Antimalarial 4(1H)-pyridones bind to the Qisite of cytochromebc1

Cytochrome bc1 is a proven drug target in the prevention and treatment of malaria. The rise in drug-resistant strains of Plasmodium falciparum, the organism responsible for malaria, has generated a global effort in designing new classes of drugs. Much of the design/redesign work on overcoming this resistance has been focused on compounds that are presumed to bind the Qo site (one of two potential binding sites within cytochrome bc1) using the known crystal structure of this large membrane-bound macromolecular complex via in silico modeling. Cocrystallization of the cytochrome bc1 complex with the 4(1H)-pyridone class of inhibitors, GSK932121 and GW844520, that have been shown to be potent antimalarial agents in vivo, revealed that these inhibitors do not bind at the Qo site but bind at the Qi site. The discovery that these compounds bind at the Qi site may provide a molecular explanation for the cardiotoxicity and eventual failure of GSK932121 in phase-1 clinical trial and highlight the need for direct experimental observation of a compound bound to a target site before chemical optimization and development for clinical trials. The binding of the 4(1H)-pyridone class of inhibitors to Qi also explains the ability of this class to overcome parasite Qo-based atovaquone resistance and provides critical structural information for future design of new selective compounds with improved safety profiles

Using indirect methods to constrain symbiotic nitrogen fixation rates : a case study from an Amazonian rain forest

© The Authors 2009. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Biogeochemistry 99 (2010): 1-13, doi:10.1007/s10533-009-9392-y.Human activities have profoundly altered the global nitrogen (N) cycle. Increases in anthropogenic N have had multiple effects on the atmosphere, on terrestrial, freshwater and marine ecosystems, and even on human health. Unfortunately, methodological limitations challenge our ability to directly measure natural N inputs via biological N fixation (BNF)—the largest natural source of new N to ecosystems. This confounds efforts to quantify the extent of anthropogenic perturbation to the N cycle. To address this gap, we used a pair of indirect methods—analytical modeling and N balance—to generate independent estimates of BNF in a presumed hotspot of N fixation, a tropical rain forest site in central Rondônia in the Brazilian Amazon Basin. Our objectives were to attempt to constrain symbiotic N fixation rates in this site using indirect methods, and to assess strengths and weaknesses of this approach by looking for areas of convergence and disagreement between the estimates. This approach yielded two remarkably similar estimates of N fixation. However, when compared to a previously published bottom-up estimate, our analysis indicated much lower N inputs via symbiotic BNF in the Rondônia site than has been suggested for the tropics as a whole. This discrepancy may reflect errors associated with extrapolating bottom-up fluxes from plot-scale measures, those resulting from the indirect analyses, and/or the relatively low abundance of legumes at the Rondônia site. While indirect methods have some limitations, we suggest that until the technological challenges of directly measuring N fixation are overcome, integrated approaches that employ a combination of model-generated and empirically-derived data offer a promising way of constraining N inputs via BNF in natural ecosystems.We acknowledge and are grateful for financial support from the Andrew W. Mellon Foundation (C.C. and B.H.), the National Science Foundation (NSF DEB-0515744 to C.C. and A.T. and DEB-0315656 to C.N.), and the NASA LBA Program (NCC5-285 to C.N.)

Student responses to the introduction of case-based learning and practical activities into a theoretical obstetrics and gynaecology teaching programme

BACKGROUND: The fourth-year Obstetrics and Gynaecology course at our institution had previously been taught using theory classes alone. A new teaching model was introduced to provide a better link with professional practice. We wished to evaluate the impact of the introduction of case discussions and other practical activities upon students' perceptions of the learning process. METHODS: Small-group discussions of cases and practical activities were introduced for the teaching of a fourth-year class in 2003 (Group II; 113 students). Comparisons were made with the fourth-year class of 2002 (Group I; 108 students), from before the new programme was introduced. Students were asked to rate their satisfaction with various elements of the teaching programme. Statistical differences in their ratings were analysed using the chi-square and Bonferroni tests. RESULTS: Group II gave higher ratings to the clarity of theory classes and lecturers' teaching abilities (p < 0.05) and lecturers' punctuality (p < 0.001) than did Group I. Group II had greater belief that the knowledge assessment tests were useful (p < 0.001) and that their understanding of the subject was good (p < 0.001) than did Group I. Group II gave a higher overall rating to the course (p < 0.05) than did Group I. However, there was no difference in the groups' assessments of the use made of the timetabled hours available for the subject or lecturers' concern for students' learning. CONCLUSIONS: Students were very receptive to the new teaching model

