Abstract: Interactions among proteins are the basis of various
life events. So, it is important to recognize and research protein
interaction sites. A control set that contains 149 protein molecules
were used here. Then 10 features were extracted and 4 sample sets
that contained 9 sliding windows were made according to features.
These 4 sample sets were calculated by Radial Basis Functional neutral
networks which were optimized by Particle Swarm Optimization
respectively. Then 4 groups of results were obtained. Finally, these 4
groups of results were integrated by decision fusion (DF) and Genetic
Algorithm based Selected Ensemble (GASEN). A better accuracy was
got by DF and GASEN. So, the integrated methods were proved to
be effective.
Abstract: The proximate composition, physical traits and
sensory properties of beef and chicken patties incorporated with
various level of dried cornsilk (Maydis stigma) were studied. The
beef and chicken patties were formulated with either 2%, 4% or 6%
of cornsilk. Both cooked beef and chicken patties incorporated with
6% cornsilk recorded the highest protein concentration at 23.3% and
28.42%, respectively. Both cooked beef and chicken patties
containing 6% cornsilk significantly recorded the lowest
concentration of fat at 11.4% and 14.60%, respectively. Beef and
chicken patties formulated with 6% cornsilk recorded the highest
cooking yield at 80.13% and 83.03% compared to other treatments.
The inclusion of cornsilk did not change the sensory properties and
consumer acceptability of cornsilk-based beef and chicken patties.
Cornsilk fibre has been effective in improving cooking yield,
moisture and fat retention of beef and chicken patties
Abstract: Rice seed expression (cDNA) library in the Lambda
Zap 11® phage constructed from the developing grain 10-20 days
after flowering was transformed into yeast for functional
complementation assays in three salt sensitive yeast mutants S.
cerevisiae strain CY162, G19 and Axt3K. Transformed cells of G19
and Axt3K with pYES vector with cDNA inserts showed enhance
tolerance than those with empty pYes vector. Sequencing of the
cDNA inserts revealed that they encode for the putative proteins with
the sequence homologous to rice putative protein PROLM24
(Os06g31070), a prolamin precursor. Expression of this cDNA did
not affect yeast growth in absence of salt. Axt3k and G19 strains
expressing the PROLM24 were able to grow upto 400 mM and 600
mM of NaCl respectively. Similarly, Axt3k mutant with PROLM24
expression showed comparatively higher growth rate in the medium
with excess LiCl (50 mM). The observation that expression of
PROLM24 rescued the salt sensitive phenotypes of G19 and Axt3k
indicates the existence of a regulatory system that ameliorates the
effect of salt stress in the transformed yeast mutants. However, the
exact function of the cDNA sequence, which shows partial sequence
homology to yeast UTR1 is not clear. Although UTR1 involved in
ferrous uptake and iron homeostasis in yeast cells, there is no
evidence to prove its role in Na+ homeostasis in yeast cells. Absence
of transmembrane regions in Os06g31070 protein indicates that salt
tolerance is achieved not through the direct functional
complementation of the mutant genes but through an alternative
mechanism.
Abstract: This study has investigated the antidiabetic and
antioxidant potential of Pseudovaria macrophylla bark extract on
streptozotocin–nicotinamide induced type 2 diabetic rats. LCMSQTOF
and NMR experiments were done to determine the chemical
composition in the methanolic bark extract. For in vivo experiments,
the STZ (60 mg/kg/b.w, 15 min after 120 mg/kg/1 nicotinamide, i.p.)
induced diabetic rats were treated with methanolic extract of
Pseuduvaria macrophylla (200 and 400 mg/kg·bw) and
glibenclamide (2.5 mg/kg) as positive control respectively.
