Abstract: In this paper, a simple microfluidic device for monitoring algal cell behavior is proposed. An array of algal microwells is fabricated by PDMS soft-lithography using X-ray LIGA mold, placed on a glass substrate. Two layers of replicated PDMS and substrate are attached by oxygen plasma bonding, creating a microchannel for the microfluidic system. Algal cell are loaded into the microfluidic device, which provides positive charge on the bottom surface of wells. Algal cells, which are negative charged, can be attracted to the bottom of the wells via electrostatic interaction. By varying the concentration of algal cells in the loading suspension, it is possible to obtain wells with a single cell. Liquid medium for cells monitoring are flown continuously over the wells, providing nutrient and waste exchange between the well and the main flow. This device could lead to the uncovering of the quantitative biology of the algae, which is a key to effective and extensive algal utilizations in the field of biotechnology, food industry and bioenergy research and developments.
Abstract: Macrophomina phaseolina is a devastating soil-borne
fungal plant pathogen that causes charcoal rot disease in many
economically important crops worldwide. So far, no registered
fungicide is available against this plant pathogen. This study was
planned to examine the antifungal activity of an allelopathic grass
Cenchrus pennisetiformis (Hochst. & Steud.) Wipff. for the
management of M. phaseolina isolated from cowpea [Vigna
unguiculata (L.) Walp.] plants suffering from charcoal rot disease.
Different parts of the plants viz. inflorescence, shoot and root were
extracted in methanol. Laboratory bioassays were carried out using
different concentrations (0, 0.5, 1.0, …, 3.0 g mL-1) of methanolic
extracts of the test allelopathic grass species to assess the antifungal
activity against the pathogen. In general, extracts of all parts of the
grass exhibited antifungal activity. All the concentrations of
methanolic extracts of shoot and root significantly reduced fungal
biomass by 20–73% and 40–80%, respectively. Methanolic shoot
extract was fractionated using n-hexane, chloroform, ethyl acetate
and n-butanol. Different concentrations of these fractions (3.125,
6.25, …, 200 mg mL-1) were analyzed for their antifungal activity.
All the concentrations of n-hexane fraction significantly reduced
fungal biomass by 15–96% over corresponding control treatments.
Higher concentrations (12.5–200 mg mL-1) of chloroform, ethyl
acetate and n-butanol also reduced the fungal biomass significantly
by 29–100%, 46–100% and 24–100%, respectively.
Abstract: Alcohol and water extracts of Cymbopogon citratus
was investigated for anti-bacterial properties and phytochemical
constituents. The extract was screened against four gram-negative
bacteria Escherichia coli, Klebsiella pneumoniae, Pseudomonas
aeruginosa, Proteus vulgaris) and two grampositive bacteria Bacillus
subtilis and Staphylococcus aureus at four different concentrations
(1:1, 1:5, 1:10 and 1:20) using disc diffusion method. The antibacterial
examination was by disc diffusion techniques, while the
photochemical constituents were investigated using standard
chemical methods. Results showed that the extracts inhibited the
growth of standard and local strains of the organisms used. The
treatments were significantly different (P = 0.05). The minimum
inhibitory concentration of the extracts against the tested
microorganisms ranged between 150mg/ml and 50mg/ml. The
alcohol extracts were found to be generally more effective than the
water extract. The photochemical analysis revealed the presence of
alkaloids and phenol but absence of cardiac and cyanogenic
glycosides. The presence of alkaloid and phenols were inferred as
being responsible for the anti-bacterial properties of the extracts.
Abstract: Human amniotic membrane (HAM) is a useful
biological material for the reconstruction of damaged ocular surface.
The processing and preservation of HAM is critical to prevent the
patients undergoing amniotic membrane transplant (AMT) from cross
infections. For HAM preparation human placenta is obtained after an
elective cesarean delivery. Before collection, the donor is screened
for seronegativity of HCV, Hbs Ag, HIV and Syphilis. After
collection, placenta is washed in balanced salt solution (BSS) in
sterile environment. Amniotic membrane is then separated from the
placenta as well as chorion while keeping the preparation in BSS.
Scrapping of HAM is then carried out manually until all the debris is
removed and clear transparent membrane is acquired. Nitrocellulose
membrane filters are then placed on the stromal side of HAM, cut
around the edges with little membrane folded towards other side
making it easy to separate during surgery. HAM is finally stored in
solution of glycerine and Dulbecco-s Modified Eagle Medium
(DMEM) in 1:1 ratio containing antibiotics. The capped borosil vials
containing HAM are kept at -80°C until use. This vial is thawed to
room temperature and opened under sterile operation theatre
conditions at the time of surgery.
