Abstract: Carbonic anhydrases (CAs) has been focused as
biological catalysis for CO2 sequestration process because it can
catalyze the conversion of CO2 to bicarbonate. Here, codon-optimized
sequence of α type-CA cloned from Duneliala species. (DsCAopt) was
constructed, expressed, and characterized. The expression level in E.
coli BL21(DE3) was better for codon-optimized DsCAopt than intact
sequence of DsCAopt. DsCAopt enzyme shows high-stability at pH
7.6/10.0. In final, we demonstrated that in the Ca2+ solution, DsCAopt
enzyme can catalyze well the conversion of CO2 to CaCO3, as the
calcite form.
Abstract: The purpose of this research was develop a biological
nutrient removal (BNR) system which has low energy consumption, sludge production, and land usage. These indicate that BNR system could be a alternative of future wastewater treatment in ubiquitous
city(U-city). Organics and nitrogen compounds could be removed by this system so that secondary or tertiary stages of wastewater treatment satisfy their standards. This system was composed of oxic and anoxic
filter filed with PVDC and POM media. Anoxic/oxic filter system operated under empty bed contact time of 4 hours by increasing
recirculation ratio from 0 to 100 %. The system removals of total nitrogen and COD were 76.3% and 93%, respectively. To be observed
internal behavior in this system SCOD, NH3-N, and NO3-N were
conducted and removal shows range of 25~100%, 59~99%, and
70~100%, respectively.
Abstract: The stem cells have ability to differentiated
themselves through mitotic cell division and various range of
specialized cell types. Cellular differentiation is a way by which few
specialized cell develops into more specialized.This paper studies the
fundamental problem of computational schema for an artificial neural
network based on chemical, physical and biological variables of
state. By doing this type of study system could be model for a viable
propagation of various economically important stem cells
differentiation. This paper proposes various differentiation outcomes
of artificial neural network into variety of potential specialized cells
on implementing MATLAB version 2009. A feed-forward back
propagation kind of network was created to input vector (five input
elements) with single hidden layer and one output unit in output
layer. The efficiency of neural network was done by the assessment
of results achieved from this study with that of experimental data
input and chosen target data. The propose solution for the efficiency
of artificial neural network assessed by the comparatative analysis of
“Mean Square Error" at zero epochs. There are different variables of
data in order to test the targeted results.
Abstract: Biological data has several characteristics that strongly differentiate it from typical business data. It is much more complex, usually large in size, and continuously changes. Until recently business data has been the main target for discovering trends, patterns or future expectations. However, with the recent rise in biotechnology, the powerful technology that was used for analyzing business data is now being applied to biological data. With the advanced technology at hand, the main trend in biological research is rapidly changing from structural DNA analysis to understanding cellular functions of the DNA sequences. DNA chips are now being used to perform experiments and DNA analysis processes are being used by researchers. Clustering is one of the important processes used for grouping together similar entities. There are many clustering algorithms such as hierarchical clustering, self-organizing maps, K-means clustering and so on. In this paper, we propose a clustering algorithm that imitates the ecosystem taking into account the features of biological data. We implemented the system using an Ant-Colony clustering algorithm. The system decides the number of clusters automatically. The system processes the input biological data, runs the Ant-Colony algorithm, draws the Topic Map, assigns clusters to the genes and displays the output. We tested the algorithm with a test data of 100 to1000 genes and 24 samples and show promising results for applying this algorithm to clustering DNA chip data.
Abstract: Discovering new biological knowledge from the highthroughput biological data is a major challenge to bioinformatics today. To address this challenge, we developed a new approach for protein classification. Proteins that are evolutionarily- and thereby functionally- related are said to belong to the same classification. Identifying protein classification is of fundamental importance to document the diversity of the known protein universe. It also provides a means to determine the functional roles of newly discovered protein sequences. Our goal is to predict the functional classification of novel protein sequences based on a set of features extracted from each protein sequence. The proposed technique used datasets extracted from the Structural Classification of Proteins (SCOP) database. A set of spectral domain features based on Fast Fourier Transform (FFT) is used. The proposed classifier uses multilayer back propagation (MLBP) neural network for protein classification. The maximum classification accuracy is about 91% when applying the classifier to the full four levels of the SCOP database. However, it reaches a maximum of 96% when limiting the classification to the family level. The classification results reveal that spectral domain contains information that can be used for classification with high accuracy. In addition, the results emphasize that sequence similarity measures are of great importance especially at the family level.
