Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements

Background  

Many DNA regulatory elements occur as multiple instances within a target promoter. Gibbs sampling programs for finding DNA regulatory elements de novo can be prohibitively slow in locating all instances of such an element in a sequence set.     

GATA elements control repression of cardiac troponin I promoter activity in skeletal muscle cells

Background  

We reported previously that the cardiac troponin I (cTnI) promoter drives cardiac-specific expression of reporter genes in cardiac muscle cells and in transgenic mice, and that disruption of GATA elements inactivates the cTnI promoter in cultured cardiomyocytes. We have now examined the role of cTnI promoter GATA elements in skeletal muscle cells.     

Mechanisms of matrix metalloproteinase-2 (mmp-2) transcriptional repression by progesterone in jar choriocarcinoma cells

Background  

Although the MMP-2 promoter lacks a canonical progesterone response element (PRE), the hormone inhibits MMP-2 expression and is part of treatment protocols in gynecological invasive pathologies, including endometriosis and endometrial hyperplasia. This study aimed to explore the mechanism by which progesterone inhibits MMP-2 expression.     

Analysis of the lambdoid prophage element e14 in the E. coli K-12 genome

Background  

Many sequenced bacterial genomes harbor phage-like elements or cryptic prophages. These elements have been implicated in pathogenesis, serotype conversion and phage immunity. The e14 element is a defective lambdoid prophage element present at 25 min in the E. coli K-12 genome. This prophage encodes important functional genes such as lit (T4 exclusion), mcrA (modified cytosine restriction activity) and pin (recombinase).     

Transcriptome analysis of the mobile genome ICE<Emphasis Type="Italic">clc</Emphasis> in <Emphasis Type="Italic">Pseudomonas knackmussii</Emphasis> B13

Background  

Integrative and conjugative elements (ICE) form a diverse group of DNA elements that are integrated in the chromosome of the bacterial host, but can occasionally excise and horizontally transfer to a new host cell. ICE come in different families, typically with a conserved core for functions controlling the element's behavior and a variable region providing auxiliary functions to the host. The ICEclc element of Pseudomonas knackmussii strain B13 is representative for a large family of chromosomal islands detected by genome sequencing approaches. It provides the host with the capacity to degrade chloroaromatics and 2-aminophenol.     

Three cis-elements required for rice α-amylase Amy3D expression during sugar starvation

Expression of -amylase genes during seedling development plays a key role in production of sugar from the starch stored in the cereal seed. Rice -amylase Amy3D promoter/GUS constructs in transgenic rice cell lines were studied to identify cis elements in the promoter of this metabolite-regulated gene. Three sequences having the greatest effects on Amy3D gene expression included the amylase element (TATCCAT), the CGACG element, and a G box-related element (CTACGTGGCCA). These promoter cis elements are needed for high-level expression of Amy3D under conditions of sugar starvation. The involvement of G box cis-elements in environmental stress responses suggest a link between the nutrient stress and the environmental stress responses of the plant.     

A convenient scheme for coupling a finite element curvilinear mesh to a finite element voxel mesh: application to the heart

Background  

In some cases, it may be necessary to combine distinct finite element meshes into a single system. The present work describes a scheme for coupling a finite element mesh, which may have curvilinear elements, to a voxel based finite element mesh.     

A Protein Similarity Approach For Detecting Prophage Regions In Bacterial Genomes

Background  

Numerous completely sequenced bacterial genomes harbor prophage elements. These elements have been implicated in increasing the virulence of the host and in phage immunity. The e14 element is a defective lambdoid prophage element present at 25 min in the Escherichia coli K-12 genome. e14 is a well-characterized prophage element and has been subjected to in-depth bioinformatic analysis.