Abstract: MiRNAs participate in gene regulation of translation.
Some studies have investigated the interactions between genes and
intragenic miRNAs. It is important to study the miRNA binding sites
of genes involved in carcinogenesis. RNAHybrid 2.1 and ERNAhybrid
programmes were used to compute the hybridization free
energy of miRNA binding sites. Of these 54 mRNAs, 22.6%, 37.7%,
and 39.7% of miRNA binding sites were present in the 5'UTRs,
CDSs, and 3'UTRs, respectively. The density of the binding sites for
miRNAs in the 5'UTR ranged from 1.6 to 43.2 times and from 1.8 to
8.0 times greater than in the CDS and 3'UTR, respectively. Three
types of miRNA interactions with mRNAs have been revealed: 5'-
dominant canonical, 3'-compensatory, and complementary binding
sites. MiRNAs regulate gene expression, and information on the
interactions between miRNAs and mRNAs could be useful in
molecular medicine. We recommend that newly described sites
undergo validation by experimental investigation.
Abstract: Segmentation, filtering out of measurement errors and
identification of breakpoints are integral parts of any analysis of
microarray data for the detection of copy number variation (CNV).
Existing algorithms designed for these tasks have had some successes
in the past, but they tend to be O(N2) in either computation time or
memory requirement, or both, and the rapid advance of microarray
resolution has practically rendered such algorithms useless. Here we
propose an algorithm, SAD, that is much faster and much less thirsty
for memory – O(N) in both computation time and memory requirement
-- and offers higher accuracy. The two key ingredients of SAD are the
fundamental assumption in statistics that measurement errors are
normally distributed and the mathematical relation that the product of
two Gaussians is another Gaussian (function). We have produced a
computer program for analyzing CNV based on SAD. In addition to
being fast and small it offers two important features: quantitative
statistics for predictions and, with only two user-decided parameters,
ease of use. Its speed shows little dependence on genomic profile.
Running on an average modern computer, it completes CNV analyses
for a 262 thousand-probe array in ~1 second and a 1.8 million-probe
array in 9 seconds
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: In this study, a mathematical model was proposed and
the accuracy of this model was assessed to predict the growth of
Pseudomonas aeruginosa and rhamnolipid production under nitrogen
limiting (sodium nitrate) fed-batch fermentation. All of the
parameters used in this model were achieved individually without
using any data from the literature.
The overall growth kinetic of the strain was evaluated using a
dual-parallel substrate Monod equation which was described by
several batch experimental data. Fed-batch data under different
glycerol (as the sole carbon source, C/N=10) concentrations and feed
flow rates were used to describe the proposed fed-batch model and
other parameters. In order to verify the accuracy of the proposed
model several verification experiments were performed in a vast
range of initial glycerol concentrations. While the results showed an
acceptable prediction for rhamnolipid production (less than 10%
error), in case of biomass prediction the errors were less than 23%. It
was also found that the rhamnolipid production by P. aeruginosa was
more sensitive at low glycerol concentrations.
Based on the findings of this work, it was concluded that the
proposed model could effectively be employed for rhamnolipid
production by this strain under fed-batch fermentation on up to 80 g l-
1 glycerol.
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: Viral influenza A subtypes H5N1 and pandemic
H1N1 (pH1N1) have worldwide emerged and transmitted. The most
common anti-influenza drug for treatment of both seasonal and
pandemic influenza viruses is oseltamivir that nowadays becomes
resistance to influenza neuraminidase. The novel long-acting drug,
laninamivir, was discovered for treatment of the patients infected
with influenza B and influenza A viruses. In the present study,
laninamivir complexed with wild-type strain of both H5N1 and
pH1N1 viruses were comparatively determined the structures and
drug-target interactions by means of molecular dynamics (MD)
simulations. The results show that the hydrogen bonding interactions
formed between laninamivir and its binding residues are likely
similar for the two systems. Additionally, the presence of
intermolecular interactions from laninamivir to the residues in the
binding pocket is established through their side chains in accordance
with hydrogen bond interactions.
Abstract: Acute toxicity of nano SiO2, ZnO, MCM-41 (Meso
pore silica), Cu, Multi Wall Carbon Nano Tube (MWCNT), Single
Wall Carbon Nano Tube (SWCNT) , Fe (Coated) to bacteria Vibrio
fischeri using a homemade luminometer , was evaluated. The values
of the nominal effective concentrations (EC), causing 20% and 50%
inhibition of biouminescence, using two mathematical models at two
times of 5 and 30 minutes were calculated. Luminometer was
designed with Photomultiplier (PMT) detector. Luminol
chemiluminescence reaction was carried out for the calibration graph.
