Virtual chemical reactions for drug design

Two methods for the fast, fragment-based combinatorial molecule assembly were developed. The software COLIBREE® (Combinatorial Library Breeding) generates candidate structures from scratch, based on stochastic optimization [1]. Result structures of a COLIBREE design run are based on a fixed scaffold and variable linkers and side-chains. Linkers representing virtual chemical reactions and side-chain building blocks obtained from pseudo-retrosynthetic dissection of large compound databases are exchanged during optimization. The process of molecule design employs a discrete version of Particle Swarm Optimization (PSO) [2]. Assembled compounds are scored according to their similarity to known reference ligands. Distance to reference molecules is computed in the space of the topological pharmacophore descriptor CATS [3]. In a case study, the approach was applied to the de novo design of potential peroxisome proliferator-activated receptor (PPAR gamma) selective agonists. In a second approach, we developed the formal grammar Reaction-MQL [4] for the in silico representation and application of chemical reactions. Chemical transformation schemes are defined by functional groups participating in known organic reactions. The substructures are specified by the linear Molecular Query Language (MQL) [5]. The developed software package contains a parser for Reaction-MQL-expressions and enables users to design, test and virtually apply chemical reactions. The program has already been used to create combinatorial libraries for virtual screening studies. It was also applied in fragmentation studies with different sets of retrosynthetic reactions and various compound libraries

Hydrologic Conditions Describe West Nile Virus Risk in Colorado

We examine the relationship between hydrologic variability and the incidence of human disease associated with West Nile virus (WNV; family Flaviviridae, genus Flavivirus) infection (hereafter termed “human WN cases”) in Colorado from 2002 to 2007. We find that local hydrologic conditions, as simulated by the Mosaic hydrology model, are associated with differences in human WN cases. In Colorado’s eastern plains, wetter spring conditions and drier summer conditions predict human WN cases. In Colorado’s western mountains, drier spring and summer conditions weakly predict human WN cases. These findings support two working hypotheses: (1) wet spring conditions increase the abundance of Culex tarsalis vectors in the plains, and (2) dry summer conditions, and respondent irrigational practices during such droughts, favor Cx. pipiens and Cx. tarsalis abundance throughout Colorado. Both of these processes potentially increase the local vector-to-host ratio, favoring WNV amplification among competent avian hosts and bridging to humans

Health effects of smoke from planned burns: a study protocol

Abstract Background Large populations are exposed to smoke from bushfires and planned burns. Studies investigating the association between bushfire smoke and health have typically used hospital or ambulance data and been done retrospectively on large populations. The present study is designed to prospectively assess the association between individual level health outcomes and exposure to smoke from planned burns. Methods/design A prospective cohort study will be conducted during a planned burn season in three locations in Victoria (Australia) involving 50 adult participants who undergo three rounds of cardiorespiratory medical tests, including measurements for lung inflammation, endothelial function, heart rate variability and markers of inflammation. In addition daily symptoms and twice daily lung function are recorded. Outdoor particulate air pollution is continuously measured during the study period in these locations. The data will be analysed using mixed effect models adjusting for confounders. Discussion Planned burns depend on weather conditions and dryness of ‘fuels’ (i.e. forest). It is potentially possible that no favourable conditions occur during the study period. To reduce the risk of this occurring, three separate locations have been identified as having a high likelihood of planned burn smoke exposure during the study period, with the full study being rolled out in two of these three locations. A limitation of this study is exposure misclassification as outdoor measurements will be conducted as a measure for personal exposures. However this misclassification will be reduced as participants are only eligible if they live in close proximity to the monitors

Is remaining indoors an effective way of reducing exposure to fine particulate matter during biomass burning events?

