Essential requirements for robust signaling in Hfq dependent small RNA networks

Bacteria possess networks of small RNAs (sRNAs) that are important for modulating gene expression. At the center of many of these sRNA networks is the Hfq protein. Hfq's role is to quickly match cognate sRNAs and target mRNAs from among a large number of possible combinations and anneal them to form duplexes. Here we show using a kinetic model that Hfq can efficiently and robustly achieve this difficult task by minimizing the sequestration of sRNAs and target mRNAs in Hfq complexes. This sequestration can be reduced by two non-mutually exclusive kinetic mechanisms. The first mechanism involves heterotropic cooperativity (where sRNA and target mRNA binding to Hfq is influenced by other RNAs bound to Hfq); this cooperativity can selectively decrease singly-bound Hfq complexes and ternary complexes with non-cognate sRNA-target mRNA pairs while increasing cognate ternary complexes. The second mechanism relies on frequent RNA dissociation enabling the rapid cycling of sRNAs and target mRNAs among different Hfq complexes; this increases the probability the cognate ternary complex forms before the sRNAs and target mRNAs degrade. We further demonstrate that the performance of sRNAs in isolation is not predictive of their performance within a network. These findings highlight the importance of experimentally characterizing duplex formation in physiologically relevant contexts with multiple RNAs competing for Hfq. The model will provide a valuable framework for guiding and interpreting these experiments.     

Influence of Plant Community Composition on Biomass Production in Planted Grasslands

United States energy policy mandates increased use of renewable fuels. Restoring grasslands could contribute to a portion of this requirement through biomass harvest for bioenergy use. We investigated which plant community characteristics are associated with differences in biomass yield from a range of realistic native prairie plantings (n = 11; i.e., conservation planting, restoration, and wildlife cover). Our primary goal was to understand whether patterns in plant community composition and the Floristic Quality Index (FQI) were related to productivity as evidenced by dormant season biomass yield. FQI is an objective measure of how closely a plant community represents that of a pre-European settlement community. Our research was conducted in planted fields of native tallgrass prairie species, and provided a gradient in floristic quality index, species richness, species diversity, and species evenness in south-central Wisconsin during 2008 and 2009. We used a network of 15 randomly located 1 m² plots within each field to characterize the plant community and estimate biomass yield by clipping the plots at the end of each growing season. While plant community composition and diversity varied significantly by planting type, biomass yield did not vary significantly among planting types (ANOVA; P >0.05). Biomass yield was positively correlated with plant community evenness, richness, C4 grass cover, and floristic quality index, but negatively correlated with plant species diversity in our multi-season multiple linear mixed effects models. Concordantly, plots with biomass yield in the lowest quartile (biomass yield < 3500 kh/ha) had 8% lower plant community evenness and 9% lower FQI scores than those in the upper quartile (biomass yield > 5800 kh/ha). Our results suggest that promoting the establishment of fields with high species evenness and floristic quality may increase biomass yield, while simultaneously supporting biodiversity.     

Increased nuclear envelope permeability and Pep4p-dependent degradation of nucleoporins during hydrogen peroxide-induced cell death

The death of yeast treated with hydrogen peroxide (H(2)O(2)) shares a number of morphological and biochemical features with mammalian apoptosis. In this study, we report that the permeability of yeast nuclear envelopes (NE) increased during H(2)O(2)-induced cell death. Similar phenomena have been observed during apoptosis in mammalian tissue culture cells. Increased NE permeability in yeast was temporally correlated with an increase in the production of reactive-oxygen species (ROS). Later, after ROS levels began to decline and viability was lost, specific nuclear pore complex (NPC) proteins (nucleoporins) were degraded. Although caspases are responsible for the degradation of mammalian nucleoporins during apoptosis, the deletion of the metacaspase gene YCA1 had no effect on the stability of yeast nucleoporins. Instead, Pep4p, a vacuolar cathepsin D homolog, was responsible for the proteolysis of nucleoporins. Coincident with nucleoporin degradation, a Pep4p-EGFP reporter migrated out of the vacuole in H(2)O(2)-treated cells. We conclude that increases in ROS and NPC permeability occur relatively early during H(2)O(2)-induced cell death. Later, Pep4p migrates out of vacuoles and degrades nucleoporins after the cells are effectively dead.     

