Abstract: Attempts were made to identify anuran glial cells. They were found as nervous tissue resident. Having stage dependent morphotype changes, whereby, appeared as an ovoid to oval in resting state and amoeboid mrophotypes in activated state, stained fairly with methylene blue and take up Pelikane blue 10% aqueous solution, as well as having the ability to phagocytize heat killed Staphylococcus aureus. They were delineated from the migrating peripheral monocytes by morphotypic and morphometeric differences. Such criteria were consistence with glial cells. Thus, the anuran glial cells are being identified in the frog Rana ridibunda Pallas 1771 and this animal can be of use as a simple model for the immunobiology of glial cells.
Abstract: Cardiovascular diseases, principally atherosclerosis, are responsible for 30% of world deaths. Atherosclerosis is due to the formation of plaque. The fatty plaque may be at risk of rupture, leading typically to stroke and heart attack. The plaque is usually associated with a high degree of lumen reduction, called a stenosis.It is increasingly recognized that the initiation and progression of disease and the occurrence of clinical events is a complex interplay between the local biomechanical environment and the local vascular biology. The aim of this study is to investigate the flow behavior through a stenosed artery. A physical experiment was performed using an artery model and blood analogue fluid. An axisymmetric model constructed consists of contraction and expansion region that follow a mathematical form of cosine function. A 30% diameter reduction was used in this study. The flow field was measured using particle image velocimetry (PIV). Spherical particles with 20μm diameter were seeded in a water-glycerol-NaCl mixture. Steady flow Reynolds numbers are 250. The area of interest is the region after the stenosis where the flow separation occurs. The velocity field was measured and the velocity gradient was investigated. There was high particle concentration in the recirculation zone. High velocity gradient formed immediately after the stenosis throat created a lift force that enhanced particle migration to the flow separation area.
Abstract: Stochastic models of biological networks are well established in systems biology, where the computational treatment of such models is often focused on the solution of the so-called chemical master equation via stochastic simulation algorithms. In contrast to this, the development of storage-efficient model representations that are directly suitable for computer implementation has received significantly less attention. Instead, a model is usually described in terms of a stochastic process or a "higher-level paradigm" with graphical representation such as e.g. a stochastic Petri net. A serious problem then arises due to the exponential growth of the model-s state space which is in fact a main reason for the popularity of stochastic simulation since simulation suffers less from the state space explosion than non-simulative numerical solution techniques. In this paper we present transition class models for the representation of biological network models, a compact mathematical formalism that circumvents state space explosion. Transition class models can also serve as an interface between different higher level modeling paradigms, stochastic processes and the implementation coded in a programming language. Besides, the compact model representation provides the opportunity to apply non-simulative solution techniques thereby preserving the possible use of stochastic simulation. Illustrative examples of transition class representations are given for an enzyme-catalyzed substrate conversion and a part of the bacteriophage λ lysis/lysogeny pathway.
Abstract: Micro droplet formation is considered as a growing
emerging area of research due to its wide-range application in
chemistry as well as biology. The mechanism of micro droplet
formation using two immiscible liquids running through a T-junction
has been widely studied.
We believe that the flow of these two immiscible phases can be of
greater important factor that could have an impact on out-flow
hydrodynamic behavior, the droplets generated and the size of the
droplets. In this study, the type of the capillary tubes used also
represents another important factor that can have an impact on the
generation of micro droplets.
The tygon capillary tubing with hydrophilic inner surface doesn't
allow regular out-flows due to the fact that the continuous phase
doesn't adhere to the wall of the capillary inner surface.
Teflon capillary tubing, presents better wettability than tygon
tubing, and allows to obtain steady and regular regimes of out-flow,
and the micro droplets are homogeneoussize.
The size of the droplets is directly dependent on the flows of the
continuous and dispersed phases. Thus, as increasing the flow of the
continuous phase, to flow of the dispersed phase stationary, the size
of the drops decreases. Inversely, while increasing the flow of the
dispersed phase, to flow of the continuous phase stationary, the size
of the droplet increases.