Biochemical parameters were assayed in the blood samples of all
groups of rats. The pro-inflammatory cytokines, antioxidant status
and plasma transforming growth factor βeta-1 (TGF-β1) were
evaluated. The histological study of the pancreas was examined and
its expression level of insulin was observed by
immunohistochemistry. In addition, the expression of glucose
transporters (GLUT 1, 2 and 4) were assessed in pancreas tissue by
western blot analysis. The outcomes of the study displayed that the
bark methanol extract of Pseuduvaria macrophylla has potentially
normalized the elevated blood glucose levels and improved serum
insulin and C-peptide levels with significant increase in the
antioxidant enzyme, reduced glutathione (GSH) and decrease in the
level of lipid peroxidation (LPO). Additionally, the extract has
markedly decreased the levels of serum pro-inflammatory cytokines
and transforming growth factor beta-1 (TGF-β1). Histopathology
analysis demonstrated that Pseuduvaria macrophylla has the
potential to protect the pancreas of diabetic rats against peroxidation
damage by downregulating oxidative stress and elevated
hyperglycaemia. Furthermore, the expression of insulin protein,
GLUT-1, GLUT-2 and GLUT-4 in pancreatic cells was enhanced.
The findings of this study support the anti-diabetic claims of
Pseudovaria macrophylla bark.
Abstract: We investigated the response of testosterone (T),
growth hormone (GH), cortisol (C), steroid hormone binding
globulin (SHBG), insulin-like growth factor (IGF-1), insulin-like
growth factor binding protein-3 (IGFBP-3), and some anaboliccatabolic
indexes, i.e.: T/C, T/SHBG, and IGF-1/IGFBP-3 to
maximal exercise in endurance-trained athletes (TREN) and
untrained subjects (CG). The baseline concentration of IGF-1 was
higher in athletes (TREN) when compared to the CG (p
Abstract: The main objective of this study was to demonstrate that differentiation of infected and vaccinated animals (DIVA) strategy using different ELISA tests is possible when a subunit vaccine (Haemagglutinin protein) is used to prevent Avian influenza. Special emphasis was placed on the differentiation in the serological response to different components of the AIV (Nucleoprotein, Neuraminidase, Haemagglutinin, Nucleocapsid) between chickens that were vaccinated with a whole virus kill vaccine and recombinant vaccine. Furthermore, the potential use of this DIVA strategy using ELISA assays to detect Neuraminidase 1 (N1) was analyzed as strategy in countries where the field virus is H5N1 and the vaccine used is formulated with H5N2. Detection of AIV-s antibodies to any component in serum was negative for all animals on the study days 0-13. At study day 14 the titers of antibodies against Nucleoprotein (NP) and Nucleocapsid (NC) rose in the experimental groups vaccinated with Volvac® AI KV and were negatives during all the trial in the experimental groups vaccinated with a subunit H5; significant statistically differences were observed between these groups (p < 0.05). The seroconversion either Haemagglutinin or Neuraminidase was evident after 21 days post-vaccination in the experimental groups vaccinated with the respective viral fraction. Regarding the main aim of this study and according with the results that were obtained, use a combination of different ELISA test as a DIVA strategy is feasible when the vaccination is carry out with a subunit H5 vaccine. Also is possible to use the ELISA kit to detect Neuraminidase (either N1 or N2) as a DIVA concept in countries where H5N1 is present and the vaccination programs are done with H5N2 vaccine.
Abstract: The PRAF family of proteins is a plant specific family of proteins with distinct domain architecture and various unique sequence/structure traits. We have carried out an extensive search of the Arabidopsis genome using an automated pipeline and manual methods to verify previously known and identify unknown instances of PRAF proteins, characterize their sequence and build 3D structures of their individual domains. Integrating the sequence, structure and whatever little known experimental details for each of these proteins and their domains, we present a comprehensive characterization of the different domains in these proteins and their variant properties.
Abstract: The paper presents the influence of the conventional
ploughing tillage technology in comparison with the minimum
tillage, upon the soil properties, weed control and yield in the case of
maize (Zea mays L.), soya-bean (Glycine hispida L.) and winter
wheat (Triticum aestivum L.) in a three years crop rotation. A
research has been conducted at the University of Agricultural
Sciences and Veterinary Medicine Cluj-Napoca, Romania. The use of
minimum soil tillage systems within a three years rotation: maize,
soya-bean, wheat favorites the rise of the aggregates hydro stability
with 5.6-7.5% on a 0-20 cm depth and 5-11% on 20-30 cm depth.
