Abstract: This study aims to demonstrate the quantification of
peptides based on isotope dilution surface enhanced Raman
scattering (IDSERS). SERS spectra of phenylalanine (Phe), leucine
(Leu) and two peptide sequences TGQIFK (T13) and
YSFLQNPQTSLCFSESIPTPSNR (T6) as part of the 22-kDa
human growth hormone (hGH) were obtained on Ag-nanoparticle
covered substrates. On the basis of the dominant Phe and Leu
vibrational modes, precise partial least squares (PLS) prediction
models were built enabling the determination of unknown T13 and
T6 concentrations. Detection of hGH in its physiological
concentration in order to investigate the possibility of protein
quantification has been achieved.
Abstract: Background: Dialign is a DNA/Protein alignment tool
for performing pairwise and multiple pairwise alignments through the
comparison of gap-free segments (fragments) between sequence
pairs. An alignment of two sequences is a chain of fragments, i.e
local gap-free pairwise alignments, with the highest total score.
METHOD: A new approach is defined in this article which relies on
the concept of using three-dimensional fragments – i.e. local threeway
alignments -- in the alignment process instead of twodimensional
ones. These three-dimensional fragments are gap-free
alignments constituting of equal-length segments belonging to three
distinct sequences. RESULTS: The obtained results showed good
improvments over the performance of DIALIGN.
Abstract: The objective of the present study was to evaluate the
potential of hollow microneedles for enhancing the transdermal
delivery of Bovine Serum Albumin (MW~66,000 Da)-Fluorescein
Isothiocyanate (BSA-FITC) conjugate, a hydrophilic large molecular
compound. Moreover, the effect of different formulations was
evaluated. The series of binary mixtures composed of propylene
glycol (PG) and pH 7.4 phosphate buffer solution (PBS) was
prepared and used as a medium for BSA-FITC. The results showed
that there was no permeation of BSA-FITC solution across the
neonatal porcine skin without using hollow microneedles, whereas
the cumulative amount of BSA-FITC released at 8 h through the
neonatal porcine skin was about 60-70% when using hollow
microneedles. Furthermore, the results demonstrated that the higher
volume of PG in binary mixtures injected, the lower cumulative
amount of BSA-FITC released and release rate of BSA-FITC from
skin. These release profiles of BSA-FITC in binary mixtures were
expressed by Fick-s law of diffusion. These results suggest the
utilization of hollow microneedle to enhance transdermal delivery of
protein and provide useful information for designing an effective
hollow microneedle system.
Abstract: Due to the ever growing amount of publications about
protein-protein interactions, information extraction from text is
increasingly recognized as one of crucial technologies in
bioinformatics. This paper presents a Protein Interaction Extraction
System using a Link Grammar Parser from biomedical abstracts
(PIELG). PIELG uses linkage given by the Link Grammar Parser to
start a case based analysis of contents of various syntactic roles as
well as their linguistically significant and meaningful combinations.
The system uses phrasal-prepositional verbs patterns to overcome
preposition combinations problems. The recall and precision are
74.4% and 62.65%, respectively. Experimental evaluations with two
other state-of-the-art extraction systems indicate that PIELG system
achieves better performance. For further evaluation, the system is
augmented with a graphical package (Cytoscape) for extracting
protein interaction information from sequence databases. The result
shows that the performance is remarkably promising.
Abstract: The purpose of research was to know the role of
immunogenic protein of 49 kDa from V.alginolyticus which capable
to initiate molecule expression of MHC Class II in receptor of
Cromileptes altivelis. The method used was in vivo experimental
research through testing of immunogenic protein 49 kDa from
V.alginolyticus at Cromileptes altivelis (size of 250 - 300 grams)
using 3 times booster by injecting an immunogenic protein in a
intramuscular manner. Response of expressed MHC molecule was
shown using immunocytochemistry method and SEM. Results
indicated that adhesin V.alginolyticus 49 kDa which have
immunogenic character could trigger expression of MHC class II on
receptor of grouper and has been proven by staining using
immunocytochemistry and SEM with labeling using antibody anti
MHC (anti mouse). This visible expression based on binding between
epitopes antigen and antibody anti MHC in the receptor. Using
immunocytochemistry, intracellular response of MHC to in vivo
induction of immunogenic adhesin from V.alginolyticus was shown.