Abstract: Anaerobic treatment has many advantages over other
biological method particularly when used to treat complex
wastewater such as petroleum refinery wastewater. In this study two
Up-flow Anaerobic Sludge Blanket (UASB) reactors were operated
in parallel to treat six volumetric organic loads (0.58, 1.21, 0.89,
2.34, 1.47 and 4.14 kg COD/m3·d) to evaluate the chemical oxygen
demand (COD) removal efficiency. The reactors were continuously
adapting to the changing of operation condition with increase in the
removal efficiency or slight decrease until the last load which was
more than two times the load, at which the reactor stressed and the
removal efficiency decreased to 75% with effluent concentration of
1746 mg COD/L. Other parameters were also monitored such as pH,
alkalinity, volatile fatty acid and gas production rate. The UASB
reactor was suitable to treat petroleum refinery wastewater and the
highest COD removal rate was 83% at 1215 kg/m3·d with COD
concentration about 356 mg/L in the effluent.
Abstract: Biological reactions of individuals of a testing animal
to toxic substance are unique and can be used as an indication of the
existing of toxic substance. However, to distinguish such phenomenon
need a very complicate system and even more complicate to analyze
data in 3 dimensional. In this paper, a system to evaluate in vitro
biological activities to acute toxicity of stochastic self-affine
non-stationary signal of 3D goldfish swimming by using fractal
analysis is introduced. Regular digital camcorders are utilized by
proposed algorithm 3DCCPC to effectively capture and construct 3D
movements of the fish. A Critical Exponent Method (CEM) has been
adopted as a fractal estimator. The hypothesis was that the swimming
of goldfish to acute toxic would show the fractal property which
related to the toxic concentration. The experimental results supported
the hypothesis by showing that the swimming of goldfish under the
different toxic concentration has fractal properties. It also shows that
the fractal dimension of the swimming related to the pH value of FD Ôëê
0.26pH + 0.05. With the proposed system, the fish is allowed to swim
freely in all direction to react to the toxic. In addition, the trajectories
are precisely evaluated by fractal analysis with critical exponent
method and hence the results exhibit with much higher degree of
confidence.
Abstract: The value of overall oxygen transfer Coefficient
(KLa), which is the best measure of oxygen transfer in water through
aeration, is obtained by a simple approach, which sufficiently
explains the utility of the method to eliminate the discrepancies due
to inaccurate assumption of saturation dissolved oxygen
concentration. The rate of oxygen transfer depends on number of
factors like intensity of turbulence, which in turns depends on the
speed of rotation, size, and number of blades, diameter and
immersion depth of the rotor, and size and shape of aeration tank, as
well as on physical, chemical, and biological characteristic of water.
An attempt is made in this paper to correlate the overall oxygen
transfer Coefficient (KLa), as an independent parameter with other
influencing parameters mentioned above. It has been estimated that
the simulation equation developed predicts the values of KLa and
power with an average standard error of estimation of 0.0164 and
7.66 respectively and with R2 values of 0.979 and 0.989 respectively,
when compared with experimentally determined values. The
comparison of this model is done with the model generated using
Computational fluid dynamics (CFD) and both the models were
found to be in good agreement with each other.
Abstract: The Beshar River is one aquatic ecosystem, which is
located next to the city of Yasuj in southern Iran. The Beshar river
has been contaminated by industrial factories such as effluent of
sugar factory, agricultural and other activities in this region such as,
Imam Sajjad hospital, drainage from agricultural farms, Yasuj urban
surface runoff and effluent of wastewater treatment plants ,specially
Yasuj waste water treatment plant. In order to evaluate the effects of
these pollutants on the quality of the Beshar river, five monitoring
stations were selected along its course. The first station is located
upstream of Yasuj near the Dehnow village; stations 2 to 4 are
located east, south and west of city; and the 5th station is located
downstream of Yasuj. Several water quality parameters were
sampled. These include pH, dissolved oxygen, biological oxygen
demand (BOD), temperature, conductivity, turbidity, total dissolved
solids and discharge or flow measurements. Water samples from the
five stations were collected and analyzed to determine the following
physicochemical parameters: EC, pH, T.D.S, T.H, No2, DO, BOD5,
COD during 2008 to 2010. The study shows that the BOD5 value of
station 1 is at a minimum (1.7 ppm) and increases downstream from
stations 2 to 4 to a maximum (11.6 ppm), and then decreases at
station 5. The DO values of station 1 is a maximum (8.45 ppm),
decreases downstream to stations 2 - 4 which are at a minimum (3.1
ppm), before increasing at station 5. The amount of BOD and TDS
are highest at the 4th station and the amount of DO is lowest at this
station, marking the 4th station as more highly polluted than the
other stations .This study shows average amount of the water quality
parameters in first year of sampling (2008) have had a better quality
relation to third year in 2010 because of recent drought in this region
and pollutant increasing .As the Beshar river path after 5th station
goes through the mountain area with more slope and flow velocity
,so the physicochemical parameters improve at the 5th station due to
pollutant degradation and dilution. Finally the point and nonpoint
pollutant sources of Beshar river were determined and compared to
the monitoring results.
