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

Mapping the Spatial Distribution of a Disease-Transmitting Insect in the Presence of Surveillance Error and Missing Data

Maps of the distribution of epidemiological data often ignore surveillance error or possible correlations between missing information and outcomes. We analyse presence–absence data at the household level (12050 points) of a disease‐carrying insect in Mariano Melgar, Peru, collected as part of the Arequipan Ministry of Health\u27s efforts to control Chagas disease. We construct a Bayesian hierarchical model to locate regions that are vulnerable to under‐reporting due to surveillance error, accounting for variability in participation due to infestation status. The spatial correlation in the data allows us to identify relative inspector sensitivity and to elucidate the relationship between participation and infestation. We show that naive estimates of prevalence would be biased by surveillance error and missingness at random assumptions. We validate our results through simulations and observe how randomized inspector assignments may improve prevalence estimates. Our results suggests that bias due to imperfect observations and missingness at random can be assessed and corrected in prevalence estimates of spatially auto-correlated binary variables

Nitric oxide and coronary vascular endothelium adaptations in hypertension

This review highlights a number of nitric oxide (NO)-related mechanisms that contribute to coronary vascular function and that are likely affected by hypertension and thus become important clinically as potential considerations in prevention, diagnosis, and treatment of coronary complications of hypertension. Coronary vascular resistance is elevated in hypertension in part due to impaired endothelium-dependent function of coronary arteries. Several lines of evidence suggest that other NO synthase isoforms and dilators other than NO may compensate for impairments in endothelial NO synthase (eNOS) to protect coronary artery function, and that NO-dependent function of coronary blood vessels depends on the position of the vessel in the vascular tree. Adaptations in NOS isoforms in the coronary circulation to hypertension are not well described so the compensatory relationship between these and eNOS in hypertensive vessels is not clear. It is important to understand potential functional consequences of these adaptations as they will impact the efficacy of treatments designed to control hypertension and coronary vascular disease. Polymorphisms of the eNOS gene result in significant associations with incidence of hypertension, although mechanistic details linking the polymorphisms with alterations in coronary vasomotor responses and adaptations to hypertension are not established. This understanding should be developed in order to better predict those individuals at the highest risk for coronary vascular complications of hypertension. Greater endothelium-dependent dilation observed in female coronary arteries is likely related to endothelial Ca2+ control and eNOS expression and activity. In hypertension models, the coronary vasculature has not been studied extensively to establish mechanisms for sex differences in NO-dependent function. Genomic and nongenomic effects of estrogen on eNOS and direct and indirect antioxidant activities of estrogen are discussed as potential mechanisms of interest in coronary circulation that could have implications for sex- and estrogen status-dependent therapy for hypertension and coronary dysfunction. The current review identifies some important basic knowledge gaps and speculates on the potential clinical relevance of hypertension adaptations in factors regulating coronary NO function

Implications of Electronics Constraints for Solid-State Quantum Error Correction and Quantum Circuit Failure Probability

In this paper we present the impact of classical electronics constraints on a solid-state quantum dot logical qubit architecture. Constraints due to routing density, bandwidth allocation, signal timing, and thermally aware placement of classical supporting electronics significantly affect the quantum error correction circuit's error rate. We analyze one level of a quantum error correction circuit using nine data qubits in a Bacon-Shor code configured as a quantum memory. A hypothetical silicon double quantum dot quantum bit (qubit) is used as the fundamental element. A pessimistic estimate of the error probability of the quantum circuit is calculated using the total number of gates and idle time using a provably optimal schedule for the circuit operations obtained with an integer program methodology. The micro-architecture analysis provides insight about the different ways the electronics impact the circuit performance (e.g., extra idle time in the schedule), which can significantly limit the ultimate performance of any quantum circuit and therefore is a critical foundation for any future larger scale architecture analysis.Comment: 10 pages, 7 figures, 3 table

Isotopic Signature of Massive, Buried Ice in Eastern Taylor Valley, Antarctica: Implications for Its Origin

The coastal regions of the McMurdo Dry Valleys, Antarctica, contain deposits of the Ross Sea Drift, sedimentary material left from the Ross Sea ice sheet from the advance of the West Antarctic ice sheet during the Last Glacial Maximum. Much of this deposit is ice-cored, but data on the stable isotopic composition of water from this ice, which may contain a valuable climate archive, are sparse or incomplete. Widespread thermokarstic ground subsidence in this “coastal thaw zone” of the McMurdo Dry Valleys suggests that these potential records are rapidly being lost due to the melting of ground ice and permafrost. We collected samples of massive buried ice from the Ross Sea Drift in eastern Taylor Valley for δ18O-H2O and δ2H-H2O and measured a broad range of values (δ18O = −27.7 to −37.3 ‰; δ2H = −210 to −295 ‰). These buried ice deposits do not show evidence of alteration through sublimation or evaporation, plot along the local meteoric water line, and have values that indicate ice deposition under a colder climate than present conditions. We propose that this ice was sourced from the Ross Sea ice sheet during the Last Glacial Maximum and contains a valuable and accessible climate record

