External and internal detection of Nosema ceranae on honey bees using real-time PCR

Numerous methods exist for molecular-based detection of Nosema ceranae. Here we determine location of parasite loads, the optimal tissue for pathogen detection, and the likely sources of variability among assays. Bee washes and head/thorax samples revealed substantial N. ceranae loads (2.67×10(4)±1.12×10(4) and 1.83×10(4)±4.14×10(3)). Midgut samples carried the highest parasite loads (3.42×10(6)±1.84×10(6)), followed by the hindgut (5.50×10(5)±3.24×10(5)). We recommend using midgut samples for molecular-based detection and quantification of N. ceranae because of the low variability among samples.     

Renovascular reactivity measured by near-infrared spectroscopy

Hypotension and shock are risk factors for death, renal insufficiency, and stroke in preterm neonates. Goal-directed neonatal hemodynamic management lacks end-organ monitoring strategies to assess the adequacy of perfusion. Our aim is to develop a clinically viable, continuous metric of renovascular reactivity to gauge renal perfusion during shock. We present the renovascular reactivity index (RVx), which quantifies passivity of renal blood volume to spontaneous changes in arterial blood pressure. We tested the ability of the RVx to detect reductions in renal blood flow. Hemorrhagic shock was induced in 10 piglets. The RVx was monitored as a correlation between slow waves of arterial blood pressure and relative total hemoglobin (rTHb) obtained with reflectance near-infrared spectroscopy (NIRS) over the kidney. The RVx was compared with laser-Doppler measurements of red blood cell flux, and renal laser-Doppler measurements were compared with cerebral laser-Doppler measurements. Renal blood flow decreased to 75%, 50%, and 25% of baseline at perfusion pressures of 60, 45, and 40 mmHg, respectively, whereas in the brain these decrements occurred at pressures of 30, 25, and 15 mmHg, respectively. The RVx compared favorably to the renal laser-Doppler data. Areas under the receiver operator characteristic curves using renal blood flow thresholds of 50% and 25% of baseline were 0.85 (95% CI, 0.83-0.87) and 0.90 (95% CI, 0.88-0.92). Renovascular autoregulation can be monitored and is impaired in advance of cerebrovascular autoregulation during hemorrhagic shock.     

Computational identification of gene over-expression targets for metabolic engineering of taxadiene production

Taxadiene is the first dedicated intermediate in the biosynthetic pathway of the anticancer compound Taxol. Recent studies have taken advantage of heterologous hosts to produce taxadiene and other isoprenoid compounds, and such ventures now offer research opportunities that take advantage of the engineering tools associated with the surrogate host. In this study, metabolic engineering was applied in the context of over-expression targets predicted to improve taxadiene production. Identified targets included genes both within and outside of the isoprenoid precursor pathway. These targets were then tested for experimental over-expression in a heterologous Escherichia coli host designed to support isoprenoid biosynthesis. Results confirmed the computationally predicted improvements and indicated a synergy between targets within the expected isoprenoid precursor pathway and those outside this pathway. The presented algorithm is broadly applicable to other host systems and/or product choices.     

Burrowing behavior and burrowing energetics of a bioindicator under human disturbance

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Parasite modification of predator functional response

Parasite alteration of the host (predator) functional response provides a mechanism by which parasites can alter predator–prey population dynamics and stability. We tested the hypothesis that parasitic infection of a crab (Eurypanopeus depressus) by a rhizocephalan barnacle (Loxothylacus panopei) can modify the crab’s functional response to mussel (Brachidontes exustus) prey and investigated behavioral mechanisms behind a potential change in the response. Infection dramatically reduced mussel consumption by crabs across mussel densities, resulting in a decreased attack rate parameter and a nearly eightfold reduction in maximum consumption (i.e. the asymptote, or inverse of the handling time parameter) in a type II functional response model. To test whether increased handling time of infected crabs drove the decrease in maximum consumption rate, we independently measured handling time through observation. Infection had no effect on handling time and thus could not explain the reduction in consumption. Infection did, however, increase the time that it took crabs to begin handling prey after the start of the handling time experiment. Furthermore, crabs harboring relatively larger parasites remained inactive longer before making contact with prey. This behavioral modification likely contributed to the reduced mussel consumption of infected crabs. A field survey revealed that 20 % of crabs inhabiting oyster reefs at the study site (North Inlet estuary, Georgetown, South Carolina, USA) are infected by the barnacle parasite, indicating that parasite infection could have a substantial effect on the population level crab-mussel interaction.     

