Metagenome skimming of insect specimen pools: potential for comparative genomics

Metagenomic analyses are challenging in metazoans, but high-copy number and repeat regions can be assembled from lowcoverage sequencing by “genome skimming,” which is applied here as a new way of characterizing metagenomes obtained in an ecological or taxonomic context. Illumina shotgun sequencing on two pools of Coleoptera (beetles) of approximately 200 species each were assembled into tens of thousands of scaffolds. Repeated low-coverage sequencing recovered similar scaffold sets consistently, although approximately 70% of scaffolds could not be identified against existing genome databases. Identifiable scaffolds included mitochondrial DNA, conserved sequences with hits to expressed sequence tag and protein databases, and knownrepeatelementsof high and low complexity, includingnumerous copies ofrRNAandhistone genes.Assemblies of histones captured a diversity of gene order and primary sequence in Coleoptera. Scaffolds with similarity to multiple sites in available coleopteran genome sequences for Dendroctonus and Tribolium revealed high specificity of scaffolds to either of these genomes, in particular for high-copy number repeats. Numerous “clusters” of scaffolds mapped to the same genomic site revealed intraand/or intergenomic variation within a metagenome pool. In addition to effect of taxonomic composition of the metagenomes, the number of mapped scaffolds also revealed structural differences between the two reference genomes, although the significance of this striking finding remains unclear. Finally, apparently exogenous sequences were recovered, including potential food plants, fungal pathogens, and bacterial symbionts. The “metagenome skimming” approach is useful for capturing the genomic diversity of poorly studied, species-rich lineages and opens new prospects in environmental genomic

Uncovering trophic interactions in arthropod predators through DNA shotgun-sequencing of gut contents

Characterizing trophic networks is fundamental to many questions in ecology, but this typically requires painstaking efforts, especially to identify the diet of small generalist predators. Several attempts have been devoted to develop suitable molecular tools to determine predatory trophic interactions through gut content analysis, and the challenge has been to achieve simultaneously high taxonomic breadth and resolution. General and practical methods are still needed, preferably independent of PCR amplification of barcodes, to recover a broader range of interactions. Here we applied shotgun-sequencing of the DNA from arthropod predator gut contents, extracted from four common coccinellid and dermapteran predators co-occurring in an agroecosystem in Brazil. By matching unassembled reads against six DNA reference databases obtained from public databases and newly assembled mitogenomes, and filtering for high overlap length and identity, we identified prey and other foreign DNA in the predator guts. Good taxonomic breadth and resolution was achieved (93% of prey identified to species or genus), but with low recovery of matching reads. Two to nine trophic interactions were found for these predators, some of which were only inferred by the presence of parasitoids and components of the microbiome known to be associated with aphid prey. Intraguild predation was also found, including among closely related ladybird species. Uncertainty arises from the lack of comprehensive reference databases and reliance on low numbers of matching reads accentuating the risk of false positives. We discuss caveats and some future prospects that could improve the use of direct DNA shotgun-sequencing to characterize arthropod trophic networks

Efeito do diluidor e da temperatura de congelação sobre o sêmen congelado de ovino da raça Santa Inês.

Objetivou-se verificar a influência do tipo de diluidor e da temperatura sobre motilidade do sêmen ovino. A coleta do sêmen foi efetuada uma vez por semana em cinco ovinos da raça Santa Inês, após feito um pool dos ejaculados e avaliado quanto ao volume, à motilidade, vigor, concentração e diluído no Leite e Tris. As amostras foram envasadas em palhetas de 0,25 ml e congeladas em três temperaturas (- 79o C, -90o C, -120o C) no equipamento TK 3000. Quando atingida a primeira temperatura, um grupo de palhetas foi transferido para o botijão criogênico e assim sucessivamente, para às demais temperaturas testadas. Após 30 dias, as palhetas foram descongeladas e o sêmen avaliado pelo método CASA. Procedeu-se a ANOVA para testar o efeito da temperatura de congelação sobre os diluidores. Para o diluidor leite, a motilidade progressiva e a percentagem de espermatozóide rápidos diferiu significativamente para temperatura de -79o C em relação às de -90o C e -120o C. No diluidor Tris não houve diferença significativa entre as temperaturas de congelação, entretanto foi significativo e superior ao diluidor a base leite em todas as temperaturas testadas. O diluidor Tris e a temperatura de congelação de -79o C mostraram ser o protocolo de congelação mais apropriado para sêmen de carneiros Santa Inês, entretanto estudos utilizando a inseminação artificial precisam ser conduzidos para validar sua qualidade. Abstract:: This study aimed to verify the influence of the temperature and the extender type on the motility of ram semen. The semen was collected a time per week in five ?Santa Inês? ram, after it was made one pool of the ejaculated and evaluated how much to the volume, motility, vigor, concentration and diluted with Milk and Tris.The samples were stored in straw of 0,25 mL to be frozen in three temperatures (-79°C,-90°C,-120°C) employing the TK 3000 equipment. When reached the first temperature, a group of straws was transferred to the cryogenic container and thus successively, for the the others tested temperatures. After 30 days, the straws had been thawed and the semen evaluated for the CASA method. It was used the ANOVA to test the effect of the temperature of freezing on the extenders. For the Milk, the progressive motility and the fast spermatozoid percentage for the temperature of -79°C differed significantly when compared to the temperatures of -90°C and -120°C. In the extender Tris did not have significant difference between the temperatures of freezing, however it was significant and superior to the extender milk in all tested temperatures. The extender Tris and the freezing temperature of -79°C showed to be the more appropriate freezing protocol for ?Santa Inês? ram semen. However more studies using the artificial insemination need to be lead to validate its quality