Approaches for advancing scientific understanding of macrosystems

The emergence of macrosystems ecology (MSE), which focuses on regional- to continental-scale ecological patterns and processes, builds upon a history of long-term and broad-scale studies in ecology. Scientists face the difficulty of integrating the many elements that make up macrosystems, which consist of hierarchical processes at interacting spatial and temporal scales. Researchers must also identify the most relevant scales and variables to be considered, the required data resources, and the appropriate study design to provide the proper inferences. The large volumes of multi-thematic data often associated with macrosystem studies typically require validation, standardization, and assimilation. Finally, analytical approaches need to describe how cross-scale and hierarchical dynamics and interactions relate to macroscale phenomena. Here, we elaborate on some key methodological challenges of MSE research and discuss existing and novel approaches to meet them

Vascular endothelial growth factor (VEGF) fails to improve blood flow and to promote collateralization in a diabetic mouse ischemic hindlimb model

BACKGROUND: Angiogenic therapy with vascular endothelial growth factor (VEGF) has been proposed as a treatment paradigm for patients suffering from an insufficiency of collateral vessels. Diabetes is associated with increase in the production of VEGF and therefore additional VEGF may not be beneficial. Accordingly, we sought to determine the efficacy of VEGF therapy to augment collateral formation and tissue perfusion in a diabetic mouse ischemic hindlimb model. METHODS: Diabetic and non-diabetic mice were studied in parallel for the efficacy of VEGF administration. Diabetes was induced with streptozotocin. Hindlimb ischemia was produced by severing the left iliac artery. An outlet tube from an osmotic infusion pump with placebo/ 500 micrograms of plasmid-DNA encoding VEGF was fenestrated and tunneled into the left quadriceps muscle. RESULTS: VEGF induced more rapid and complete restoration of blood flow in normal mice. However, in the setting of diabetes there was no difference between VEGF Vs. placebo in the rate or adequacy of flow restoration. There was a significant increase in smooth muscle actin and Factor-VIII antigen densities in diabetic animals and in animals which received VEGF. CONCLUSIONS: Angiogenic therapy with VEGF in the setting of diabetes does not appear to have the beneficial effects seen in the absence of diabetes

Accelerated Thermokarst Formation in the McMurdo Dry Valleys, Antarctica

Thermokarst is a land surface lowered and disrupted by melting ground ice. Thermokarst is a major driver of landscape change in the Arctic, but has been considered to be a minor process in Antarctica. Here, we use ground-based and airborne LiDAR coupled with timelapse imaging and meteorological data to show that 1) thermokarst formation has accelerated in Garwood Valley, Antarctica; 2) the rate of thermokarst erosion is presently,10 times the average Holocene rate; and 3) the increased rate of thermokarst formation is driven most strongly by increasing insolation and sediment/albedo feedbacks. This suggests that sediment enhancement of insolation-driven melting may act similarly to expected increases in Antarctic air temperature (presently occurring along the Antarctic Peninsula), and may serve as a leading indicator of imminent landscape change in Antarctica that will generate thermokarst landforms similar to those in Arctic periglacial terrains

The global carbon budget 1959-2011

Accurate assessments of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere is important to better understand the global carbon cycle, support the climate policy process, and project future climate change. Present-day analysis requires the combination of a range of data, algorithms, statistics and model estimates and their interpretation by a broad scientific community. Here we describe datasets and a methodology developed by the global carbon cycle science community to quantify all major components of the global carbon budget, including their uncertainties. We discuss changes compared to previous estimates, consistency within and among components, and methodology and data limitations. CO2 emissions from fossil fuel combustion and cement production (EFF) are based on energy statistics, while emissions from Land-Use Change (ELUC), including deforestation, are based on combined evidence from land cover change data, fire activity in regions undergoing deforestation, and models. The global atmospheric CO2 concentration is measured directly and its rate of growth (GATM) is computed from the concentration. The mean ocean CO2 sink (SOCEAN) is based on observations from the 1990s, while the annual anomalies and trends are estimated with ocean models. Finally, the global residual terrestrial CO2 sink (SLAND) is estimated by the difference of the other terms. For the last decade available (2002–2011), EFF was 8.3 ± 0.4 PgC yr−1, ELUC 1.0 ± 0.5 PgC yr−1, GATM 4.3 ± 0.1PgC yr−1, SOCEAN 2.5 ± 0.5 PgC yr−1, and SLAND 2.6 ± 0.8 PgC yr−1. For year 2011 alone, EFF was 9.5 ± 0.5 PgC yr−1, 3.0 percent above 2010, reflecting a continued trend in these emissions; ELUC was 0.9 ± 0.5 PgC yr−1, approximately constant throughout the decade; GATM was 3.6 ± 0.2 PgC yr−1, SOCEAN was 2.7 ± 0.5 PgC yr−1, and SLAND was 4.1 ± 0.9 PgC yr−1. GATM was low in 2011 compared to the 2002–2011 average because of a high uptake by the land probably in response to natural climate variability associated to La Niña conditions in the Pacific Ocean. The global atmospheric CO2 concentration reached 391.31 ± 0.13 ppm at the end of year 2011. We estimate that EFF will have increased by 2.6% (1.9–3.5%) in 2012 based on projections of gross world product and recent changes in the carbon intensity of the economy. All uncertainties are reported as ±1 sigma (68% confidence assuming Gaussian error distributions that the real value lies within the given interval), reflecting the current capacity to characterise the annual estimates of each component of the global carbon budget. This paper is intended to provide a baseline to keep track of annual carbon budgets in the future