Metabolic flux analysis and pharmaceutical production

Rational engineering of biological systems is an inherently complex process due to their evolved nature. Metabolic engineering emerged and developed over the past 20 years as a field in which methodologies for the rational engineering of biological systems is now being applied to specific industrial, medical, or scientific problems. Of considerable interest is the determination of metabolic fluxes within the cell itself, called metabolic flux analysis. This special issue and this review have a particular interest in the application of metabolic flux analysis for improving the pharmaceutical production process (for both small and large molecules). Though metabolic flux analysis has been somewhat limited in application towards pharmaceutical production, the overall goal is to: (1) have a better understanding of the organism and/or process in question, and (2) provide a rational basis to further engineer (on both metabolic and process scales) improved pharmaceutical production in these organisms. The focus of this review article is to present how experimental and computational methods of metabolic flux analysis have matured, mirroring the maturation of the metabolic engineering field itself, while highlighting some of the successful applications towards both small- and large-molecule pharmaceuticals.     

Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme

To try to resolve the loss of stability in the temperature‐sensitive mutant of T4 lysozyme, Arg 96 → His, all of the remaining 18 naturally occurring amino acids were substituted at site 96. Also, in response to suggestions that the charged residues Lys85 and Asp89, which are 5–8 Å away, may have important effects, each of these amino acids was replaced with alanine. Crystal structures were determined for many of the variants. With the exception of the tryptophan and valine mutants R96W and R96V, the crystallographic analysis shows that the substituted side chain following the path of Arg96 in wildtype (WT). The melting temperatures of the variants decrease by up to ～16°C with WT being most stable. There are two site 96 replacements, with lysine or glutamine, that leave the stability close to that of WT. The only element that the side chains of these residues have in common with the WT arginine is the set of three carbon atoms at the C^α, C^β, and C^γ positions. Although each side chain is long and flexible with a polar group at the distal position, the details of the hydrogen bonding to the rest of the protein differ in each case. Also, the glutamine replacement lacks a positive charge. This shows that there is some adaptability in achieving full stabilization at this site. At the other extreme, to be maximally destabilizing a mutation at site 96 must not only eliminate favorable interactions but also introduce an unfavorable element such as steric strain or a hydrogen‐bonding group that remains unsatisfied. Overall, the study highlights the essential need for atomic resolution site‐specific structural information to understand and to predict the stability of mutant proteins. It can be very misleading to simply assume that conservative amino acid substitutions cause small changes in stability, whereas large stability changes are associated with nonconservative replacements.     

Evaluation at atomic resolution of the role of strain in destabilizing the temperature‐sensitive T4 lysozyme mutant Arg 96 → His

Mutant R96H is a classic temperature‐sensitive mutant of bacteriophage T4 lysozyme. It was in fact the first variant of the protein to be characterized structurally. Subsequently, it has been studied extensively by a variety of experimental and computational techniques, but the reasons for the loss of stability of the mutant protein remain controversial. In the crystallographic refinement of the mutant structure at 1.9 Å resolution one of the bond angles at the site of substitution appeared to be distorted by about 11^°, and it was suggested that this steric strain was one of the major factors in destabilizing the mutant. Different computationally‐derived models of the mutant structure, however, did not show such distortion. To determine the geometry at the site of mutation more reliably, we have extended the resolution of the data and refined the wildtype (WT) and mutant structures to be better than 1.1 Å resolution. The high‐resolution refinement of the structure of R96H does not support the bond angle distortion seen in the 1.9 Å structure determination. At the same time, it does confirm other manifestations of strain seen previously including an unusual rotameric state for His96 with distorted hydrogen bonding. The rotamer strain has been estimated as about 0.8 kcal/mol, which is about 25% of the overall reduction in stability of the mutant. Because of concern that contacts from a neighboring molecule in the crystal might influence the geometry at the site of mutation we also constructed and analyzed supplemental mutant structures in which this crystal contact was eliminated. High‐resolution refinement shows that the crystal contacts have essentially no effect on the conformation of Arg96 in WT or on His96 in the R96H mutant.