Abstract: Multi-agent system approach has proven to be an effective and appropriate abstraction level to construct whole models of a diversity of biological problems, integrating aspects which can be found both in "micro" and "macro" approaches when modeling this type of phenomena. Taking into account these considerations, this paper presents the important computational characteristics to be gathered into a novel bioinformatics framework built upon a multiagent architecture. The version of the tool presented herein allows studying and exploring complex problems belonging principally to structural biology, such as protein folding. The bioinformatics framework is used as a virtual laboratory to explore a minimalist model of protein folding as a test case. In order to show the laboratory concept of the platform as well as its flexibility and adaptability, we studied the folding of two particular sequences, one of 45-mer and another of 64-mer, both described by an HP model (only hydrophobic and polar residues) and coarse grained 2D-square lattice. According to the discussion section of this piece of work, these two sequences were chosen as breaking points towards the platform, in order to determine the tools to be created or improved in such a way to overcome the needs of a particular computation and analysis of a given tough sequence. The backwards philosophy herein is that the continuous studying of sequences provides itself important points to be added into the platform, to any time improve its efficiency, as is demonstrated herein.
Abstract: Understanding the cell's large-scale organization is an
interesting task in computational biology. Thus, protein-protein
interactions can reveal important organization and function of the
cell. Here, we investigated the correspondence between protein
interactions and function for the yeast. We obtained the correlations
among the set of proteins. Then these correlations are clustered using
both the hierarchical and biclustering methods. The detailed analyses
of proteins in each cluster were carried out by making use of their
functional annotations. As a result, we found that some functional
classes appear together in almost all biclusters. On the other hand, in
hierarchical clustering, the dominancy of one functional class is
observed. In brief, from interaction data to function, some correlated
results are noticed about the relationship between interaction and
function which might give clues about the organization of the
proteins.
Abstract: Classification is one of the primary themes in
computational biology. The accuracy of classification strongly
depends on quality of a dataset, and we need some method to
evaluate this quality. In this paper, we propose a new graphical
analysis method using 'Membership-Deviation Graph (MDG)' for
analyzing quality of a dataset. MDG represents degree of
membership and deviations for instances of a class in the dataset. The
result of MDG analysis is used for understanding specific feature and
for selecting best feature for classification.
Abstract: The paper attempts to elucidate the columnar structure
of the cortex by answering the following questions. (1) Why the
cortical neurons with similar interests tend to be vertically arrayed
forming what is known as cortical columns? (2) How to describe the
cortex as a whole in concise mathematical terms? (3) How to design
efficient digital models of the cortex?
Abstract: In molecular biology, microarray technology is widely and successfully utilized to efficiently measure gene activity. If working with less studied organisms, methods to design custom-made microarray probes are available. One design criterion is to select probes with minimal melting temperature variances thus ensuring similar hybridization properties. If the microarray application focuses on the investigation of metabolic pathways, it is not necessary to cover the whole genome. It is more efficient to cover each metabolic pathway with a limited number of genes. Firstly, an approach is presented which minimizes the overall melting temperature variance of selected probes for all genes of interest. Secondly, the approach is extended to include the additional constraints of covering all pathways with a limited number of genes while minimizing the overall variance. The new optimization problem is solved by a bottom-up programming approach which reduces the complexity to make it computationally feasible. The new method is exemplary applied for the selection of microarray probes in order to cover all fungal secondary metabolite gene clusters for Aspergillus terreus.
Abstract: The scientific achievements coming from molecular
biology depend greatly on the capability of computational
applications to analyze the laboratorial results. A comprehensive
analysis of an experiment requires typically the simultaneous study
of the obtained dataset with data that is available in several distinct
public databases. Nevertheless, developing a centralized access to
these distributed databases rises up a set of challenges such as: what
is the best integration strategy, how to solve nomenclature clashes,
how to solve database overlapping data and how to deal with huge
datasets. In this paper we present GeNS, a system that uses a simple and yet innovative approach to address several biological data integration issues. Compared with existing systems, the main
advantages of GeNS are related to its maintenance simplicity and to its coverage and scalability, in terms of number of supported
databases and data types. To support our claims we present the current use of GeNS in two concrete applications. GeNS currently contains more than 140 million of biological relations and it can be
publicly downloaded or remotely access through SOAP web services.
