EcoCyc (EcoCyc.org) is a freely accessible, comprehensive database that collects and summarizes experimental data for Escherichia coli K-12, the best-studied bacterial model organism. New ...experimental discoveries about gene products, their function and regulation, new metabolic pathways, enzymes and cofactors are regularly added to EcoCyc. New SmartTable tools allow users to browse collections of related EcoCyc content. SmartTables can also serve as repositories for user- or curator-generated lists. EcoCyc now supports running and modifying E. coli metabolic models directly on the EcoCyc website.
Abstract
RegulonDB, first published 20 years ago, is a comprehensive electronic resource about regulation of transcription initiation of Escherichia coli K-12 with decades of knowledge from classic ...molecular biology experiments, and recently also from high-throughput genomic methodologies. We curated the literature to keep RegulonDB up to date, and initiated curation of ChIP and gSELEX experiments. We estimate that current knowledge describes between 10% and 30% of the expected total number of transcription factor- gene regulatory interactions in E. coli. RegulonDB provides datasets for interactions for which there is no evidence that they affect expression, as well as expression datasets. We developed a proof of concept pipeline to merge binding and expression evidence to identify regulatory interactions. These datasets can be visualized in the RegulonDB JBrowse. We developed the Microbial Conditions Ontology with a controlled vocabulary for the minimal properties to reproduce an experiment, which contributes to integrate data from high throughput and classic literature. At a higher level of integration, we report Genetic Sensory-Response Units for 200 transcription factors, including their regulation at the metabolic level, and include summaries for 70 of them. Finally, we summarize our research with Natural language processing strategies to enhance our biocuration work.
Our understanding of the regulation of gene expression has benefited from the availability of high-throughput technologies that interrogate the whole genome for the binding of specific transcription ...factors and gene expression profiles. In the case of widely used model organisms, such as Escherichia coli K-12, the new knowledge gained from these approaches needs to be integrated with the legacy of accumulated knowledge from genetic and molecular biology experiments conducted in the pre-genomic era in order to attain the deepest level of understanding possible based on the available data.
In this paper, we describe an expansion of RegulonDB, the database containing the rich legacy of decades of classic molecular biology experiments supporting what we know about gene regulation and operon organization in E. coli K-12, to include the genome-wide dataset collections from 32 ChIP and 19 gSELEX publications, in addition to around 60 genome-wide expression profiles relevant to the functional significance of these datasets and used in their curation. Three essential features for the integration of this information coming from different methodological approaches are: first, a controlled vocabulary within an ontology for precisely defining growth conditions; second, the criteria to separate elements with enough evidence to consider them involved in gene regulation from isolated transcription factor binding sites without such support; and third, an expanded computational model supporting this knowledge. Altogether, this constitutes the basis for adequately gathering and enabling the comparisons and integration needed to manage and access such wealth of knowledge.
This version 10.0 of RegulonDB is a first step toward what should become the unifying access point for current and future knowledge on gene regulation in E. coli K-12. Furthermore, this model platform and associated methodologies and criteria can be emulated for gathering knowledge on other microbial organisms.
Global biodiversity is negatively affected by anthropogenic climate change. As species distributions shift due to increasing temperatures and precipitation fluctuations, many species face the risk of ...extinction. In this study, we explore the expected trend for plant species distributions in Central America and southern Mexico under two alternative Representative Concentration Pathways (RCPs) portraying moderate (RCP4.5) and severe (RCP8.5) increases in greenhouse gas emissions, combined with two species dispersal assumptions (limited and unlimited), for the 2061-2080 climate forecast. Using an ensemble approach employing three techniques to generate species distribution models, we classified 1924 plant species from the region's (sub)tropical forests according to IUCN Red List categories. To infer the spatial and taxonomic distribution of species' vulnerability under each scenario, we calculated the proportion of species in a threat category (Vulnerable, Endangered, Critically Endangered) at a pixel resolution of 30 arc seconds and by family. Our results show a high proportion (58-67%) of threatened species among the four experimental scenarios, with the highest proportion under RCP8.5 and limited dispersal. Threatened species were concentrated in montane areas and avoided lowland areas where conditions are likely to be increasingly inhospitable. Annual precipitation and diurnal temperature range were the main drivers of species' relative vulnerability. Our approach identifies strategic montane areas and taxa of conservation concern that merit urgent inclusion in management plans to improve climatic resilience in the Mesoamerican biodiversity hotspot. Such information is necessary to develop policies that prioritize vulnerable elements and mitigate threats to biodiversity under climate change.
In the present work we study the transcription-factor regulatory network that controls the synthesis of flagella in E. coli. Our objective is to address how the transcription-factor dynamics (in ...terms of their promoter activities and associated rates) correlate with their positions in the hierarchical organization of this regulatory network. Our results suggest that global-regulator promoters express at higher rates than those of local regulators, particularly when the bacterial populations are actively growing. Furthermore, promoter activity decreases together with the rate of cellular division. And finally, local-regulator promoters reach their maximal activity later than global-regulator promoters do. In summary, our results suggest a strong correlation between promoter activities and their hierarchical organization in this particular regulatory network.
As the skin is the main protective organ of the body, it is exposed to wounds or injuries which carry out a healing process during a period of approximately 15 days depending on the severity of the ...injury. In the present research, the development of chitosan-based hydrogels loaded with silver nanoparticles and calendula extract (Ch-AgNPs-Ce) was proposed. This can be used to fulfill the hemostatic, anti-infective, antibacterial, healing and anti-inflammatory functions through controlled release of the nanoparticles and calendula extract in substitution of commonly used drugs. The physical properties of the silver nanoparticles were analyzed by UV–visible spectroscopy, scanning and transmission electron microscopy, showing a size between 50 and 100 nm. The antibacterial properties were evaluated by the agar well diffusion method. Antimicrobial testing of the hydrogels showed that the inclusion of silver nanoparticles provides concentration-dependent antibacterial behavior against E. coli and S. aureus. The healing properties of the system were tested in two diabetic patients to whom said hydrogels were placed, obtaining a positive curative result after a few weeks. Therefore, it can be concluded that Ch-AgNPs-Ce hydrogels can achieve healing in chronic or exposed wounds after a period of time which can be used in alternative treatments in patients with poor healing capacity.