Bushfires, prescribed burns, and residential wood burning are significant sources of fine particles (aerodynamic diameter 2.5) affecting the health and well-being of many communities. Despite the lack of evidence, a common public health recommendation is to remain indoors, assuming that the home provides a protective barrier against ambient PM2.5. The study aimed to assess to what extent houses provide protection against peak concentrations of outdoor PM2.5 and whether remaining indoors is an effective way of reducing exposure to PM2.5. The effectiveness of this strategy was evaluated by conducting simultaneous week-long indoor and outdoor measurements of PM2.5 at 21 residences in regional areas of Victoria, Australia. During smoke plume events, remaining indoors protected residents from peak outdoor PM2.5 concentrations, but the level of protection was highly variable, ranging from 12% to 76%. Housing stock (e.g., age of the house) and ventilation (e.g., having windows/doors open or closed) played a significant role in the infiltration of outdoor PM2.5 indoors. The results also showed that leaving windows and doors closed once the smoke plume abates trapped PM2.5 indoors and increased indoor exposure to PM2.5. Furthermore, for approximately 50% of households, indoor sources such as cooking activities, smoking, and burning candles or incense contributed significantly to indoor PM2.5. Implications: Smoke from biomass burning sources can significantly impact on communities. Remaining indoors with windows and doors closed is a common recommendation by health authorities to minimize exposures to peak concentrations of fine particles during smoke plume events. Findings from this study have shown that the protection from fine particles in biomass burning smoke is highly variable among houses, with information on housing age and ventilation status providing an approximate assessment on the protection of a house. Leaving windows closed once a smoke plume abates traps particles indoors and increases exposures

Male mating biology

Before sterile mass-reared mosquitoes are released in an attempt to control local populations, many facets of male mating biology need to be elucidated. Large knowledge gaps exist in how both sexes meet in space and time, the correlation of male size and mating success and in which arenas matings are successful. Previous failures in mosquito sterile insect technique (SIT) projects have been linked to poor knowledge of local mating behaviours or the selection of deleterious phenotypes during colonisation and long-term mass rearing. Careful selection of mating characteristics must be combined with intensive field trials to ensure phenotypic characters are not antagonistic to longevity, dispersal, or mating behaviours in released males. Success has been achieved, even when colonised vectors were less competitive, due in part to extensive field trials to ensure mating compatibility and effective dispersal. The study of male mating biology in other dipterans has improved the success of operational SIT programmes. Contributing factors include inter-sexual selection, pheromone based attraction, the ability to detect alterations in local mating behaviours, and the effects of long-term colonisation on mating competitiveness. Although great strides have been made in other SIT programmes, this knowledge may not be germane to anophelines, and this has led to a recent increase in research in this area

Nontarget Effects of the Mosquito Adulticide Pyrethrin Applied Aerially During a West Nile Virus Outbreak in an Urban California Environment

In August 2006, a pyrethrin insecticide synergized with piperonyl butoxide (EverGreen Crop Protection EC 60-6, McLaughlin Gormley King Company, Golden Valley, MN) was sprayed in ultralow volumes over the city of Davis, CA, by the Sacramento-Yolo Mosquito and Vector Control District to control mosquitoes transmitting West Nile virus. Concurrently, we evaluated the impact of the insecticide on nontarget arthropods by 1) comparing mortality of treatment and control groups of sentinel arthropods, and 2) measuring the diversity and abundance of dead arthropods found on treatment and control tarps placed on the ground. We found no effect of spraying on nontarget sentinel species including dragonflies (Sympetrum corruptum), spiders (Argiope aurantia), butterflies (Colias eurytheme), and honeybees (Apis mellifera). In contrast, significantly higher diversity and numbers of nontarget arthropods were found on ground tarps placed in sprayed versus unsprayed areas. All of the dead nontarget species were small-bodied arthropods as opposed to the large-bodied sentinels that were not affected. The mortality of sentinel mosquitoes placed at the same sites as the nontarget sentinels and ground tarps ranged from 0% to 100%. Dead mosquitoes were not found on the ground tarps. We conclude that aerial spraying with pyrethrins had no impact on the large-bodied arthropods placed in the spray zone, but did have a measurable impact on a wide range of small-bodied organisms

Comparison of Argentinean Saint Louis Encephalitis Virus Non-Epidemic and Epidemic Strain Infections in an Avian Model

