A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes

Helitron transposons capture and mobilize gene fragments in eukaryotes, but experimental evidence for their transposition is lacking in the absence of an isolated active element. Here we reconstruct Helraiser, an ancient element from the bat genome, and use this transposon as an experimental tool to unravel the mechanism of Helitron transposition. A hairpin close to the 3'-end of the transposon functions as a transposition terminator. However, the 3'-end can be bypassed by the transposase, resulting in transduction of flanking sequences to new genomic locations. Helraiser transposition generates covalently closed circular intermediates, suggestive of a replicative transposition mechanism, which provides a powerful means to disseminate captured transcriptional regulatory signals across the genome. Indeed, we document the generation of novel transcripts by Helitron promoter capture both experimentally and by transcriptome analysis in bats. Our results provide mechanistic insight into Helitron transposition, and its impact on diversification of gene function by genome shuffling

The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes

Over 95% of all metazoan (animal) species comprise the invertebrates, but very few genomes from these organisms have been sequenced. We have, therefore, formed a Global Invertebrate Genomics Alliance (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site (http://giga.nova.edu) has been launched to facilitate this collaborative venture

The 'evil twin syndrome' in chronic pelvic pain: A systematic review of prevalence studies of bladder pain syndrome and endometriosis

AbstractBackgroundChronic pelvic pain (CPP), a common gynaecological presentation, may be due to bladder pain syndrome (BPS) or the co-existence of BPS and endometriosis, known as the ‘evil twins syndrome’.ObjectivesTo estimate the prevalence of BPS and the co-existence of BPS and endometriosis in women with CPP.Data sourcesWe searched until March 2012: The Cochrane Library, DARE (1997–2012), EMBASE (1980–2012), Medline (1950–2012), PSYCHINFO (1806–2012), Web of knowledge (1900–2012), LILACS (1982–2012) and SIGLE (1990–2012) with no language restrictions. We manually searched through bibliographies and conference proceedings of the International Continence Society.Study selectionObservational studies of women suffering from CPP, who were not pregnant or suffering from cancer, who underwent a laparoscopy and cystoscopy to investigate their symptoms. Study selection, data extraction and quality assessment was performed independently by two reviewers. Statistical analysis was performed to estimate prevalence and confidence intervals (CI).ResultsNine studies were included with 1016 patients with CPP. Study quality and diagnostic assessment varied. The mean prevalence of BPS was 61% (range 11–97%, CI 58–64%, I2 = 98%). The mean prevalence of endometriosis was 70% (range 28–93%, CI 67–73%, I2 = 93%) and co-existing BPS and endometriosis was 48% (range 16–78%, CI 44–51%, I2 = 96%).ConclusionAlmost two thirds of women presenting with CPP have BPS. Large variations in prevalence may be due to variable study selection and quality. Clinicians need to actively investigate patients for BPS, a condition that appears to co-exist with endometriosis

Escarificação mecânica e biológica para a redução da compactação em argissolo franco-arenoso sob plantio direto Mechanical and biological chiseling to reduce compaction of a sandy loam alfisol under no-tillage

O manejo influi nas propriedades físicas no campo, alterando a dinâmica do ar, da água e de solutos no solo. Propriedades físicas em sistemas de manejo conservacionista do solo foram avaliadas em um Argissolo Vermelho-Amarelo distrófico arênico (Typic Hapludalf) de textura franco-arenosa no horizonte A. Os tratamentos foram estabelecidos em solo com histórico de 10 anos de plantio direto, a saber: soja em sistema plantio direto; soja em solo escarificado; crotalária em cultivo mínimo e solo descoberto sem preparo. Foram determinadas: a resistência mecânica à penetração; a densidade do solo; a porosidade total; a distribuição do tamanho de poros; a condutividade hidráulica do solo saturado e não saturado; a infiltração de água no solo pelos métodos de anéis concêntricos e sob chuva natural; a variação da umidade volumétrica do solo durante o ciclo das culturas e a curva característica de água no solo. Observou-se que a resistência mecânica à penetração (RP) foi máxima na camada de 0,075 m, nos tratamentos sem preparo do solo, enquanto, no solo escarificado (Esc-soja), a RP máxima ocorreu em maior profundidade (0,175 m). A mobilização subsuperficial (escarificação) e a superficial (discagem e semeadura) do solo não se refletiram em redução na densidade do solo (Ds). O solo sob plantio direto de soja apresentou maior volume de macroporos que o solo sob cultivo de crotalária e descoberto, na profundidade 0,02 a 0,05 m, favorecendo a maior condutividade hidráulica do solo saturado e a menor retenção de água no solo em situação de déficit hídrico. Dentre as propriedades físico-mecânicas analisadas, a RP mostrou-se mais sensível em detectar a compactação do que a Ds e porosidades, especialmente para camadas de solo pouco espessas. A eficácia da ruptura da camada compactada do solo depende da propriedade hídrica ou mecânica do solo usada como indicadora. Usando a condutividade hidráulica do solo saturado, em médio prazo, a "escarificação biológica" (CM-crot) mostrou-se mais eficaz na ruptura da camada compactada e estabelecimento de poros condutores de água do que a escarificação mecânica (Esc-soja) do solo. Em contrapartida, se o indicador for a RP, o resultado é inverso. Assim, a propriedade hídrica ou mecânica do solo a ser usada como indicadora para a avaliação da eficácia da ruptura da camada compactada do solo depende do processo físico priorizado: a infiltração e redistribuição de água ou a penetração e crescimento de raízes.<br>Soil management alters the physical soil properties and changes the soil air, water, and solute dynamics. Physical soil properties as affected by conservationist soil management systems were studied in a sandy loam Typic Hapludalf. The treatments were established on a soil that has been under no-tillage for 10 years, and consisted of: no-tillage soybeans, chisel tillage soybeans, reduced tillage Crotalaria, and bare soil without tillage. The evaluated soil properties were soil penetration resistance, bulk density, porosity, pore size distribution, saturated and unsaturated hydraulic conductivity, water infiltration using concentric rings or natural rainfall, variation of the volumetric soil moisture throughout the cropping cycle, and water retention curve. Soil penetration resistance (PR) was highest at 0.075 m and 0.175 m depth in no-tillage and chiseled soil, respectively. Soil subsurface mobilization with chiseling and surface mobilization due to disking and sowing did not influence the bulk density (BD) after the crop harvest. No-till soil under soybean crop had greater macroporosity than reduced tillage crotalaria and bare soil at 0.02 to 0.05 m depth, resulting in a greater saturated hydraulic conductivity and lower water retention during periods of low water availability. Among the analyzed soil physical-mechanical properties, PR seemed to be more sensitive to detect soil compaction than BD or porosities, particularly for thinner soil layers. The effectiveness in rupturing compacted soil depended on the hydraulic or mechanical soil property used as indicator. When using K(thetas) as indicator, in the medium term (4.5 months), "biological chiseling" by Crotalaria roots was more efficient at ameliorating soil compaction and establishing a network of conductive pores compared to mechanical chiseling. However, inverse results were observed when PR was used as indicator. Thus, the choice of a soil physical property as indicator to evaluate the effectiveness of compaction reduction depends on which physical process is considered more important: water infiltration and redistribution or root penetration and growth