Abstract: Water is the key of national development. Wherever a spring has been dried out or a river has changed its course, the area-s people have migrated and have been scattered and the area-s civilization has lost its brilliance. Today, air pollution, global warming and ozone layer damage are as the problems of countries, but certainly in the next decade the shortage and pollution of waters will be important issues of the world. The polluted waters are more dangerous in when they are used in agriculture. Because they infect plants and these plants are used in human and livestock consumption in food chain. With the increasing population growth and after that, the increase need to facilities and raw materials, human beings has started to do haste actions and wanted or unwanted destroyed his life basin. They try to overuse and capture his environment extremely, instead of having futurism approach in sustainable use of nature. This process includes Zayanderood recession, and caused its pollution after the transition from industrial and urban areas. Zayandehrood River in Isfahan is a vital artery of a living ecosystem. Now is the location of disposal waste water of many cities, villages and existing industries. The central area of the province is an important industrial place, and its environmental situation has reached a critical stage. Not only a large number of pollution-generating industries are active in the city limits, but outside of the city and adjacent districts Zayandehrood River, heavy industries like steel, Mobarakeh Steel and other tens great units pollute wild life. This article tries to study contaminant sources of Zayanderood and their severity, and determine and discuss the share of each of these resources by major industrial centers located in areas. At the end, we represent suitable strategy.
Abstract: The PAX6, a transcription factor, is essential for the morphogenesis of the eyes, brain, pituitary and pancreatic islets. In rodents, the loss of Pax6 function leads to central nervous system defects, anophthalmia, and nasal hypoplasia. The haplo-insufficiency of Pax6 causes microphthalmia, aggression and other behavioral abnormalities. It is also required in brain patterning and neuronal plasticity. In human, heterozygous mutation of Pax6 causes loss of iris [aniridia], mental retardation and glucose intolerance. The 3- deletion in Pax6 leads to autism and aniridia. The phenotypes are variable in peneterance and expressivity. However, mechanism of function and interaction of PAX6 with other proteins during development and associated disease are not clear. It is intended to explore interactors of PAX6 to elucidated biology of PAX6 function in the tissues where it is expressed and also in the central regulatory pathway. This report describes In-silico approaches to explore interacting proteins of PAX6. The models show several possible proteins interacting with PAX6 like MITF, SIX3, SOX2, SOX3, IPO13, TRIM, and OGT. Since the Pax6 is a critical transcriptional regulator and master control gene of eye and brain development it might be interacting with other protein involved in morphogenesis [TGIF, TGF, Ras etc]. It is also presumed that matricelluar proteins [SPARC, thrombospondin-1 and osteonectin etc] are likely to interact during transport and processing of PAX6 and are somewhere its cascade. The proteins involved in cell survival and cell proliferation can also not be ignored.
Abstract: Lectins have a good scope in current clinical
microbiology research. In the present study evaluated the
antimicrobial activities of a D-galactose binding lectin (PnL) was
purified from the annelid, Perinereis nuntia (polychaeta) by affinity
chromatography. The molecular mass of the lectin was determined to
be 32 kDa as a single polypeptide by SDS-PAGE under both reducing
and non-reducing conditions. The hemagglutinating activity of the
PnL showed against trypsinized and glutaraldehyde-fixed human
erythrocytes was specifically inhibited by D-Gal, GalNAc,
Galβ1-4Glc and Galα1-6Glc. PnL was evaluated for in vitro
antibacterial screening studies against 11 gram-positive and
gram-negative microorganisms. From the screening results, it was
revealed that PnL exhibited significant antibacterial activity against
gram-positive bacteria. Bacillus megaterium showed the highest
growth inhibition by the lectin (250 μg/disc). However, PnL did not
inhibit the growth of gram-negative bacteria such as Vibrio cholerae
and Pseudomonas sp. PnL was also examined for in vitro antifungal
activity against six fungal phytopathogens. PnL (100 μg/mL) inhibited
the mycelial growth of Alternaria alternata (24.4%). These results
indicate that future findings of lectin applications obtained from
annelids may be of importance to life sciences.
Abstract: The paper discusses the mathematics of pattern
indexing and its applications to recognition of visual patterns that are
found in video clips. It is shown that (a) pattern indexes can be
represented by collections of inverted patterns, (b) solutions to
pattern classification problems can be found as intersections and
histograms of inverted patterns and, thus, matching of original
patterns avoided.