Runoff sources and land cover change in the Amazon : an end-member mixing analysis from small watersheds

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Biogeochemistry 105 (2011): 7-18, doi:10.1007/s10533-011-9597-8.The flowpaths by which water moves from watersheds to streams has important consequences for the runoff dynamics and biogeochemistry of surface waters in the Amazon Basin. The clearing of Amazon forest to cattle pasture has the potential to change runoff sources to streams by shifting runoff to more surficial flow pathways. We applied end member mixing analysis (EMMA) to ten small watersheds throughout the Amazon in which solute composition of streamwater and groundwater, overland flow, soil solution, throughfall and rainwater were measured, largely as part of the Large-Scale Biosphere-Atmosphere Experiment in Amazonia. We found a range in the extent to which streamwater samples fell within the mixing space determined by potential flowpath end members, suggesting that some water sources to streams were not sampled. The contribution of overland flow as a source of stream flow was greater in pasture watersheds than in forest watersheds of comparable size. Increases in overland flow contribution to pasture streams ranged in some cases from 0% in forest to 27 to 28% in pasture and were broadly consistent with results from hydrometric sampling of Amazon forest and pasture watersheds that indicate 17- to 18-fold increase in the overland flow contribution to stream flow in pastures. In forest, overland flow was an important contribution to stream flow (45 to 57%) in ephemeral streams where flows were dominated by stormflow. Overland flow contribution to stream flow decreased in importance with increasing watershed area, from 21 to 57% in forest and 60 to 89% in pasture watersheds 100 ha. Soil solution contributions to stream flow were similar across watershed area and groundwater inputs generally increased in proportion to decreases in overland flow. Application of EMMA across multiple watersheds indicated patterns across gradients of stream size and land cover that were consistent with patterns determined by detailed hydrometric sampling.This work was supported by National Science Foundation (DEB-0315656, DEB-0640661), the NASA LBA Program (NCC5-686, NCC5-69, NCC5-705, NNG066E88A) and by grants from Brazilian agencies FAPESP (03/13172-2) and CNPq (20199/2005-5)

Prevalence of Disorders Recorded in Dogs Attending Primary-Care Veterinary Practices in England

Purebred dog health is thought to be compromised by an increasing occurence of inherited diseases but inadequate prevalence data on common disorders have hampered efforts to prioritise health reforms. Analysis of primary veterinary practice clinical data has been proposed for reliable estimation of disorder prevalence in dogs. Electronic patient record (EPR) data were collected on 148,741 dogs attending 93 clinics across central and south-eastern England. Analysis in detail of a random sample of EPRs relating to 3,884 dogs from 89 clinics identified the most frequently recorded disorders as otitis externa (prevalence 10.2%, 95% CI: 9.1-11.3), periodontal disease (9.3%, 95% CI: 8.3-10.3) and anal sac impaction (7.1%, 95% CI: 6.1-8.1). Using syndromic classification, the most prevalent body location affected was the head-and-neck (32.8%, 95% CI: 30.7-34.9), the most prevalent organ system affected was the integument (36.3%, 95% CI: 33.9-38.6) and the most prevalent pathophysiologic process diagnosed was inflammation (32.1%, 95% CI: 29.8-34.3). Among the twenty most-frequently recorded disorders, purebred dogs had a significantly higher prevalence compared with crossbreds for three: otitis externa (P = 0.001), obesity (P = 0.006) and skin mass lesion (P = 0.033), and popular breeds differed significantly from each other in their prevalence for five: periodontal disease (P = 0.002), overgrown nails (P = 0.004), degenerative joint disease (P = 0.005), obesity (P = 0.001) and lipoma (P = 0.003). These results fill a crucial data gap in disorder prevalence information and assist with disorder prioritisation. The results suggest that, for maximal impact, breeding reforms should target commonly-diagnosed complex disorders that are amenable to genetic improvement and should place special focus on at-risk breeds. Future studies evaluating disorder severity and duration will augment the usefulness of the disorder prevalence information reported herein

Action potentials in abscisic acid-deficient tomato mutant generated spontaneously and evoked by electrical stimulation

