mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences.

BACKGROUND: Formation of operational taxonomic units (OTU) is a common approach to data aggregation in microbial ecology studies based on amplification and sequencing of individual gene targets. The de novo assembly of OTU sequences has been recently demonstrated as an alternative to widely used clustering methods, providing robust information from experimental data alone, without any reliance on an external reference database. RESULTS: Here we introduce mPUMA (microbial Profiling Using Metagenomic Assembly, http://mpuma.sourceforge.net), a software package for identification and analysis of protein-coding barcode sequence data. It was developed originally for Cpn60 universal target sequences (also known as GroEL or Hsp60). Using an unattended process that is independent of external reference sequences, mPUMA forms OTUs by DNA sequence assembly and is capable of tracking OTU abundance. mPUMA processes microbial profiles both in terms of the direct DNA sequence as well as in the translated amino acid sequence for protein coding barcodes. By forming OTUs and calculating abundance through an assembly approach, mPUMA is capable of generating inputs for several popular microbiota analysis tools. Using SFF data from sequencing of a synthetic community of Cpn60 sequences derived from the human vaginal microbiome, we demonstrate that mPUMA can faithfully reconstruct all expected OTU sequences and produce compositional profiles consistent with actual community structure. CONCLUSIONS: mPUMA enables analysis of microbial communities while empowering the discovery of novel organisms through OTU assembly

SPECULOOS exoplanet search and its prototype on TRAPPIST

One of the most significant goals of modern science is establishing whether life exists around other suns. The most direct path towards its achievement is the detection and atmospheric characterization of terrestrial exoplanets with potentially habitable surface conditions. The nearest ultracool dwarfs (UCDs), i.e. very-low-mass stars and brown dwarfs with effective temperatures lower than 2700 K, represent a unique opportunity to reach this goal within the next decade. The potential of the transit method for detecting potentially habitable Earth-sized planets around these objects is drastically increased compared to Earth-Sun analogs. Furthermore, only a terrestrial planet transiting a nearby UCD would be amenable for a thorough atmospheric characterization, including the search for possible biosignatures, with near-future facilities such as the James Webb Space Telescope. In this chapter, we first describe the physical properties of UCDs as well as the unique potential they offer for the detection of potentially habitable Earth-sized planets suitable for atmospheric characterization. Then, we present the SPECULOOS ground-based transit survey, that will search for Earth-sized planets transiting the nearest UCDs, as well as its prototype survey on the TRAPPIST telescopes. We conclude by discussing the prospects offered by the recent detection by this prototype survey of a system of seven temperate Earth-sized planets transiting a nearby UCD, TRAPPIST-1.Comment: Submitted as a chapter in the "Handbook of Exoplanets" (editors: H. Deeg & J.A. Belmonte; Section Editor: N. Narita). 16 pages, 4 figure

Neurospora from natural populations: Population genomics insights into the Life history of a model microbial Eukaryote

The ascomycete filamentous fungus Neurospora crassa played a historic role in experimental biology and became a model system for genetic research. Stimulated by a systematic effort to collect wild strains initiated by Stanford geneticist David Perkins, the genus Neurospora has also become a basic model for the study of evolutionary processes, speciation, and population biology. In this chapter, we will first trace the history that brought Neurospora into the era of population genomics. We will then cover the major contributions of population genomic investigations using Neurospora to our understanding of microbial biogeography and speciation, and review recent work using population genomics and genome-wide association mapping that illustrates the unique potential of Neurospora as a model for identifying the genetic basis of (potentially adaptive) phenotypes in filamentous fungi. The advent of population genomics has contributed to firmly establish Neurospora as a complete model system and we hope our review will entice biologists to include Neurospora in their research

Social gradient in the cost of oral pain and related dental service utilisation among South African adults

Background: Oral pain affects people's daily activities and quality of life. The burden of oral pain may vary across socio-economic positions. Currently, little is known about the social gradient in the cost of oral pain among South Africans. This study therefore assessed the social gradient in the cost of oral pain and the related dental service utilisation pattern among South African adults. Methods: Data were obtained from a nationally representative cross-sectional survey of South African adults ?16 year-old (n = 2651) as part of the South African Social Attitudes Survey conducted by the South African Human Sciences Research Council. The survey included demographic data, individual-level socio-economic position (SEP), self-reported oral health status, past six months' oral pain experience and cost. The area-level SEP was obtained from the 2010 General Household Survey (n = 25,653 households) and the 2010/2011Quarterly Labour Force Survey conducted in South Africa. The composite indices used for individual-level SEP (? = 0.76) and area-level SEP (? = 0. 88) were divided into tertiles. Data analysis was done using t-tests and ANOVA. Significance was set at p < 0.05. Results: The prevalence of oral pain among the adult South Africans was 19.4 % (95 % CI = 17.2-21.9). The most commonly reported form of oral pain was 'toothache' (78.9 %). The majority of the wealthiest participants sought care from private dental clinics (64.7 %), or from public dental clinics (19.7 %), while the poorest tended to visit a public dental clinic (45 %) or nurse/general medical practitioner (17.4 %). In the poorest areas, 21 % responded to pain by 'doing nothing'. The individual expenditure for oral pain showed a social gradient from an average of ZAR61.44 spent by those of lowest SEP to ZAR433.83 by the wealthiest (national average ZAR170.92). Average time lost from school/work was two days over the six-month period, but days lost was highest for those living in middle class neighbourhoods (3.41), while those from the richest neighbourhood had lost significantly fewer days from oral pain (0.64). Conclusions: There is a significant social gradient in the burden of oral pain. Improved access to dental care, possibly through carefully planned universal National Health Insurance (NHI), may reduce oral health disparities in South Africa.Scopus 201

Entomological Surveillance of Behavioural Resilience and Resistance in Residual Malaria Vector Populations.

