Search results for " sequence"

Validation and application of a PCR primer set to quantify fungal communities in the soil environment by real-time quantitative PCR

2011

Fungi constitute an important group in soil biological diversity and functioning. However, characterization and knowledge of fungal communities is hampered because few primer sets are available to quantify fungal abundance by real-time quantitative PCR (real-time Q-PCR). The aim in this study was to quantify fungal abundance in soils by incorporating, into a real-time Q-PCR using the SYBRGreen (R) method, a primer set already used to study the genetic structure of soil fungal communities. To satisfy the real-time Q-PCR requirements to enhance the accuracy and reproducibility of the detection technique, this study focused on the 18S rRNA gene conserved regions. These regions are little affec…

Gene expression in TGFbeta-induced epithelial cell differentiation in a three-dimensional intestinal epithelial cell differentiation model

2006

Abstract Background The TGFβ1-induced signal transduction processes involved in growth and differentiation are only partly known. The three-dimensional epithelial differentiation model, in which T84 epithelial cells are induced to differentiate either with TGFβ1 or IMR-90 mesenchymal cell-secreted soluble factors, is previously shown to model epithelial cell differentiation seen in intestine. That model has not been used for large scale gene expression studies, such as microarray method. Therefore the gene expression changes were studied in undifferentiated and differentiated three-dimensional T84 cultures with cDNA microarray method in order to study the molecular changes and find new play…

A nonlinear optimization procedure to estimate GTR-distances

2006

Interaction of glutamic-acid-rich proteins with the cGMP signalling pathway in rod photoreceptors.

1999

The assembly of signalling molecules into macromolecular complexes (transducisomes) provides specificity, sensitivity and speed in intracellular signalling pathways. Rod photoreceptors in the eye contain an unusual set of glutamic-acid-rich proteins (GARPs) of unknown function. GARPs exist as two soluble forms, GARP1 and GARP2, and as a large cytoplasmic domain (GARP' part) of the beta-subunit of the cyclic GMP-gated channel. Here we identify GARPs as multivalent proteins that interact with the key players of cGMP signalling, phosphodiesterase and guanylate cyclase, and with a retina-specific ATP-binding cassette transporter (ABCR), through four, short, repetitive sequences. In electron mic…

Genome-wide association study and mouse expression data identify a highly conserved 32 kb intergenic region between WNT3 and WNT9b as possible suscep…

2014

Item does not contain fulltext Bladder exstrophy-epispadias complex (BEEC), the severe end of the urorectal malformation spectrum, has a profound impact on continence as well as sexual and renal functions. It is widely accepted that for the majority of cases the genetic basis appears to be multifactorial. Here, we report the first study which utilizes genome-wide association methods to analyze a cohort comprising patients presenting the most common BEEC form, classic bladder exstrophy (CBE), to identify common variation associated with risk for isolated CBE. We employed discovery and follow-up samples comprising 218 cases/865 controls and 78 trios in total, all of European descent. Our disc…

In vitro evolution of an atrazine-degrading population under cyanuric acid selection pressure: Evidence for the selective loss of a 47kb region on th…

2011

International audience; The adaptation of microorganisms to pesticide biodegradation relies on the recruitment of catabolic genes by horizontal gene transfer and homologous recombination mediated by insertion sequences (IS). This environment-friendly function is maintained in the degrading population but it has a cost which could diminish its fitness. The loss of genes in the course of evolution being a major mechanism of ecological specialization, we mimicked evolution in vitro by sub-culturing the atrazine-degrading Pseudomonas sp. ADP in a liquid medium containing cyanuric acid as the sole source of nitrogen. After 120 generations, a new population evolved, which replaced the original on…

The influence of backslopping on lactic acid bacteria diversity in tarhana fermentation

2020

Tarhana is produced at batch systems in which the microbiota has changed accordingly to the microbial load from ingredients. In order to stabilize the microbiota, the effects of backslopping carried out under different temperature regimes (25 and 30 °C), pH (3.70 and 4.00) and inoculation rates (5, 10 and 15%) on lactic acid bacteria (LAB) diversity were determined in tarhana dough. LAB and Total Aerobic Mesophilic Bacteria (TAMB) numbers increased in all tarhana dough samples subjected to backslopping. Temperature and pH significantly affected the microbiological diversity of tarhana whereas the different inoculation rates did not. Tarhana dough showed complex tarhana microbiota following …

Plio-Pleistocene geological evolution of the northern Sicily continental margin (southern Tyrrhenian Sea): new insights from high-resolution, multi-e…

2003

High-resolution seismic profiles were acquired in the north Sicily offshore region with an innovative, multi-tip sparker array which lacks ringing and has a base frequency around 600 Hz. The new data, combined with published data, suggest that intra-slope and extensional basins formed as a consequence of the late Miocene (?)–early Pliocene shortening and thrusting, and the middle (?)–late Pliocene continental rifting affecting the internal side of the Sicilian-Maghrebian chain. Early (?) Pleistocene to Holocene high-amplitude and high-frequency sea-level changes resulted in repeated sub-aerial exposure and flooding of the shelf, and the deposition of cyclically arranged hemipelagic and shel…

Vertical movements in NE Sicily and its offshore: Outcome of tectonic uplift during the last 125 ky

2013

New data in the coastal area between Acquedolci and Patti (northeastern Sicily, Italy) have been collected to calculate vertical tectonic rates in a key sector between the Kabilian-Calabrian and the Sicilian-Maghrebian chain. The comparison among marine geology data (multibeam and seismic reflection profiles) on the continental shelf-slope system and the radiocarbon ages on geomorphological markers collected during a coastal survey, provided new stratigraphic, geomorphological and biological data, contributing to the knowledge of the geological evolution of this sector for the last 125 ky.This coastal area is framed between two main structural features active during the Pleistocene in north…

Microbial succession of nitrate-reducing bacteria in the rhizosphere of Poa alpina across a glacier foreland in the Central Alps

2006

International audience; Changes in community structure and activity of the dissimilatory nitrate-reducing community were investigated across a glacier foreland in the Central Alps to gain insight into the successional pattern of this functional group and the driving environmental factors. Bulk soil and rhizosphere soil of Poa alpina was sampled in five replicates in August during the flowering stage and in September after the first snowfalls along a gradient from 25 to 129 years after deglaciation and at a reference site outside the glacier foreland (> 2000 years deglaciated). In a laboratory-based assay, nitrate reductase activity was determined colorimetrically after 24 h of anaerobic inc…