Concordant evolution of mitochondrial and nuclear genomes in the wheat pathogen Phaeosphaeria nodorum

We compared patterns of mitochondrial restriction fragment length polymorphism (RFLP) diversity with patterns of nuclear RFLP diversity to investigate the effects of selection, gene flow, and sexual reproduction on the population genetic structure and evolutionary history of the wheat pathogen Phaeosphaeria nodorum. A total of 315 fungal isolates from Texas, Oregon, and Switzerland were analyzed using seven nuclear RFLP probes that hybridized to discrete loci and purified mitochondrial DNA that hybridized to the entire mtDNA genome. Forty-two different mitochondrial haplotypes and 298 different nuclear haplotypes were detected. The two most frequent mtDNA haplotypes were present in every population and represented 32% of all isolates. High levels of gene flow, low levels of population subdivision, no evidence for either host specificity or cyto-nuclear disequilibrium were inferred from the analysis of both genomes. The concordance in estimates of these population genetic parameters from both genomes suggests that the two genomes experienced similar degrees of migration, genetic drift and selection.     

Anthropology and the Dialectic of Enlightenment: A Discourse on the Definition and Ideals of a Threatened Discipline

The knowledge practices of social and cultural anthropology can be conceived as undergoing constant methodological reconsideration or reformulation as a consequence of internal critique and of institutional change effected in the larger educational and political environment. Neo‐liberal shifts affecting the institutional context may have influenced a deepening of the crisis in anthropology where the nature of its project has become less certain or has threatened a reconfiguration of such proportion that anthropology may be losing sight of its direction. This essay explores some of the Enlightenment roots of social and cultural anthropology. It is presented as very much an idea that embodies and reflects what Adorno and Horkheimer discussed as the dialectic of Enlightenment. The argument presented is less pessimistic claiming that the distinction of anthropology is in its pursuit of Enlightenment ideals that it has maintained and rehoned as a consequence of its own routine internal critique. The vital implication of the discussion is that anthropology is in a situation of serious threat in largely a post‐Enlightenment world. In such a context, the methodological ideals that emerged as integral to the spirit of anthropology are well worth maintaining rather than abandoning. The ideals that are addressed are conceived to be integral to the importance of anthropology as critique and as a knowledge practice capable of sustaining a profound contribution to the understanding of the potential that is human being.     

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.     

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.