Efeito da concentração espermática sobre sêmen congelado de carneiros da raça Santa Inês.

Objetivou-se verificar o efeito da concentração final dos espermatozóide de ovinos sobre os parâmetros de motilidade do sêmen congelado. Foram coletados seis ejaculados de cinco carneiros Santa Inês, uma vez por semana feito um pool e avaliado o volume, motilidade, vigor, concentração espermática e, fracionado em três alíquotas para testar diluições diferentes (1000x106, 800x106, 600x106 espermatozóides por mL). As amostras foram envasadas em palhetas de 0,25 mL, congeladas no equipamento TK 3000 e conservadas no botijão criogênico. Decorridos 30 dias foram descongeladas e, o sêmen avaliado pelo método CASA. Procedeu-se a ANOVA para testar o resultado da concentração de espermatozóides sobre os parâmetros de motilidade. A concentração de 600 x 106 sptz/ mL para as variáveis percentagens de espermatozóides móveis, motilidade progressiva, percentagem de espermatozóides de velocidade rápida e média mostrou-se superior a de 800 x 106 sptz /mL e 1000 x 106 sptz /ml. Para a variável velocidade média da trajetória do espermatozóide rápido (VAPR) não foi observada diferença significativa entre as concentrações testadas. Neste estudo, a concentração de 600 x 106 sptz/ ml apresentou a melhor preservação dos parâmetros de motilidade após a congelação, tornandose adequada para o uso na inseminação artificial. No entanto necessita-se de mais estudos in vivo para avaliar a eficiência desta técnica

Spatiotemporal patterns of population in mainland China, 1990 to 2010

According to UN forecasts, global population will increase to over 8 billion by 2025, with much of this anticipated population growth expected in urban areas. In China, the scale of urbanization has, and continues to be, unprecedented in terms of magnitude and rate of change. Since the late 1970s, the percentage of Chinese living in urban areas increased from ~18% to over 50%. To quantify these patterns spatially we use time-invariant or temporally-explicit data, including census data for 1990, 2000, and 2010 in an ensemble prediction model. Resulting multi-temporal, gridded population datasets are unique in terms of granularity and extent, providing fine-scale (~100 m) patterns of population distribution for mainland China. For consistency purposes, the Tibet Autonomous Region, Taiwan, and the islands in the South China Sea were excluded. The statistical model and considerations for temporally comparable maps are described, along with the resulting datasets. Final, mainland China population maps for 1990, 2000, and 2010 are freely available as products from the WorldPop Project website and the WorldPop Dataverse Repository

Comportamento de ovinos confinados e alimentados com torta de mamona destoxificada em substituição ao farelo de soja.