The minimum soil tillage systems – paraplow, chisel or rotary grape
– are polyvalent alternatives for basic preparation, germination bed
preparation and sowing, for fields and crops with moderate loose
requirements being optimized technologies for: soil natural fertility
activation and rationalization, reduction of erosion, increasing the
accumulation capacity for water and realization of sowing in the
optimal period. The soil tillage system influences the productivity
elements of cultivated species and finally the productions thus
obtained. Thus, related to conventional working system, the
productions registered in minimum tillage working represented 89-
97% in maize, 103-112% in soya-bean, 93-99% in winter-wheat. The
results of investigations showed that the yield is a conclusion soil
tillage systems influence on soil properties, plant density assurance
and on weed control. Under minimum tillage systems in the case of
winter weat as an option for replacing classic ploughing, the best
results in terms of quality indices were obtained from version worked
with paraplow, followed by rotary harrow and chisel. At variants
worked with paraplow were obtained quality indices close to those of
the variant worked with plow, and protein and gluten content was
even higher. At Ariesan variety, highest protein content, 12.50% and
gluten, 28.6% was obtained for the variant paraplow.
Abstract: Processes of plant breeding, testing and licensing of new varieties, patent protection in seed production, relations in trade and protection of copyright are dependent on identification, differentiation and characterization of plant genotypes. Therefore, we focused our research on utilization of wheat storage proteins as genetic markers suitable not only for differentiation of individual genotypes, but also for identification and characterization of their considerable properties. We analyzed a collection of 102 genotypes of bread wheat (Triticum aestivum L.), 41 genotypes of spelt wheat (Triticum spelta L.), and 35 genotypes of durum wheat (Triticum durum Desf.), in this study. Our results show, that genotypes of bread wheat and durum wheat were homogenous and single line, but spelt wheat genotypes were heterogenous. We observed variability of HMW-GS composition according to environmental factors and level of breeding and predict technological quality on the basis of Glu-score calculation.
Abstract: Chemical reaction and diffusion are important phenomena in quantitative neurobiology and biophysics. The knowledge of the dynamics of calcium Ca2+ is very important in cellular physiology because Ca2+ binds to many proteins and regulates their activity and interactions Calcium waves propagate inside cells due to a regenerative mechanism known as calcium-induced calcium release. Buffer-mediated calcium diffusion in the cytosol plays a crucial role in the process. A mathematical model has been developed for calcium waves by assuming the buffers are in equilibrium with calcium i.e., the rapid buffering approximation for a one dimensional unsteady state case. This model incorporates important physical and physiological parameters like dissociation rate, diffusion rate, total buffer concentration and influx. The finite difference method has been employed to predict [Ca2+] and buffer concentration time course regardless of the calcium influx. The comparative studies of the effect of the rapid buffered diffusion and kinetic parameters of the model on the concentration time course have been performed.
Abstract: Protein and Esterase electrophoresis were used to
genetically identify two Saudi tick species. Engorged females of the
camel tick Hyalomma dromedarii (Koch) (Acari: Ixodidae) and the
cattle tick Boophilus annulatus (Say) (Acari: Ixodidae) ticks
collected from infested camels and cattle in the animals resting
house at Hail region in KSA were used. The results showed that
there are a variation in both of protein and esterase activity levels and
a high polymorphism within and between the genera and species of
Hyalomma and Boophilus . In conclusion, the protein and esterase
electrophoretic analysis used in the present study could successfully
distinguish among tick species, commonly found in Saudi Arabia.
