Abstract: Bean common mosaic necrosis virus (BCMNV) is a
potyvirus with a worldwide distribution. This virus causes serious
economic losses in Iran in many leguminoses. During 20008,
samples were collected from soybeans fields in Tehran Province.
Four isolates (S1, S2 and S3) were inoculated on 15 species of
Cucurbitaceae, Chenopodiaceae, Solanacae and Leguminosae.
Chenopodium quinoa and C. amaranticolor.
Did not developed any symptoms.all isolates caused mosaic
symptoms on Phaseolus vulgaris cv. Red Kidney and P. vulgaris cv.
Bountiful. The molecular weights of coat protein using SDS-PAGE
and western blotting were estimated at 33 kDa. Reverse transcription
polymerase chain reaction (RT-PCR) was performed using one
primer pairs designed by L. XU et al. An approximately 920 bp
fragment was amplified with a specific primer.
Abstract: Ten lactating multiparous Holstein cows were used in
a cross-over design with two dietary treatments and 28-d periods
(with 14 d as an adaptation) to study the effect of restaurant fat on
milk production and composition. Each cow was offered 14.7 kg
DM /d of the basal concentrate diet based on barley and corn (crude
protein = 17.7%, neutral detergent fiber = 23.5%, and acid detergent
fiber = 5.8% of dry matter) with free access to alfalfa. Dietary
treatments were arranged as supplying each cow with 0 (CONTROL)
or 150 g/day (RF) of restaurant fat. Supplemental RF did not
significantly (P > 0.25) affect milk yield, composition, and
composition yields, except for milk fat contents. Milk fat contents
were depressed (P < 0.05) with supplemental RF. Our results indicate
that RF could depress milk fat without affecting milk yield and that
the depression in milk fat in response to RF precedes the depression
in milk yield.
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: Portuguese diet has been gradually diverging from the basic principles of healthy eating, leading to an unbalanced dietary pattern which, associated with increasing sedentary lifestyle, has a negative impact on public health. The main objective of this work was to characterize the dietary habits of university students in Viseu, Portugal. The study consisted of a sample of 80 university students, aged between 18 and 28 years. Anthropometric data (weight (kg) and height (m)) were collected and Body Mass Index (BMI) was calculated. The dietary habits were assessed through a three-day food record and the software Medpoint was used to convert food into energy and nutrients. The results showed that students present a normal body mass index. Female university students made a higher number of daily meals than male students, and these last skipped breakfast more frequently. The values of average daily intake of energy, macronutrients and calcium were higher in males. The food pattern was characterized by a predominant consumption of meat, cereal, fats and sugar. Dietary intake of dairy products, fruits, vegetables and legumes does not meet the recommendations, revealing inadequate food habits such as hypoglycemic, hyperprotein and hyperlipidemic diet. Our findings suggest that preventive interventions should be focus in promoting healthy eating habits and physical activity in adulthood.
Abstract: Sensitive and predictive DILI (Drug Induced Liver
Injury) biomarkers are needed in drug R&D to improve early
detection of hepatotoxicity. The discovery of DILI biomarkers that
demonstrate the predictive power to identify individuals at risk to
DILI would represent a major advance in the development of
personalized healthcare approaches. In this healthy volunteer
acetaminophen study (4g/day for 7 days, with 3 monitored nontreatment
days before and 4 after), 450 serum samples from 32
subjects were analyzed using protein profiling by antibody
suspension bead arrays. Multiparallel protein profiles were generated
using a DILI target protein array with 300 antibodies, where the
antibodies were selected based on previous literature findings of
putative DILI biomarkers and a screening process using pre dose
samples from the same cohort. Of the 32 subjects, 16 were found to
develop an elevated ALT value (2Xbaseline, responders). Using the
plasma profiling approach together with multivariate statistical
analysis some novel findings linked to lipid metabolism were found
and more important, endogenous protein profiles in baseline samples
(prior to treatment) with predictive power for ALT elevations were
identified.
Abstract: Many digital signal processing, techniques have been used to automatically distinguish protein coding regions (exons) from non-coding regions (introns) in DNA sequences. In this work, we have characterized these sequences according to their nonlinear dynamical features such as moment invariants, correlation dimension, and largest Lyapunov exponent estimates. We have applied our model to a number of real sequences encoded into a time series using EIIP sequence indicators. In order to discriminate between coding and non coding DNA regions, the phase space trajectory was first reconstructed for coding and non-coding regions. Nonlinear dynamical features are extracted from those regions and used to investigate a difference between them. Our results indicate that the nonlinear dynamical characteristics have yielded significant differences between coding (CR) and non-coding regions (NCR) in DNA sequences. Finally, the classifier is tested on real genes where coding and non-coding regions are well known.