Avaliou-se o comportamento de ovinos confinados e alimentados com níveis de 0, 33, 67 e 100% de substituição do farelo de soja (FS) pela torta de mamona destoxificada (TMD), ao longo de 24 h do quadragésimo quinto dia num delineamento inteiramente casualizado com cinco repetições (ovinos). Estimouse a porcentagem do tempo total de Ingestão de Ração (IR), Ruminação (TR), em ?Outras Atividades? (TA), em Ócio Acordado (OA) e em Ócio Dormindo (OD), dividindo-se o dia em oito períodos (5-8 h; 8-11 h; 11-14 h; 14-17 h; 17-20 h; 20-23 h; 23-2 h; 2-5 h). Não foi observada interação entre níveis de substituição do FS pela TMD para a variável IR. Entretanto, quanto ao período do dia, observou-se maior tempo de IR entre 8-11 h. O TR não foi afetado pelos níveis de substituição do FS pela TMD. Quanto à variável TA, o nível de 67% TMD foi superior àquele de 100%. Quanto às variáveis OA e OD, não foram observados efeitos dos níveis de substituição do FS pela TMD. A TMD não afetou o comportamento dos ovinos, sendo este afetado pelos períodos do dia

The SERTS-97 Rocket Experiment on Study Activity on the Sun: Flight 36.167-GS on 1997 November 18

This paper describes mainly the 1997 version of the Solar EUV Rocket Telescope and Spectrograph (SERTS-97), a scientific experiment that operated on NASA's suborbital rocket flight 36.167-GS. Its function was to study activity on the Sun and to provide a cross calibration for the CDS instrument on the SOHO satellite. The experiment was designed, built, and tested by the Solar Physics Branch of the Laboratory for Astronomy and Solar Physics at the Goddard Space Flight Center (GSFC). Other essential sections of the rocket were built under the management of the Sounding Rockets Program Office. These sections include the electronics, timers, IGN despin, the SPARCS pointing controls, the S-19 flight course correction section, the rocket motors, the telemetry, ORSA, and OGIVE

The geographical distribution and burden of trachoma in Africa.

BACKGROUND: There remains a lack of epidemiological data on the geographical distribution of trachoma to support global mapping and scale up of interventions for the elimination of trachoma. The Global Atlas of Trachoma (GAT) was launched in 2011 to address these needs and provide standardised, updated and accessible maps. This paper uses data included in the GAT to describe the geographical distribution and burden of trachoma in Africa. METHODS: Data assembly used structured searches of published and unpublished literature to identify cross-sectional epidemiological data on the burden of trachoma since 1980. Survey data were abstracted into a standardised database and mapped using geographical information systems (GIS) software. The characteristics of all surveys were summarized by country according to data source, time period, and survey methodology. Estimates of the current population at risk were calculated for each country and stratified by endemicity class. RESULTS: At the time of writing, 1342 records are included in the database representing surveys conducted between 1985 and 2012. These data were provided by direct contact with national control programmes and academic researchers (67%), peer-reviewed publications (17%) and unpublished reports or theses (16%). Prevalence data on active trachoma are available in 29 of the 33 countries in Africa classified as endemic for trachoma, and 1095 (20.6%) districts have representative data collected through population-based prevalence surveys. The highest prevalence of active trachoma and trichiasis remains in the Sahel area of West Africa and Savannah areas of East and Central Africa and an estimated 129.4 million people live in areas of Africa confirmed to be trachoma endemic. CONCLUSION: The Global Atlas of Trachoma provides the most contemporary and comprehensive summary of the burden of trachoma within Africa. The GAT highlights where future mapping is required and provides an important planning tool for scale-up and surveillance of trachoma control

Milder winters in northern Scandinavia may contribute to larger outbreaks of haemorrhagic fever virus

The spread of zoonotic infectious diseases may increase due to climate factors such as temperature, humidity and precipitation. This is also true for hantaviruses, which are globally spread haemorrhagic fever viruses carried by rodents. Hantaviruses are frequently transmitted to humans all over the world and regarded as emerging viral diseases. Climate variations affect the rodent reservoir populations and rodent population peaks coincide with increased number of human cases of hantavirus infections. In northern Sweden, a form of haemorrhagic fever called nephropathia epidemica (NE), caused by the Puumala hantavirus (PUUV) is endemic and during 2006–2007 an unexpected, sudden and large outbreak of NE occurred in this region. The incidence was 313 cases/100,000 inhabitants in the most endemic areas, and from January through March 2007 the outbreak had a dramatic and sudden start with 474 cases in the endemic region alone. The PUUV rodent reservoir is bank voles and immediately before and during the peak of disease outbreak the affected regions experienced extreme climate conditions with a record-breaking warm winter, registering temperatures 6–9°C above normal. No protective snow cover was present before the outbreak and more bank voles than normal came in contact with humans inside or in close to human dwellings. These extreme climate conditions most probably affected the rodent reservoir and are important factors for the severity of the outbreak