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.
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: Identifying the nature of protein-nanoparticle
interactions and favored binding sites is an important issue in
functional characterization of biomolecules and their physiological
responses. Herein, interaction of silver nanoparticles with lysozyme
as a model protein has been monitored via fluorescence spectroscopy.
Formation of complex between the biomolecule and silver
nanoparticles (AgNPs) induced a steady state reduction in the
fluorescence intensity of protein at different concentrations of
nanoparticles. Tryptophan fluorescence quenching spectra suggested
that silver nanoparticles act as a foreign quencher, approaching the
protein via this residue. Analysis of the Stern-Volmer plot showed
quenching constant of 3.73 μM−1. Moreover, a single binding site in
lysozyme is suggested to play role during interaction with AgNPs,
having low affinity of binding compared to gold nanoparticles.
Unfolding studies of lysozyme showed that complex of lysozyme-
AgNPs has not undergone structural perturbations compared to the
bare protein. Results of this effort will pave the way for utilization of
sensitive spectroscopic techniques for rational design of
nanobiomaterials in biomedical applications.
Abstract: In this study, a synthetic pathway was created by
assembling genes from Clostridium butyricum and Escherichia coli
in different combinations. Among the genes were dhaB1 and dhaB2
from C. butyricum VPI1718 coding for glycerol dehydratase (GDHt)
and its activator (GDHtAc), respectively, involved in the conversion
of glycerol to 3-hydroxypropionaldehyde (3-HPA). The yqhD gene
from E.coli BL21 was also included which codes for an NADPHdependent
1,3-propanediol oxidoreductase isoenzyme (PDORI)
reducing 3-HPA to 1,3-propanediol (1,3-PD). Molecular modeling
analysis indicated that the conformation of fusion protein of YQHD
and DHAB1 was favorable for direct molecular channeling of the
intermediate 3-HPA. According to the simulation results, the yqhD
and dhaB1 gene were assembled in the upstream of dhaB2 to express
a fusion protein, yielding the recombinant strain E. coliBL21
(DE3)//pET22b+::yqhD-dhaB1_dhaB2 (strain BP41Y3). Strain
BP41Y3 gave 10-fold higher 1,3-PD concentration than E. coliBL21
(DE3)//pET22b+::yqhD-dhaB1_dhaB2 (strain BP31Y2) expressing
the recombinant enzymes simultaneously but in a non-fusion mode.
This is the first report using a gene fusion approach to enhance the
biological conversion of glycerol to the value added compound 1,3-
PD.
Abstract: Solid state fermentation of cassava peel with emphasis on protein enrichment using Trichoderma viride was evaluated. The effect of five variables: moisture content, pH, particle size (p), nitrogen source and incubation temperature; on the true protein and total sugars of cassava peel was investigated. The optimum fermentation period was established to be 8 days. Total sugars were 5-fold higher at pH 6 relative to pH 4 and 7-fold higher when cassava peels were fermented at 30oC relative to 25oC as well as using ammonium sulfate as the nitrogen source relative to urea or a combination of both. Total sugars ranged between 123.21mg/g at 50% initial moisture content to 374mg/g at 60% and from 190.59mg/g with particle size range of 2.00>p>1.41mm to 310.10mg/g with 4.00>p>3.35mm.True protein ranged from 229.70 mg/g at pH 4 to 284.05 mg/g at pH 6; from 200.87 mg/g with urea as nitrogen source and to 254.50mg/g with ammonium sulfate; from 213.82mg/g at 50% initial moisture content to 254.50mg/g at 60% moisture content, from 205.75mg/g in cassava peel with 5.6>p> 4.75mm to 268.30 in cassava peel with particle size 4.00>p>3.35mm, from 207.57mg/g at 25oC to 254.50mg/g at 30oC Cassava peel with particle size 4.00>p>3.35 mm and initial moisture content of 60% at pH 6.0, 30oC incubation temperature with ammonium sulfate (10g N / kg substrate) was most suitable for protein enrichment with Trichoderma viride. Crude protein increased from 4.21 % in unfermented cassava peel samples to 10.43 % in fermented samples.
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: Deaminated lesions were produced via nitrosative oxidation of natural nucleobases; uracul (Ura, U) from cytosine (Cyt, C), hypoxanthine (Hyp, H) from adenine (Ade, A), and xanthine (Xan, X) and oxanine (Oxa, O) from guanine (Gua, G). Such damaged nucleobases may induce mutagenic problems, so that much attentions and efforts have been poured on the revealing of their mechanisms in vivo or in vitro. In this study, we employed these deaminated lesions as useful probes for analysis of DNA-binding/recognizing proteins or enzymes. Since the pyrimidine lesions such as Hyp, Oxa and Xan are employed as analogues of guanine, their comparative uses are informative for analyzing the role of Gua in DNA sequence in DNA-protein interaction. Several DNA oligomers containing such Hyp, Oxa or Xan substituted for Gua were designed to reveal the molecular interaction between DNA and protein. From this approach, we have got useful information to understand the molecular mechanisms of the DNA-recognizing enzymes, which have not ever been observed using conventional DNA oligomer composed of just natural nucleobases.