23,415 research outputs found
Extraction of Transcript Diversity from Scientific Literature
Transcript diversity generated by alternative splicing and associated mechanisms contributes heavily to the functional complexity of biological systems. The numerous examples of the mechanisms and functional implications of these events are scattered throughout the scientific literature. Thus, it is crucial to have a tool that can automatically extract the relevant facts and collect them in a knowledge base that can aid the interpretation of data from high-throughput methods. We have developed and applied a composite text-mining method for extracting information on transcript diversity from the entire MEDLINE database in order to create a database of genes with alternative transcripts. It contains information on tissue specificity, number of isoforms, causative mechanisms, functional implications, and experimental methods used for detection. We have mined this resource to identify 959 instances of tissue-specific splicing. Our results in combination with those from EST-based methods suggest that alternative splicing is the preferred mechanism for generating transcript diversity in the nervous system. We provide new annotations for 1,860 genes with the potential for generating transcript diversity. We assign the MeSH term âalternative splicingâ to 1,536 additional abstracts in the MEDLINE database and suggest new MeSH terms for other events. We have successfully extracted information about transcript diversity and semiautomatically generated a database, LSAT, that can provide a quantitative understanding of the mechanisms behind tissue-specific gene expression. LSAT (Literature Support for Alternative Transcripts) is publicly available at http://www.bork.embl.de/LSAT/
The Jones polynomial and graphs on surfaces
The Jones polynomial of an alternating link is a certain specialization of
the Tutte polynomial of the (planar) checkerboard graph associated to an
alternating projection of the link. The Bollobas-Riordan-Tutte polynomial
generalizes the Tutte polynomial of planar graphs to graphs that are embedded
in closed oriented surfaces of higher genus.
In this paper we show that the Jones polynomial of any link can be obtained
from the Bollobas-Riordan-Tutte polynomial of a certain oriented ribbon graph
associated to a link projection. We give some applications of this approach.Comment: 19 pages, 9 figures, minor change
A Pseudo DNA Cryptography Method
The DNA cryptography is a new and very promising direction in cryptography
research. DNA can be used in cryptography for storing and transmitting the
information, as well as for computation. Although in its primitive stage, DNA
cryptography is shown to be very effective. Currently, several DNA computing
algorithms are proposed for quite some cryptography, cryptanalysis and
steganography problems, and they are very powerful in these areas. However, the
use of the DNA as a means of cryptography has high tech lab requirements and
computational limitations, as well as the labor intensive extrapolation means
so far. These make the efficient use of DNA cryptography difficult in the
security world now. Therefore, more theoretical analysis should be performed
before its real applications.
In this project, We do not intended to utilize real DNA to perform the
cryptography process; rather, We will introduce a new cryptography method based
on central dogma of molecular biology. Since this method simulates some
critical processes in central dogma, it is a pseudo DNA cryptography method.
The theoretical analysis and experiments show this method to be efficient in
computation, storage and transmission; and it is very powerful against certain
attacks. Thus, this method can be of many uses in cryptography, such as an
enhancement insecurity and speed to the other cryptography methods. There are
also extensions and variations to this method, which have enhanced security,
effectiveness and applicability.Comment: A small work that quite some people asked abou
Exploration of alternative splicing events in ten different grapevine cultivars
Background: The complex dynamics of gene regulation in plants are still far from being fully understood. Among many factors involved, alternative splicing (AS) in particular is one of the least well documented. For many years, AS has been considered of less relevant in plants, especially when compared to animals, however, since the introduction of next generation sequencing techniques the number of plant genes believed to be alternatively spliced has increased exponentially.
Results: Here, we performed a comprehensive high-throughput transcript sequencing of ten different grapevine cultivars, which resulted in the first high coverage atlas of the grape berry transcriptome. We also developed findAS, a software tool for the analysis of alternatively spliced junctions. We demonstrate that at least 44 % of multi-exonic genes undergo AS and a large number of low abundance splice variants is present within the 131.622 splice junctions we have annotated from Pinot noir.