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 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.
Abstract: β-Glucosidase is an important enzyme for production
of ethanol from lignocellulose. With hydrolytic activity on
cellooligosaccharides, especially cellobiose, β-glucosidase removes
product inhibitory effect on cellulases and forms fermentable sugars.
In this study, β-glucosidase encoding gene (BGL1) from traditional
starter yeast Saccharomycosis fibuligera BMQ908 was cloned and
expressed in Pichia pastoris. BGL1 of S. fibuligera BMQ 908 shared
98% nucleotide homology with the closest GenBank sequence
(M22475) but identity in amino-acid sequences of catalytic domains.
Recombinant plasmid pPICZαA/BGL1 containing the sequence
encoding BGL1 mature protein and α-factor secretion signal was
constructed and transformed into methylotrophic yeast P. pastoris by
electroporation. The recombinant strain produced single extracellular
protein with molecular weight of 120 kDa and cellobiase activity of
60 IU/ml. The optimum pH of the recombinant β-glucosidase was 5.0
and the optimum temperature was 50°C.
Abstract: The experiment was conducted to evaluate
digestibility quantities of protein in Canola Meals (CMs) between
caecectomised and intact adult Rhode Island Red (RIR) cockerels
with using conventional addition method (CAM) for 7 d: a 4-d
adaptation and a 3-d experiment period on the basis of a completely
randomized design with 4 replicates. Results indicated that
caecectomy decreased (P
Abstract: The paper presents a part of the results obtained in a
complex research project on Romanian Grey Steppe breed, owner of
some remarkable qualities such as hardiness, longevity, adaptability,
special resistance to ban weather and diseases and included in the
genetic fund (G.D. no. 822/2008.) from Romania.
Following the researches effectuated, we identified alleles of six
loci, codifying the six types of major milk proteins: alpha-casein S1
(α S1-cz); beta-casein (β-cz); kappa-casein (K-cz); beta-lactoglobulin
(β-lg); alpha-lactalbumin (α-la) and alpha-casein S2 (α S2-cz). In
system αS1-cz allele αs1-Cn B has the highest frequency (0.700), in
system β-cz allele β-Cn A2 ( 0.550 ), in system K-cz allele k-CnA2 (
0.583 ) and heterozygote genotype AB ( 0.416 ) and BB (0.375), in
system β-lg allele β-lgA1 has the highest frequency (0.542 ) and
heterozygote genotype AB ( 0.500 ), in system α-la there is
monomorphism for allele α-la B and similarly in system αS2-cz for
allele αs2-Cn A.
The milk analysis by the isoelectric focalization technique (I.E.F.)
allowed the identification of a new allele for locus αS1-casein, for two
of the individuals under analysis, namely allele called αS1-casein
IRV. When experiments were repeated, we noticed that this is not a
proteolysis band and it really was a new allele that has not been
registered in the specialized literature so far. We identified two
heterozygote individuals, carriers of this allele, namely: BIRV and
CIRV. This discovery is extremely important if focus is laid on the
national genetic patrimony.
Abstract: Proteins levels produced by bacteria may be increased
in stressful surroundings, such as in the presence of antibiotics. It
appears that many antimicrobial agents or antibiotics, when used at
low concentrations, have in common the ability to activate or repress
gene transcription, which is distinct from their inhibitory effect.