Vegetation and climate controls on potential CO2, DOC and DON production in northern latitude soils

Climatic change may influence decomposition dynamics in arctic and boreal ecosystems, affecting both atmospheric CO₂ levels, and the flux of dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) to aquatic systems. In this study, we investigated landscape‐scale controls on potential production of these compounds using a one‐year laboratory incubation at two temperatures (10° and 30 °C). We measured the release of CO₂, DOC and DON from tundra soils collected from a variety of vegetation types and climatic regimes: tussock tundra at four sites along a latitudinal gradient from the interior to the north slope of Alaska, and soils from additional vegetation types at two of those sites (upland spruce at Fairbanks, and wet sedge and shrub tundra at Toolik Lake in northern Alaska). Vegetation type strongly influenced carbon fluxes. The highest CO₂ and DOC release at the high incubation temperature occurred in the soils of shrub tundra communities. Tussock tundra soils exhibited the next highest DOC fluxes followed by spruce and wet sedge tundra soils, respectively. Of the fluxes, CO₂ showed the greatest sensitivity to incubation temperatures and vegetation type, followed by DOC. DON fluxes were less variable. Total CO₂ and total DOC release were positively correlated, with DOC fluxes approximately 10% of total CO₂ fluxes. The ratio of CO₂ production to DOC release varied significantly across vegetation types with Tussock soils producing an average of four times as much CO₂ per unit DOC released compared to Spruce soils from the Fairbanks site. Sites in this study released 80–370 mg CO₂‐C g soil C^?1 and 5–46 mg DOC g soil C^?1 at high temperatures. The magnitude of these fluxes indicates that arctic carbon pools contain a large proportion of labile carbon that could be easily decomposed given optimal conditions. The size of this labile pool ranged between 9 and 41% of soil carbon on a g soil C basis, with most variation related to vegetation type rather than climate.     

A Formal Representation of the WHO and UNICEF Estimates of National Immunization Coverage: A Computational Logic Approach

Production of official statistics frequently requires expert judgement to evaluate and reconcile data of unknown and varying quality from multiple and potentially conflicting sources. Moreover, exceptional events may be difficult to incorporate in modelled estimates. Computational logic provides a methodology and tools for incorporating analyst''s judgement, integrating multiple data sources and modelling methods, ensuring transparency and replicability, and making documentation computationally accessible. Representations using computational logic can be implemented in a variety of computer-based languages for automated production. Computational logic complements standard mathematical and statistical techniques and extends the flexibility of mathematical and statistical modelling. A basic overview of computational logic is presented and its application to official statistics is illustrated with the WHO & UNICEF estimates of national immunization coverage.     

The Polymorphic Pseudokinase ROP5 Controls Virulence in Toxoplasma gondii by Regulating the Active Kinase ROP18

Secretory polymorphic serine/threonine kinases control pathogenesis of Toxoplasma gondii in the mouse. Genetic studies show that the pseudokinase ROP5 is essential for acute virulence, but do not reveal its mechanism of action. Here we demonstrate that ROP5 controls virulence by blocking IFN-γ mediated clearance in activated macrophages. ROP5 was required for the catalytic activity of the active S/T kinase ROP18, which phosphorylates host immunity related GTPases (IRGs) and protects the parasite from clearance. ROP5 directly regulated activity of ROP18 in vitro, and both proteins were necessary to avoid IRG recruitment and clearance in macrophages. Clearance of both the Δrop5 and Δrop18 mutants was reversed in macrophages lacking Irgm3, which is required for IRG function, and the virulence defect was fully restored in Irgm3^−/− mice. Our findings establish that the pseudokinase ROP5 controls the activity of ROP18, thereby blocking IRG mediated clearance in macrophages. Additionally, ROP5 has other functions that are also Irgm3 and IFN-γ dependent, indicting it plays a general role in governing virulence factors that block immunity.     

Endemic Foci of the Tick-Borne Relapsing Fever Spirochete Borrelia crocidurae in Mali,West Africa,and the Potential for Human Infection

Background

Tick-borne relapsing fever spirochetes are maintained in endemic foci that involve a diversity of small mammals and argasid ticks in the genus Ornithodoros. Most epidemiological studies of tick-borne relapsing fever in West Africa caused by Borrelia crocidurae have been conducted in Senegal. The risk for humans to acquire relapsing fever in Mali is uncertain, as only a few human cases have been identified. Given the high incidence of malaria in Mali, and the potential to confuse the clinical diagnosis of these two diseases, we initiated studies to determine if there were endemic foci of relapsing fever spirochetes that could pose a risk for human infection.

