism's survival and well-being. We use this example to argue that the collection of Mendelian Disease Genes can, and should, be used to study the rules governing systems vulnerability in living organisms.
Abstract: Mushrooms are a group of fleshy macroscopic fungi.
They have been valued throughout the world as both edible and
medicine. They are highly nutritious with good amount of quality
proteins, vitamins and minerals. An edible mushroom, Calocybe
indica was selected to validate its nutritional and medicinal
properties. Since tissue damage in hyperglycemia has been related to
oxidative stress, we evaluated the enzymatic and non-enzymatic
antioxidant status in the serum, liver and kidney since they are the
target organs in diabetic complications. From the results, increased
oxidative stress and decreased antioxidants might be related to the
causation of diabetes mellitus. The treatment in the diabetic rats with
the Calocybe indica showed an increase in the antioxidant system
and decrease in the production of free radicals. The mushrooms
which contain antioxidant phytochemicals has potential free radical
scavenging capacity and hence can induce the antioxidant system in
the body significantly reduces the generated free radicals thereby
maintaining the normal levels of the antioxidants
Abstract: The study of proteomics reached unexpected levels of
interest, as a direct consequence of its discovered influence over some
complex biological phenomena, such as problematic diseases like
cancer. This paper presents the latest authors- achievements regarding
the analysis of the networks of proteins (interactome networks), by
computing more efficiently the betweenness centrality measure. The
paper introduces the concept of betweenness centrality, and then
describes how betweenness computation can help the interactome net-
work analysis. Current sequential implementations for the between-
ness computation do not perform satisfactory in terms of execution
times. The paper-s main contribution is centered towards introducing
a speedup technique for the betweenness computation, based on
modified shortest path algorithms for sparse graphs. Three optimized
generic algorithms for betweenness computation are described and
implemented, and their performance tested against real biological
data, which is part of the IntAct dataset.
Abstract: This study proposes a basic molecular formula for all
proteins. A total of 10,739 proteins belonging to 9 different protein
groups classified on the basis of their functions were selected
randomly. They included enzymes, storage proteins, hormones,
signalling proteins, structural proteins, transport proteins,
immunoglobulins or antibodies, motor proteins and receptor proteins.
After obtaining the protein molecular formula using the ProtParam
tool, the H/C, N/C, O/C, and S/C ratios were determined for each
randomly selected sample. In this case, H, N, O, and S coefficients
were specified per carbon atom. Surprisingly, the results
demonstrated that H, N, O, and S coefficients for all 10,739 proteins
are similar and highly correlated. This study demonstrates that
despite differences in the structure and function, all known proteins
have a similar basic molecular formula CnH1.58 ± 0.015nN0.28 ± 0.005nO0.30
± 0.007nS0.01 ± 0.002n. The total correlation between all coefficients was
found to be 0.9999.
Abstract: The study of proteomics reached unexpected levels of
interest, as a direct consequence of its discovered influence over
some complex biological phenomena, such as problematic diseases
like cancer. This paper presents a new technique that allows for an
accurate analysis of the human interactome network. It is basically
a two-step analysis process that involves, at first, the detection of
each protein-s absolute importance through the betweenness centrality
computation. Then, the second step determines the functionallyrelated
communities of proteins. For this purpose, we use a community
detection technique that is based on the edge betweenness
calculation. The new technique was thoroughly tested on real biological
data and the results prove some interesting properties of those proteins that are involved in the carcinogenesis process. Apart from its
experimental usefulness, the novel technique is also computationally
effective in terms of execution times. Based on the analysis- results, some topological features of cancer mutated proteins are presented
and a possible optimization solution for cancer drugs design is suggested.
Abstract: The drug discovery process starts with protein
identification because proteins are responsible for many functions
required for maintenance of life. Protein identification further needs
determination of protein function. Proposed method develops a
classifier for human protein function prediction. The model uses
decision tree for classification process. The protein function is
predicted on the basis of matched sequence derived features per each
protein function. The research work includes the development of a
tool which determines sequence derived features by analyzing
different parameters. The other sequence derived features are
determined using various web based tools.
Abstract: Graph has become increasingly important in modeling
complicated structures and schemaless data such as proteins, chemical
compounds, and XML documents. Given a graph query, it is desirable
to retrieve graphs quickly from a large database via graph-based
indices. Different from the existing methods, our approach, called
VFM (Vertex to Frequent Feature Mapping), makes use of vertices
and decision features as the basic indexing feature. VFM constructs
two mappings between vertices and frequent features to answer graph
queries. The VFM approach not only provides an elegant solution to
the graph indexing problem, but also demonstrates how database
indexing and query processing can benefit from data mining,
especially frequent pattern mining. The results show that the proposed
method not only avoids the enumeration method of getting subgraphs
of query graph, but also effectively reduces the subgraph isomorphism
tests between the query graph and graphs in candidate answer set in
verification stage.