There have been comparatively few studies on the potential of
antibiotics or natural compounds in nature as a specific chemical
signal that can trigger a variety of biological functions. Therefore,
this study was focusing on the effect of essential oils from
Cymbopogon flexuosus and C. nardus in regulating proteins
production by Bacillus subtilis ATCC 21332. The Minimum
Inhibition Concentrations (MICs) of both essential oils on B. subtilis
were determined by using microdilution assay, resulting 0.2% and
1.56% for each C. flexuosus and C. nardus subsequently. The
bacteria were further exposed to each essential oils at concentration
of 0.01XMIC for 2 days. The proteins were then isolated and
analyzed by sodium dodecyl sulfate polyacrylamide gel
electrophoresis (SDS-PAGE). Protein profile showed that a band
with approximate size of 250 kD was appeared for the treated
bacteria with essential oils. Thus, Bacillus subtilis ATCC 21332 in
stressful condition with the presence of essential oils at low
concentration could induce the protein production.
Abstract: Sorghum flour was supplemented with 15 and 30%
chickpea flour. Sorghum flour and the supplement were fermented at
35 oC for 0, 8, 16, and 24 h. Changes in pH, titrable acidity, total
soluble solids, protein content, in vitro protein digestibility and
amino acid composition were investigated during fermentation and/or
after supplementation of sorghum flour with chickpea. The pH of the
fermenting material decreased sharply with a concomitant increase in
the titrable acidity. The total soluble solids remained unchanged with
progressive fermentation time. The protein content of sorghum
cultivar was found to be 9.27 and that of chickpea was 22.47%. The
protein content of sorghum cultivar after supplementation with15 and
30% chickpea was significantly (P ≤ 0.05) increased to 11.78 and
14.55%, respectively. The protein digestibility also increased after
fermentation from 13.35 to 30.59 and 40.56% for the supplements,
respectively. Further increment in protein content and digestibility
was observed when supplemented and unsupplemented samples were
fermented for different periods of time. Cooking of fermented
samples was found to increase the protein content slightly and
decreased digestibility for both supplements. Amino acid content of
fermented and fermented and cooked supplements was determined.
Supplementation was found to increase the lysine and therionine
content. Cooking following fermentation decreased lysine,
isoleucine, valine and sulfur containg amino acids.
Abstract: A thin coating of hexamethyldisiloxane and subsequent O2-plasma treatment was performed on mirror-polished titanium in order to regulate the wide range of wettability including 106 and almost 0 degrees of contact angles. The adsorption behavior of
fibronectin and albumin in both individual and competitive mode,
and initial attachment of fibroblasts and osteoblasts were investigated.
Individually, fibronectin adsorption showed a biphasic inclination, whereas albumin showed greater adsorption to hydrophobic surfaces.
In competitive mode, in solution containing both fibronectin and albumin, fibronectin showed greater adsorption on hydrophilic
surfaces, whereas Alb predominantly adsorbed on hydrophobic
surfaces. Initial attachment of both cells increased with increase in
surface wettability, in particular, on super-hydrophilic surface, which
correlated well with fibronectin adsorption in competitive mode.
These results suggest that a cold plasma-surface modification enabled
to regulate the surface wettability, and fibronectin adsorption may be
responsible for increasing cell adhesion on hydrophilic surfaces in a
body fluid
Abstract: A. niger XP isolated from Vietnam produces very low amount of acidic phytase with optimal pH at 2.5 and 5.5. The phytase production of this strain was successfully improved through gene cloning and expression. A 1.4 - kb DNA fragment containing the coding region of the phyA gene was amplified by PCR and inserted into the expression vector pPICZαA with a signal peptide α- factor, under the control of AOX1 promoter. The recombined plasmid was transformed into the host strain P. pastoris KM71H and X33 by electroporation. Both host strains could efficiently express and secret phytase. The multicopy strains were screened for over expression of phytase. All the selected multicopy strains of P. pastoris X33 were examined for phytase activity, the maximum phytase yield of 1329 IU/ml was obtained after 4 days of incubation in medium BMM. The recombinant protein with MW of 97.4 KW showed to be the only one protein secreted in the culture broth. Multicopy transformant P. pastoris X33 supposed to be potential candidate for producing the commercial preparation of phytase.