Methodology/Principal Findings

We investigated 20 villages across southern Mali for the presence of relapsing fever spirochetes. Small mammals were captured, thin blood smears were examined microscopically for spirochetes, and serum samples were tested for antibodies to relapsing fever spirochetes. Ornithodoros sonrai ticks were collected and examined for spirochetal infection. In total, 11.0% of the 663 rodents and 14.3% of the 63 shrews tested were seropositive and 2.2% of the animals had active spirochete infections when captured. In the Bandiagara region, the prevalence of infection was higher with 35% of the animals seropositive and 10% infected. Here also Ornithodoros sonrai were abundant and 17.3% of 278 individual ticks tested were infected with Borrelia crocidurae. Fifteen isolates of B. crocidurae were established and characterized by multi-locus sequence typing.

Conclusions/Significance

The potential for human tick-borne relapsing fever exists in many areas of southern Mali.     

Effectiveness of Cognitive Behavioral Therapy for Depression in Patients Receiving Disability Benefits: A Systematic Review and Individual Patient Data Meta-Analysis

Objectives

To systematically summarize the randomized trial evidence regarding the relative effectiveness of cognitive behavioural therapy (CBT) in patients with depression in receipt of disability benefits in comparison to those not receiving disability benefits.

Data Sources

All relevant RCTs from a database of randomized controlled and comparative studies examining the effects of psychotherapy for adult depression (http://www.evidencebasedpsychotherapies.org), electronic databases (MEDLINE, EMBASE, PSYCINFO, AMED, CINAHL and CENTRAL) to June 2011, and bibliographies of all relevant articles.

Study Eligibility Criteria, Participants and Intervention

Adult patients with major depression, randomly assigned to CBT versus minimal/no treatment or care-as-usual.

Study Appraisal and Synthesis Methods

Three teams of reviewers, independently and in duplicate, completed title and abstract screening, full text review and data extraction. We performed an individual patient data meta-analysis to summarize data.

Results

Of 92 eligible trials, 70 provided author contact information; of these 56 (80%) were successfully contacted to establish if they captured receipt of benefits as a baseline characteristic; 8 recorded benefit status, and 3 enrolled some patients in receipt of benefits, of which 2 provided individual patient data. Including both patients receiving and not receiving disability benefits, 2 trials (227 patients) suggested a possible reduction in depression with CBT, as measured by the Beck Depression Inventory, mean difference [MD] (95% confidence interval [CI]) = −2.61 (−5.28, 0.07), p = 0.06; minimally important difference of 5. The effect appeared larger, though not significantly, in those in receipt of benefits (34 patients) versus not receiving benefits (193 patients); MD (95% CI) = −4.46 (−12.21, 3.30), p = 0.26.

Conclusions

Our data does not support the hypothesis that CBT has smaller effects in depressed patients receiving disability benefits versus other patients. Given that the confidence interval is wide, a decreased effect is still possible, though if the difference exists, it is likely to be small.     

Adult Cardiac Progenitor Cell Aggregates Exhibit Survival Benefit Both In Vitro and In Vivo

Background

A major hurdle in the use of exogenous stems cells for therapeutic regeneration of injured myocardium remains the poor survival of implanted cells. To date, the delivery of stem cells into myocardium has largely focused on implantation of cell suspensions.

Methodology and Principal Findings

We hypothesize that delivering progenitor cells in an aggregate form would serve to mimic the endogenous state with proper cell-cell contact, and may aid the survival of implanted cells. Microwell methodologies allow for the culture of homogenous 3D cell aggregates, thereby allowing cell-cell contact. In this study, we find that the culture of cardiac progenitor cells in a 3D cell aggregate augments cell survival and protects against cellular toxins and stressors, including hydrogen peroxide and anoxia/reoxygenation induced cell death. Moreover, using a murine model of cardiac ischemia-reperfusion injury, we find that delivery of cardiac progenitor cells in the form of 3D aggregates improved in vivo survival of implanted cells.

Conclusion

Collectively, our data support the notion that growth in 3D cellular systems and maintenance of cell-cell contact improves exogenous cell survival following delivery into myocardium. These approaches may serve as a strategy to improve cardiovascular cell-based therapies.