Abstract: The two-dimensional gel electrophoresis method
(2-DE) is widely used in Proteomics to separate thousands of proteins
in a sample. By comparing the protein expression levels of proteins in
a normal sample with those in a diseased one, it is possible to identify
a meaningful set of marker proteins for the targeted disease. The major
shortcomings of this approach involve inherent noises and irregular
geometric distortions of spots observed in 2-DE images. Various
experimental conditions can be the major causes of these problems. In
the protein analysis of samples, these problems eventually lead to
incorrect conclusions. In order to minimize the influence of these
problems, this paper proposes a partition based pair extension method
that performs spot-matching on a set of gel images multiple times and
segregates more reliable mapping results which can improve the
accuracy of gel image analysis. The improved accuracy of the
proposed method is analyzed through various experiments on real
2-DE images of human liver tissues.
Abstract: SeqWord Gene Island Sniffer, a new program for
the identification of mobile genetic elements in sequences of bacterial chromosomes is presented. This program is based on the
analysis of oligonucleotide usage variations in DNA sequences. 3,518 mobile genetic elements were identified in 637 bacterial
genomes and further analyzed by sequence similarity and the
functionality of encoded proteins. The results of this study are stored in an open database http://anjie.bi.up.ac.za/geidb/geidbhome.
php). The developed computer program and the database provide the information valuable for further investigation of the
distribution of mobile genetic elements and virulence factors among bacteria. The program is available for download at www.bi.up.ac.za/SeqWord/sniffer/index.html.
Abstract: The halophilic proteinase showed a maximal activity
at 50°C and pH 9~10, in 20% NaCl and was highly stabilized by
NaCl. It was able to hydrolyse natural actomyosin (NAM), collagen
and anchovy protein. For NAM hydrolysis, the myosin heavy chain
was completely digested by halophilic proteinase as evidenced by the
lowest band intensity remaining, but partially hydrolysed actin. The
SR5-3 proteinase was also capable hydrolyzing two major
components of collagen, β- and α-compounds, effectively. The
degree of hydrolysis (DH) of the halophilic proteinase and
commercial proteinases (Novozyme, Neutrase, chymotrypsin and
Flavourzyme) on the anchovy protein, were compared, and it was
found that the proteinase showed a greater degree of hydrolysis
towards anchovy protein than that from commercial proteinases. DH
of halophilic proteinase was sharply enhanced according to the
increase in the concentration of enzyme from 0.035 U to 0.105 U.
The results warranting that the acceleration of the production of fish
sauce with higher quality, may be achieved by adding of the
halophilic proteinase from this bacterium.
Abstract: In the last few years, the Semantic Web gained scientific acceptance as a means of relationships identification in knowledge base, widely known by semantic association. Query about complex relationships between entities is a strong requirement for many applications in analytical domains. In bioinformatics for example, it is critical to extract exchanges between proteins. Currently, the widely known result of such queries is to provide paths between connected entities from data graph. However, they do not always give good results while facing the user need by the best association or a set of limited best association, because they only consider all existing paths but ignore the path evaluation. In this paper, we present an approach for supporting association discovery queries. Our proposal includes (i) a query language PmSPRQL which provides a multiparadigm query expressions for association extraction and (ii) some quantification measures making easy the process of association ranking. The originality of our proposal is demonstrated by a performance evaluation of our approach on real world datasets.
Abstract: Tandem mass spectrometry (MS/MS) is the engine
driving high-throughput protein identification. Protein mixtures possibly
representing thousands of proteins from multiple species are
treated with proteolytic enzymes, cutting the proteins into smaller
peptides that are then analyzed generating MS/MS spectra. The
task of determining the identity of the peptide from its spectrum
is currently the weak point in the process. Current approaches to de
novo sequencing are able to compute candidate peptides efficiently.
The problem lies in the limitations of current scoring functions. In this
paper we introduce the concept of proteome signature. By examining
proteins and compiling proteome signatures (amino acid usage) it is
possible to characterize likely combinations of amino acids and better
distinguish between candidate peptides. Our results strongly support
the hypothesis that a scoring function that considers amino acid usage
patterns is better able to distinguish between candidate peptides. This
in turn leads to higher accuracy in peptide prediction.