Abstract: Banana is one of the most consumed fruits in the tropics and subtropics. Brazil accounts for about 9% of the world banana production. However, the production losses are as high as 30 to 40% and even much higher in some developing countries. The green banana flour is a complex carbohydrate source, including a high total starch (73.4%), resistant starch (17.5%) with functional properties. Gamma irradiation is considered to be an alternative method for food preservation. It has been performed due to the need of extending the shelf - life of foods, whilst maintaining their safety and avoiding one of the main concerns: the nutrient loss. In this work data about on the effects of ionizing radiation on the physicochemical analysis (carbohydrate, proteins, lipids, alimentary fiber, moistures and ashes) of Brazilian functional products (biscuits and bread) of the green banana pulp are presented. The caloric value was calculated. No significant difference was observed between the samples of irradiated and non – irradiated green banana biscuits with the following determinations: carbohydrates, proteins, alimentary fiber and ashes. Only a small significant difference was found in lipids (macronutrients). The results of physical chemical analysis of the irradiated and non- irradiated green banana bread non- irradiated showed no significant difference with the following determinations: carbohydrates, lipids (macronutrients), moisture, ashes and caloric value. A small difference was found in proteins (macronutrients). Irradiation of functional products (biscuits and bread) with doses of 1 and 3kGy maintained their original macronutrients content, showing good radioresistance.
Abstract: Sixteen female Holstein calves allocated in three
treatments including: 1: control, 2: fed raw fiber concentrate (RFC)
for 45 days and 3: fed RFC for 90 days. RFC supplement (Vitacel®
200) was added to milk immediately before feeding (10 g/L milk).
Withers height and body weights of calves were measured monthly.
Individual dry matter intake was recorded daily. Blood samples were
taken monthly. The result showed that calves consumed RFC had
significantly greater weaning and final body weight. Treatment effect
on dry matter intake was not significant (p>0.05). Calves fed RFC
had better feed efficiency. Withers height of calves fed RFC were
taller than the control group (p
Abstract: A new strategy for oriented immobilization of proteins was proposed. The strategy contains two steps. The first step is to search for a docking site away from the active site on the protein surface. The second step is trying to find a ligand that is able to grasp the targeted site of the protein. To avoid ligand binding to the active site of protein, the targeted docking site is selected to own opposite charges to those near the active site. To enhance the ligand-protein binding, both hydrophobic and electrostatic interactions need to be included. The targeted docking site should therefore contain hydrophobic amino acids. The ligand is then selected through the help of molecular docking simulations. The enzyme α-amylase derived from Aspergillus oryzae (TAKA) was taken as an example for oriented immobilization. The active site of TAKA is surrounded by negatively charged amino acids. All the possible hydrophobic sites on the surface of TAKA were evaluated by the free energy estimation through benzene docking. A hydrophobic site on the opposite side of TAKA-s active site was found to be positive in net charges. A possible ligand, 3,3-,4,4- – Biphenyltetra- carboxylic acid (BPTA), was found to catch TAKA by the designated docking site. Then, the BPTA molecules were grafted onto silica gels and measured the affinity of TAKA adsorption and the specific activity of thereby immobilized enzymes. It was found that TAKA had a dissociation constant as low as 7.0×10-6 M toward the ligand BPTA on silica gel. The increase in ionic strength has little effect on the adsorption of TAKA, which indicated the existence of hydrophobic interaction between ligands and proteins. The specific activity of the immobilized TAKA was compared with the randomly adsorbed TAKA on primary amine containing silica gel. It was found that the orderly immobilized TAKA owns a specific activity twice as high as the one randomly adsorbed by ionic interaction.
Abstract: Understanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by making use of their functional annotations. As a result, we found that some functional classes appear together in almost all biclusters. On the other hand, in hierarchical clustering, the dominancy of one functional class is observed. In the light of the clustering data, we have verified some interactions which were not identified as core interactions in DIP and also, we have characterized some functionally unknown proteins according to the interaction data and functional correlation. In brief, from interaction data to function, some correlated results are noticed about the relationship between interaction and function which might give clues about the organization of the proteins, also to predict new interactions and to characterize functions of unknown proteins.
Abstract: Aim of this work was to compare the efficacy of two
loading methods of proteins onto polymeric nanocarriers: adsorption
and encapsulation methods. Preliminary studies of protein loading
were done using Bovine Serum Albumin (BSA) as model protein.
Nanocarriers were prepared starting from polylactic co-glycolic acid
(PLGA) polymer; production methods used are two different variants
of emulsion evaporation method. Nanoparticles obtained were
analyzed in terms of dimensions by Dynamic Light Scattering and
Loading Efficiency of BSA by Bradford Assay. Loaded
nanoparticles were then submitted to in-vitro protein dissolution test
in order to study the effect of the delivery system on the release rate
of the protein.