St. Louis encephalitis virus (SLEV, Flavivirus, Flaviviridae) is an emerging mosquito-borne pathogen in South America, with human SLEV encephalitis cases reported in Argentina and Brazil. Genotype III strains of SLEV were isolated from Culex quinquefasciatus mosquitoes in Cordoba, Argentina in 2005, during the largest SLEV outbreak ever reported in South America. The present study tested the hypothesis that the recent, epidemic SLEV strain exhibits greater virulence in birds as compared with a non-epidemic genotype III strain isolated from mosquitoes in Santa Fe Province 27 years earlier. The observed differences in infection parameters between adult House sparrows (Passer domesticus) that were needle-inoculated with either the epidemic or historic SLEV strain were not statistically significant. However, only the House sparrows that were infected with the epidemic strain achieved infectious-level viremia titers sufficient to infect Cx. spp. mosquitoes vectors. Furthermore, the vertebrate reservoir competence index values indicated an approximately 3-fold increase in amplification potential of House sparrows infected with the epidemic strain when pre-existing flavivirus-reactive antibodies were present, suggesting the possibility that antibody-dependent enhancement may increase the risk of avian-amplified transmission of SLEV in South America

Sources and transformations of particle-bound polycyclic aromatic hydrocarbons in Mexico City

Understanding sources, concentrations, and transformations of polycyclic aromatic hydrocarbons (PAHs) in the atmosphere is important because of their potent mutagenicity and carcinogenicity. The measurement of particle-bound PAHs by three different methods during the Mexico City Metropolitan Area field campaign in April 2003 presents a unique opportunity for characterization of these compounds and intercomparison of the methods. The three methods are (1) collection and analysis of bulk samples for time-integrated gas- and particle-phase speciation by gas chromatography/mass spectrometry; (2) aerosol photoionization for fast detection of PAHs on particles' surfaces; and (3) aerosol mass spectrometry for fast analysis of size and chemical composition. This research represents the first time aerosol mass spectrometry has been used to measure ambient PAH concentrations and the first time that fast, real-time methods have been used to quantify PAHs alongside traditional filter-based measurements in an extended field campaign. Speciated PAH measurements suggest that motor vehicles and garbage and wood burning are important sources in Mexico City. The diurnal concentration patterns captured by aerosol photoionization and aerosol mass spectrometry are generally consistent. Ambient concentrations of particle-phase PAHs typically peak at ~110 ng m^-3 during the morning rush hour and rapidly decay due to changes in source activity patterns and dilution as the boundary layer rises, although surface-bound PAH concentrations decay faster. The more rapid decrease in surface versus bulk PAH concentrations during the late morning suggests that freshly emitted combustion-related particles are quickly coated by secondary aerosol material in Mexico City's atmosphere and may also be transformed by heterogeneous reactions

British container breeding mosquitoes: the impact of urbanisation and climate change on community composition and phenology

The proliferation of artificial container habitats in urban areas has benefitted urban adaptable mosquito species globally. In areas where mosquitoes transmit viruses and parasites, it can promote vector population productivity and fuel mosquito-borne disease outbreaks. In Britain, storage of water in garden water butts is increasing, potentially expanding mosquito larval habitats and influencing population dynamics and mosquito-human contact. Here we show that the community composition, abundance and phenology of mosquitoes breeding in experimental water butt containers were influenced by urbanisation. Mosquitoes in urban containers were less species-rich but present in significantly higher densities (100.4±21.3) per container than those in rural containers (77.7±15.1). Urban containers were dominated by Culex pipiens (a potential vector of West Nile Virus [WNV]) and appear to be increasingly exploited by Anopheles plumbeus (a human-biting potential WNV and malaria vector). Culex phenology was influenced by urban land use type, with peaks in larval abundances occurring earlier in urban than rural containers. Among other factors, this was associated with an urban heat island effect which raised urban air and water temperatures by 0.9°C and 1.2°C respectively. Further increases in domestic water storage, particularly in urban areas, in combination with climate changes will likely alter mosquito population dynamics in the UK