Abstract: Protein-protein interactions (PPI) play a crucial role in many biological processes such as cell signalling, transcription, translation, replication, signal transduction, and drug targeting, etc. Structural information about protein-protein interaction is essential for understanding the molecular mechanisms of these processes. Structures of protein-protein complexes are still difficult to obtain by biophysical methods such as NMR and X-ray crystallography, and therefore protein-protein docking computation is considered an important approach for understanding protein-protein interactions. However, reliable prediction of the protein-protein complexes is still under way. In the past decades, several grid-based docking algorithms based on the Katchalski-Katzir scoring scheme were developed, e.g., FTDock, ZDOCK, HADDOCK, RosettaDock, HEX, etc. However, the success rate of protein-protein docking prediction is still far from ideal. In this work, we first propose a more practical measure for evaluating the success of protein-protein docking predictions,the rate of first success (RFS), which is similar to the concept of mean first passage time (MFPT). Accordingly, we have assessed the ZDOCK bound and unbound benchmarks 2.0 and 3.0. We also createda new benchmark set for protein-protein docking predictions, in which the complexes have experimentally determined binding affinity data. We performed free energy calculation based on the solution of non-linear Poisson-Boltzmann equation (nlPBE) to improve the binding mode prediction. We used the well-studied thebarnase-barstarsystem to validate the parameters for free energy calculations. Besides,thenlPBE-based free energy calculations were conducted for the badly predicted cases by ZDOCK and ZRANK. We found that direct molecular mechanics energetics cannot be used to discriminate the native binding pose from the decoys.Our results indicate that nlPBE-based calculations appeared to be one of the promising approaches for improving the success rate of binding pose predictions.
Abstract: Two species of Physalis, P.angulataL. and P.
peruviana L. were used as models for comparative study to
understand the values of micro-morphological, -anatomical and
architectural characteristics of leaf for taxonomic purposes and
possibly breeding and commercial applications. Both speciespossess
amphistomaticleaves with 1-layer epidermis, 3-4-layer spongy
mesophyll andbicollateral bundle midrib. Palisade parenchyma cells
of P. angulatawere almost twice longer (65-75 μm) than the other
one. Type of stomata was similar as anomocyticbut stomatal
index(SI) at adaxial surface and abaxial surface of P. angulata were
less than of P. peruvianaas 3.57, 4.00 and6.25, 6.66 respectively.
Some leaf architectural characteristics such as leaf shape, order of
venationalsoprovided information of taxonomic significance
Abstract: In a 10-week (May – August, 2008) Phase I trial, 840, 1+ rainbow trout, Oncorhynchus mykiss, received a commercial oral immunomodulator, Fin Immune™, at four different dosages (0, 10, 20 and 30 mg g-1) to evaluate immune response and growth. The overall objective of was to determine an optimal dosage of this product for rainbow trout that provides enhanced immunity with maximal growth and health. Biweekly blood samples were taken from 10 randomly selected fish in each tank (30 samples per treatment) to evaluate the duration of enhanced immunity conferred by Fin-Immune™. The immunological assessment included serum white blood cell (lymphocyte, neutrophil) densities and blood hematocrit (packed cell volume %). Of these three variables, only lymphocyte density increased significantly among trout fed Fin- Immune™ at 20 and 30 mg g-1 which peaked at week 6. At week 7, all trout were switched to regular feed (lacking Fin-Immune™) and by week 10, lymphocyte levels decreased among all levels but were still greater than at week 0. There was growth impairment at the highest dose of Fin-Immune™ tested (30 mg g-1) which can be associated with a physiological compensatory mechanism due to a dose-specific threshold level. Thus, our main objective of this Phase I study was achieved, the 20 mg g-1 dose of Fin-Immune™ should be the most efficacious (of those we tested) to use for a Phase II disease challenge trial.
Abstract: Bio-electrical responses obtained from freshwater
sediments by employing microbial fuel cell (MFC) technology were
investigated in this experimental study. During the electricity
generation, organic matter in the sediment was microbially oxidized
under anaerobic conditions with an electrode serving as a terminal
electron acceptor. It was found that the sediment organic matter
(SOM) associated with electrochemically-active electrodes became
more humified, aromatic, and polydispersed, and had a higher average
molecular weight, together with the decrease in the quantity of SOM.
The alteration of characteristics of the SOM was analogous to that
commonly observed in the early stage of SOM diagenetic process (i.e.,
humification). These findings including an elevation of the sediment
redox potential present a possibility of the MFC technology as a new
soil/sediment remediation technique based on its potential benefits:
non-destructive electricity generation and bioremediation.
Abstract: The purpose of the present work was to study the
production and process parameters optimization for the synthesis of
cellulase from Trichoderma viride in solid state fermentation (SSF)
using an agricultural wheat straw as substrates; as fungal conversion
of lignocellulosic biomass for cellulase production is one among the
major increasing demand for various biotechnological applications.