In the linear calibration range, the correlation coefficients and
coefficient of Variation (CV) were 0.988 and 3.21% respectively
which demonstrate the accuracy and reproducibility of the instrument
that are suitable. The important part of this research depends on how
to optimize the best condition for maximum bioluminescence. The
culture of Vibrio fischeri with optimal conditions in liquid media,
were stirring at 120 rpm at a temperature of 150C to 180C and were
incubated for 24 to 72 hours while solid medium was held at 180C
and for 48 hours. Suspension of nanoparticles ZnO, after 30 min
contact time to bacteria Vibrio fischeri, showed the highest toxicity
while SiO2 nanoparticles showed the lowest toxicity. After 5 min
exposure time, the toxicity of ZnO was the strongest and MCM-41
was the weakest toxicant component.
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: The in vitro culture procedure of purple nutsedge
(Cyperus rotundus L.) for multiple shoot induction and tuber
formation was established. Multiple shoots were significantly
induced from a single shoot of about 0.5 – 0.8 cm long, on Murashige
and Skoog (MS) medium supplemented with 4.44 μM 6-
benzyladinine (BA) alone or in combination with 2.85 μM 1-
indoleacetic acid (IAA), providing 17.6 and 15.3 shoots per explant
with 31.2 and 27.5 leaves per explant, respectively, within 6 weeks of
culturing. Moreover, MS medium supplemented with 4.44 μM BA
and 2.85 μM IAA was suitable for tuber induction, obtaining 5.9
tubers with 3.4 rhizomes per explant. In combination with ancymidol
and higher concentration of sucrose, 11.1 μM BA and 60 g/L sucrose
or 11.1 μM BA, 7.8 μM ancymidol and 60 g/L sucrose induced 3.5
tubers with 1.6 rhizomes or 3.5 tubers without rhizome, respectively.
However, MS medium containing 3.9 or 7.8 μM ancymidol in
combination with either 60 or 80 g/L sucrose enchanced significant
root formation at 20.9 – 23.6 roots per explant.
Abstract: Gastric ulceration is a discontinuity in gastric mucosa, usually occurs due to imbalance between the gastric mucosal protective factors, that is called gastric mucosal barrier, and the aggressive factors, to which the mucosa is exposed. This study was carried out on sixty male Sprague-Dowely rats (12- 16 weeks old) allocated into two groups. The first control group and the second Gastric lesion group which induced by oral administration of a single daily dose of aspirin at a dose of 300 mg/kg body weight for 7 consecutive-days (6% aspirin solution will be prepared and each rat will be given 5 ml of that solution/kg body weight). Blood is collected 1, 2 and 3 weeks after induction of gastric ulceration. Significant increase in serum copper, nitric oxide, and prostaglandin E2 all over the period of experiment. Significant decrease in erythrocyte superoxide dismutase (t-SOD) activities, serum (calcium, phosphorus, glucose and insulin) levels. Non-significant changes in serum sodium and potassium levels are obtained.
Abstract: Cytogenetic analysis still remains the gold standard method for prenatal diagnosis of trisomy 21 (Down syndrome, DS). Nevertheless, the conventional cytogenetic analysis needs live cultured cells and is too time-consuming for clinical application. In contrast, molecular methods such as FISH, QF-PCR, MLPA and quantitative Real-time PCR are rapid assays with results available in 24h. In the present study, we have successfully used a novel MGB TaqMan probe-based real time PCR assay for rapid diagnosis of trisomy 21 status in Down syndrome samples. We have also compared the results of this molecular method with corresponding results obtained by the cytogenetic analysis. Blood samples obtained from DS patients (n=25) and normal controls (n=20) were tested by quantitative Real-time PCR in parallel to standard G-banding analysis. Genomic DNA was extracted from peripheral blood lymphocytes. A high precision TaqMan probe quantitative Real-time PCR assay was developed to determine the gene dosage of DSCAM (target gene on 21q22.2) relative to PMP22 (reference gene on 17p11.2). The DSCAM/PMP22 ratio was calculated according to the formula; ratio=2 -ΔΔCT. The quantitative Real-time PCR was able to distinguish between trisomy 21 samples and normal controls with the gene ratios of 1.49±0.13 and 1.03±0.04 respectively (p value
Abstract: Some Chromium (III) complexes were synthesized
with three amino acids: L Glutamic Acid, Glycine, and L-cysteine as
the ligands, in order to provide a new supplement containing Cr(III)
for patients with type 2 diabetes mellitus. The complexes have been
prepared by refluxing a mixture of Chromium(III) chloride in
aqueous solution with L-glutamic acid, Glycine, and L-cysteine after
pH adjustment by sodium hydroxide. These complexes were
characterized by Infrared and Uv-Vis spectrophotometer and
Elemental analyzer. The product yields of four products were 87.50
and 56.76% for Cr-Glu complexes, 46.70% for Cr-Gly complex and
40.08% for Cr-Cys complex respectively. The predicted structure of
the complexes are [Cr(glu)2(H2O)2].xH2O, Cr(gly)3..xH2O and
Cr(cys)3.xH2O., respectively.