Abstract: Austenite and Martensite indicate the phases of solids undergoing phase transformation which we usually associate with materials and not with living organisms. This article provides an overview of bacterial proteins and structures that are undergoing phase transformation and suggests its probable effect on mechanical behavior. The context is mainly within the role of phase transformations occurring in the flagellum of bacteria. The current knowledge of molecular mechanism leading to phase variation in living organisms is reviewed. Since in bacteria, each flagellum is driven by a separate motor, similarity to a Differential drive in case of four-wheeled vehicles is suggested. It also suggests the application of the mechanism in which bacteria changes its direction of movement to facilitate single point turning of a multi-wheeled vehicle. Finally, examples are presented to illustrate that the motion due to phase transformation of flagella in bacteria can start a whole new research on motion mechanisms.
Abstract: Poly (ethylene glycol) (PEG) molecules attached to surfaces have shown high potential as a protein repellent due to their flexibility and highly water solubility. A quartz crystal microbalance recording frequency and dissipation changes (QCM-D) has been used to study the adsorption from aqueous solutions, of lysozyme and α-lactalbumin proteins (the last with and without calcium) onto modified stainless steel surfaces. Surfaces were coated with poly(ethylene imine) (PEI) and silicate before grafting on PEG molecules. Protein adsorption was also performed on the bare stainless steel surface as a control. All adsorptions were conducted at 23°C and pH 7.2. The results showed that the presence of PEG molecules significantly reduced the adsorption of lysozyme and α- lactalbumin (with calcium) onto the stainless steel surface. By contrast, and unexpected, PEG molecules enhanced the adsorption of α-lactalbumin (without calcium). It is suggested that the PEG -α- lactalbumin hydrophobic interaction plays a dominant role which leads to protein aggregation at the surface for this latter observation. The findings also lead to the general conclusion that PEG molecules are not a universal protein repellent. PEG-on-PEI surfaces were better at inhibiting the adsorption of lysozyme and α-lactalbumin (with calcium) than with PEG-on-silicate surfaces.
Abstract: Discovering new biological knowledge from the highthroughput biological data is a major challenge to bioinformatics today. To address this challenge, we developed a new approach for protein classification. Proteins that are evolutionarily- and thereby functionally- related are said to belong to the same classification. Identifying protein classification is of fundamental importance to document the diversity of the known protein universe. It also provides a means to determine the functional roles of newly discovered protein sequences. Our goal is to predict the functional classification of novel protein sequences based on a set of features extracted from each protein sequence. The proposed technique used datasets extracted from the Structural Classification of Proteins (SCOP) database. A set of spectral domain features based on Fast Fourier Transform (FFT) is used. The proposed classifier uses multilayer back propagation (MLBP) neural network for protein classification. The maximum classification accuracy is about 91% when applying the classifier to the full four levels of the SCOP database. However, it reaches a maximum of 96% when limiting the classification to the family level. The classification results reveal that spectral domain contains information that can be used for classification with high accuracy. In addition, the results emphasize that sequence similarity measures are of great importance especially at the family level.
Abstract: The zinc and iron environments in different growth
stages have been studied with EXAFS and XANES with Brookhaven
Synchrotron Light Source. Tissue samples included meat, organ,
vegetable, leaf, and yeast. The project studied the EXAFS and
XANES of tissue samples using Zn and Fe K-edges. Duck embryo
samples show that brain and intestine would contain shorter EXFAS
determined Zn-N/O bond; as with the cases of fresh yeast versus
reconstituted live yeast and green leaf versus yellow leaf. The
XANES Fourier transform characteristic-length would be useful as a
functionality index for selected types of tissue samples in various
physical states. The extension to the development of functional
synchrotron imaging for tissue engineering application based on
spectroscopic technique is discussed.
