Secretory phospholipases A2 stimulate mucus secretion, induce airway inflammation, and produce secretory hyperresponsiveness to neutrophil elastase in ferret trachea

Secretory phospholipases A(2) (sPLA(2)) are increased in the bronchoalveolar lavage fluid of patients with asthma and acute respiratory distress syndrome. Intratracheal sPLA(2) instillation induces acute lung injury in the rat and guinea pig. We hypothesized that sPLA(2) would stimulate mucus secretion in vitro and that intratracheal sPLA(2) exposure would induce mucus hypersecretion and airway inflammation in the ferret trachea in vivo. In vitro, porcine pancreatic sPLA(2) at a concentration of 0.5 or 5 U/ml significantly increased mucous glycoconjugate (MG) secretion from the excised ferret trachea. P-bromophenacylbromide (a sPLA(2) inhibitor), quercetin (a lipoxygenase inhibitor), or MK-886 (a 5-lipoxygenase inhibitor), each at 10(-4) M, significantly reduced sPLA(2)-induced MG secretion. sPLA(2)-stimulated MG secretion was decreased in Ca(2+)-free medium. In vivo, ferrets were intubated for 30 min once per day for 3 days using an ETT coated with 20 units of porcine pancreatic sPLA(2) mixed in water-soluble jelly. Constitutive MG secretion increased 1 day after sPLA(2) exposure and returned to control 5 days later. Human neutrophil elastase (HNE) at 10(-8) M increased MG secretion in the sPLA(2)-exposed trachea compared with that in the control trachea, but methacholine at 10(-7) M did not. sPLA(2)-induced secretory hyperresponsiveness continued for at least 5 days after sPLA(2) exposure ended. sPLA(2) increased tracheal inflammation, MG secretion, and secretory hyperresponsiveness to HNE probably through enzymatic action rather than by activation of its receptor.     

Sustained biological effects of porcine interleukin 5 delivered to pigs as recombinant protein or via a DNA vector

The ability of cytokines to act as natural immunotherapeutics to enhance the health and the disease resistance of animals is of particular interest to the intensive livestock industries. Antibiotics have been used for such purposes over a long period of time, however, there is growing concern that this practice will enhance the development of antibiotic resistance in a range of bacterial pathogens. In several species, interleukin 5 (IL-5) is known to enhance B cell activity and to increase the numbers of eosinophils in blood and tissues. In this report, IL-5 was delivered to pigs, either as a recombinant protein or via a DNA delivery vector and was shown to elevate eosinophils in blood over a sustained period. Interleukin 3, a potent haemopoietic factor, did not synergise with IL-5 when both cytokines were given together, but did prime the pigs for a stronger response to IL-5. These results demonstrate that IL-5 can readily be delivered to commercial pigs to elicit a significant biological effect.     

Six months of supervised high-intensity low-volume resistance training improves strength independent of changes in muscle mass in young overweight men

To determine the effects of a 6-month supervised low-volume resistance training (RT) program (1 set, 85-90%, one repetition maximum, 1RM, 3 d x wk(-1)) on muscular strength (1RM) and skeletal muscle mass (SMM) in previously sedentary, overweight men on an ad libitum diet. Nineteen men were randomly assigned to a control (CON, n = 8) or RT (n = 11) group. The exercise protocol consisted of 5 upper- and 4 lower-body exercises using weight machines. CON maintained their sedentary lifestyle. One RM for upper body (chest press [CP] + lat pull-down [LPD]) and lower body (leg press [LP]) and SMM were assessed at baseline, and at 3 and 6 months. Adherence was 96 +/- 2% with an average time to complete each exercise session of 15 +/- 2 minutes. Volume completed per exercise session significantly increased from baseline (2,812 +/- 670 kg) to 6 months (6,411 +/- 2,128 kg). There was a group by time interaction in 1RM for CP, LPD, and LP. Upper-body strength increased significantly (p < 0.001) (31.3 +/- 9.3%) from baseline to 3 months and from 3 to 6 months (17.9 +/- 8.7%). Lower-body strength also increased significantly from baseline to 3 months (17.8 +/- 16.6%) and from 3 to 6 months (32.0 +/- 33.7%). No changes in upper- or lower-body strength occurred in the CON group. There was no group by time interaction for SMM (CON, 34.5 +/- 2.9 kg vs. RT, 34.2 +/- 2.9 kg; p > 0.05) or for energy intake (p > 0.05). In conclusion, a single set resistance training program at 85% of 1RM, 3 d x wk(-1) resulted in continued increases in muscular strength and a very high adherence rate over a 6-month period in sedentary, overweight men independent of significant changes in SMM. This training protocol may increase adherence and produce long-term increases in muscular fitness as part of an adult fitness program.     