Belowground organisms play critical roles in maintaining multiple ecosystem processes, including plant productivity, decomposition, and nutrient cycling. Despite their importance, however, we have a ...limited understanding of how and why belowground biodiversity (bacteria, fungi, protists, and invertebrates) may change as soils develop over centuries to millennia (pedogenesis). Moreover, it is unclear whether belowground biodiversity changes during pedogenesis are similar to the patterns observed for aboveground plant diversity. Here we evaluated the roles of resource availability, nutrient stoichiometry, and soil abiotic factors in driving belowground biodiversity across 16 soil chronosequences (from centuries to millennia) spanning a wide range of globally distributed ecosystem types. Changes in belowground biodiversity during pedogenesis followed two main patterns. In lower-productivity ecosystems (i.e., drier and colder), increases in belowground biodiversity tracked increases in plant cover. In more productive ecosystems (i.e., wetter and warmer), increased acidification during pedogenesis was associated with declines in belowground biodiversity. Changes in the diversity of bacteria, fungi, protists, and invertebrates with pedogenesis were strongly and positively correlated worldwide, highlighting that belowground biodiversity shares similar ecological drivers as soils and ecosystems develop. In general, temporal changes in aboveground plant diversity and belowground biodiversity were not correlated, challenging the common perception that belowground biodiversity should follow similar patterns to those of plant diversity during ecosystem development. Taken together, our findings provide evidence that ecological patterns in belowground biodiversity are predictable across major globally distributed ecosystem types and suggest that shifts in plant cover and soil acidification during ecosystem development are associated with changes in belowground biodiversity over centuries tomillennia.
The cardiovascular disease pandemic has promoted the cardiovascular polypill as one of the most scalable public health strategies to improve cardiovascular risk by increasing accessibility and ...adherence to treatments. Data from randomized clinical trials has shown that the polypill strategy significantly improves adherence as well as risk factor control (cholesterol and blood pressure), however, to date, no information from phase IV registries has been available.
We conducted a multicentre, observational and prospective registry of a polypill-based treatment strategy. A total of 1193 patients in Mexico were included. Patient demographics, clinical history, blood pressure, analysis of blood lipids and the Framingham risk score were measured at baseline and after 12 months of treatment with the CNIC-Ferrer polypill.
At one year with the polypill, systolic blood pressure (SBP) and diastolic blood pressure (DBP) levels changed from mean 146.9 mmHg to 128 mmHg (p <0.001), and from 89.1 mmHg to 80.4 mmHg (p <0.001) respectively. LDLc levels were significantly reduced 132.5–107.6 mg/dL (p <0.001). The 10 year Framingham cardiovascular disease risk was also reduced in the high-risk group (33.7 + 22.0 vs. 21.2 + 14.8; p <0.001) and in the intermediate risk group (23.7 + 14.8 vs. 12.7 + 11.4; p <0.001).
To our knowledge, the results of the current study constitute the first real life data on the impact of a polypill therapy on cardiovascular risk factor control. The results show major improvements on the primary outcome, above and beyond those presented previously in the setting of randomized clinical trials.
Introduction
Over half of all gallbladder carcinoma (GBC) is discovered incidentally after cholecystectomy for benign disease. There are scant data comparing presentation and outcome for patients ...with incidental versus suspected GBC. The goal of this study is to determine the clinical differences between these two entities.
Study Design
Patients with GBC were identified retrospectively from records at academic healthcare institutions in Temuco, Chile; Atlanta, GA; and Rochester, MN between 1984 and 2008. Overall survival was compared for patients with and without preoperative suspicion using Kaplan–Meier curves and a multivariate Cox proportional hazards model.
Results
Of 571 patients, 128 (22.4 %) had preoperative suspicion of malignancy, and 443 (77.6 %) were discovered incidentally. Incidental tumors were of lower stage, better differentiated, and with lower rates of metastases. Median survival for incidentally discovered GBC was 32.3 versus 5.8 months for suspected GBC (
p
< 0.0001). In a Cox proportional hazards model controlling for operation extent, T stage, differentiation, and other factors, preoperative suspicion remains a strong risk factor (odds ratio, 2.0; confidence interval, 1.5–2.9;
p
< 0.0001).
Conclusions
Tumor characteristics differed significantly between patients with incidentally discovered versus preoperatively suspected GBC. Incidental GBC has a significantly better median survival.
Identifying the global drivers of soil priming is essential to understanding C cycling in terrestrial ecosystems. We conducted a survey of soils across 86 globally-distributed locations, spanning a ...wide range of climates, biotic communities, and soil conditions, and evaluated the apparent soil priming effect using
C-glucose labeling. Here we show that the magnitude of the positive apparent priming effect (increase in CO
release through accelerated microbial biomass turnover) was negatively associated with SOC content and microbial respiration rates. Our statistical modeling suggests that apparent priming effects tend to be negative in more mesic sites associated with higher SOC contents. In contrast, a single-input of labile C causes positive apparent priming effects in more arid locations with low SOC contents. Our results provide solid evidence that SOC content plays a critical role in regulating apparent priming effects, with important implications for the improvement of C cycling models under global change scenarios.
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