Abstract: The dynamics of Min proteins plays a center role in
accurate cell division. Although the nucleoids may presumably play
an important role in prokaryotic cell division, there is a lack of
models to account for its participation. In this work, we apply the
lattice Boltzmann method to investigate protein oscillation based on a
mesoscopic model that takes into account the nucleoid-s role. We
found that our numerical results are in reasonably good agreement
with the previous experimental results On comparing with the other
computational models without the presence of nucleoids, the
highlight of our finding is that the local densities of MinD and MinE
on the cytoplasmic membrane increases, especially along the cell
width, when the size of the obstacle increases, leading to a more
distinct cap-like structure at the poles. This feature indicated the
realistic pattern and reflected the combination of Min protein
dynamics and nucleoid-s role.
Abstract: Multiple sequence alignment is a fundamental part in
many bioinformatics applications such as phylogenetic analysis.
Many alignment methods have been proposed. Each method gives a
different result for the same data set, and consequently generates a
different phylogenetic tree. Hence, the chosen alignment method
affects the resulting tree. However in the literature, there is no
evaluation of multiple alignment methods based on the comparison of
their phylogenetic trees. This work evaluates the following eight
aligners: ClustalX, T-Coffee, SAGA, MUSCLE, MAFFT, DIALIGN,
ProbCons and Align-m, based on their phylogenetic trees (test trees)
produced on a given data set. The Neighbor-Joining method is used
to estimate trees. Three criteria, namely, the dNNI, the dRF and the
Id_Tree are established to test the ability of different alignment
methods to produce closer test tree compared to the reference one
(true tree). Results show that the method which produces the most
accurate alignment gives the nearest test tree to the reference tree.
MUSCLE outperforms all aligners with respect to the three criteria
and for all datasets, performing particularly better when sequence
identities are within 10-20%. It is followed by T-Coffee at lower
sequence identity (30%), trees scores of all methods
become similar.
Abstract: Reactiondiffusion systems are mathematical models that describe how the concentration of one or more substances distributed in space changes under the influence of local chemical reactions in which the substances are converted into each other, and diffusion which causes the substances to spread out in space. The classical representation of a reaction-diffusion system is given by semi-linear parabolic partial differential equations, whose general form is ÔêétX(x, t) = DΔX(x, t), where X(x, t) is the state vector, D is the matrix of the diffusion coefficients and Δ is the Laplace operator. If the solute move in an homogeneous system in thermal equilibrium, the diffusion coefficients are constants that do not depend on the local concentration of solvent and of solutes and on local temperature of the medium. In this paper a new stochastic reaction-diffusion model in which the diffusion coefficients are function of the local concentration, viscosity and frictional forces of solvent and solute is presented. Such a model provides a more realistic description of the molecular kinetics in non-homogenoeus and highly structured media as the intra- and inter-cellular spaces. The movement of a molecule A from a region i to a region j of the space is described as a first order reaction Ai k- → Aj , where the rate constant k depends on the diffusion coefficient. Representing the diffusional motion as a chemical reaction allows to assimilate a reaction-diffusion system to a pure reaction system and to simulate it with Gillespie-inspired stochastic simulation algorithms. The stochastic time evolution of the system is given by the occurrence of diffusion events and chemical reaction events. At each time step an event (reaction or diffusion) is selected from a probability distribution of waiting times determined by the specific speed of reaction and diffusion events. Redi is the software tool, developed to implement the model of reaction-diffusion kinetics and dynamics. It is a free software, that can be downloaded from http://www.cosbi.eu. To demonstrate the validity of the new reaction-diffusion model, the simulation results of the chaperone-assisted protein folding in cytoplasm obtained with Redi are reported. This case study is redrawing the attention of the scientific community due to current interests on protein aggregation as a potential cause for neurodegenerative diseases.