The most potent malaria vectors rely heavily upon human blood so they are vulnerable to attack with insecticide-treated nets (ITNs) and indoor residual spraying (IRS) within houses. Mosquito taxa that can avoid feeding or resting indoors, or by obtaining blood from animals, mediate a growing proportion of the dwindling transmission that persists as ITNs and IRS are scaled up. Increasing frequency of behavioural evasion traits within persisting residual vector systems usually reflect the successful suppression of the most potent and vulnerable vector taxa by IRS or ITNs, rather than their failure. Many of the commonly observed changes in mosquito behavioural patterns following intervention scale-up may well be explained by modified taxonomic composition and expression of phenotypically plastic behavioural preferences, rather than altered innate preferences of individuals or populations. Detailed review of the contemporary evidence base does not yet provide any clear-cut example of true behavioural resistance and is, therefore, consistent with the hypothesis presented. Caution should be exercised before over-interpreting most existing reports of increased frequency of behavioural traits which enable mosquitoes to evade fatal contact with insecticides: this may simply be the result of suppressing the most behaviourally vulnerable of the vector taxa that constituted the original transmission system. Mosquito taxa which have always exhibited such evasive traits may be more accurately described as behaviourally resilient, rather than resistant. Ongoing national or regional entomological monitoring surveys of physiological susceptibility to insecticides should be supplemented with biologically and epidemiologically meaningfully estimates of malaria vector population dynamics and the behavioural phenotypes that determine intervention impact, in order to design, select, evaluate and optimize the implementation of vector control measures

Identifying the most productive breeding sites for malaria mosquitoes in The Gambia

BACKGROUND: Ideally larval control activities should be targeted at sites that generate the most adult vectors, thereby reducing operational costs. Despite the plethora of potential mosquito breeding sites found in the floodplains of the Gambia River, about 150 km from its mouth, during the rainy season, only a small proportion are colonized by anophelines on any day. This study aimed to determine the characteristics of larval habitats most frequently and most densely populated by anopheline larvae and to estimate the numbers of adults produced in different habitats. METHODS: A case-control design was used to identify characteristics of sites with or without mosquitoes. Sites were surveyed for their physical water properties and invertebrate fauna. The characteristics of 83 sites with anopheline larvae (cases) and 75 sites without (controls) were collected between June and November 2005. Weekly adult productivity was estimated with emergence traps in water-bodies commonly containing larvae. RESULTS: The presence of anopheline larvae was associated with high invertebrate diversity (Odds Ratio, OR 11.69, 95% CI 5.61-24.34, p < 0.001), the presence of emergent vegetation (OR 2.83, 95% CI 1.35-5.95, p = 0.006), and algae (at borderline significance; OR 1.87, 95% CI 0.96-3.618, p = 0.065). The density of larvae was reduced in sites that were larger than 100 m in perimeter (OR 0.151; 95% CI 0.060-0.381, p < 0.001), where water was tidal (OR 0.232; 95% CI 0.101-0.533, p = 0.001), vegetation shaded over 25% of the habitat (OR 0.352; 95% CI 0.136-0.911, p = 0.031) and water conductivity was above 2,000 muS/cm (OR 0.458; 95% CI 0.220-0.990, p = 0.048). Pools produced the highest numbers of Anopheles gambiae adults compared with rice fields, floodwater areas close to the edge of the floodplain or close to the river, and stream fringes. Pools were characterized by high water temperature and turbidity, low conductivity, increased presence of algae, and absence of tidal water. CONCLUSION: There are few breeding sites that produce a high number of adult vectors in the middle reaches of the river in The Gambia, whereas those with low productivity are larger in area and can be found throughout the rainy season. Even though risk factors could be identified for the presence and density of larvae and productivity of habitats, the results indicate that anti-larval interventions in this area of The Gambia cannot be targeted in space or time during the rainy season

A dearth of small particles in the transiting material around the white dwarfWD 1145+017

White dwarf WD 1145+017 is orbited by several clouds of dust, possibly emanating from actively disintegrating bodies. These dust clouds reveal themselves through deep, broad, and evolving transits in the star's light curve. Here, we report two epochs of multi-wavelength photometric observations of WD 1145+017, including several filters in the optical, K$_\mathrm{s}$ and 4.5 $\mu$m bands in 2016 and 2017. The observed transit depths are different at these wavelengths. However, after correcting for excess dust emission at K$_\mathrm{s}$ and 4.5 $\mu$m, we find the transit depths for the white dwarf itself are the same at all wavelengths, at least to within the observational uncertainties of $\sim$5%-10%. From this surprising result, and under the assumption of low optical depth dust clouds, we conclude that there is a deficit of small particles (with radii $s \lesssim$ 1.5 $\mu$m) in the transiting material. We propose a model wherein only large particles can survive the high equilibrium temperature environment corresponding to 4.5 hr orbital periods around WD 1145+017, while small particles sublimate rapidly. In addition, we evaluate dust models that are permitted by our measurements of infrared emission

Effects of Irritant Chemicals on Aedes aegypti Resting Behavior: Is There a Simple Shift to Untreated “Safe Sites”?