Genome-level longitudinal expression of signaling pathways and gene networks in pediatric septic shock

We have conducted longitudinal studies focused on the expression profiles of signaling pathways and gene networks in children with septic shock. Genome-level expression profiles were generated from whole blood-derived RNA of children with septic shock (n=30) corresponding to day one and day three of septic shock, respectively. Based on sequential statistical and expression filters, day one and day three of septic shock were characterized by differential regulation of 2,142 and 2,504 gene probes, respectively, relative to controls (n=15). Venn analysis demonstrated 239 unique genes in the day one dataset, 598 unique genes in the day three dataset, and 1,906 genes common to both datasets. Functional analyses demonstrated time-dependent, differential regulation of genes involved in multiple signaling pathways and gene networks primarily related to immunity and inflammation. Notably, multiple and distinct gene networks involving T cell- and MHC antigen-related biology were persistently downregulated on both day one and day three. Further analyses demonstrated large scale, persistent downregulation of genes corresponding to functional annotations related to zinc homeostasis. These data represent the largest reported cohort of patients with septic shock subjected to longitudinal genome-level expression profiling. The data further advance our genome-level understanding of pediatric septic shock and support novel hypotheses.     

Dead-end elimination with backbone flexibility

MOTIVATION: Dead-End Elimination (DEE) is a powerful algorithm capable of reducing the search space for structure-based protein design by a combinatorial factor. By using a fixed backbone template, a rotamer library, and a potential energy function, DEE identifies and prunes rotamer choices that are provably not part of the Global Minimum Energy Conformation (GMEC), effectively eliminating the majority of the conformations that must be subsequently enumerated to obtain the GMEC. Since a fixed-backbone model biases the algorithm predictions against protein sequences for which even small backbone movements may result in a significantly enhanced stability, the incorporation of backbone flexibility can improve the accuracy of the design predictions. If explicit backbone flexibility is incorporated into the model, however, the traditional DEE criteria can no longer guarantee that the flexible-backbone GMEC, the lowest-energy conformation when the backbone is allowed to flex, will not be pruned. RESULTS: We derive a novel DEE pruning criterion, flexible-backbone DEE (BD), that is provably accurate with backbone flexibility, guaranteeing that no rotamers belonging to the flexible-backbone GMEC are pruned; we also present further enhancements to BD for improved pruning efficiency. The results from applying our novel algorithms to redesign the beta1 domain of protein G and to switch the substrate specificity of the NRPS enzyme GrsA-PheA are then compared against the results from previous fixed-backbone DEE algorithms. We confirm experimentally that traditional-DEE is indeed not provably-accurate with backbone flexibility and that BD is capable of generating conformations with significantly lower energies, thus confirming the feasibility of our novel algorithms. AVAILABILITY: Contact authors for source code.     

Branched Chain Keto-Acids Exert Biphasic Effects on α-Ketoglutarate-Stimulated Respiration in Intact Rat Liver Mitochondria

Pathophysiological concentrations of branched chain keto-acids (BCKAs), such as those that occur in maple syrup urine disease, inhibit oxygen consumption in liver homogenates and brain slices and the enzymatic activity of α-ketoglutarate- and pyruvate dehydrogenase complexes. Consistent with previous work, studies in isolated rat liver mitochondria indicate that three BCKAs, α-ketoisocaproate (KIC), α-keto-β-methylvalerate (KMV) and α-ketoisovalerate (KIV), preferentially inhibited State 3 respiration supported by α-ketoglutarate relative to succinate or glutamate/malate (KIC, >100-fold; KMV, >10-fold; KIV, >4-fold). KIC was also the most potent inhibitor (K_i,app 13 ± 2 μM). Surprisingly, sub-inhibitory concentrations of KIC and KMV can markedly stimulate State 3 respiration of mitochondria utilizing α-ketoglutarate and glutamate/malate, but not succinate. The data suggest that physiological concentrations of the BCKAs may modulate mitochondrial respiration. Special issue dedicated to John P. Blass.     