Abstract: Ontology is widely being used as a tool for organizing
information, creating the relation between the subjects within the
defined knowledge domain area. Various fields such as Civil,
Biology, and Management have successful integrated ontology in
decision support systems for managing domain knowledge and to
assist their decision makers. Gross pollutant traps (GPT) are devices
used in trapping and preventing large items or hazardous particles in
polluting and entering our waterways. However choosing and
determining GPT is a challenge in Malaysia as there are inadequate
GPT data repositories being captured and shared. Hence ontology is
needed to capture, organize and represent this knowledge into
meaningful information which can be contributed to the efficiency of
GPT selection in Malaysia urbanization. A GPT Ontology framework
is therefore built as the first step to capture GPT knowledge which
will then be integrated into the decision support system. This paper
will provide several examples of the GPT ontology, and explain how
it is constructed by using the Protégé tool.
Abstract: The amount of the information being churned out by the field of biology has jumped manifold and now requires the extensive use of computer techniques for the management of this information. The predominance of biological information such as protein sequence similarity in the biological information sea is key information for detecting protein evolutionary relationship. Protein sequence similarity typically implies homology, which in turn may imply structural and functional similarities. In this work, we propose, a learning method for detecting remote protein homology. The proposed method uses a transformation that converts protein sequence into fixed-dimensional representative feature vectors. Each feature vector records the sensitivity of a protein sequence to a set of amino acids substrings generated from the protein sequences of interest. These features are then used in conjunction with support vector machines for the detection of the protein remote homology. The proposed method is tested and evaluated on two different benchmark protein datasets and it-s able to deliver improvements over most of the existing homology detection methods.
Abstract: The present study has been taken to explore the
screening of in vitro antimicrobial activities of D-galactose-binding
sponge lectin (HOL-30). HOL-30 was purified from the marine
demosponge Halichondria okadai by affinity chromatography. The
molecular mass of the lectin was determined to be 30 kDa with a
single polypeptide by SDS-PAGE under non-reducing and reducing
conditions. HOL-30 agglutinated trypsinized and glutaraldehydefixed
rabbit and human erythrocytes with preference for type O
erythrocytes. The lectin was subjected to evaluation for inhibition of
microbial growth by the disc diffusion method against eleven human
pathogenic gram-positive and gram-negative bacteria. The lectin
exhibited strong antibacterial activity against gram-positive bacteria,
such as Bacillus megaterium and Bacillus subtilis. However, it did
not affect against gram-negative bacteria such as Salmonella typhi
and Escherichia coli. The largest zone of inhibition was recorded of
Bacillus megaterium (12 in diameter) and Bacillus subtilis (10 mm in
diameter) at a concentration of the lectin (250 μg/disc). On the other
hand, the antifungal activity of the lectin was investigated against six
phytopathogenic fungi based on food poisoning technique. The lectin
has shown maximum inhibition (22.83%) of mycelial growth of
Botrydiplodia theobromae at a concentration of 100 μg/mL media.
These findings indicate that the lectin may be of importance to
clinical microbiology and have therapeutic applications.
Abstract: Bioinformatics and computational biology involve
the use of techniques including applied mathematics,
informatics, statistics, computer science, artificial intelligence,
chemistry, and biochemistry to solve biological problems
usually on the molecular level. Research in computational
biology often overlaps with systems biology. Major research
efforts in the field include sequence alignment, gene finding,
genome assembly, protein structure alignment, protein structure
prediction, prediction of gene expression and proteinprotein
interactions, and the modeling of evolution. Various
global rearrangements of permutations, such as reversals and
transpositions,have recently become of interest because of their
applications in computational molecular biology. A reversal is
an operation that reverses the order of a substring of a permutation.
A transposition is an operation that swaps two adjacent
substrings of a permutation. The problem of determining the
smallest number of reversals required to transform a given
permutation into the identity permutation is called sorting by
reversals. Similar problems can be defined for transpositions
and other global rearrangements. In this work we perform a
study about some genome rearrangement primitives. We show
how a genome is modelled by a permutation, introduce some
of the existing primitives and the lower and upper bounds
on them. We then provide a comparison of the introduced
primitives.
Abstract: The most common result of analysis of highthroughput
data in molecular biology represents a global list of
genes, ranked accordingly to a certain score. The score can be a
measure of differential expression. Recent work proposed a new
method for selecting a number of genes in a ranked gene list from
microarray gene expression data such that this set forms the
Optimally Functionally Enriched Network (OFTEN), formed by
known physical interactions between genes or their products. Here
we present calculation results of relative connectivity of genes from
META-OFTEN network and tentative biological interpretation of the
most reproducible signal. The relative connectivity and
inbetweenness values of genes from META-OFTEN network were
estimated.