Abstract: A new approach to predict the 3D structures of proteins by combining the knowledge-based method and Molecular Dynamics Simulation is presented on the chicken villin headpiece subdomain (HP-36). Comparative modeling is employed as the knowledge-based method to predict the core region (Ala9-Asn28) of the protein while the remaining residues are built as extended regions (Met1-Lys8; Leu29-Phe36) which then further refined using Molecular Dynamics Simulation for 120 ns. Since the core region is built based on a high sequence identity to the template (65%) resulting in RMSD of 1.39 Å from the native, it is believed that this well-developed core region can act as a 'nucleation center' for subsequent rapid downhill folding. Results also demonstrate that the formation of the non-native contact which tends to hamper folding rate can be avoided. The best 3D model that exhibits most of the native characteristics is identified using clustering method which then further ranked based on the conformational free energies. It is found that the backbone RMSD of the best model compared to the NMR-MDavg is 1.01 Å and 3.53 Å, for the core region and the complete protein, respectively. In addition to this, the conformational free energy of the best model is lower by 5.85 kcal/mol as compared to the NMR-MDavg. This structure prediction protocol is shown to be effective in predicting the 3D structure of small globular protein with a considerable accuracy in much shorter time compared to the conventional Molecular Dynamics simulation alone.
Abstract: The nutrient composition and sensory properties of
poultry-based patties (PBPs) incorporated with various levels of grey
oyster mushroom (Pleurotus sajor-caju, PSC) were studied. The
PBPs were formulated with either 0%, 25% or 50% of fresh ground
PSC. Results show poultry patty formulated with 25% PSC had
protein content of 17.46% lower than the control patty which had
18.13% but it was not significant. Meanwhile, both cooked poultry
patties containing 25% and 50% PSC significantly recorded lower
concentration of fat at 10.67% and 7.15%, respectively. On the other
hand, poultry patty added with 50% ground PSC shows the highest
concentration of total dietary fibre (TDF) of 4.90 g/100g compared to
poultry patty containing 25% of mushroom (3.40 g/100g) and to the
control (1.90g/100g). In addition, patty incorporated with 25% PSC
had moisture content of 57.91% which is significantly lower than
patty formulated with 50% which had moisture of 61.80%. In the
sensory evaluation, there were no differences recorded in all sensory
attributes of PSC-based patties judged by untrained panelists. In
conclusion, the addition of PSC to replace poultry meat can be
recommended for the purpose of lowering production cost, enhancing
nutritional composition and maintaining the acceptability of poultry
patties.
Abstract: Pearson-s correlation coefficient and sequential path
analysis has been used for determining the interrelationship among
yield, yield components, soil minerals and aroma of Khao Dawk Mali
(KDML) 105 rice grown in the area of Tungkularonghai in Roi-Et
province, located in the northeast of Thailand. Pearson-s correlation
coefficient in this study showed that the number of panicles was the
only factor that had positive significant (0.790**) effect on grain
yield. Sequential path analysis revealed that the number of panicles
followed by the number of fertile spikelets and 100-grain weight
were the first-order factors which had positive direct effects on grain
yield. Whereas, other factors analyzed had indirect effects
influencing grain yield. This study also indicated that no significant
relationship was found between the aroma level and any of the
factors analyzed.
Abstract: Toxoplasma gondii is an intracellular parasite capable
of infecting all nucleated cells in a diverse array of species.
Toxoplasma plaque assay have been described using Bacto Agar.
Because of its experimental advantages carboxymethyl cellulose
overlay, medium viscosity was choosing and the aim of this work
was to develop alternative method for formation of T. gondii plaques.
Tachyzoites were inoculated onto monolayers of Vero cells and
cultured at 37° C under 5 % CO2. The cultures were followed up by
microscopy inspection. Small plaques were visible by naphtol blue
stain 4 days after infection. Larger plaques could be observed by day
10 of culture. The carboxymethyl cellulose is a cheap reagent and the
methodology is easier, faster than assays under agar overlay. This is
the first description of the carboxymethyl cellulose overlay use for
obtaining the formation of T. gondii plaques and may be useful in
consequent obtaining tachyzoites for detailed studies.
