Synthesis and antiviral activity of novel HCV NS3 protease inhibitors with P4 capping groups

We have synthesized and evaluated a series of novel HCV NS3 protease inhibitors with various P4 capping groups, which include urea, carbamate, methoxy-carboxamide, cyclic carbamate and amide, pyruvic amide, oxamate, oxalamide and cyanoguanidine. Most of these compounds are remarkably potent, exhibiting single-digit to sub-nanomolar activity in the enzyme assay and cell-based replicon assay. Selected compounds were also evaluated in the protease-inhibitor-resistant mutant transient replicon assay, and they were found to show quite different potency profiles against a panel of HCV protease-inhibitor-resistant mutants.     

Temporal dynamics of roost snags of long-legged myotis in the Pacific Northwest,USA

Snags are used as roosting sites by many bats living in coniferous forests of western North America. Thus, providing sufficient numbers of snags both spatially and temporally in forested landscapes is critical to sustaining populations of these species. One aspect that remains poorly understood is length of time that roost snags persist on the landscape in a form suitable for use by bats. This information is critical for forest-planning efforts in ensuring long-term availability of snag resources on forested landscapes. We monitored condition of 339 snags used as roosting sites by long-legged myotis (Myotis volans) 1–5 years post-discovery from 2001 to 2006 across 6 watersheds in Washington, Oregon, and Idaho, USA. Persistence rates (i.e., probability a snag remains standing from year x to x + 1) of roost snags declined with year post-discovery in all study areas. Fir snags (Abies spp.) exhibited lower persistence rates than other conifer species. Data for the Washington area indicated only 4.3% of roost snags likely remain standing 10 years post-discovery, with half-lives of all snag species <3 roost-years. Model ranking of habitat models predicting fall year of roost snags revealed that snag condition models were the most parsimonious in all geographic locations. Roost snags larger in diameter, shorter in height, and with fewer branches on the bole were likely to persist for more years. These data indicate that snags used as roosts by long-legged myotis are suitable as roosting sites for only a few years before falling. We recommend management policies for coniferous forests in the Pacific Northwest, USA, that promote sufficient leave-trees in set-aside areas to provide for future suitable, large-diameter snags for bats in managed, forested landscapes. © 2012 The Wildlife Society.     

Grenadier abundance examined at varying spatial scales in deep waters off Newfoundland, Canada, with special focus on the influence of corals

There is a growing body of research examining the effects of corals on fish communities, species abundances, and biodiversity. Yet, few studies have quantitatively examined what factors are influencing the distribution of individual fish species. In general, many researchers believe they know what influences the distribution of grenadiers on large spatial scales, but numerous studies have shown the distributions of organisms are often determined by various factors that change in relative importance when viewed at differing scales. Our study used video collected from three deep canyons off Newfoundland, Canada (North west Atlantic) to examine how the factors apparently influencing the distribution of four grenadiers (Macrouridae: Coryphaenoides rupestris, Coryphaenoides carapinus, Nezumia bairdii, and Macrourus berglax) change when assessed at varying spatial scales. We paid special attention to the influence of deep-water corals found in the study area (large gorgonians/antipatharians, small gorgonians, sea pens, soft corals, and cup corals). The factors that influenced grenadier presence and/or abundance (and the magnitude of this effect) varied as different sampling resolutions were examined. We found C. rupestris abundance was positively related to cup coral abundance in transects longer than 10 m, likely as a result of similar habitat preferences between both taxa. When significant relationships between depth and C. rupestris presence and/or abundance were found, they were always negative. Depth was a significant predictor of C. carapinus abundance in transects longer than 10 m. Very few predictors of M. berglax abundance or presence could be found. Depth and the number of small gorgonians were consistent predictors of N. bairdii abundance.     

The design and synthesis of indazole and pyrazolopyridine based glucokinase activators for the treatment of Type 2 diabetes mellitus

Glucokinase activators represent a promising potential treatment for patients with Type 2 diabetes. Herein, we report the identification and optimization of a series of novel indazole and pyrazolopyridine based activators leading to the identification of 4-(6-(azetidine-1-carbonyl)-5-fluoropyridin-3-yloxy)-2-ethyl-N-(5-methylpyrazin-2-yl)-2H-indazole-6-carboxamide (42) as a potent activator with favorable preclinical pharmacokinetic properties and in vivo efficacy.     

Robust design and optimization of retroaldol enzymes

Enzyme catalysts of a retroaldol reaction have been generated by computational design using a motif that combines a lysine in a nonpolar environment with water-mediated stabilization of the carbinolamine hydroxyl and β-hydroxyl groups. Here, we show that the design process is robust and repeatable, with 33 new active designs constructed on 13 different protein scaffold backbones. The initial activities are not high but are increased through site-directed mutagenesis and laboratory evolution. Mutational data highlight areas for improvement in design. Different designed catalysts give different borohydride-reduced reaction intermediates, suggesting a distribution of properties of the designed enzymes that may be further explored and exploited.     

Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths,and an Early Cretaceous origin of modern birds

The origin and timing of the diversification of modern birds remains controversial, primarily because phylogenetic relationships are incompletely resolved and uncertainty persists in molecular estimates of lineage ages. Here, we present a species tree for the major palaeognath lineages using 27 nuclear genes and 27 archaic retroposon insertions. We show that rheas are sister to the kiwis, emu and cassowaries, and confirm ratite paraphyly because tinamous are sister to moas. Divergence dating using 10 genes with broader taxon sampling, including emu, cassowary, ostrich, five kiwis, two rheas, three tinamous, three extinct moas and 15 neognath lineages, suggests that three vicariant events and possibly two dispersals are required to explain their historical biogeography. The age of crown group birds was estimated at 131 Ma (95% highest posterior density 122–138 Ma), similar to previous molecular estimates. Problems associated with gene tree discordance and incomplete lineage sorting in birds will require much larger gene sets to increase species tree accuracy and improve error in divergence times. The relatively rapid branching within neoaves pre-dates the extinction of dinosaurs, suggesting that the genesis of the radiation within this diverse clade of birds was not in response to the Cretaceous–Paleogene extinction event.     