An optimization of process parameters is a necessary step to get
higher yield of product. Several kinetic parameters like pretreatment,
extraction solvent, substrate concentration, initial moisture content,
pH, incubation temperature and inoculum size were optimized for
enhanced production of third most demanded industrially important
cellulase. The maximum cellulase enzyme activity 398.10±2.43
μM/mL/min was achieved when proximally analyzed lignocellulosic
substrate wheat straw inocubated at 2% HCl as pretreatment tool
along with distilled water as extraction solvent, 3% substrate
concentration 40% moisture content with optimum pH 5.5 at 45°C
incubation temperature and 10% inoculum size.
Abstract: The growing health hazardous impact of arsenic (As)
contamination in environment is the impetus of the present
investigation. Application of lactic acid bacteria (LAB) for the
removal of toxic and heavy metals from water has been reported.
This study was performed in order to isolate and characterize the Asresistant
LAB from mud and sludge samples for using as efficient As
uptaking probiotic. Isolation of As-resistant LAB colonies was
performed by spread plate technique using bromocresol purple
impregnated-MRS (BP-MRS) agar media provided with As @ 50
μg/ml. Isolated LAB were employed for probiotic characterization
process, acid and bile tolerance, lactic acid production, antibacterial
activity and antibiotic tolerance assays. After As-resistant and
removal characterizations, the LAB were identified using 16S rDNA
sequencing. A total of 103 isolates were identified as As-resistant
strains of LAB. The survival of 6 strains (As99-1, As100-2, As101-3,
As102-4, As105-7, and As112-9) was found after passing through the
sequential probiotic characterizations. Resistant pattern pronounced
hollow zones at As concentration >2000 μg/ml in As99-1, As100-2,
and As101-3 LAB strains, whereas it was found at ~1000 μg/ml in
rest 3 strains. Among 6 strains, the As uptake efficiency of As102-4
(0.006 μg/h/mg wet weight of cell) was higher (17 – 209%)
compared to remaining LAB. 16S rDNA sequencing data of 3 (As99-
1, As100-2, and As101-3) and 3 (As102-4, As105-7, and As112-9)
LAB strains clearly showed 97 to 99% (340 bp) homology to
Pediococcus dextrinicus and Pediococcus acidilactici, respectively.
Though, there was no correlation between the metal resistant and
removal efficiency of LAB examined but identified elevated As
removing LAB would probably be a potential As uptaking probiotic
agent. Since present experiment concerned with only As removal
from pure water, As removal and removal mechanism in natural
condition of intestinal milieu should be assessed in future studies.
Abstract: Numerical parametric study is conducted to study the effects of ampoule rotation on the flows and the dopant segregation in vertical bridgman (vb) crystal growth. Calculations were performed in unsteady state. The extended darcy model, which includes the time derivative and coriolis terms, has been employed in the momentum equation. It’s found that the convection, and dopant segregation can be affected significantly by ampoule rotation, and the effect is similar to that by an axial magnetic field. Ampoule rotation decreases the intensity of convection and stretches the flow cell axially. When the convection is weak, the flow can be suppressed almost completely by moderate ampoule rotation and the dopant segregation becomes diffusion-controlled. For stronger convection, the elongated flow cell by ampoule rotation may bring dopant mixing into the bulk melt reducing axial segregation at the early stage of the growth. However, if the cellular flow cannot be suppressed completely, ampoule rotation may induce larger radial segregation due to poor mixing.
Abstract: The hybridization of artificial immune system with
cellular automata (CA-AIS) is a novel method. In this hybrid model,
the cellular automaton within each cell deploys the artificial immune
system algorithm under optimization context in order to increase its
fitness by using its neighbor-s efforts. The hybrid model CA-AIS is
introduced to fix the standard artificial immune system-s weaknesses.
The credibility of the proposed approach is evaluated by simulations
and it shows that the proposed approach achieves better results
compared to standard artificial immune system.
Abstract: The number of users supported in a DS-CDMA
cellular system is typically less than spreading factor (N), and the
system is said to be underloaded. Overloading is a technique to
accommodate more number of users than the spreading factor N. In
O/O overloading scheme, the first set is assigned to the N
synchronous users and the second set is assigned to the additional
synchronous users. An iterative multistage soft decision interference
cancellation (SDIC) receiver is used to remove high level of
interference between the two sets. Performance is evaluated in terms
of the maximum number acceptable users so that the system
performance is degraded slightly compared to the single user
performance at a specified BER. In this paper, the capacity of CDMA
based O/O overloading scheme is evaluated with SDIC receiver. It is
observed that O/O scheme using orthogonal Gold codes provides
25% channel overloading (N=64) for synchronous DS-CDMA
system on an AWGN channel in the uplink at a BER of 1e-5.For a
Rayleigh faded channel, the critical capacity is 40% at a BER of 5e-5
assuming synchronous users. But in practical systems, perfect chip
timing is very difficult to maintain in the uplink.. We have shown that
the overloading performance reduces to 11% for a timing
synchronization error of 0.02Tc for a BER of 1e-5.