Abstract: Microbial oil was produced by soil isolated
oleaginous yeast YU5/2 in flask-batch fermentation. The yeast was
identified by molecular genetics technique based on sequence
analysis of the variable D1/D2 domain of the large subunit (26S)
ribosomal DNA and it was identified as Torulaspora globosa. T.
globosa YU5/2 supported maximum values of 0.520 g/L/d, 0.472 g
lipid/g cells, 4.16 g/L, and 0.156 g/L/d for volumetric lipid
production rate, and specific yield of lipid, lipid concentration, and
specific rate of lipid production respectively, when culture was
performed in nitrogen-limiting medium supplemented with 80g/L
glucose. Among the carbon sources tested, maximum cell yield
coefficient (YX/S, g/L), maximum specific yield of lipid (YP/X, g
lipid/g cells) and volumetric lipid production rate (QP, g/L/d) were
found of 0.728, 0.237, and 0.619, respectively, using sweet potato
tubers hydrolysates as carbon source.
Abstract: The importance for manipulating an incorporated
scaffold and directing cell behaviors is well appreciated for tissue
engineering. Here, we developed newly nano-topographic oxidized
silicon nanosponges capable of being various chemical modifications
to provide much insight into the fundamental biology of how cells
interact with their surrounding environment in vitro. A wet etching
technique is exerted to allow us fabricated the silicon nanosponges in a
high-throughput manner. Furthermore, various organo-silane
chemicals enabled self-assembled on the surfaces by vapor deposition.
We have found that Chinese hamster ovary (CHO) cells displayed
certain distinguishable morphogenesis, adherent responses, and
biochemical properties while cultured on these chemical modified
nano-topographic structures in compared with the planar oxidized
silicon counterparts, indicating that cell behaviors can be influenced
by certain physical characteristic derived from nano-topography in
addition to the hydrophobicity of contact surfaces crucial for cell
adhesion and spreading. Of particular, there were predominant
nano-actin punches and slender protrusions formed while cells were
cultured on the nano-topographic structures. This study shed potential
applications of these nano-topographic biomaterials for controlling
cell development in tissue engineering or basic cell biology research.
Abstract: We investigated oxidative DNA damage caused by
radio frequency radiation using 8-oxo-7, 8-dihydro-2'-
deoxyguanosine (8-oxodG) generated in mice tissues after exposure
to 900 MHz mobile phone radio frequency in three independent
experiments. The RF was generated by a Global System for Mobile
Communication (GSM) signal generator. The radio frequency field
was adjusted to 25 V/m. The whole body specific absorption rate
(SAR) was 1.0 W/kg. Animals were exposed to this field for 30 min
daily for 30 days. 24 h post-exposure, blood serum, brain and spleen
were removed and DNA was isolated. Enzyme-linked
immunosorbent assay (ELISA) was used to measure 8-oxodG
concentration. All animals survived the whole experimental period.
The body weight of animals did not change significantly at the end of
the experiment. No statistically significant differences observed in
the levels of oxidative stress. Our results are not in favor of the
hypothesis that 900 MHz RF induces oxidative damage.
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: Candida spp. are common and aggressive pathogens.
Because of the growing resistance of Candida spp. to current
antifungals, novel targets, found in Candida spp. but not in humans
or other flora, have to be identified. The alternative oxidase (AOX)
is one such possibility. This enzyme is insensitive to cyanide, but is
sensitive to compounds such as salicylhydroxamic acid (SHAM),
disulfiram and n-alkyl gallates. The growth Candida albicans was
inhibited by SHAM (Ki = 9-15 mM) and cyanide (Ki = 2-4 mM),
albeit to differing extents. The rate of O2 uptake was inhibited by
less than 10% by 25 mM SHAM and by about 90% by 250 μM
KCN. Although SHAM substantially inhibited the growth of C.
albicans, it is unlikely that the inhibition of AOX was the cause.
Salicylhydroxamic acid is used therapeutically in the treatment of
urinary tract infections and urolithiasis, but it also has some potential
in the treatment of C. albicans infection.
