Engineering stochasticity in gene expression

Stochastic fluctuations (noise) in gene expression can cause members of otherwise genetically identical populations to display drastically different phenotypes. An understanding of the sources of noise and the strategies cells employ to function reliably despite noise is proving to be increasingly important in describing the behavior of natural organisms and will be essential for the engineering of synthetic biological systems. Here we describe the design of synthetic constructs, termed ribosome competing RNAs (rcRNAs), as a means to rationally perturb noise in cellular gene expression. We find that noise in gene expression increases in a manner proportional to the ability of an rcRNA to compete for the cellular ribosome pool. We then demonstrate that operons significantly buffer noise between coexpressed genes in a natural cellular background and can even reduce the level of rcRNA enhanced noise. These results demonstrate that synthetic genetic constructs can significantly affect the noise profile of a living cell and, importantly, that operons are a facile genetic strategy for buffering against noise

Quantifying the potential exposure hazard due to energetic releases of CO2 from a failed sequestration well

AbstractWells are designed to bring fluids from depth to the earth’s surface quickly. As such they are the most likely pathway for CO2 to return to the surface in large quantities and present a hazard without adequate management. We surveyed oil industry experience of CO2 well failures, and separately, calculated the maximal CO2 flow rate from a 5000 ft depth supercritical CO2 reservoir. The calculated maximum of 20,000 tonne/day was set by the sound speed and the seven-inch well casing diameter, and was greater than any observed event. We used this flux to simulate atmospheric releases and the associated hazard utilizing the National Atmospheric Release Advisory Center (NARAC) tools and real meteorology at a representative location in the High Plains of the United States. Three cases representing a maximum hazard day (quiet winds <1 m s−1 near the wellhead) and medium and minimal hazard days (average winds 3 m s−1 and 7 m s−1) were assessed. As expected for such large releases, there is a near-well hazard when there is little or no wind. In all three cases the hazardous Temporary Emergency Exposure Levels (TEEL) 2 or 3 only occurred within the first few hundreds of meters. Because the preliminary 3-D model runs may not have been run at high enough resolution to accurately simulate very small distances, we also used a simple Gaussian plume model to provide an upper bound on the distance at which hazardous conditions might exist. This extremely conservative model, which ignores inhomogeneity in the mean wind and turbulence fields, also predicts possible hazardous concentrations up to several hundred meters downwind from a maximal release

Deficiency of Th17 cells in hyper IgE syndrome due to mutations in STAT3

Hyper–immunoglobulin E syndrome (HIES) is a primary immune deficiency characterized by abnormal and devastating susceptibility to a narrow spectrum of infections, most commonly Staphylococcus aureus and Candida albicans. Recent investigations have identified mutations in STAT3 in the majority of HIES patients studied. Despite the identification of the genetic cause of HIES, the mechanisms underlying the pathological features of this disease remain to be elucidated. Here, we demonstrate a failure of CD4+ T cells harboring heterozygous STAT3 mutations to generate interleukin 17–secreting (i.e., T helper [Th]17) cells in vivo and in vitro due to a failure to express sufficient levels of the Th17-specific transcriptional regulator retinoid-related orphan receptor γt. Because Th17 cells are enriched for cells with specificities against fungal antigens, our results may explain the pattern of infection susceptibility characteristic of patients with HIES. Furthermore, they underscore the importance of Th17 responses in normal host defense against the common pathogens S. aureus and C. albicans

Planet Hunters. V. A Confirmed Jupiter-Size Planet in the Habitable Zone and 42 Planet Candidates from the Kepler Archive Data