Aedes aegypti, the primary vector mosquito of dengue virus, typically lives near or inside human dwellings, and feeds preferentially on humans. The control of this mosquito vector remains the most important dengue prevention method. The use of chemicals at levels toxic to mosquitoes is currently the only confirmed effective adult vector control strategy with interventions usually applied following epidemic onset. However, research indicates that sub-lethal chemical approaches to prevent human-vector contact at the house level exist: contact irritancy and spatial repellency. The optimum efficacy of an intervention based on contact irritant actions of chemicals will, however, require full knowledge of variables that will influence vector resting behavior and thereby chemical uptake from treated sources. Here we characterize the resting patterns of female Ae. aegypti on two material types at various dark:light surface area coverage ratios and contrast configurations under chemical-free and treated conditions using a laboratory behavioral assay. Change in resting behavior between baseline and treatment conditions was quantified to determine potential negative effects of untreated surfaces (“safe sites”) when irritant responses are elicited. We show that treatment of preferred resting sites with known irritant compounds do not stimulate mosquitoes to move to safe sites after making contact with treated surfaces

Target product profile choices for intra-domiciliary malaria vector control pesticide products: repel or kill?

BACKGROUND\ud \ud The most common pesticide products for controlling malaria-transmitting mosquitoes combine two distinct modes of action: 1) conventional insecticidal activity which kills mosquitoes exposed to the pesticide and 2) deterrence of mosquitoes away from protected humans. While deterrence enhances personal or household protection of long-lasting insecticidal nets and indoor residual sprays, it may also attenuate or even reverse communal protection if it diverts mosquitoes to non-users rather than killing them outright.\ud \ud METHODS\ud \ud A process-explicit model of malaria transmission is described which captures the sequential interaction between deterrent and toxic actions of vector control pesticides and accounts for the distinctive impacts of toxic activities which kill mosquitoes before or after they have fed upon the occupant of a covered house or sleeping space.\ud \ud RESULTS\ud \ud Increasing deterrency increases personal protection but consistently reduces communal protection because deterrent sub-lethal exposure inevitably reduces the proportion subsequently exposed to higher lethal doses. If the high coverage targets of the World Health Organization are achieved, purely toxic products with no deterrence are predicted to generally provide superior protection to non-users and even users, especially where vectors feed exclusively on humans and a substantial amount of transmission occurs outdoors. Remarkably, this is even the case if that product confers no personal protection and only kills mosquitoes after they have fed.\ud \ud CONCLUSIONS\ud \ud Products with purely mosquito-toxic profiles may, therefore, be preferable for programmes with universal coverage targets, rather than those with equivalent toxicity but which also have higher deterrence. However, if purely mosquito-toxic products confer little personal protection because they do not deter mosquitoes and only kill them after they have fed, then they will require aggressive "catch up" campaigns, with behaviour change communication strategies that emphasize the communal nature of protection, to achieve high coverage rapidly

Plant Products Affect Growth and Digestive Efficiency of Cultured Florida Pompano (Trachinotus carolinus) Fed Compounded Diets

Costs of compounded diets containing fish meal as a primary protein source can be expected to rise as fish meal prices increase in response to static supply and growing demand. Alternatives to fish meal are needed to reduce production costs in many aquaculture enterprises. Some plant proteins are potential replacements for fish meal because of their amino acid composition, lower cost and wide availability. In this study, we measured utilization of soybean meal (SBM) and soy protein concentrate (SPC) by Florida pompano fed compounded diets, to determine the efficacy of these products as fish meal replacements. We also calculated apparent digestibility coefficients (ADCs) for canola meal (CM), corn gluten meal (CGM), and distillers dried grains with solubles (DDGS), following typical methods for digestibility trials. Juvenile Florida pompano were fed fish-meal-free diets containing graded levels of SBM and SPC, and weight gain was compared to a control diet that contained SBM, SPC, and fish meal. Fish fed diets that contained 25–30 percent SBM in combination with 43–39 percent SPC had weight gain equivalent to fish fed the control diet with fish meal, while weight gain of fish fed other soy combinations was significantly less than that of the control group. Apparent crude protein digestibility of CGM was significantly higher than that of DDGS but not significantly different from CM. Apparent energy digestibility of DDGS was significantly lower than CGM but significantly higher than CM. Findings suggested that composition of the reference diet used in a digestibility trial affects the values of calculated ADCs, in addition to the chemical and physical attributes of the test ingredient