Abstract: In this study, we used a two-stage process and
potassium hydroxide (KOH) to transform waste biomass (rice straw)
into activated carbon and then evaluated the adsorption capacity of the
waste for removing carbofuran from an aqueous solution. Activated
carbon was fast and effective for the removal of carbofuran because of
its high surface area. The native and carbofuran-loaded adsorbents
were characterized by elemental analysis. Different adsorption
parameters, such as the initial carbofuran concentration, contact time,
temperature and pH for carbofuran adsorption, were studied using a
batch system. This study demonstrates that rice straw can be very
effective in the adsorption of carbofuran from bodies of water.
Abstract: The efficient operation of any biological treatment
process requires pre-treatment of incompatible pollutants such as
acids, bases, oil, toxic substances, etc. which hamper the treatment
of other major components which are otherwise degradable. The
pre-treatment of alkaline waste-waters, generated from various
industries like textile, paper & pulp, potato-processing industries,
etc., having a pH of 10 or higher, is essential. The pre-treatment,
i.e., neutralization of such alkaline waste-waters can be achieved by
chemical as well as biological means. However, the biological pretreatment
offers better package over the chemical means by being
safe and economical. The biological pre-treatment can be
accomplished by using a blend of microorganisms able to withstand
such harsh alkaline conditions. In the present study, for the proper
pre-treatment of alkaline waste-waters, a package of alkalophilic
bacteria is formulated to neutralise the alkaline pH of the industrial
waste-waters. The developed microbial package is cost-effective as
well as environmental friendly.
Abstract: The objective of this work is to produce heterotrophic
microalgal lipid in flask-batch fermentation. Chlorella sp. KKU-S2
supported maximum values of 0.374 g/L/d, 0.478 g lipid/g cells, and
0.112 g/L/d for volumetric lipid production rate, and specific yield of
lipid, and specific rate of lipid production, respectively when culture
was performed on BG-11 medium supplemented with 50g/L glucose.
Among the carbon sources tested, maximum cell yield coefficient
(YX/S, g/L), maximum specific yield of lipid (YP/X, g lipid/g cells) and
volumetric lipid production rate (QP, g/L/d) were found of 0.728,
0.237, and 0.619, respectively, using sugarcane molasses as carbon
source. The main components of fatty acid from extracted lipid were
palmitic acid, stearic acid, oleic acid and linoleic acid which similar
to vegetable oils and suitable for biodiesel production.
Abstract: Composting is the process in which municipal solid
waste (MSW) and other organic waste materials such as biosolids
and manures are decomposed through the action of bacteria and other
microorganisms into a stable granular material which, applied to
land, as soil conditioner. Microorganisms, especially those that are
able to degrade polymeric organic material have a key role in speed
up this process. The aim of this study has been established to
isolation of microorganisms with high ability to production
extracellular enzymes for degradation of natural polymers that are
exists in MSW for decreasing time of degradation phase. Our
experimental study for isolation designed in two phases: in first
phase we isolated degrading microorganism with selected media that
consist a special natural polymer such as cellulose, starch, lipids and
etc as sole source of carbon. In second phase we selected
microorganism that had high degrading enzyme production with
enzymatic assay for seed production. However, our findings in pilot
scale have indicated that usage of this microbial consortium had high
efficiency for decreasing degradation phase.
Abstract: Calcium is a vital second messenger used in signal transduction. Calcium controls secretion, cell movement, muscular contraction, cell differentiation, ciliary beating and so on. Two theories have been used to simplify the system of reaction-diffusion equations of calcium into a single equation. One is excess buffer approximation (EBA) which assumes that mobile buffer is present in excess and cannot be saturated. The other is rapid buffer approximation (RBA), which assumes that calcium binding to buffer is rapid compared to calcium diffusion rate. In the present work, attempt has been made to develop a model for calcium diffusion under excess buffer approximation in neuron cells. This model incorporates the effect of [Na+] influx on [Ca2+] diffusion,variable calcium and sodium sources, sodium-calcium exchange protein, Sarcolemmal Calcium ATPase pump, sodium and calcium channels. The proposed mathematical model leads to a system of partial differential equations which have been solved numerically using Forward Time Centered Space (FTCS) approach. The numerical results have been used to study the relationships among different types of parameters such as buffer concentration, association rate, calcium permeability.