Abstract: An implant elicits a biological response in the
surrounding tissue which determines the acceptance and long-term
function of the implant. Dental implants have become one of the
main therapy methods in clinic after teeth lose. A successful implant
is in contact with bone and soft tissue represent by fibroblasts. In our
study we focused on the interaction between six different chemically
and physically modified titanium implants (Tis-MALP, Tis-O, Tis-
OA, Tis-OPAAE, Tis-OZ, Tis-OPAE) with alveolar fibroblasts as
well as with five type of microorganisms (S. epidermis, S.mutans, S.
gordonii, S. intermedius, C.albicans). The analysis of microorganism
adhesion was determined by CFU (colony forming unite) and biofilm
formation. The presence of α3β1 and vinculin expression on alveolar
fibroblasts was demonstrated using phospho specific cell based
ELISA (PACE). Alveolar fibroblasts have the highest expression of
these proteins on Tis-OPAAE and Tis-OPAE. It corresponds with
results from bacterial adhesion and biofilm formation and it was
related to the lowest production of collagen I by alveolar fibroblasts
on Tis-OPAAE titanium disc.
Abstract: Transcription factors are a group of proteins that
helps for interpreting the genetic information in DNA.
Protein-protein interactions play a major role in the execution
of key biological functions of a cell. These interactions are
represented in the form of a graph with nodes and edges.
Studies have showed that some nodes have high degree of
connectivity and such nodes, known as hub nodes, are the
inevitable parts of the network. In the present paper a method
is proposed to identify hub transcription factor proteins using
sequence information. On a complete data set of transcription
factor proteins available from the APID database, the
proposed method showed an accuracy of 77%, sensitivity of
79% and specificity of 76%.
Abstract: Ethanol is generally used as a therapeutic reagent against Hepatocellular carcinoma (HCC or hepatoma) worldwide, as it can induce Hepatocellular carcinoma cell apoptosis at low concentration through a multifactorial process regulated by several unknown proteins. This paper provides a simple and available proteomic strategy for exploring differentially expressed proteins in the apoptotic pathway. The appropriate concentrations of ethanol required to induce HepG2 cell apoptosis were first assessed by MTT assay, Gisma and fluorescence staining. Next, the central proteins involved in the apoptosis pathway processs were determined using 2D-PAGE, SDS-PAGE, and bio-software analysis. Finally the downregulation of two proteins, AFP and survivin, were determined by immunocytochemistry and reverse transcriptase PCR (RT-PCR) technology. The simple, useful method demonstrated here provides a new approach to proteomic analysis in key bio-regulating process including proliferation, differentiation, apoptosis, immunity and metastasis.
Abstract: The aim of this in vitro study was to evaluate the possible interference of a Nectandra membranacea extract (i) on the labeling of blood cells (BC), (ii) on the labeling process of BC and plasma (P) proteins with technetium-99m (Tc-99m) and (iii) on the morphology of red blood cells (RBC). Blood samples were incubated with a Nectandra membranacea crude extract, stannous chloride, Tc- 99m (sodium pertechnetate) was added, and soluble (SF) and insoluble (IF) fractions were isolated. Morphometry studies were performed with blood samples incubated with Nectandra membranacea extract. The results show that the Nectandra membranacea extract does not promote significant alteration of the labeling of BC, IF-P and IF-BC. The Nectandra membranacea extract was able to alter the erythrocyte membrane morphology, but these morphological changes were not capable to interfere on the labeling of blood constituents with Tc-99m.
Abstract: Bovine viral diarrhea virus (BVDV) can cause lifelong
persistent infection. One reason for the phenomena is attributed to
BVDV infection to placenta tissue. However the mechanisms that
BVDV invades into placenta tissue remain unclear. To clarify the
molecular mechanisms, we investigated the possible means that
BVDV entered into bovine trophoblast cells (TPC). Yeast two-hybrid
system was used to identify proteins extracted from TPC, which
interact with BVDV envelope glycoprotein E2. A PGbkt7-E2 yeast
expression vector and TPC cDNA library were constructed. Through
two rounds of screening, three positive clones were identified.
Sequencing analysis indicated that all the three positive clones
encoded the same protein clathrin. Physical interaction between
clathrin and BVDV E2 protein was further confirmed by
coimmunoprecipitation experiments. This result suggested that the
clathrin might play a critical role in the process of BVDV entry into
placenta tissue and might be a novel antiviral target for preventing
BVDV infection.
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: 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: 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 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: 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.