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

Effects of red clover isoflavones on tall fescue seed fermentation and microbial populations \u3ci\u3ein vitro\u3c/i\u3e

Negative impacts of endophyte-infected Lolium arundinaceum (Darbyshire) (tall fescue) are responsible for over $2 billion in losses to livestock producers annually. While the influence of endophyte-infected tall fescue has been studied for decades, mitigation methods have not been clearly elucidated. Isoflavones found in Trifolium pratense (red clover) have been the subject of recent research regarding tall fescue toxicosis mitigation. Therefore, the aim of this study was to determine the effect of ergovaline and red clover isoflavones on rumen microbial populations, fiber degradation, and volatile fatty acids (VFA) in an in vitro system. Using a dose of 1.10 mg × L-1, endophyte-infected or endophyte-free tall fescue seed was added to ANKOM fiber bags with or without 2.19 mg of isoflavones in the form of a control, powder, or pulverized tablet, resulting in a 2 × 3 factorial arrangements of treatments. Measurements of pH, VFA, bacterial taxa, as well as the disappearance of neutral detergent fiber (aNDF), acid detergent fiber (ADF), and crude protein (CP) were taken after 48 h of incubation. aNDF disappearance values were significantly altered by seed type (P = 0.003) and isoflavone treatment (P = 0.005), and ADF disappearance values were significantly different in a seed × isoflavone treatment interaction (P ≤ 0.05). A seed × isoflavone treatment interaction was also observed with respect to CP disappearance (P ≤ 0.05). Eighteen bacterial taxa were significantly altered by seed × isoflavone treatment interaction groups (P ≤ 0.05), eight bacterial taxa were increased by isoflavones (P ≤ 0.05), and ten bacterial taxa were altered by seed type (P ≤ 0.05). Due to the beneficial effect of isoflavones on tall fescue seed fiber degradation, these compounds may be viable options for mitigating fescue toxicosis. Further research should be conducted to determine physiological implications as well as microbiological changes in vivo

Effects of Red Clover Isoflavones on Tall Fescue Seed Fermentation and Microbial Populations \u3cem\u3eIn Vitro\u3c/em\u3e

Negative impacts of endophyte-infected Lolium arundinaceum (Darbyshire) (tall fescue) are responsible for over $2 billion in losses to livestock producers annually. While the influence of endophyte-infected tall fescue has been studied for decades, mitigation methods have not been clearly elucidated. Isoflavones found in Trifolium pratense (red clover) have been the subject of recent research regarding tall fescue toxicosis mitigation. Therefore, the aim of this study was to determine the effect of ergovaline and red clover isoflavones on rumen microbial populations, fiber degradation, and volatile fatty acids (VFA) in an in vitro system. Using a dose of 1.10 mg × L-1, endophyte-infected or endophyte-free tall fescue seed was added to ANKOM fiber bags with or without 2.19 mg of isoflavones in the form of a control, powder, or pulverized tablet, resulting in a 2 × 3 factorial arrangements of treatments. Measurements of pH, VFA, bacterial taxa, as well as the disappearance of neutral detergent fiber (aNDF), acid detergent fiber (ADF), and crude protein (CP) were taken after 48 h of incubation. aNDF disappearance values were significantly altered by seed type (P = 0.003) and isoflavone treatment (P = 0.005), and ADF disappearance values were significantly different in a seed × isoflavone treatment interaction (P ≤ 0.05). A seed × isoflavone treatment interaction was also observed with respect to CP disappearance (P ≤ 0.05). Eighteen bacterial taxa were significantly altered by seed × isoflavone treatment interaction groups (P ≤ 0.05), eight bacterial taxa were increased by isoflavones (P ≤ 0.05), and ten bacterial taxa were altered by seed type (P ≤ 0.05). Due to the beneficial effect of isoflavones on tall fescue seed fiber degradation, these compounds may be viable options for mitigating fescue toxicosis. Further research should be conducted to determine physiological implications as well as microbiological changes in vivo

When one phenotype is not enough: divergent evolutionary trajectories govern venom variation in a widespread rattlesnake species

Artículo 10 páginas, 3 figuras 1 tablaUnderstanding the origin and maintenance of phenotypic variation, particularly across a continuous spatial distribution, represents a key challenge in evolutionary biology. For this, animal venoms represent ideal study systems: they are complex, variable, yet easily quantifiable molecular phenotypes with a clear function. Rattlesnakes display tremendous variation in their venom composition, mostly through strongly dichotomous venom strategies, which may even coexist within a single species. Here, through dense, widespread population-level sampling of the Mojave rattlesnake, Crotalus scutulatus, we show that genomic structural variation at multiple loci underlies extreme geographical variation in venom composition, which is maintained despite extensive gene flow. Unexpectedly, neither diet composition nor neutral population structure explain venom variation. Instead, venom divergence is strongly correlated with environmental conditions. Individual toxin genes correlate with distinct environmental factors, suggesting that different selective pressures can act on individual loci independently of their co-expression patterns or genomic proximity. Our results challenge common assumptions about diet composition as the key selective driver of snake venom evolution and emphasize how the interplay between genomic architecture and local-scale spatial heterogeneity in selective pressures may facilitate the retention of adaptive functional polymorphisms across a continuous space.Funding: Leverhulme Trust Grant RPG 2013-315 to WW, Santander Early Career Research Scholarship to GZ, Ministerio de Economía y Competitividad Grant BFU2013-42833-P to JJC.Peer reviewe

