Search results for "script"

Transcriptional regulation of theNε‐fructoselysine metabolism inEscherichia coliby global and substrate‐specific cues

2020

Thermally processed food is an important part of the human diet. Heat-treatment, however, promotes the formation of so-called Amadori rearrangement products, such as fructoselysine. The gut microbiota including Escherichia coli can utilize these compounds as a nutrient source. While the degradation route for fructoselysine is well described, regulation of the corresponding pathway genes frlABCD remained poorly understood. Here, we used bioinformatics combined with molecular and biochemical analyses and show that fructoselysine metabolism in E. coli is tightly controlled at the transcriptional level. The global regulator CRP (CAP) as well as the alternative sigma factor σ32 (RpoH) contribute…

The GATA3 X308_Splice breast cancer mutation is a hormone context-dependent oncogenic driver

2019

AbstractAs the catalogue of oncogenic driver mutations is expanding, it is becoming clear that alterations in a given gene should not be lumped into one single class, since they might have different functions. The transcription factorGATA3is a paradigm of this. Here, we address the functions of the most commonGATA3mutation (X308_Splice) which generates a neoprotein that we designate as neoGATA3, associated with good patient prognosis. Based on extensive analyses of molecular and clinical data from approximately 3000 breast cancer patients, supported by mechanistic studiesin vitro, we show that neoGATA3 interferes with the transcriptional programs controlled by estrogen and progesterone rece…

Network motif-based analysis of regulatory patterns in paralogous gene pairs

2020

Current high-throughput experimental techniques make it feasible to infer gene regulatory interactions at the whole-genome level with reasonably good accuracy. Such experimentally inferred regulatory networks have become available for a number of simpler model organisms such as S. cerevisiae, and others. The availability of such networks provides an opportunity to compare gene regulatory processes at the whole genome level, and in particular, to assess similarity of regulatory interactions for homologous gene pairs either from the same or from different species. We present here a new technique for analyzing the regulatory interaction neighborhoods of paralogous gene pairs. Our central focu…

The Hippo Show Must Go On: YAP Activation as a Therapeutic Strategy in Colorectal Cancer

2020

The role of Hippo pathway in colorectal cancer (CRC) initiation and progression has been controversial. In this issue of Cell Stem Cell, Cheung et al. (2020) shed new light on a distinct function of the transcriptional co-activator YAP as a tumor suppressor and Wnt pathway inhibitor in CRC.

When age means safety: Data to assess trends and differences on rule knowledge, risk perception, aberrant and positive road behaviors, and traffic cr…

2019

This data article examines the association between age, knowledge of traffic rules, risk perception, risky and positive behaviors on the road and traffic safety outcomes of cyclists. The data was collected using a structured self-administrable and online-based questionnaire, applied to a full sample of 1064 cyclists. The data contains 4 parts: descriptive statistics; graphical trends for each study variable according to age; Post-Hoc (Tukey-HSD) comparisons between cyclists classified in the different age groups; and, finally, the dataset for further explorations in this regard. For further information, it is convenient to read the full article entitled "Explaining Self-Reported Traffic Cra…

Comparison of odour sensory profiles performed by two independent trained panels following the same descriptive analysis procedures

2000

Odour sensory profiling of 28 associations of cheese ripening micro-organisms was performed by two panels of 10 assessors on two different sites. Sample preparation, training protocols and references, tasting procedures and scoring were similar in the two laboratories. Panel 2 used 10 attributes and panel 1 used these terms plus 4 extra descriptors. Analysis of variance and multivariate methods (canonical variate analysis, generalised procrustes analysis and STATIS) exhibited differences between assessors within a panel and between panels concerning the use of the scoring scale and the strength of product discrimination by attribute. Panel 1 was more sensitive to fruity notes and panel 2 to…

Sodium chloride is an ionic checkpoint for human TH2 cells and shapes the atopic skin microenvironment.

2019

The incidence of allergic diseases has increased over the past 50 years, likely due to environmental factors. However, the nature of these factors and the mode of action by which they induce the type 2 immune deviation characteristic of atopic diseases remain unclear. It has previously been reported that dietary sodium chloride promotes the polarization of T helper 17 (T(H)17) cells with implications for autoimmune diseases such as multiple sclerosis. Here, we demonstrate that sodium chloride also potently promotes T(H)2 cell responses on multiple regulatory levels. Sodium chloride enhanced interleukin-4 (IL-4) and IL-13 production while suppressing interferon-gamma (IFN-gamma) production i…

Vanillin cell sensor

2007

Our project for iGEM 2006 consisted of designing a cellular vanillin biosensor. We used an EnvZ -E. coli strain as a chassis, and constructed two different devices: a sensor and an actuator, assembled using OmpR-P as a standardised mediator. The sensor device contained a computation- ally designed vanillin receptor and a synthetic two-component signal transduction protein (Trz). The receptor protein was based on a ribose-binding protein as scaffold. The Trz was built by fusion of the periplasmic and transmembrane domains of a Trg protein with an EnvZ kinase domain. When the receptor complex binds Trg, an allosteric motion is propagated to the cyto- plasmic EnvZ kinase domain, resulting in a…

2020

AbstractDeveloping methods for accurate detection of RNA modifications remains a major challenge in epitranscriptomics. Next-generation sequencing-based mapping approaches have recently emerged but, often, they are not quantitative and lack specificity. Pseudouridine (ψ), produced by uridine isomerization, is one of the most abundant RNA modification. ψ mapping classically involves derivatization with soluble carbodiimide (CMCT), which is prone to variation making this approach only semi-quantitative. Here, we developed ‘HydraPsiSeq’, a novel quantitative ψ mapping technique relying on specific protection from hydrazine/aniline cleavage. HydraPsiSeq is quantitative because the obtained sign…

Betweenness Centrality for Networks with Non-Overlapping Community Structure

2018

Evaluating the centrality of nodes in complex networks is one of the major research topics being explored due to its wide range of applications. Among the various measures that have been developed over the years, Betweenness centrality is one of the most popular. Indeed, it has proved to be efficient in many real-world situations. In this paper, we propose an extension of the Betweenness centrality designed for networks with nonoverlapping community structure. It is a linear combination of the so-called “local” and “global” Betweenness measures. The Local measure takes into account the influence of a node at the community level while the global measure depends only on the interactions betwe…