Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway.

The ability to biosynthetically produce chemicals beyond what is commonly found in Nature requires the discovery of novel enzyme function. Here we utilize two approaches to discover enzymes that enable specific production of longer-chain (C5-C8) alcohols from sugar. The first approach combines bioinformatics and molecular modelling to mine sequence databases, resulting in a diverse panel of enzymes capable of catalysing the targeted reaction. The median catalytic efficiency of the computationally selected enzymes is 75-fold greater than a panel of naively selected homologues. This integrative genomic mining approach establishes a unique avenue for enzyme function discovery in the rapidly expanding sequence databases. The second approach uses computational enzyme design to reprogramme specificity. Both approaches result in enzymes with >100-fold increase in specificity for the targeted reaction. When enzymes from either approach are integrated in vivo, longer-chain alcohol production increases over 10-fold and represents >95% of the total alcohol products

Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta

Summary: Foldit Standalone is an interactive graphical interface to the Rosetta molecular modeling package. In contrast to most command-line or batch interactions with Rosetta, Foldit Standalone is designed to allow easy, real-time, direct manipulation of protein structures, while also giving access to the extensive power of Rosetta computations. Derived from the user interface of the scientific discovery game Foldit (itself based on Rosetta), Foldit Standalone has added more advanced features and removed the competitive game elements. Foldit Standalone was built from the ground up with a custom rendering and event engine, configurable visualizations and interactions driven by Rosetta. Foldit Standalone contains, among other features: electron density and contact map visualizations, multiple sequence alignment tools for template-based modeling, rigid body transformation controls, RosettaScripts support and an embedded Lua interpreter

Prevalence of overweight, obesity and thinness in 9-10 year old children in Mauritius.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.OBJECTIVE: To document the prevalence of overweight, obesity and thinness in 9-10 year old children in Mauritius. METHODS: 412 boys and 429 girls aged 9-10 years from 23 primary schools were selected using stratified cluster random sampling. All data was cross-sectional and collected via anthropometry and self-administered questionnaire. Outcome measures were BMI (kg/m2), prevalence of overweight, obesity (International Obesity Task Force definitions) and thinness (low BMI for age). Linear and logistic regression analyses, accounting for clustering at the school level, were used to assess associations between gender, ethnicity, school location, and school's academic performance (average) to each outcome measure. RESULTS: The distribution of BMI was marginally skewed with a more pronounced positive tail in the girls. Median BMI was 15.6 kg/m2 in boys and 15.4 kg/m2 in girls, respectively. In boys, prevalence of overweight was 15.8% (95% CI: 12.6, 19.6), prevalence of obesity 4.9% (95% CI: 3.2, 7.4) and prevalence of thinness 12.4% (95% CI: 9.5, 15.9). Among girls, 18.9% (95% CI: 15.5, 22.9) were overweight, 5.1% (95% CI: 3.4, 7.7) were obese and 13.1% (95% CI: 10.2, 16.6) were thin. Urban children had a slightly higher mean BMI than rural children (0.5 kg/m2, 95% CI: 0.01, 1.00) and were nearly twice as likely to be obese (6.7% vs. 4.0%; adjusted odds ratio 1.6; 95% CI: 0.9, 3.5). Creole children were less likely to be classified as thin compared to Indian children (adjusted odds ratio 0.3, 95% CI: 0.2, 0.6). CONCLUSION: Mauritius is currently in the midst of nutritional transition with both a high prevalence of overweight and thinness in children aged 9-10 years. The coexistence of children representing opposite sides of the energy balance equation presents a unique challenge for policy and interventions. Further exploration is needed to understand the specific causes of the double burden of malnutrition and to make appropriate policy recommendations

The pyruvate decarboxylase activity of IpdC is a limitation for isobutanol production by Klebsiella pneumoniae

BACKGROUND: Klebsiella pneumoniae contains an endogenous isobutanol synthesis pathway. The ipdC gene annotated as an indole-3-pyruvate decarboxylase (Kp-IpdC), was identified to catalyze the formation of isobutyraldehyde from 2-ketoisovalerate. RESULTS: Compared with 2-ketoisovalerate decarboxylase from Lactococcus lactis (KivD), a decarboxylase commonly used in artificial isobutanol synthesis pathways, Kp-IpdC has an 2.8-fold lower Km for 2-ketoisovalerate, leading to higher isobutanol production without induction. However, expression of ipdC by IPTG induction resulted in a low isobutanol titer. In vitro enzymatic reactions showed that Kp-IpdC exhibits promiscuous pyruvate decarboxylase activity, which adversely consume the available pyruvate precursor for isobutanol synthesis. To address this, we have engineered Kp-IpdC to reduce pyruvate decarboxylase activity. From computational modeling, we identified 10 amino acid residues surrounding the active site for mutagenesis. Ten designs consisting of eight single-point mutants and two double-point mutants were selected for exploration. Mutants L546W and T290L that showed only 5.1% and 22.1% of catalytic efficiency on pyruvate compared to Kp-IpdC, were then expressed in K. pneumoniae for in vivo testing. Isobutanol production by K. pneumoniae T290L was 25% higher than that of the control strain, and a final titer of 5.5 g/L isobutanol was obtained with a substrate conversion ratio of 0.16 mol/mol glucose. CONCLUSIONS: This research provides a new way to improve the efficiency of the biological route of isobutanol production