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: The aim of this study was to estimate the frequency of
EBV infection in Hodgkin's lymphoma (HL) and non-Hodgkin's
lymphoma (NHL) occurring in Jordanian patients. A total of 55
patients with lymphoma were examined in this study. Of 55 patients,
30 and 25 were diagnosed as HL and NHL, respectively. The four
HL subtypes were observed with the majority of the cases exhibited
the mixed cellularity (MC) subtype followed by the nodular sclerosis
(NS). The high grade was found to be the commonest subtype of
NHL in our sample, followed by the low grade. The presence of EBV
virus was detected by immunostating for expression of latent
membrane protein-1 (LMP-1). The frequency of LMP-1 expression
occurred more frequent in patients with HL (60.0%) than in patients
with NHL (32.0%). The frequency of LMP-1 expression was also
higher in patients with MC subtype (61.11%) than those patients with
NS (28.57%). No age or gender difference in occurrence of EBV
infection was observed among patient with HL. By contrast, the
prevalence of EBV infection in NHL patients aged below 50 was
lower (16.66%) than in NHL patients aged 50 or above (46.15%). In
addition, EBV infection was more frequent in females with NHL
(38.46%) than in male with NHL (25%). In NHL cases, the
frequency of EBV infection in intermediate grade (60.0%) was high
when compared with frequency of low (25%) or high grades (25%).
In conclusion, analysis of LMP-1 expression indicates an important
role for this viral oncogene in the pathogenesis of EBV-associated
malignant lymphomas. These data also support the previous findings
that people with EBV may develop lymphoma and that efforts to
maintain low lymphoma should be considered for people with EBV
infection.
Abstract: This experiment was conducted to investigate the
effect of dietary supplementation of different levels of black seed
(Nigella sativa L.) on the performance and immune response of broiler chicks. A total 240 day-old broiler chicks were used and
randomly allotted equally into six experimental groups designated as 1, 2, 3, 4, 5 and 6 having black seed at the rate of 0, 2, 4, 6, 8 and
10 g /kg diet respectively. The study was lasted for 42 days. Average body weight, weight gain, relative growth rate, feed
conversion, antibody titer against Newcastle disease, phagocytic activity and phagocytic index, some blood parameters(GOT, GPT,
Glucose, Cholesterol, Triglyceride, Total protein, Albumen, WBCs,
RBCs, Hb and PCV), dressing percentage, weight of different body
organs, abdominal fat weight, were determined. It was found that, N. Sativa significantly improved final body weight, total body gain
and feed conversion ratio of groups 2 and 3 when compared with the control group. Higher levels of N. Sativa did not improve
growth performance of the chicks. Non significant differences were
observed for antibody titer against Newcastle virus, WBCs count,
serum GOT, glucose level, dressing %, relative liver, spleen, heart and head percentages. Lymphoid organs (Bursa and Thymus)
improved significantly with increasing N. Sativa level in all supplemented groups. Serum cholesterol, triglyceride and visible fat
% significantly decreased with Nigella sativa supplementation while
serum GPT level significantly increased with nigella sativa
supplementation.
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: Annotation of a protein sequence is pivotal for the understanding of its function. Accuracy of manual annotation provided by curators is still questionable by having lesser evidence strength and yet a hard task and time consuming. A number of computational methods including tools have been developed to tackle this challenging task. However, they require high-cost hardware, are difficult to be setup by the bioscientists, or depend on time intensive and blind sequence similarity search like Basic Local Alignment Search Tool. This paper introduces a new method of assigning highly correlated Gene Ontology terms of annotated protein sequences to partially annotated or newly discovered protein sequences. This method is fully based on Gene Ontology data and annotations. Two problems had been identified to achieve this method. The first problem relates to splitting the single monolithic Gene Ontology RDF/XML file into a set of smaller files that can be easy to assess and process. Thus, these files can be enriched with protein sequences and Inferred from Electronic Annotation evidence associations. The second problem involves searching for a set of semantically similar Gene Ontology terms to a given query. The details of macro and micro problems involved and their solutions including objective of this study are described. This paper also describes the protein sequence annotation and the Gene Ontology. The methodology of this study and Gene Ontology based protein sequence annotation tool namely extended UTMGO is presented. Furthermore, its basic version which is a Gene Ontology browser that is based on semantic similarity search is also introduced.