Factors influencing the distribution of Subantarctic deep-sea benthic foraminifera,Campbell and Bounty Plateaux,New Zealand

We investigate the combination of environmental factors that influence the distribution patterns of benthic foraminiferal tests (> 63 μm) in a topographically varied region crossed by both the Subtropical and Subantarctic Fronts, south-east of New Zealand. Seafloor sample sites, extending from outer shelf (50 m) to abyssal (5000 m) depths, are bathed by five different water masses, and receive phytodetritus from Subtropical, Subantarctic and Circumpolar surface water masses. Eight mappable associations are recognised by Q-mode cluster analysis of the benthic foraminiferal census data. Similar associations are identified using cluster analysis based solely on the presence or absence of species. Canonical correspondence analysis and a correlation coefficient matrix were used to relate the faunal data to a set of environmental proxies. These show that factors related to water depth (especially decreasing food supply with increasing depth) are the most significant in determining the overall foraminiferal distribution. Other contributing factors include surface water productivity and its seasonality; bottom water ventilation; energetic state of the benthic boundary layer and resulting substrate texture; and bottom water carbonate corrosiveness. Three shallow-water associations (50–700 m), dominated by Cassidulina carinata, Trifarina angulosa, Globocassidulina canalisuturata, Gavelinopsis praegeri, and Bolivina robusta, occur in coarse substrates on the continental shelf, and on the crests and upper slopes of four seamounts under well-oxygenated, high energy regimes, and high food input. Three mid bathyal to upper abyssal associations (500–3300 m), dominated by Alabaminella weddellensis, C. carinata, and Epistominella exigua, occur in biopelagic sandy mud, beneath a region of strongly seasonal food supply, with their composition influenced by total food flux, ventilation (Oxygen Minimum Zone), and bottom current strength. An unusual lower bathyal association (1200–2100 m), dominated by T. angulosa and Ehrenbergina glabra, occurs in a belt of coarser sandy substrate that runs along the crest of the submarine plateaux slopes beneath the strongly-flowing Subantarctic Front-related currents. A deep abyssal association (3500–5000 m), dominated by Nuttallides umbonifer and Globocassidulina subglobosa, occurs on the abyssal plain beneath oligotrophic lower Circumpolar Water south-east of the Subantarctic Front and is strongly influenced by the cold, carbonate-corrosive conditions.     

Origin and domestication of the fungal wheat pathogen Mycosphaerella graminicola via sympatric speciation

The Fertile Crescent represents the center of origin and earliest known place of domestication for many cereal crops. During the transition from wild grasses to domesticated cereals, many host-specialized pathogen species are thought to have emerged. A sister population of the wheat-adapted pathogen Mycosphaerella graminicola was identified on wild grasses collected in northwest Iran. Isolates of this wild grass pathogen from 5 locations in Iran were compared with 123 M. graminicola isolates from the Middle East, Europe, and North America. DNA sequencing revealed a close phylogenetic relationship between the pathogen populations. To reconstruct the evolutionary history of M. graminicola, we sequenced 6 nuclear loci encompassing 464 polymorphic sites. Coalescence analyses indicated a relatively recent origin of M. graminicola, coinciding with the known domestication of wheat in the Fertile Crescent around 8,000-9,000 BC. The sympatric divergence of populations was accompanied by strong genetic differentiation. At the present time, no genetic exchange occurs between pathogen populations on wheat and wild grasses although we found evidence that gene flow may have occurred since genetic differentiation of the populations.     

A mathematical model for the kinetics of Methanobacterium bryantii M.o.H. considering hydrogen thresholds

We develop a kinetic model that builds on the foundation of classic Monod kinetics, but incorporates new phenomena such as substrate thresholds and survival mode observed in experiments with the H2-oxidizing methanogen Methanobacterium bryantii M.o.H. We apply our model to the experimental data presented in our companion paper on H2 thresholds. The model accurately describes H2 consumption, CH4 generation, biomass growth, substrate thresholds, and survival state during batch experiments. Methane formation stops when its Gibbs free energy is equal zero, although this does not interrupt H2 oxidation. The thermodynamic threshold for H2 oxidation occurs when the free energy for oxidizing H2 and transferring electrons to biomass is no longer negative, at approximately 0.4 nM. This threshold is not controlled by the Gibbs free energy equation of methanogenesis from H2 + HCO3- as we show in our companion paper. Beyond this threshold, the microorganisms shift to a low-maintenance metabolism called "the survival state" in response to extended H2 starvation; adding the starvation response as another new feature of the kinetic model. A kinetic threshold (or S (min)), a natural feature of the Monod kinetics, is also captured by the model at H2 concentration of around approximately 2,400 nM. S (min) is the minimum substrate concentration to maintain steady-state biomass concentration. Our model will be useful for interpreting threshold results and designing new studies to understand thresholds and their ecological implications.