Conclusions: Our analysis shows that similar to 70 % of AS events have relatively low expression levels, furthermore alternative splice sites seem to be enriched near the constitutive ones in some extent showing the noise of the splicing mechanisms. However, AS seems to be extensively conserved among the 10 cultivars
Drip and Mate Operations Acting in Test Tube Systems and Tissue-like P systems
The operations drip and mate considered in (mem)brane computing resemble the
operations cut and recombination well known from DNA computing. We here
consider sets of vesicles with multisets of objects on their outside membrane
interacting by drip and mate in two different setups: in test tube systems, the
vesicles may pass from one tube to another one provided they fulfill specific
constraints; in tissue-like P systems, the vesicles are immediately passed to
specified cells after having undergone a drip or mate operation. In both
variants, computational completeness can be obtained, yet with different
constraints for the drip and mate operations
Identifying statistical dependence in genomic sequences via mutual information estimates
Questions of understanding and quantifying the representation and amount of
information in organisms have become a central part of biological research, as
they potentially hold the key to fundamental advances. In this paper, we
demonstrate the use of information-theoretic tools for the task of identifying
segments of biomolecules (DNA or RNA) that are statistically correlated. We
develop a precise and reliable methodology, based on the notion of mutual
information, for finding and extracting statistical as well as structural
dependencies. A simple threshold function is defined, and its use in
quantifying the level of significance of dependencies between biological
segments is explored. These tools are used in two specific applications. First,
for the identification of correlations between different parts of the maize
zmSRp32 gene. There, we find significant dependencies between the 5'
untranslated region in zmSRp32 and its alternatively spliced exons. This
observation may indicate the presence of as-yet unknown alternative splicing
mechanisms or structural scaffolds. Second, using data from the FBI's Combined
DNA Index System (CODIS), we demonstrate that our approach is particularly well
suited for the problem of discovering short tandem repeats, an application of
importance in genetic profiling.Comment: Preliminary version. Final version in EURASIP Journal on
Bioinformatics and Systems Biology. See http://www.hindawi.com/journals/bsb
A rule-based kinetic model of RNA polymerase II C-terminal domain phosphorylation
The complexity ofmany RNA processing pathways is such that a conventional systemsmodelling approach is inadequate to represent all themolecular species involved. We demonstrate that rule-based modelling permits a detailed model of a complex RNA signalling pathway to be defined. Phosphorylation of the RNApolymerase II (RNAPII)C-terminal domain (CTD; a flexible tail-like extension of the largest subunit) couples pre-messenger RNA capping, splicing and 30 end maturation to transcriptional elongation and termination, and plays a central role in integrating these processes. The phosphorylation states of the serine residues of many heptapeptide repeats of the CTD alter along the coding region of genes as a function of distance from the promoter. From a mechanistic perspective, both the changes in phosphorylation and the location atwhich they take place on the genes are a function of the time spent byRNAPII in elongation as this interval provides the opportunity for the kinases and phosphatases to interactwith theCTD.On this basis,we synthesize the available data to create a kinetic model of the action of the known kinases and phosphatases to resolve the phosphorylation pathways and their kinetics.</p
Complexity of Model Testing for Dynamical Systems with Toric Steady States
In this paper we investigate the complexity of model selection and model
testing for dynamical systems with toric steady states. Such systems frequently
arise in the study of chemical reaction networks. We do this by formulating
these tasks as a constrained optimization problem in Euclidean space. This
optimization problem is known as a Euclidean distance problem; the complexity
of solving this problem is measured by an invariant called the Euclidean
distance (ED) degree. We determine closed-form expressions for the ED degree of
the steady states of several families of chemical reaction networks with toric
steady states and arbitrarily many reactions. To illustrate the utility of this
work we show how the ED degree can be used as a tool for estimating the
computational cost of solving the model testing and model selection problems
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