University of Kentucky Measurements of Wind, Temperature, Pressure and Humidity in Support of LAPSE-RATE Using Multisite Fixed-Wing and Rotorcraft Unmanned Aerial Systems

In July 2018, unmanned aerial systems (UASs) were deployed to measure the properties of the lower atmosphere within the San Luis Valley, an elevated valley in Colorado, USA, as part of the Lower Atmospheric Profiling Studies at Elevation – a Remotely-piloted Aircraft Team Experiment (LAPSE-RATE). Measurement objectives included detailing boundary layer transition, canyon cold-air drainage and convection initiation within the valley. Details of the contribution to LAPSE-RATE made by the University of Kentucky are provided here, which include measurements by seven different fixed-wing and rotorcraft UASs totaling over 178 flights with validated data. The data from these coordinated UAS flights consist of thermodynamic and kinematic variables (air temperature, humidity, pressure, wind speed and direction) and include vertical profiles up to 900 m above the ground level and horizontal transects up to 1500 m in length. These measurements have been quality controlled and are openly available in the Zenodo LAPSE-RATE community data repository (https://zenodo.org/communities/lapse-rate/, last access: 23 July 2020), with the University of Kentucky data available at https://doi.org/10.5281/zenodo.3701845 (Bailey et al., 2020)

Lifestyle, dietary factors and antibody levels to oral bacteria in cancer-free participants of a European cohort study

Background—Increasing evidence suggests that oral microbiota play a pivotal role in chronic diseases, in addition to the well-established role in periodontal disease. Moreover, recent studies suggest that oral bacteria may also be involved in carcinogenesis; periodontal disease has been linked several cancers. In this study, we examined whether lifestyle factors have an impact on antibody levels to oral bacteria. Methods—Data on demographic characteristics, lifestyle factors, and medical conditions were obtained at the time of blood sample collection. For the current analysis, we measured antibody levels to 25 oral bacteria in 395 cancer-free individuals using an immunoblot array. Combined total immunglobin G (IgG) levels were obtained by summing concentrations for all oral bacteria measured. Results—IgG antibody levels were substantially lower among current and former smokers (1697 and 1677 ng/mL, respectively) than never smokers (1960 ng/mL; p-trend = 0.01), but did not vary by other factors, including BMI, diabetes, physical activity, or by dietary factors, after adjusting for age, sex, education, country and smoking status. The highest levels of total IgG were found among individuals with low education (2419 ng/mL). Conclusions—Our findings on smoking are consistent with previous studies and support the notion that smokers have a compromised humoral immune response. Moreover, other major factors known to be associated with inflammatory markers, including obesity, were not associated with antibody levels to a large number of oral bacteria

TESS Asteroseismology of α\alpha Mensae: Benchmark Ages for a G7 Dwarf and its M-dwarf Companion

Asteroseismology of bright stars has become increasingly important as a method to determine fundamental properties (in particular ages) of stars. The Kepler Space Telescope initiated a revolution by detecting oscillations in more than 500 main-sequence and subgiant stars. However, most Kepler stars are faint, and therefore have limited constraints from independent methods such as long-baseline interferometry. Here, we present the discovery of solar-like oscillations in $\alpha$ Men A, a naked-eye (V=5.1) G7 dwarf in TESS's Southern Continuous Viewing Zone. Using a combination of astrometry, spectroscopy, and asteroseismology, we precisely characterize the solar analog alpha Men A (Teff = 5569 +/- 62 K, R = 0.960 +/- 0.016 Rsun, M = 0.964 +/- 0.045 Msun). To characterize the fully convective M dwarf companion, we derive empirical relations to estimate mass, radius, and temperature given the absolute Gaia magnitude and metallicity, yielding M = 0.169 +/- 0.006, R = 0.19 +/- 0.01 and Teff = 3054 +/- 44 K. Our asteroseismic age of 6.2 +/- 1.4 (stat) +/- 0.6 (sys) Gyr for the primary places $\alpha$ Men B within a small population of M dwarfs with precisely measured ages. We combined multiple ground-based spectroscopy surveys to reveal an activity cycle of 13.1 +/- 1.1 years, a period similar to that observed in the Sun. We used different gyrochronology models with the asteroseismic age to estimate a rotation period of ~30 days for the primary. Alpha Men A is now the closest (d=10pc) solar analog with a precise asteroseismic age from space-based photometry, making it a prime target for next-generation direct imaging missions searching for true Earth analogs.Comment: Accepted to The Astrophysical Journal; 15 pages, 10 figure

Ribosome-associated vesicles: A dynamic subcompartment of the endoplasmic reticulum in secretory cells

The endoplasmic reticulum (ER) is a highly dynamic network of membranes. Here, we combine live-cell microscopy with in situ cryo–electron tomography to directly visualize ER dynamics in several secretory cell types including pancreatic β-cells and neurons under near-native conditions. Using these imaging approaches, we identify a novel, mobile form of ER, ribosome-associated vesicles (RAVs), found primarily in the cell periphery, which is conserved across different cell types and species. We show that RAVs exist as distinct, highly dynamic structures separate from the intact ER reticular architecture that interact with mitochondria via direct intermembrane contacts. These findings describe a new ER subcompartment within cells