Abstract: Hepatitis C is an infectious disease transmitted by
blood and due to hepatitis C virus (HCV), which attacks the liver.
The infection is characterized by liver inflammation (hepatitis) that is
often asymptomatic but can progress to chronic hepatitis and later
cirrhosis and liver cancer. Our problem tends to highlight on the one
hand the prevalence of infectious disease in the population of the
region of Batna and on other hand the biological characteristics of
this disease by a screening and a specific diagnosis based on
serological tests, liver checkup (measurement of haematological and
biochemical parameters).
The results showed:
The serology of hepatitis C establishes the diagnosis of infection
with hepatitis C. In this study and with the serological test, 24 cases
of the disease of hepatitis C were found in 1000 suspected cases (7
cases with normal transaminases and 17 cases with elevated
transaminases). The prevalence of this disease in this study
population was 2.4%.
The presence of hepatitis C disrupts liver function including the
onset of cytolysis, cholestasis, jaundice, thrombocytopenia, and
coagulation disorders.
Abstract: Gene expression profiling is rapidly evolving into a
powerful technique for investigating tumor malignancies. The
researchers are overwhelmed with the microarray-based platforms
and methods that confer them the freedom to conduct large-scale
gene expression profiling measurements. Simultaneously,
investigations into cross-platform integration methods have started
gaining momentum due to their underlying potential to help
comprehend a myriad of broad biological issues in tumor diagnosis,
prognosis, and therapy. However, comparing results from different
platforms remains to be a challenging task as various inherent
technical differences exist between the microarray platforms. In this
paper, we explain a simple ratio-transformation method, which can
provide some common ground for cDNA and Affymetrix platform
towards cross-platform integration. The method is based on the
characteristic data attributes of Affymetrix- and cDNA- platform. In
the work, we considered seven childhood leukemia patients and their
gene expression levels in either platform. With a dataset of 822
differentially expressed genes from both these platforms, we carried
out a specific ratio-treatment to Affymetrix data, which subsequently
showed an improvement in the relationship with the cDNA data.
Abstract: An implant elicits a biological response in the
surrounding tissue which determines the acceptance and long-term
function of the implant. Dental implants have become one of the
main therapy methods in clinic after teeth lose. A successful implant
is in contact with bone and soft tissue represent by fibroblasts. In our
study we focused on the interaction between six different chemically
and physically modified titanium implants (Tis-MALP, Tis-O, Tis-
OA, Tis-OPAAE, Tis-OZ, Tis-OPAE) with alveolar fibroblasts as
well as with five type of microorganisms (S. epidermis, S.mutans, S.
gordonii, S. intermedius, C.albicans). The analysis of microorganism
adhesion was determined by CFU (colony forming unite) and biofilm
formation. The presence of α3β1 and vinculin expression on alveolar
fibroblasts was demonstrated using phospho specific cell based
ELISA (PACE). Alveolar fibroblasts have the highest expression of
these proteins on Tis-OPAAE and Tis-OPAE. It corresponds with
results from bacterial adhesion and biofilm formation and it was
related to the lowest production of collagen I by alveolar fibroblasts
on Tis-OPAAE titanium disc.
Abstract: Sociological models (e.g., social network analysis, small-group dynamic and gang models) have historically been used to predict the behavior of terrorist groups. However, they may not be the most appropriate method for understanding the behavior of terrorist organizations because the models were not initially intended to incorporate violent behavior of its subjects. Rather, models that incorporate life and death competition between subjects, i.e., models utilized by scientists to examine the behavior of wildlife populations, may provide a more accurate analysis. This paper suggests the use of biological models to attain a more robust method for understanding the behavior of terrorist organizations as compared to traditional methods. This study also describes how a biological population model incorporating predator-prey behavior factors can predict terrorist organizational recruitment behavior for the purpose of understanding the factors that govern the growth and decline of terrorist organizations. The Lotka-Volterra, a biological model that is based on a predator-prey relationship, is applied to a highly suggestive case study, that of the Irish Republican Army. This case study illuminates how a biological model can be utilized to understand the actions of a terrorist organization.
Abstract: Transcription factors are a group of proteins that
helps for interpreting the genetic information in DNA.
Protein-protein interactions play a major role in the execution
of key biological functions of a cell. These interactions are
represented in the form of a graph with nodes and edges.
