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Regulatory Module (regulatory + module)

Distribution by Scientific Domains

Life Sciences	60%

Selected Abstracts

Dynamics and function of intron sequences of the wingless gene during the evolution of the Drosophila genus

EVOLUTION AND DEVELOPMENT, Issue 5 2004
J. Costas
Summary To understand the function and evolution of genes with complex patterns of expression, such as the Drosophila wingless gene, it is essential to know how their transcription is regulated. However, extracting the relevant regulatory information from a genome is still a complex task. We used a combination of comparative genomics and functional approaches to identify putative regulatory sequences in two introns (1 and 3) of the wingless gene and to infer their evolution. Comparison of the sequences obtained from several Drosophila species revealed colinear and well-conserved sequence blocks in both introns. Drosophila willistoni showed a rate of evolution, in both introns, faster than expected from its phylogenetic position. Intron 3 appeared to be composed of two separate modules, one of them lost in the willistoni group. We tested whether sequence conservation in noncoding regions is a reliable indicator of regulatory function and, if this function is conserved, by analyzing D. melanogaster transgenic reporter lines harboring intron 3 sequences from D. melanogaster (Sophophora subgenus) and the species from the Drosophila subgenus presenting the most divergent sequence, D. americana. The analysis indicated that intron 3 contains pupal enhancers conserved during the evolution of the genus, despite the fact that only 30% of the D. melanogaster intron 3 sequences lie in conserved blocks. Additional analysis of D. melanogaster transgenic reporter lines harboring intron 3 sequences from D. willistoni revealed the absence of an abdomen-specific expression pattern, probably due to the above-mentioned loss of a regulatory module in this species. [source]

Comprehensive Analysis of Expressed Sequence Tags from the Pulp of the Red Mutant ,Cara Cara' Navel Orange (Citrus sinensis Osbeck)

JOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 10 2010
Jun-Li Ye
Expressed sequence tag (EST) analysis of the pulp of the red-fleshed mutant ,Cara Cara' navel orange provided a starting point for gene discovery and transcriptome survey during citrus fruit maturation. Interpretation of the EST datasets revealed that the mutant pulp transcriptome held a high section of stress responses related genes, such as the type III metallothionein-like gene (6.0%), heat shock protein (2.8%), Cu/Zn superoxide dismutase (0.8%), late embryogenesis abundant protein 5 (0.8%), etc. 133 transcripts were detected to be differentially expressed between the red mutant and its orange-color wild genotype ,Washington' via digital expression analysis. Among them, genes involved in metabolism, defense/stress and signal transduction were statistical overrepresented. Fifteen transcription factors, composed of NAM, ATAF, and CUC transcription factor (NAC); myeloblastosis (MYB); myelocytomatosis (MYC); basic helix-loop-helix (bHLH); basic leucine zipper (bZIP) domain members, were also included. The data reflected the distinct expression profile and the unique regulatory module associated with these two genotypes. Eight differently expressed genes analyzed in digital were validated by quantitative real-time polymerase chain reaction. For structural polymorphism, both simple sequence repeats and single nucleotide polymorphisms (SNP) loci were surveyed; dinucleotide presentation revealed a bias toward AG/GA/TC/CT repeats (52.5%), against GC/CG repeats (0%). SNPs analysis found that transitions (73%) outnumbered transversions (27%). Seventeen potential cultivar-specific and 387 heterozygous SNP loci were detected from ,Cara Cara' and ,Washington' EST pool. [source]

Statistical Reconstruction of Transcription Factor Activity Using Michaelis,Menten Kinetics

BIOMETRICS, Issue 3 2007
R. Khanin
Summary The basic building block of a gene regulatory network consists of a gene encoding a transcription factor (TF) and the gene(s) it regulates. Considerable efforts have been directed recently at devising experiments and algorithms to determine TFs and their corresponding target genes using gene expression and other types of data. The underlying problem is that the expression of a gene coding for the TF provides only limited information about the activity of the TF, which can also be controlled posttranscriptionally. In the absence of a reliable technology to routinely measure the activity of regulators, it is of great importance to understand whether this activity can be inferred from gene expression data. We here develop a statistical framework to reconstruct the activity of a TF from gene expression data of the target genes in its regulatory module. The novelty of our approach is that we embed the deterministic Michaelis,Menten model of gene regulation in this statistical framework. The kinetic parameters of the gene regulation model are inferred together with the profile of the TF regulator. We also obtain a goodness-of-fit test to verify the fit of the model. The model is applied to a time series involving the Streptomyces coelicolor bacterium. We focus on the transcriptional activator cdaR, which is partly responsible for the production of a particular type of antibiotic. The aim is to reconstruct the activity profile of this regulator. Our approach can be extended to include more complex regulatory relationships, such as multiple regulatory factors, competition, and cooperativity. [source]

Synthetic morphology: prospects for engineered, self-constructing anatomies

JOURNAL OF ANATOMY, Issue 6 2008
Jamie A. Davies
Abstract This paper outlines prospects for applying the emerging techniques of synthetic biology to the field of anatomy, with the aim of programming cells to organize themselves into specific, novel arrangements, structures and tissues. There are two main reasons why developing this hybrid discipline , synthetic morphology , would be useful. The first is that having a way to engineer self-constructing assemblies of cells would provide a powerful means of tissue engineering for clinical use in surgery and regenerative medicine. The second is that construction of simple novel systems according to theories of morphogenesis gained from study of real embryos will provide a means of testing those theories rigorously, something that is very difficult to do by manipulation of complex embryos. This paper sets out the engineering requirements for synthetic morphology, which include the development of a library of sensor modules, regulatory modules and effector modules that can be connected functionally within cells. A substantial number of sensor and regulatory modules already exist and this paper argues that some potential effector modules have already been identified. The necessary library may therefore be within reach. The paper ends by suggesting a set of challenges, ranging from simple to complex, the achievement of which would provide valuable proofs of concept. [source]

Computational Biology: Toward Deciphering Gene Regulatory Information in Mammalian Genomes

BIOMETRICS, Issue 3 2006
Hongkai Ji
Summary Computational biology is a rapidly evolving area where methodologies from computer science, mathematics, and statistics are applied to address fundamental problems in biology. The study of gene regulatory information is a central problem in current computational biology. This article reviews recent development of statistical methods related to this field. Starting from microarray gene selection, we examine methods for finding transcription factor binding motifs and cis -regulatory modules in coregulated genes, and methods for utilizing information from cross-species comparisons and ChIP-chip experiments. The ultimate understanding of cis -regulatory logic in mammalian genomes may require the integration of information collected from all these steps. [source]