Abstract: The protein domain structure has been widely used as the most informative sequence feature to computationally predict protein-protein interactions. However, in a recent study, a research group has reported a very high accuracy of 94% using hydrophobicity feature. Therefore, in this study we compare and verify the usefulness of protein domain structure and hydrophobicity properties as the sequence features. Using the Support Vector Machines (SVM) as the learning system, our results indicate that both features achieved accuracy of nearly 80%. Furthermore, domains structure had receiver operating characteristic (ROC) score of 0.8480 with running time of 34 seconds, while hydrophobicity had ROC score of 0.8159 with running time of 20,571 seconds (5.7 hours). These results indicate that protein-protein interaction can be predicted from domain structure with reliable accuracy and acceptable running time.
Abstract: The organic farmers use wider range of crop varieties than the conventional farming. Bread wheat is the most favorite and the most common food crop. The organic bread wheat is usually of worse technological quality. Therefore, it is supposed to be an attractive alternative to the hulled wheat species (einkorn, emmer wheat and spelt). Twenty-five hulled bread wheat varieties and control bread wheat ones were grown on the certified organic parcel in České Budějovice (the Czech Republic) between 2009 and 2012. Their baking quality was measured and evaluated with standard methods, and in accordance with ICC. The results have shown that the grain of hulled wheat varieties contain a lot of proteins in grains (up to 18 percent); even the organic hulled bread wheat varieties are characterized by such good baking quality. Einkorn and emmer wheat are of worse technological quality of proteins (low values of gluten index and Zeleny test), which is a disadvantage of these two wheat species. On the other hand, spelt wheat is of better technological quality and is similar to the control bread wheat varieties. Mixtures consisting of bread wheat, among others, are considered good alternatives; they may contribute to wider range of use of the hulled wheat species. It is one of the possibilities which may increase the proportion of proteins in bread wheat grains; the nutrition-rich hulled wheat grains may be also used in such way at the same time.
Abstract: Twelve lactating Etawah Crossedbred goats were used
in this study. Goat feed consisted of Cally andra callothyrsus,
Pennisetum purpureum, wheat bran and dried fermented cassava
peel. The cassava peels were fermented with a traditional culture
called “ragi tape" (mixed culture of Saccharomyces cerevisae,
Aspergillus sp, Candida, Hasnula and Acetobacter). The goats were
divided into 2 groups (Control and Treated) of six does. The
experimental diet of the Control group consisted of 70% of roughage
(fresh Callyandra callothyrsus and Pennisetum purpureum 60:40)
and 30% of wheat bran on dry matter (DM) base. In the Treated
group 30% of wheat bran was replaced with dried fermented cassava
peels. Data were statistically analyzed using analysis of variance
followed SPSS program. The concentration of HCN in fermented
cassava peel decreased to non toxic level. Nutrient composition of
dried fermented cassava peel consisted of 85.75% dry matter;
5.80% crude protein and 82.51% total digestible nutrien (TDN).
Substitution of 30% of wheat bran with dried fermented cassava peel
in the diet had no effect on dry matter and organic matter intake but
significantly (P< 0.05) decreased crude protein and TDN
consumption as well as milk yields and milk composition. The study
recommended to reduced the level of substitution to less than 30% of
concentrates in the diet in order to avoid low nutrient intake and milk
production of goats.
Abstract: One field experiment was conducted on corn (Zea
mays L.Var. SC 704) to study the effect of three different basic levels
of nitrogen (90, 140and 190 Kg/ha as urea) with 0.01% and 0.02%
pyridoxine pre-sowing seed soaking for 8 hours. Water-soaked seeds
were treated as controled. biomass production was recorded on 45,
70 and 95 days after sowing. Total dry material (TDM), leaf area
index (LAI), crop growth rate (CGR), relative growth rate (RGR) and
net assimilation rate (NAR) was calculated form 45until 95 days after
sowing. Yield and its components such as kernel yield, grain weight,
biologic yield, harvest index and protein percentage was measured at
harvest. In general, 0.02% pyridoxine and 190 Kg pure nitrogen/ha
was shown gave maximum value for growth and yield parameters.
N190 + 0.02 % pyridoxine enhanced seed yield and biologic yield by
57.15% and 62.98% compared to 90kg N and water – soaked
treatment.