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: Among all microRNAs (miRNAs) in 12 plant species investigated in this study, only miR398 targeted the copper chaperone for superoxide dismutase (CCS). The nucleotide sequences of miRNA binding sites were located in the mRNA protein-coding sequence (CDS) and were highly homologous. These binding sites in CCS mRNA encoded a conservative GDLGTL hexapeptide. The binding sites for miR398 in the CDS of superoxide dismutase 1 mRNA encoded GDLGN pentapeptide. The conservative miR398 binding site located in the CDS of superoxide dismutase 2 mRNA encoded the GDLGNI hexapeptide. The miR398 binding site in the CDS of superoxide dismutase 3 mRNA encoded the GDLGNI or GDLGNV hexapeptide. Gene expression of the entire superoxide dismutase family in the studied plant species was regulated only by miR398. All members of the miR398 family, i.e. miR398a,b,c were connected to one site for each CuZnSOD and chaperone mRNA.
Abstract: Integrins are a large family of multidomain α/β cell
signaling receptors. Some integrins contain an additional inserted I
domain, whose earliest expression appears to be with the chordates,
since they are observed in the urochordates Ciona intestinalis (vase
tunicate) and Halocynthia roretzi (sea pineapple), but not in integrins
of earlier diverging species. The domain-s presence is viewed as a
hallmark of integrins of higher metazoans, however in vertebrates,
there are clearly three structurally-different classes: integrins without
I domains, and two groups of integrins with I domains but separable
by the presence or absence of an additional αC helix. For example,
the αI domains in collagen-binding integrins from Osteichthyes
(bony fish) and all higher vertebrates contain the specific αC helix,
whereas the αI domains in non-collagen binding integrins from
vertebrates and the αI domains from earlier diverging urochordate
integrins, i.e. tunicates, do not. Unfortunately, within the early
chordates, there is an evolutionary gap due to extinctions between the
tunicates and cartilaginous fish. This, coupled with a knowledge gap
due to the lack of complete genomic data from surviving species,
means that the origin of collagen-binding αC-containing αI domains
remains unknown. Here, we analyzed two available genomes from
Callorhinchus milii (ghost shark/elephant shark; Chondrichthyes –
cartilaginous fish) and Petromyzon marinus (sea lamprey;
Agnathostomata), and several available Expression Sequence Tags
from two Chondrichthyes species: Raja erinacea (little skate) and
Squalus acanthias (dogfish shark); and Eptatretus burgeri (inshore
hagfish; Agnathostomata), which evolutionary reside between the
urochordates and osteichthyes. In P. marinus, we observed several
fragments coding for the αC-containing αI domain, allowing us to
shed more light on the evolution of the collagen-binding integrins.
Abstract: A statistical optimization of the saccharification
process of EFB was studied. The statistical analysis was done by
applying faced centered central composite design (FCCCD) under
response surface methodology (RSM). In this investigation, EFB
dose, enzyme dose and saccharification period was examined, and the
maximum 53.45% (w/w) yield of reducing sugar was found with 4%
(w/v) of EFB, 10% (v/v) of enzyme after 120 hours of incubation. It
can be calculated that the conversion rate of cellulose content of the
substrate is more than 75% (w/w) which can be considered as a
remarkable achievement. All the variables, linear, quadratic and
interaction coefficient, were found to be highly significant, other than
two coefficients, one quadratic and another interaction coefficient.
The coefficient of determination (R2) is 0.9898 that confirms a
satisfactory data and indicated that approximately 98.98% of the
variability in the dependent variable, saccharification of EFB, could
be explained by this model.