TarO : a target optimisation system for structural biology

This work was funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC) Structural Proteomics of Rational Targets (SPoRT) initiative, (Grant BBS/B/14434). Funding to pay the Open Access publication charges for this article was provided by BBSRC.TarO (http://www.compbio.dundee.ac.uk/taro) offers a single point of reference for key bioinformatics analyses relevant to selecting proteins or domains for study by structural biology techniques. The protein sequence is analysed by 17 algorithms and compared to 8 databases. TarO gathers putative homologues, including orthologues, and then obtains predictions of properties for these sequences including crystallisation propensity, protein disorder and post-translational modifications. Analyses are run on a high-performance computing cluster, the results integrated, stored in a database and accessed through a web-based user interface. Output is in tabulated format and in the form of an annotated multiple sequence alignment (MSA) that may be edited interactively in the program Jalview. TarO also simplifies the gathering of additional annotations via the Distributed Annotation System, both from the MSA in Jalview and through links to Dasty2. Routes to other information gateways are included, for example to relevant pages from UniProt, COG and the Conserved Domains Database. Open access to TarO is available from a guest account with private accounts for academic use available on request. Future development of TarO will include further analysis steps and integration with the Protein Information Management System (PIMS), a sister project in the BBSRC Structural Proteomics of Rational Targets initiative.Publisher PDFPeer reviewe

Experiment to Determine Properties of Packed Particle Beds and Regenerators at Cryogenic Temperatures

The testing of the properties of packed-particle beds and regenerators at cryogenic temperatures as low as 4 K is an essential part of the magnetic refrigeration research and development program at the Los Alamos National Laboratory. We envision magnetic refrigeration and heat pump systems operating in various ranges from 4 K to ambient temperature and above. Only pressurized helium gas appears suitable as the heat exchange fluid for the low-temperature applications. Because published data on the properties of porous beds at low temperatures is sparse, we have found it necessary to develop an experimental test apparatus to study the properties of various configurations of beds and regenerators. Two of the well-known methods for such studies are the steady-enthalpy-flux method and the single-blow transient method. We have developed an experimental system in which gas flow can be suddenly switched to an alternate better (or colder) flow in step-function fashion at temperatures from 4 to 300 K. This apparatus will yield information on steady-state heat transfer and friction factors as well as on the transient behavior. Such information is very important to the design of high-efficiency magnetic refrigeration systems. This paper describes this experimental apparatus and presents the results and analysis of recent measurements on packed-particle beds in the liquid helium and liquid nitrogen temperature ranges

Apparatus to Determine the Heat Capacity and Thermal Conductivity of a Material From 1 to 300 K in Magnetic Fields Up to 9 T

Magnetic refrigeration is a new technology that potentially offers refrigeration efficiencies > 50% of Carnot, compactness, and high reliability. Studies indicate that approx. 35% of Carnot efficiency is generally the best that is now possible for gas compression/expansion systems and, at that, only for very large plants; for smaller machines, the fraction of Carnot efficiency can become very small, e.g., 1-W refrigerators generally operate at 2 to 8% of Carnot efficiency. For magnetic refrigerators, the compression/expansion processes are replaced by a cycle involving the application/removal of a magnetic field to either a paramagnetic or ferromagnetic material (generally, paramagnets are used below approx. 20K and ferromagnets above). The thermodynamic cycles in gas and magnetic systems are analogous. Central to the development of magnetic refrigerators is the characterization of magnetic working substances. Among the key properties for which we require data are the heat capacity (from which we derive the entropy) and the thermal conductivity as functions of temperature and magnetic field. Accordingly, at the Los Alamos National Laboratory, we have designed and constructed an apparatus to make measurements of these quantities over the range 1 to 300 K at fields up to 9 T. We describe the methodology of these measurements, the versatile apparatus for making them, and results on GdNi, the first sample measured