Action potentials generated spontaneously (SAPs) and evoked by electrical stimulation (APs) in tomato plants (Solanum lycopersicum L.) cv. Micro-Tom ABA-deficient mutants (sitiens—MTsit) and its wild type (MTwt) were characterized by continuous monitoring of electrical activity for 66 h and by application of an electrical stimulation supplied extracellularly. MTsit generated SAPs which spread along the stem, including petioles and roots with an amplitude of 44.6 ± 4.4 mV, half-time (t½) of 33.1 ± 2.9 s and velocity of 5.4 ± 1.0 cm min−1. Amplitude and velocity were 43 and 108 % higher in MTsit than in MTwt, respectively. The largest number of SAPs was registered in the early morning in both genotypes. MTsit was less responsive to electrical stimuli. The excitation threshold and the refractory period were greater in MTsit than in MTwt. After current application, APs were generated in the MTwt with 21.2 ± 2.4 mV amplitude and propagated with 5.6 ± 0.5 cm min−1 velocity. Lower intensity stimuli did not trigger APs in these plants. In MTsit APs were measured with amplitude of 26.8 ± 4.8 mV and propagated with velocity of 8.5 ± 0.1 cm min−1

Observational and Physical Classification of Supernovae

This chapter describes the current classification scheme of supernovae (SNe). This scheme has evolved over many decades and now includes numerous SN Types and sub-types. Many of these are universally recognized, while there are controversies regarding the definitions, membership and even the names of some sub-classes; we will try to review here the commonly-used nomenclature, noting the main variants when possible. SN Types are defined according to observational properties; mostly visible-light spectra near maximum light, as well as according to their photometric properties. However, a long-term goal of SN classification is to associate observationally-defined classes with specific physical explosive phenomena. We show here that this aspiration is now finally coming to fruition, and we establish the SN classification scheme upon direct observational evidence connecting SN groups with specific progenitor stars. Observationally, the broad class of Type II SNe contains objects showing strong spectroscopic signatures of hydrogen, while objects lacking such signatures are of Type I, which is further divided to numerous subclasses. Recently a class of super-luminous SNe (SLSNe, typically 10 times more luminous than standard events) has been identified, and it is discussed. We end this chapter by briefly describing a proposed alternative classification scheme that is inspired by the stellar classification system. This system presents our emerging physical understanding of SN explosions, while clearly separating robust observational properties from physical inferences that can be debated. This new system is quantitative, and naturally deals with events distributed along a continuum, rather than being strictly divided into discrete classes. Thus, it may be more suitable to the coming era where SN numbers will quickly expand from a few thousands to millions of events.Comment: Extended final draft of a chapter in the "SN Handbook". Comments most welcom

Estradiol inhibits the effects of extracellular ATP in human sperm by a non genomic mechanism of action

Steroid hormones, beside their classical genomic mechanism of action, exert rapid, non genomic effects in different cell types. These effects are mediated by still poorly characterized plasma membrane receptors that appear to be distinct from the classic intracellular receptors. In the present study we evaluated the non genomic effects of estradiol (17βE2) in human sperm and its effects on sperm stimulation by extracellular ATP, a potent activator of sperm acrosome reaction. In human sperm 17βE2 induced a rapid increase of intracellular calcium (Ca2+) concentrations dependent on an influx of Ca2+ from the extracellular medium. The monitoring of the plasma membrane potential variations induced by 17βE2 showed that this steroid induces a rapid plasma membrane hyperpolarization that was dependent on the presence of Ca2+ in the extracellular medium since it was absent in Ca2+ free-medium. When sperm were pre-incubated in the presence of the K+ channel inhibitor tetra-ethylammonium, the 17βE2 induced plasma membrane hyperpolarization was blunted suggesting the involvement of K+ channels in the hyperpolarizing effects of 17βE2. Extracellular ATP induced a rapid plasma membrane depolarization followed by acrosome reaction. Sperm pre-incubation with 17βE2 inhibited the effects of extracellular ATP on sperm plasma membrane potential variations and acrosome reaction. The effects of 17βE2 were specific since its inactive steroisomer 17αE2 was inactive. Furthermore the effects of 17βE2 were not inhibited by tamoxifen, an antagonist of the classic 17βE2 intracellular receptor