Abstract: This paper presents an algebraic approach to optimize
queries in domain-specific database management system
for protein structure data. The approach involves the introduction of
several protein structure specific algebraic operators to query the
complex data stored in an object-oriented database system. The
Protein Algebra provides an extensible set of high-level Genomic
Data Types and Protein Data Types along with a comprehensive
collection of appropriate genomic and protein functions. The paper
also presents a query translator that converts high-level query
specifications in algebra into low-level query specifications in
Protein-QL, a query language designed to query protein structure
data. The query transformation process uses a Protein Ontology that
serves the purpose of a dictionary.
Abstract: Eukaryotic protein-coding genes are interrupted by spliceosomal introns, which are removed from the RNA transcripts before translation into a protein. The exon-intron structures of different eukaryotic species are quite different from each other, and the evolution of such structures raises many questions. We try to address some of these questions using statistical analysis of whole genomes. We go through all the protein-coding genes in a genome and study correlations between the net length of all the exons in a gene, the number of the exons, and the average length of an exon. We also take average values of these features for each chromosome and study correlations between those averages on the chromosomal level. Our data show universal features of exon-intron structures common to animals, plants, and protists (specifically, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Cryptococcus neoformans, Homo sapiens, Mus musculus, Oryza sativa, and Plasmodium falciparum). We have verified linear correlation between the number of exons in a gene and the length of a protein coded by the gene, while the protein length increases in proportion to the number of exons. On the other hand, the average length of an exon always decreases with the number of exons. Finally, chromosome clustering based on average chromosome properties and parameters of linear regression between the number of exons in a gene and the net length of those exons demonstrates that these average chromosome properties are genome-specific features.
Abstract: This paper aims at overviewing the topics of a research project (CARDIOSENSOR) on the field of health sciences (biomaterials and biomedical engineering). The project has focused on the development of a nanosensor for the assessment of the risk of cardiovascular diseases by the monitoring of C-reactive protein (CRP), which has been currently considered as the best validated inflammatory biomarker associated to cardiovascular diseases. The project involves tasks such as: 1) the development of sensor devices based on field effect transistors (FET): assembly, optimization and validation; 2) application of sensors to the detection of CRP in standard solutions and comparison with enzyme-linked immunosorbent assay (ELISA); and 3) application of sensors to real samples such as blood and saliva and evaluation of their ability to predict the risk of cardiovascular disease.
Abstract: We have developed an energy based approach for identifying the binding sites and important residues for binding in protein-protein complexes. We found that the residues and residuepairs with charged and aromatic side chains are important for binding. These residues influence to form cation-¤Ç, electrostatic and aromatic interactions. Our observation has been verified with the experimental binding specificity of protein-protein complexes and found good agreement with experiments. The analysis on surrounding hydrophobicity reveals that the binding residues are less hydrophobic than non-binding sites, which suggests that the hydrophobic core are important for folding and stability whereas the surface seeking residues play a critical role in binding. Further, the propensity of residues in the binding sites of receptors and ligands, number of medium and long-range contacts, and influence of neighboring residues will be discussed.
Abstract: Polarization modulation infrared reflection absorption
spectroscopy (PM-IRRAS) in combination with electrochemistry,
was employed to study the influence of surface charge (potential) on
the kinetics of bovine serum albumin (BSA) adsorption on a
biomedical-grade 316LVM stainless steel surface is discussed. The
BSA adsorption kinetics was found to greatly depend on the surface
potential. With an increase in surface potential towards more
negative values, both the BSA initial adsorption rate and the
equilibrium (saturated) surface concentration also increased. Both
effects were explained on the basis of replacement of well-ordered
water molecules at the 316LVM / solution interface, i.e. by the
increase in entropy of the system.