Studies have showed that some nodes have high degree of
connectivity and such nodes, known as hub nodes, are the
inevitable parts of the network. In the present paper a method
is proposed to identify hub transcription factor proteins using
sequence information. On a complete data set of transcription
factor proteins available from the APID database, the
proposed method showed an accuracy of 77%, sensitivity of
79% and specificity of 76%.
Abstract: Microcirculation is essential for the proper supply of
oxygen and nutritive substances to the biological tissue and the
removal of waste products of metabolism. The determination of
blood flow in the capillaries is therefore of great interest to clinicians.
A comparison has been carried out using the developed non-invasive,
non-contact and whole field laser speckle contrast imaging (LSCI)
based technique and as well as a commercially available laser
Doppler blood flowmeter (LDF) to evaluate blood flow at the finger
tip and elbow and is presented here. The LSCI technique gives more
quantitative information on the velocity of blood when compared to
the perfusion values obtained using the LDF. Measurement of blood
flow in capillaries can be of great interest to clinicians in the
diagnosis of vascular diseases of the upper extremities.
Abstract: The objective of our work is to develop a new approach for discovering knowledge from a large mass of data, the result of applying this approach will be an expert system that will serve as diagnostic tools of a phenomenon related to a huge information system. We first recall the general problem of learning Bayesian network structure from data and suggest a solution for optimizing the complexity by using organizational and optimization methods of data. Afterward we proposed a new heuristic of learning a Multi-Entities Bayesian Networks structures. We have applied our approach to biological facts concerning hereditary complex illnesses where the literatures in biology identify the responsible variables for those diseases. Finally we conclude on the limits arched by this work.
Abstract: The spatial variation in plant species associated with intercropping is intended to reduce resource competition between species and increase yield potential. A field experiment was carried out on corn (Zea mays L.) and soybean (Glycine max L.) intercropping in a replacement series experiment with weed contamination consist of: weed free, infestation of redroot pigweed, infestation of jimsonweed and simultaneous infestation of redroot pigweed and jimsonweed in Karaj, Iran during 2007 growing season. The experimental design was a randomized complete block in factorial experiment with replicated thrice. Significant (P≤0.05) differences were observed in yield in intercropping. Corn yield was higher in intercropping, but soybean yield was significantly reduced by corn when intercropped. However, total productivity and land use efficiency were high under the intercropping system even in contamination of either species of weeds. Aggressivity of corn relative to soybean revealed the greater competitive ability of corn than soybean. Land equivalent ratio (LER) more than 1 in all treatments attributed to intercropping advantages and was highest in 50: 50 (corn/soybean) in weed free. These findings suggest that intercropping corn and soybean increase total productivity per unit area and improve land use efficiency. Considering the experimental findings, corn-soybean intercropping (50:50) may be recommended for yield advantage, more efficient utilization of resources, and weed suppression as a biological control.
Abstract: Nowadays, Gene Ontology has been used widely by many researchers for biological data mining and information retrieval, integration of biological databases, finding genes, and incorporating knowledge in the Gene Ontology for gene clustering. However, the increase in size of the Gene Ontology has caused problems in maintaining and processing them. One way to obtain their accessibility is by clustering them into fragmented groups. Clustering the Gene Ontology is a difficult combinatorial problem and can be modeled as a graph partitioning problem. Additionally, deciding the number k of clusters to use is not easily perceived and is a hard algorithmic problem. Therefore, an approach for solving the automatic clustering of the Gene Ontology is proposed by incorporating cohesion-and-coupling metric into a hybrid algorithm consisting of a genetic algorithm and a split-and-merge algorithm. Experimental results and an example of modularized Gene Ontology in RDF/XML format are given to illustrate the effectiveness of the algorithm.
Abstract: The highly nonlinear characteristics of drying
processes have prompted researchers to seek new nonlinear control
solutions. However, the relation between the implementation
complexity, on-line processing complexity, reliability control
structure and controller-s performance is not well established. The
present paper proposes high performance nonlinear fuzzy controllers
for a real-time operation of a drying machine, being developed under
a consistent match between those issues. A PCI-6025E data
acquisition device from National Instruments® was used, and the
control system was fully designed with MATLAB® / SIMULINK
language. Drying parameters, namely relative humidity and
temperature, were controlled through MIMOs Hybrid Bang-bang+PI
(BPI) and Four-dimensional Fuzzy Logic (FLC) real-time-based
controllers to perform drying tests on biological materials. The
performance of the drying strategies was compared through several
criteria, which are reported without controllers- retuning. Controllers-
performance analysis has showed much better performance of FLC
than BPI controller. The absolute errors were lower than 8,85 % for
Fuzzy Logic Controller, about three times lower than the
experimental results with BPI control.
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.