Abstract: A major challenge in biomaterials research is the
regulation of protein adsorption which is a key factor for controlling
the subsequent cell adhesion at implant surfaces. The aim of the
present study was to control the adsorption of fibronectin (FN) and
the attachment of MG-63 osteoblasts with an electronic
nanostructure. Shallow doping line lattices with a period of 260 nm
were produced for this purpose by implantation of phosphorous in
silicon wafers. Protein coverage was determined after incubating the
substrate with FN by means of an immunostaining procedure and the
measurement of the fluorescence intensity with a TECAN analyzer.
We observed an increased amount of adsorbed FN on the
nanostructure compared to control substrates. MG-63 osteoblasts
were cultivated for 24h on FN-incubated substrates and their
morphology was assessed by SEM. Preferred orientation and
elongation of the cells in direction of the doping lattice lines was
observed on FN-coated nanostructures.
Abstract: Methods of contemporary mathematical physics such
as chaos theory are useful for analyzing and understanding the
behavior of complex biological and physiological systems. The three
dimensional model of HIV/AIDS is the basis of active research since
it provides a complete characterization of disease dynamics and the
interaction of HIV-1 with the immune system. In this work, the
behavior of the HIV system is analyzed using the three dimensional
HIV model and a chaotic measure known as the Hurst exponent.
Results demonstrate that Hurst exponents of CD4, CD8 cells and
viral load vary nonlinearly with respect to variations in system
parameters. Further, it was observed that the three dimensional HIV
model can accommodate both persistent (H>0.5) and anti-persistent
(H
Abstract: The possibility of intrinsic electromagnetic fields
within living cells and their resonant self-interaction and interaction
with ambient electromagnetic fields is suggested on the basis of a
theoretical and experimental study. It is reported that intrinsic
electromagnetic fields are produced in the form of radio-frequency
and infra-red photons within atoms (which may be coupled or
uncoupled) in cellular structures, such as the cell cytoskeleton and
plasma membrane. A model is presented for the interaction of these
photons among themselves or with atoms under a dipole-dipole
coupling, induced by single-photon or two-photon processes. This
resonance is manifested by conspicuous field amplification and it is
argued that it is possible for these resonant photons to undergo
tunnelling in the form of evanescent waves to a short range (of a few
nanometers to micrometres). This effect, suggested as a resonant
photon tunnelling mechanism in this report, may enable these fields
to act as intracellular signal communication devices and as bridges
between macromolecules or cellular structures in the cell
cytoskeleton, organelles or membrane. A brief overview of an
experimental technique and a review of some preliminary results are
presented, in the detection of these fields produced in living cell
membranes under physiological conditions.
Abstract: Mitochondria are dynamic organelles, capable to
interact with each other. While the number of mitochondria in a cell
varies, their quality and functionality depends on the operation of
fusion, fission, motility and mitophagy. Nowadays, several
researches declare as an important factor in neurogenerative diseases
the disruptions in the regulation of mitochondrial dynamics. In this
paper a stochastic model in BioAmbients calculus is presented,
concerning mitochondrial fusion and its distribution in the renewal of
mitochondrial population in a cell. This model describes the
successive and dependent stages of protein synthesis, protein-s
activation and merging of two independent mitochondria.
Abstract: Most of the drugs used for pharmaceutical purposes
are poorly water-soluble drugs. About 40% of all newly discovered
drugs are lipophilic and the numbers of lipophilic drugs seem to
increase more and more. Drug delivery systems such as
nanoparticles, micelles or liposomes are applied to improve their
solubility and thus their bioavailability. Besides various techniques of
solubilization, oil-in-water emulsions are often used to incorporate
lipophilic drugs into the oil phase. To stabilize emulsions surface
active substances (surfactants) are generally used. An alternative
method to avoid the application of surfactants was of great interest.
One possibility is to develop O/W-emulsion without any addition of
surface active agents or the so called “surfactant-free emulsion or
SFE”. The aim of this study was to develop and characterize SFE as a
drug carrier by varying the production conditions. Lidocaine base
was used as a model drug. The injection method was developed.
Effects of ultrasound as well as of temperature on the properties of
the emulsion were studied. Particle sizes and release were
determined. The long-term stability up to 30 days was performed.
The results showed that the surfactant-free O/W emulsions with
pharmaceutical oil as drug carrier can be produced.