Abstract: The subcellular organelles called oil bodies (OBs) are lipid-filled quasi-spherical droplets produced from the endoplasmic reticulum (ER) and then released into the cytoplasm during seed development. It is believed that an OB grows by coalescence with other OBs and that its stability depends on the composition of oleosins, major proteins inserted in the hemi membrane that covers OBs. In this study, we measured the OB-volume distribution from different genotypes of A. thaliana after 7, 8, 9, 10 and 11 days of seed development. In order to test the hypothesis of OBs dynamics, we developed a simple mathematical model using non-linear differential equations inspired from the theory of coagulation. The model describes the evolution of OB-volume distribution during the first steps of seed development by taking into consideration the production of OBs, the increase of triacylglycerol volume to be stored, and the growth by coalescence of OBs. Fitted parameters values show an increase in the OB production and coalescence rates in A. thaliana oleosin mutants compared to wild type.
Abstract: Coagulation of water involves the use of coagulating
agents to bring the suspended matter in the raw water together for
settling and the filtration stage. Present study is aimed to examine the
effects of aluminum sulfate as coagulant in conjunction with Moringa
Oleifera Coagulant Protein as coagulant aid on turbidity, hardness,
and bacteria in turbid water. A conventional jar test apparatus was
employed for the tests. The best removal was observed at a pH of 7
to 7.5 for all turbidities. Turbidity removal efficiency was resulted
between % 80 to % 99 by Moringa Oleifera Coagulant Protein as
coagulant aid. Dosage of coagulant and coagulant aid decreased with
increasing turbidity. In addition, Moringa Oleifera Coagulant Protein
significantly has reduced the required dosage of primary coagulant.
Residual Al+3 in treated water were less than 0.2 mg/l and meets the
environmental protection agency guidelines. The results showed that
turbidity reduction of % 85.9- % 98 paralleled by a primary
Escherichia coli reduction of 1-3 log units (99.2 – 99.97%) was
obtained within the first 1 to 2 h of treatment. In conclusions,
Moringa Oleifera Coagulant Protein as coagulant aid can be used for
drinking water treatment without the risk of organic or nutrient
release. We demonstrated that optimal design method is an efficient
approach for optimization of coagulation-flocculation process and
appropriate for raw water treatment.
Abstract: Wheat gluten hydrolyzates (WGHs) and anchovy fine
powder hydrolyzates (AFPHs) were produced at 300 MPa using
combinations of Flavourzyme 500MG (F), Alcalase 2.4L (A),
Marugoto E (M) and Protamex (P), and then were compared to those
produced at ambient pressure concerning the contents of soluble solid
(SS), soluble nitrogen and electrophoretic profiles. The contents of SS
in the WGHs and AFPHs increased up to 87.2% according to the
increase in enzyme number both at high and ambient pressure. Based
on SS content, the optimum enzyme combinations for one-, two-,
three- and four-enzyme hydrolysis were determined as F, FA, FAM
and FAMP, respectively. Similar trends were found for the contents of
total soluble nitrogen (TSN) and TCA-soluble nitrogen (TCASN). The
contents of SS, TSN and TCASN in the hydrolyzates together with
electrophoretic mobility maps indicates that the high-pressure
treatment of this study accelerated protein hydrolysis compared to
ambient-pressure treatment.
Abstract: Multi-agent system approach has proven to be an effective and appropriate abstraction level to construct whole models of a diversity of biological problems, integrating aspects which can be found both in "micro" and "macro" approaches when modeling this type of phenomena. Taking into account these considerations, this paper presents the important computational characteristics to be gathered into a novel bioinformatics framework built upon a multiagent architecture. The version of the tool presented herein allows studying and exploring complex problems belonging principally to structural biology, such as protein folding. The bioinformatics framework is used as a virtual laboratory to explore a minimalist model of protein folding as a test case. In order to show the laboratory concept of the platform as well as its flexibility and adaptability, we studied the folding of two particular sequences, one of 45-mer and another of 64-mer, both described by an HP model (only hydrophobic and polar residues) and coarse grained 2D-square lattice. According to the discussion section of this piece of work, these two sequences were chosen as breaking points towards the platform, in order to determine the tools to be created or improved in such a way to overcome the needs of a particular computation and analysis of a given tough sequence. The backwards philosophy herein is that the continuous studying of sequences provides itself important points to be added into the platform, to any time improve its efficiency, as is demonstrated herein.