New Vectors for Urea-Inducible Recombinant Protein Production

We have developed a novel urea-inducible recombinant protein production system by exploiting the Proteus mirabilis urease ureR-ureD promoter region and the ureR AraC-family transcriptional regulator. Experiments using the expression of β-galactosidase and green fluorescent protein (GFP) showed that promoter activity is tightly regulated and that varying the concentration of urea can give up to 100-fold induction. Production of proteins of biopharmaceutical interest has been demonstrated, including human growth hormone (hGH), a single chain antibody fragment (scFv) against interleukin-1β and a potential Neisserial vaccine candidate (BamAENm). Expression levels can be fine-tuned by temperature and different urea concentrations, and can be induced with readily available garden fertilisers and even urine. As urea is an inexpensive, stable inducer, a urea-induced expression system has the potential to considerably reduce the costs of large-scale recombinant protein production

Effects of human immunodeficiency virus and metabolic complications on myocardial nutrient metabolism, blood flow, and oxygen consumption: a cross-sectional analysis

<p>Abstract</p> <p>Background</p> <p>In the general population, peripheral metabolic complications (MC) increase the risk for left ventricular dysfunction. Human immunodeficiency virus infection (HIV) and combination anti-retroviral therapy (cART) are associated with MC, left ventricular dysfunction, and a higher incidence of cardiovascular events than the general population. We examined whether myocardial nutrient metabolism and left ventricular dysfunction are related to one another and worse in HIV infected men treated with cART vs. HIV-negative men with or without MC.</p> <p>Methods</p> <p>Prospective, cross-sectional study of myocardial glucose and fatty acid metabolism and left ventricular function in HIV+ and HIV-negative men with and without MC. Myocardial glucose utilization (GLUT), and fatty acid oxidation and utilization rates were quantified using ¹¹C-glucose and ¹¹C-palmitate and myocardial positron emission tomography (PET) imaging in four groups of men: 23 HIV+ men with MC+ (HIV+/MC+, 42 ± 6 yrs), 15 HIV+ men without MC (HIV+/MC-, 41 ± 6 yrs), 9 HIV-negative men with MC (HIV-/MC+, 33 ± 5 yrs), and 22 HIV-negative men without MC (HIV-/MC-, 25 ± 6 yrs). Left ventricular function parameters were quantified using echocardiography.</p> <p>Results</p> <p>Myocardial glucose utilization was similar among groups, however when normalized to fasting plasma insulin concentration (GLUT/INS) was lower (p < 0.01) in men with metabolic complications (HIV+: 9.2 ± 6.2 vs. HIV-: 10.4 ± 8.1 nmol/g/min/μU/mL) than men without metabolic complications (HIV+: 45.0 ± 33.3 vs. HIV-: 60.3 ± 53.0 nmol/g/min/μU/mL). Lower GLUT/INS was associated with lower myocardial relaxation velocity during early diastole (r = 0.39, p < 0.001).</p> <p>Conclusion</p> <p>Men with metabolic complications, irrespective of HIV infection, had lower basal myocardial glucose utilization rates per unit insulin that were related to left ventricular diastolic impairments, indicating that well-controlled HIV infection is not an independent risk factor for blunted myocardial glucose utilization per unit of insulin.</p> <p>Trial Registration</p> <p>NIH Clinical Trials <a href="http://clinicaltrials.gov/ct2/show/NCT00656851">NCT00656851</a></p

Adultery and the Rumor Mill: les bourgeois de Molinchart and El gran galeoto

This article seeks to challenge interpretations of the adultery plot as a subversive current in nineteenth-century literature by examining two texts that are often dismissed by contemporary critics: Les bourgeois de Molinchart (1854), a novel by the French writer Champfleury (the pseudonym of Jules Husson), and El gran Galeoto (1881), a play by the Spanish playwright Jos, Echegaray. In each of these works, the rumor of the adultery precedes and to a large extent precipitates the infidelity at the end of the work. In committing adultery, therefore, the protagonists are not rising up against social norms so much as capitulating to the expectations of society, enacting a plot that has been projected upon them. The essay compares and contrasts the treatment of the rumor mill in the two works and examines the literary strategies that the writers use to undercut a transgressive reading of the infidelity plot

Inexpensive protein overexpression driven by the NarL transcription activator protein