Abstract: Expression and secretion of inflammation markers are
disturbed in obesity. Interleukin-6 reduces body fat mass. The
common G-174C polymorphism in the promoter of IL-6 gene has
been reported that effects on transcriptional regulation. The objective
was to investigate association of the common polymorphism G-174C
with obesity in Iranian population. The present study is cross
sectional association study that included 242 individuals (110 men
and 132 women). Serum IL-6 levels, C-reactive protein, fasting
blood glucose and blood lipids profile were measured .BMI and
WHR were calculated. Genotyping is carried out by PCR and RFLP.
The frequencies of G and C allele were 64.5% and 35.5%,
respectively. The G-174C polymorphism was not associated with
BMI and WHR. However in obese individual, fasting blood glucose
was significantly higher in carrier of C allele compared with the noncarrier.
The IL-6 G-174C polymorphism is not a risk factor for
obesity in Iranian population.
Abstract: A game animals – elk (Alces alces), deer (Cervus
elaphus), roe deer (Capreolus capreolus) or wild boar (Sus scrofa
scrofa) - every autumn and winter period provide an excellent
investment, diversification of many consumer meals. In last years
consumption and assortiment of game meat products significantly
increase. Investigations about biochemical composition of game meat
are not very much. The meat of wild animals is more favourable for
human health because it has lower saturated fatty acids content, but
higher content of protein. Therefore the aim of investigations was to
compare biochemical composition of ungulates obtained in
Latvia.Investigations were carried out in wild animals different
regions of Latvia. In the studied samples protein, intramuscular fat,
fatty acids and cholesterol were determined. The biochemical
analysis of 54 samples were done. Results of analysis showed that
protein content 22.36 – 22.92% of all types of meat samples is not
different statistically, significantly lower fat content 1.33 ± 0.88%
had elk meat samples and 1.59 ± 0.59% roe deer samples. Content of
cholesterol was various 64.41 – 95.07% in the ruminant meat
samples of different species. From the dietetic point of view the best
composition of fatty acids has meat samples of roe deer.
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.
Abstract: The purpose of my research proposal is to
demonstrate that there is a relationship between EEG and
endometrial cancer.
The above relationship is based on an Aristotelian Syllogism;
since it is known that the 14-3-3 protein is related to the electrical
activity of the brain via control of the flow of Na+ and K+ ions and
since it is also known that many types of cancer are associated with
14-3-3 protein, it is possible that there is a relationship between EEG
and cancer. This research will be carried out by well-defined
diagnostic indicators, obtained via the EEG, using signal processing
procedures and pattern recognition tools such as neural networks in
order to recognize the endometrial cancer type. The current research
shall compare the findings from EEG and hysteroscopy performed on
women of a wide age range. Moreover, this practice could be
expanded to other types of cancer. The implementation of this
methodology will be completed with the creation of an ontology.
This ontology shall define the concepts existing in this research-s
domain and the relationships between them. It will represent the
types of relationships between hysteroscopy and EEG findings.
Abstract: Protein residue contact map is a compact
representation of secondary structure of protein. Due to the
information hold in the contact map, attentions from researchers in
related field were drawn and plenty of works have been done
throughout the past decade. Artificial intelligence approaches have
been widely adapted in related works such as neural networks,
genetic programming, and Hidden Markov model as well as support
vector machine. However, the performance of the prediction was not
generalized which probably depends on the data used to train and
generate the prediction model. This situation shown the importance
of the features or information used in affecting the prediction
performance. In this research, support vector machine was used to
predict protein residue contact map on different combination of
features in order to show and analyze the effectiveness of the
features.
Abstract: The effect of phosphorus supplementation of ammoniated rice straw was studied. The in vitro experiment was carried out following the first stage of Tilley and Terry method. The treatments consisting of four diets were A = 50% ammoniated rice straw + 50% concentrate (control), B = A + 0.2% Phosphor (P) supplement, C = A + 0.4% Phosphor (P) supplement, and D = A + 0.6% Phosphor (P) supplement of dry matter. Completely randomized design was used as the experimental design with differences among treatment means were examined using Duncan multiple range test. Variables measured were total bacterial and cellulolytic bacterial population, cellulolytic enzyme activity, ammonia (NH3) and volatile fatty acid (VFA) concentrations, as fermentability indicators and synthesized microbial protein, as well as degradability indicators including dry matter (DM), organic matter (OM), neutral detergent fibre (NDF), acid detergent fibre (ADF) and cellulose. The results indicated that fermentability and degradability of diets consisting ammoniated rice straw with P supplementation were significantly higher than the control diet (P< 0.05). It is concluded that P supplementation is important to improve fermentability and degradability of rations containing ammoniated RS and concentrate. In terms of the most effective level of P supplementation occurred at a supplementation rate of 0.4% of dry matter.