Abstract: By using the method of coincidence degree and constructing suitable Lyapunov functional, some sufficient conditions are established for the existence and global exponential stability of antiperiodic solutions for a kind of impulsive Cohen-Grossberg shunting inhibitory cellular neural networks (CGSICNNs) on time scales. An example is given to illustrate our results.
Abstract: Polyphenolics and sugar are the components of many
fruit juices. In this work, the performance of ultra-filtration (UF) for
separating phenolic compounds from apple juice was studied by
performing batch experiments in a membrane module with an area of
0.1 m2 and fitted with a regenerated cellulose membrane of 1 kDa
MWCO. The effects of various operating conditions: transmembrane
pressure (3, 4, 5 bar), temperature (30, 35, 40 ºC), pH (2, 3, 4, 5),
feed concentration (3, 5, 7, 10, 15 ºBrix for apple juice) and feed flow
rate (1, 1.5, 1.8 L/min) on the performance were determined.
The optimum operating conditions were: transmembrane pressure
4 bar, temperature 30 ºC, feed flow rate 1 – 1.8 L/min, pH 3 and 10
Brix (apple juice). After performing ultrafiltration under these
conditions, the concentration of polyphenolics in retentate was
increased by a factor of up to 2.7 with up to 70% recovered in the
permeate and with approx. 20% of the sugar in that stream..
Application of diafiltration (addition of water to the concentrate) can
regain the flux by a factor of 1.5, which has been decreased due to
fouling. The material balance performed on the process has shown
the amount of deposits on the membrane and the extent of fouling in
the system. In conclusion, ultrafiltration has been demonstrated as a
potential technology to separate the polyphenolics and sugars from
their mixtures and can be applied to remove sugars from fruit juice.
Abstract: This paper discusses telecominication market developments in Saudi Arabia. Empirical research was carried in the holy city of Makkah to study the customer's preference for mobile cellular service and the factor influencing their subscription of the mobile phone service. Results indicate that the financial factor sicnificantly influence the customer's selection of the service provider.
Abstract: Nowadays there is a growing interest in biofuel production in most countries because of the increasing concerns about hydrocarbon fuel shortage and global climate changes, also for enhancing agricultural economy and producing local needs for transportation fuel. Ethanol can be produced from biomass by the hydrolysis and sugar fermentation processes. In this study ethanol was produced without using expensive commercial enzymes from sugarcane bagasse. Alkali pretreatment was used to prepare biomass before enzymatic hydrolysis. The comparison between NaOH, KOH and Ca(OH)2 shows NaOH is more effective on bagasse. The required enzymes for biomass hydrolysis were produced from sugarcane solid state fermentation via two fungi: Trichoderma longibrachiatum and Aspergillus niger. The results show that the produced enzyme solution via A. niger has functioned better than T. longibrachiatum. Ethanol was produced by simultaneous saccharification and fermentation (SSF) with crude enzyme solution from T. longibrachiatum and Saccharomyces cerevisiae yeast. To evaluate this procedure, SSF of pretreated bagasse was also done using Celluclast 1.5L by Novozymes. The yield of ethanol production by commercial enzyme and produced enzyme solution via T. longibrachiatum was 81% and 50% respectively.
Abstract: One of the essential components of much of DSP
application is noise cancellation. Changes in real time signals are
quite rapid and swift. In noise cancellation, a reference signal which
is an approximation of noise signal (that corrupts the original
information signal) is obtained and then subtracted from the noise
bearing signal to obtain a noise free signal. This approximation of
noise signal is obtained through adaptive filters which are self
adjusting. As the changes in real time signals are abrupt, this needs
adaptive algorithm that converges fast and is stable. Least mean
square (LMS) and normalized LMS (NLMS) are two widely used
algorithms because of their plainness in calculations and
implementation. But their convergence rates are small. Adaptive
averaging filters (AFA) are also used because they have high
convergence, but they are less stable. This paper provides the
comparative study of LMS and Normalized NLMS, AFA and new
enhanced average adaptive (Average NLMS-ANLMS) filters for noise
cancelling application using speech signals.
Abstract: Novel polystrene-bound Schiff bases and their Pt(IV)
complexes have been prepared from condensation reaction of
polystyrene-A-NH2 with 2-hydroxybenzaldehyde and 5-fluoro-3-
bromo-2-hydroxybenzaldehyde. The structures of Pt(IV) complexes
with polystyrene including Schiff bases have been determined by
elemental analyses, magnetic susceptibility, IR, 1H-NMR, UV-vis,
TG/DTA and AAS. The antibacterial and antifungal activities of the
synthesized compounds have been studied by the well-diffusion
method against some selected microorganisms: (Bacillus cereus spp.,
Listeria monocytogenes 4b, Micrococcus luteus, Staphylococcus
aureus, Staphylococcus epidermis, Brucella abortus, Escherichia
coli, Pseudomonas putida spp., Shigella dysenteria type 10,
Salmonella typhi H).