Infra-Red Stable Supersymmetry in Chern-Simons Theories with Matter and Quenched Disorder

We study Abelian Chern-Simons field theories with matter fields and global SU(N) symmetry in the presence of random weak quenched disorder. In the absence of disorder these theories possess N=2 supersymmetric fixed points and N=1 supersymmetric fixed lines in the infra-red limit. We show that although the presence of disorder forbids any supersymmetry of the bare action, infra-red stable supersymmetric fixed points and fixed lines are realized in the disorder-averaged effective theories.Comment: 8 pp., LaTeX. Explanatory remarks and references added. Version to appear in Phys. Rev. Let

Vacuum instability in external fields

We study particles creation in arbitrary space-time dimensions by external electric fields, in particular, by fields, which are acting for a finite time. The time and dimensional analysis of the vacuum instability is presented. It is shown that the distributions of particles created by quasiconstant electric fields can be written in a form which has a thermal character and seems to be universal. Its application, for example, to the particles creation in external constant gravitational field reproduces the Hawking temperature exactly.Comment: 36 pages, LaTe

Feasibility Study of Short Takeoff and Landing Urban Air Mobility Vehicles Using Geometric Programming

Electric Short Takeoff and Landing (eSTOL) vehicles are proposed as a path towards implementing an Urban Air Mobility (UAM) network that reduces critical vehicle certification risks and offers advantages in vehicle performance compared to the widely proposed Electric Vertical Takeoff and Landing (eVTOL) aircraft. An overview is given of the system constraints and key enabling technologies that must be incorporated into the design of the vehicle. The tradeoffs between vehicle performance and runway length are investigated using geometric programming, a robust optimization framework. Runway lengths as short as 100-300 ft are shown to be feasible, depending on the level of technology and the desired cruise speed. The tradeoffs between runway length and the potential to build new infrastructure in urban centers are investigated using Boston as a representative case study. The placement of some runways up to 600ft is shown to be possible in the urban center, with a significant increase in the number of potential locations for runways shorter than 300ft. Key challenges and risks to implementation are discussed

Gammaherpesvirus-Driven Plasma Cell Differentiation Regulates Virus Reactivation from Latently Infected B Lymphocytes

Gammaherpesviruses chronically infect their host and are tightly associated with the development of lymphoproliferative diseases and lymphomas, as well as several other types of cancer. Mechanisms involved in maintaining chronic gammaherpesvirus infections are poorly understood and, in particular, little is known about the mechanisms involved in controlling gammaherpesvirus reactivation from latently infected B cells in vivo. Recent evidence has linked plasma cell differentiation with reactivation of the human gammaherpesviruses EBV and KSHV through induction of the immediate-early viral transcriptional activators by the plasma cell-specific transcription factor XBP-1s. We now extend those findings to document a role for a gammaherpesvirus gene product in regulating plasma cell differentiation and thus virus reactivation. We have previously shown that the murine gammaherpesvirus 68 (MHV68) gene product M2 is dispensable for virus replication in permissive cells, but plays a critical role in virus reactivation from latently infected B cells. Here we show that in mice infected with wild type MHV68, virus infected plasma cells (ca. 8% of virus infected splenocytes at the peak of viral latency) account for the majority of reactivation observed upon explant of splenocytes. In contrast, there is an absence of virus infected plasma cells at the peak of latency in mice infected with a M2 null MHV68. Furthermore, we show that the M2 protein can drive plasma cell differentiation in a B lymphoma cell line in the absence of any other MHV68 gene products. Thus, the role of M2 in MHV68 reactivation can be attributed to its ability to manipulate plasma cell differentiation, providing a novel viral strategy to regulate gammaherpesvirus reactivation from latently infected B cells. We postulate that M2 represents a new class of herpesvirus gene products (reactivation conditioners) that do not directly participate in virus replication, but rather facilitate virus reactivation by manipulating the cellular milieu to provide a reactivation competent environment