Food security and climate change: on the potential to adapt global crop production by active selection to rising atmospheric carbon dioxide

Agricultural production is under increasing pressure by global anthropogenic changes, including rising population, diversion of cereals to biofuels, increased protein demands and climatic extremes. Because of the immediate and dynamic nature of these changes, adaptation measures are urgently needed to ensure both the stability and continued increase of the global food supply. Although potential adaption options often consider regional or sectoral variations of existing risk management (e.g. earlier planting dates, choice of crop), there may be a global-centric strategy for increasing productivity. In spite of the recognition that atmospheric carbon dioxide (CO(2)) is an essential plant resource that has increased globally by approximately 25 per cent since 1959, efforts to increase the biological conversion of atmospheric CO(2) to stimulate seed yield through crop selection is not generally recognized as an effective adaptation measure. In this review, we challenge that viewpoint through an assessment of existing studies on CO(2) and intraspecific variability to illustrate the potential biological basis for differential plant response among crop lines and demonstrate that while technical hurdles remain, active selection and breeding for CO(2) responsiveness among cereal varieties may provide one of the simplest and direct strategies for increasing global yields and maintaining food security with anthropogenic change.     

Specificity is rarely absolute in coral-algal symbiosis: implications for coral response to climate change

Some reef-building corals have been shown to respond to environmental change by shifting the composition of their algal symbiont (genus Symbiodinium) communities. These shifts have been proposed as a potential mechanism by which corals might survive climate stressors, such as increased temperatures. Conventional molecular methods suggest this adaptive capacity may not be widespread because few (～25%) coral species have been found to associate with multiple Symbiodinium clades. However, these methods can fail to detect low abundance symbionts (typically less than 10-20% of the total algal symbiont community). To determine whether additional Symbiodinium clades are present, but are not detected using conventional techniques, we applied a high-resolution, real-time PCR assay to survey Symbiodinium (in clades A-D) from 39 species of phylogenetically and geographically diverse scleractinian corals. This survey included 26 coral species thought to be restricted to hosting a single Symbiodinium clade ('symbiotic specialists'). We detected at least two Symbiodinium clades (C and D) in at least one sample of all 39 coral species tested; all four Symbiodinium clades were detected in over half (54%) of the 26 symbiotic specialist coral species. Furthermore, on average, 68 per cent of all sampled colonies within a given coral species hosted two or more symbiont clades. We conclude that the ability to associate with multiple symbiont clades is common in scleractinian (stony) corals, and that, in coral-algal symbiosis, 'specificity' and 'flexibility' are relative terms: specificity is rarely absolute. The potential for reef corals to adapt or acclimatize to environmental change via symbiont community shifts may therefore be more phylogenetically widespread than has previously been assumed.     

Effects of smoking and cessation on subclinical arterial disease: a substudy of a randomized controlled trial

Background

The mechanisms by which smoking cessation reduces cardiovascular disease risk are unclear. We evaluated longitudinal changes in carotid intima-media thickness among current smokers enrolled in a prospective, randomized smoking cessation clinical trial.

Methodology/Principal Findings

Subjects were enrolled in a randomized, double-blind, placebo-controlled trial of 5 smoking cessation pharmacotherapies and underwent carotid ultrasonography with carotid intima-media thickness measurement. Subjects were classified as continuously abstinent (biochemically confirmed abstinence at 6 months, 1 year, and 3 years post-quit attempt), intermittently abstinent (reported smoking at one of the three time points), or smoked continuously (reported smoking at all three time points). The primary endpoint was the absolute change (mm) in carotid intima-media thickness (ΔCIMT_max) before randomization and 3 years after the target quit date. Pearson correlations were calculated and multivariable regression models (controlling for baseline CIMT_max and research site) were analyzed. Among 795 subjects (45.2±10.6 years old, 58.5% female), 189 (23.8%) were continuously abstinent, 373 (46.9%) smoked continuously, and 233 (29.3%) were abstinent intermittently. There was a greater increase in carotid intima-media thickness among subjects who were continuously abstinent than among those who smoked continuously (p = 0.020), but not intermittently (p = 0.310). Antihypertensive medication use (p = 0.001) and research site (p<0.001) independently predicted ΔCIMTmax – not smoking status. The greatest increase in carotid intima-media thickness among continuous abstainers was related to increases in body-mass index (p = 0.043).

Conclusions/Significance

Smoking status did not independently predict ΔCIMT_max; increasing body-mass index and antihypertensive medication use were the most important independent predictors. The rapid reduction in cardiovascular disease events observed with smoking cessation is unlikely to be mediated by changes in subclinical atherosclerosis burden.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00332644","term_id":"NCT00332644"}}NCT00332644     

High-throughput karyotyping of human pluripotent stem cells

Genomic integrity of human pluripotent stem cell (hPSC) lines requires routine monitoring. We report here that novel karyotyping assay, utilizing bead-bound bacterial artificial chromosome probes, provides a fast and easy tool for detection of chromosomal abnormalities in hPSC lines. The analysis can be performed from low amounts of DNA isolated from whole cell pools with simple data analysis interface. The method enables routine screening of stem cell lines in a cost-efficient high-throughput manner.