Seasonal drought limits tree species across the Neotropics

AcceptedArticle in Press© 2016 Nordic Society Oikos.Within the tropics, the species richness of tree communities is strongly and positively associated with precipitation. Previous research has suggested that this macroecological pattern is driven by the negative effect of water-stress on the physiological processes of most tree species. This implies that the range limits of taxa are defined by their ability to occur under dry conditions, and thus in terms of species distributions predicts a nested pattern of taxa distribution from wet to dry areas. However, this 'dry-tolerance' hypothesis has yet to be adequately tested at large spatial and taxonomic scales. Here, using a dataset of 531 inventory plots of closed canopy forest distributed across the western Neotropics we investigated how precipitation, evaluated both as mean annual precipitation and as the maximum climatological water deficit, influences the distribution of tropical tree species, genera and families. We find that the distributions of tree taxa are indeed nested along precipitation gradients in the western Neotropics. Taxa tolerant to seasonal drought are disproportionally widespread across the precipitation gradient, with most reaching even the wettest climates sampled; however, most taxa analysed are restricted to wet areas. Our results suggest that the 'dry tolerance' hypothesis has broad applicability in the world's most species-rich forests. In addition, the large number of species restricted to wetter conditions strongly indicates that an increased frequency of drought could severely threaten biodiversity in this region. Overall, this study establishes a baseline for exploring how tropical forest tree composition may change in response to current and future environmental changes in this region.This paper is a product of the RAINFOR and ATDN networks and of ForestPlots.net researchers (http://www.forestplots.net). RAINFOR and ForestPlots have been supported by a Gordon and Betty Moore Foundation grant, the European Union’s Seventh Framework Programme (283080, ‘GEOCARBON’; 282664, ‘AMAZALERT’); European Research Council (ERC) grant ‘Tropical Forests in the Changing Earth System’ (T-FORCES), and Natural Environment Research Council (NERC) Urgency Grant and NERC Consortium Grants ‘AMAZONICA’ (NE/F005806/1) and ‘TROBIT’ (NE/D005590/1). Additional funding for fieldwork was provided by Tropical Ecology Assessment and Monitoring (TEAM) Network, a collaboration among Conservation International, the Missouri Botanical Garden, the Smithsonian Institution, and the Wildlife Conservation Society. A.E.M. receives a PhD scholarship from the T-FORCES ERC grant. O.L.P. is supported by an ERC Advanced Grant and a Royal Society Wolfson Research Merit Award. We thank Jon J. Lloyd, Chronis Tzedakis, David Galbraith, and two anonymous reviewers for helpful comments and Dylan Young for helping with the analyses. This study would not be possible without the extensive contributions of numerous field assistants and rural communities in the Neotropical forests. Alfredo Alarcón, Patricia Alvarez Loayza, Plínio Barbosa Camargo, Juan Carlos Licona, Alvaro Cogollo, Massiel Corrales Medina, Jose Daniel Soto, Gloria Gutierrez, Nestor Jaramillo Jarama, Laura Jessica Viscarra, Irina Mendoza Polo, Alexander Parada Gutierrez, Guido Pardo, Lourens Poorter, Adriana Prieto, Freddy Ramirez Arevalo, Agustín Rudas, Rebeca Sibler and Javier Silva Espejo additionally contributed data to this study though their RAINFOR participations. We further thank those colleagues no longer with us, Jean Pierre Veillon, Samuel Almeida, Sandra Patiño and Raimundo Saraiva. Many data come from Alwyn Gentry, whose example has inspired new generations to investigate the diversity of the Neotropics

Long-term decline of the Amazon carbon sink

Atmospheric carbon dioxide records indicate that the land surface has acted as a strong global carbon sink over recent decades1, 2, with a substantial fraction of this sink probably located in the tropics3, particularly in the Amazon4. Nevertheless, it is unclear how the terrestrial carbon sink will evolve as climate and atmospheric composition continue to change. Here we analyse the historical evolution of the biomass dynamics of the Amazon rainforest over three decades using a distributed network of 321 plots. While this analysis confirms that Amazon forests have acted as a long-term net biomass sink, we find a long-term decreasing trend of carbon accumulation. Rates of net increase in above-ground biomass declined by one-third during the past decade compared to the 1990s. This is a consequence of growth rate increases levelling off recently, while biomass mortality persistently increased throughout, leading to a shortening of carbon residence times. Potential drivers for the mortality increase include greater climate variability, and feedbacks of faster growth on mortality, resulting in shortened tree longevity5. The observed decline of the Amazon sink diverges markedly from the recent increase in terrestrial carbon uptake at the global scale1, 2, and is contrary to expectations based on models6