Most Escherichia coli overexpression vectors used for recombinant protein production (RPP) depend on organic inducers, for example, sugars or simple conjugates. However, these can be expensive and, sometimes, chemically unstable. To simplify this and to cut the cost of RPP, we have developed vectors controlled by the Escherichia coli nitrate-responsive NarL transcription activator protein, which use nitrate, a cheap, stable, and abundant inorganic ion, to induce high-level controlled RPP. We show that target proteins, such as green fluorescent protein, human growth hormone, and single-chain variable region antibody fragments can be expressed to high levels using our promoter systems. As nitrate levels are high in many commercial fertilizers, we demonstrate that controlled RPP can be achieved using readily available and inexpensive garden products

Reduction of aerobic and lactic acid bacteria in dairy desludge using an integrated compressed CO2 and ultrasonic process

International audienceAbstractCurrent treatment routes are not suitable to reduce and stabilise bacterial content in some dairy process streams such as separator and bactofuge desludges which currently present a major emission problem faced by dairy producers. In this study, a novel method for the processing of desludge was developed. The new method, elevated pressure sonication (EPS), uses a combination of low frequency ultrasound (20 kHz) and elevated CO2 pressure (50 to 100 bar). Process conditions (pressure, sonicator power, processing time) were optimised for batch and continuous EPS processes to reduce viable numbers of aerobic and lactic acid bacteria in bactofuge desludge by ≥3-log fold. Coagulation of proteins present in the desludge also occurred, causing separation of solid (curd) and liquid (whey) fractions. The proposed process offers a 10-fold reduction in energy compared to high temperature short time (HTST) treatment of milk

Limitations and potentials of dual-purpose cow herds in Central Coastal Veracruz, Mexico

Feed chemical and kinetic composition and animal performance information was used to evaluate productivity limitations and potentials of dual-purpose member herds of the Genesis farmer organization of central coastal Veracruz, Mexico. The Cornell Net Carbohydrate and Protein System model (Version 6.0) was systematically applied to specific groups of cows in structured simulations to establish probable input–output relationships for typical management, and to estimate probable outcomes from alternative management based on forage-based dietary improvements. Key herd vulnerabilities were pinpointed: chronic energy deficits among dry cows of all ages in late gestation and impeded growth for immature cows. Regardless of the forage season of calving, most cows, if not all, incur energy deficits in the final trimester of gestation; thus reducing the pool of tissue energy and constraining milking performance. Under typical management, cows are smaller and underweight for their age, which limits feed intake capacity, milk production and the probability of early postpartum return to ovarian cyclicity. The substitution of good-quality harvested forage for grazing increased predicted yields by about one-third over typical scenarios for underweight cows. When diets from first parturition properly supported growth and tissue repletion, milk production in second and third lactations was predicted to improve about 60%. Judiciously supplemented diets based on good quality grass and legume forages from first calving were predicted to further increase productivity by about 80% across a three-lactation cow lifetime. These dual-purpose herd owners have large incentives to increase sales income by implementing nutritional strategies like those considered in this study

A Multimetric Assessment of Stream Condition in the Northern Lakes and Forests Ecoregion Using Spatially Explicit Statistical Modeling and Regional Normalization

We sampled fish communities, water temperature, water chemistry, physical habitat, and catchment characteristics for 94 stream sites selected randomly throughout the Northern Lakes and Forests ecoregion and used those data to explicitly model reference conditions and assess ecological stream condition at each site via a regional normalization framework. The streams we sampled were first order through fourth order, and the catchments ranged from 0.9 to 458 km2. We developed multiple linear regression (MLR) models that predicted fish community metrics, water chemistry characteristics, and local physical habitat from catchment characteristics; we used these models to compare existing conditions with the conditions that would be expected based on the regression models. Our results indicated that the fish communities were relatively unimpaired because the catchment variables associated with human‐induced land use change were important in only 1 of the 10 fish metric models. Agricultural land use was a significant variable in the MLR equation for species of Lepomis (sunfish). Agricultural land use and urban land use were both significant variables in all of the MLR models predicting water chemistry variables; urban land use was a significant variable in the MLR model predicting the percent coverage of all instream cover types. Regional normalization indicated that none of the sites were impaired based on fish community attributes. However, our analysis based on water chemistry metrics indicated that 22– 35% of the sites were impaired and that, based on physical habitat, 6–14% of the sites were impaired. A comparison with other published studies of the ecoregion suggested that the regional normalization process correctly characterized stream condition.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141590/1/tafs0697.pd