We report the latest Planet Hunter results, including PH2 b, a Jupiter-size (R_PL = 10.12 \pm 0.56 R_E) planet orbiting in the habitable zone of a solar-type star. PH2 b was elevated from candidate status when a series of false positive tests yielded a 99.9% confidence level that transit events detected around the star KIC 12735740 had a planetary origin. Planet Hunter volunteers have also discovered 42 new planet candidates in the Kepler public archive data, of which 33 have at least three transits recorded. Most of these transit candidates have orbital periods longer than 100 days and 20 are potentially located in the habitable zones of their host stars. Nine candidates were detected with only two transit events and the prospective periods are longer than 400 days. The photometric models suggest that these objects have radii that range between Neptune to Jupiter. These detections nearly double the number of gas giant planet candidates orbiting at habitable zone distances. We conducted spectroscopic observations for nine of the brighter targets to improve the stellar parameters and we obtained adaptive optics imaging for four of the stars to search for blended background or foreground stars that could confuse our photometric modeling. We present an iterative analysis method to derive the stellar and planet properties and uncertainties by combining the available spectroscopic parameters, stellar evolution models, and transiting light curve parameters, weighted by the measurement errors. Planet Hunters is a citizen science project that crowd-sources the assessment of NASA Kepler light curves. The discovery of these 43 planet candidates demonstrates the success of citizen scientists at identifying planet candidates, even in longer period orbits with only two or three transit events.Comment: 35 pages, 11 figures, 6 tables, accepted and published on ApJ ApJ, 776, 1

The transfusion threshold for upper gastrointestinal bleeding is a hemoglobin of 7.0 g/dl or less

A critical appraisal and clinical application of Villanueva C, Colomo A, Bosch A, Concepcion M, Hernandez-Gea V, Aracil C. Transfusion strategies for acute upper gastrointestinal bleeding. New Eng J Med. 2013;368(1):11-21. doi: 10.1056/NEJMoa121180

U6 snRNA m6A modification is required for accurate and efficient cis- and trans-splicing of <i>C. elegans</i> mRNAs

pre-mRNA splicing is a critical feature of eukaryotic gene expression. Many eukaryotes use cis-splicing to remove intronic sequences from pre-mRNAs. In addition to cis-splicing, many organisms use trans-splicing to replace the 5′ ends of mRNAs with a non-coding spliced-leader RNA. Both cis- and trans-splicing rely on accurately recognising splice site sequences by spliceosomal U snRNAs and associated proteins. Spliceosomal snRNAs carry multiple RNA modifications with the potential to affect different stages of pre-mRNA splicing. Here, we show that m6A modification of U6 snRNA A43 by the RNA methyltransferase METT-10 is required for accurate and efficient cis- and trans-splicing of C. elegans pre-mRNAs. The absence of U6 snRNA m6A modification primarily leads to alternative splicing at 5′ splice sites. Furthermore, weaker 5′ splice site recognition by the unmodified U6 snRNA A43 affects splicing at 3′ splice sites. U6 snRNA m6A43 and the splicing factor SNRNP27K function to recognise an overlapping set of 5′ splice sites with an adenosine at +4 position. Finally, we show that U6 snRNA m6A43 is required for efficient SL trans-splicing at weak 3′ trans-splice sites. We conclude that the U6 snRNA m6A modification is important for accurate and efficient cis- and trans-splicing in C. elegans

Are different groups of patients with stroke more likely to be excluded from the new UK general medical services contract? A cross-sectional retrospective analysis of a large primary care population

Peer reviewedPublisher PD

Fruit and Vegetable Intake and Food Store Access: A Cross-Sectional Survey Study in Ypsilanti, Michigan

Given declines in supermarkets in Washtenaw County, Michigan (MI), we aim to characterize the relationship between food store access and fruit and vegetable intake in Ypsilanti, MI. A cross-sectional, convenience sample survey was conducted in March 2011 at the Ypsilanti District Library (n=83). Self-reported food store access, perceived food environment, and fruit and vegetable intake were assessed. Linear and logistic regressions were performed between store access, fruit and vegetable intake, and meeting dietary recommendations. Perception was evaluated for effect modification. Adjusting for demographics, each food store within one mile of participants’ homes increased odds of meeting recommended intake by 105% (OR 2.05, 95% CI: 1.02, 4.10). However, contrary to previous literature, each additional minute to the food store was associated with consumption of 0.37 (95% confidence interval [CI]: 0.10, 0.64) more servings of fruits and vegetables per day. Perception was not a statistically significant effect modifier, but data suggest differences for those with divergent perceptions. Food environment is associated with fruit and vegetable intake in Ypsilanti, MI. Inconsistent findings suggest that programs should focus on enhancing the food environment within the context of perceptions and preferences