RetrOryza: a database of the rice LTR-retrotransposons

Long terminal repeat (LTR)-retrotransposons comprise a significant portion of the rice genome. Their complete characterization is thus necessary if the sequenced genome is to be annotated correctly. In addition, because LTR-retrotransposons can influence the expression of neighboring genes, the complete identification of these elements in the rice genome is essential in order to study their putative functional interactions with the plant genes. The aims of the database are to (i) Assemble a comprehensive dataset of LTR-retrotransposons that includes not only abundant elements, but also low copy number elements. (ii) Provide an interface to efficiently access the resources stored in the database. This interface should also allow the community to annotate these elements. (iii) Provide a means for identifying LTR-retrotransposons inserted near genes. Here we present the results, where 242 complete LTR-retrotransposons have been structurally and functionally annotated. A web interface to the database has been made available (), through which the user can annotate a sequence or search for LTR-retrotransposons in the neighborhood of a gene of interest

From functional diversity to human well-being: A conceptual framework for agroecosystem sustainability

[EN] CONTEXT: Agricultural intensification contributes to global food security and well-being by supplying the food demand of a growing human population. However, ongoing land-use change and intensification seriously affect the abundance, diversity and distribution of species, besides many other impacts, thereby threatening the functioning of ecosystems worldwide. Despite the accumulating evidence that the current agricultural model is unsustainable, we are far from understanding the consequences of functional diversity loss for functioning and ecosystem service supply and the potential long-term threats to food security and human well-being. OBJECTIVE: In this review, we propose a conceptual framework to understand the relationships between functional diversity and human well-being that also considers agroecosystem health. To this end, we identify the most commonly assumed relationships linking functional diversity to regulating and provisioning agroecosystem services and their importance for human well-being, emphasising the most serious knowledge gaps in the in-dividual pathways of the conceptual framework. METHODS: A consortium formed by an international panel of experts from different disciplines including functional diversity, ecosystem services and human health compiled 275 articles. Members of the consortium proposed literature to exemplify each specific aspect of the conceptual framework in the text, in accordance with his/her field of expertise. The guideline for all experts was to focus mostly in current literature (38% of the references are from the last 5 years and 66% from the last decade), with special interest in reviews and synthesis articles (42% of the references), as well as meta-analyses and global studies (10% of the references). RESULTS AND CONCLUSIONS: The factors that influence agroecosystem health are extremely complex, involving both services and disservices related to land-use management and environmental conditions. The global human population needs sustainable and resilient agroecosystems and a concerted effort is needed to fundamentally redesign agricultural practices to feed the growing human population without further jeopardising the quality of life for future generations. We highlight the potential effects of land-use change and ecological intensification on the functional diversity of plant and animal communities, and the resulting consequences for ecosystem services and ultimately human health. SIGNIFICANCE: The resulting conceptual model is developed for researchers as well as policy makers high- lighting the need for a holistic approach to understand diversity impacts on human well-being. Finally, we document a major knowledge gap due to the lack of any studies focusing on the full pathway from diversity to human well-being.S

Evaluation of adjunctive HPV testing by Hybrid Capture II(® )in women with minor cytological abnormalities for the diagnosis of CIN2/3 and cost comparison with colposcopy

BACKGROUND: As a proportion of high grade cervical intraepithelial neoplasia (CIN2/3) are associated with equivocal cervical smears, which show borderline or mild dyskaryosis, follow up with repeat smears, colposcopy and biopsy is required. Since infection with oncogenic Human Papilloma Virus (HR HPV) has been found to be associated with the development of cervical cancer, HRHPV testing appears to be an alternative. OBJECTIVE: The present study assesses if HRHPV testing can predict CIN2/3 in women referred for mild dyskaryosis and borderline cytological changes in an health authority with a referral policy to colposcopy after one single mild dyskaryotic Pap smear. STUDY DESIGN: The HPV DNA Hybrid Capture II (Digene/Abbott, Maidenhead) was evaluated on 110 consenting women with mild dyskaryosis and 23 women with persistent borderline changes, who were referred for colposcopy between May and November 2001. A cost comparison between two referral policies was performed. RESULTS: CIN2/3 was diagnosed histologically in 30 of 133 women (22%) with minor cytological abnormalities. As the Receiver Operator Characteristics plot suggested a cut-off of 3 pg/ml the HRHPV HCII was evaluated at 3 RLU (relative light units) and at the manufacturer's recommendation of 1 RLU. At both cut-offs sensitivity and negative predictive value were high at 97%. Specificity was low at 37% at a cut-off of 1 pg/ml and 46% at a cut-off of 3 RLU. To remain cost neutral in comparison to immediate colposcopy the costs for one HR HPV HC II must not exceed £34.37 per test at a cut off of 3 pg/ml. CONCLUSION: The negative likelihood ratio (NLR) was of good diagnostic value with 0.089 at 1 RLU and 0.072 at 3 RLU, which reduces the post-test probability for CIN2/3 to 2% in this population. Women with minor cytological disorders can be excluded from colposcopy on a negative HR HPV result. Specificity can be improved by restricting HR HPV testing to women with persistent borderline cytological changes or to women over 30 years

Is IP-10 a Better Biomarker for Active and Latent Tuberculosis in Children than IFNγ?

Background: The blood based interferon-gamma release assays (IGRA) for the diagnosis of tuberculosis do not discriminate between active TB disease and latent TB infection (LTBI). The search for distinguishing biomarkers therefore continues, as the accurate diagnosis of tuberculosis is particularly challenging in children. IFN-c-inducible protein 10 (IP-10/CXCL10) has recently been evaluated as a marker for active TB in adults with promising results. Aim: To investigate this new biomarker for active TB and LTBI in paediatrics. Method: We measured IP-10 levels using ELISA in supernatants of whole blood samples stimulated with TB-specificantigens and negative control antigen. Results: IP-10 is produced in high levels following mycobacterial antigen stimulation in active TB (n = 17) and LTBI (n = 16) compared to controls (n = 16) and to IFN-c. The baseline levels of IP-10 are increased in active TB and in LTBI, but there is no significant difference of stimulated levels of IP-10 between active TB and LTBI. Conclusions: IP-10 is a biomarker for tuberculosis in children. However like IFNc, IP-10 also does not distinguish between active TB and LTBI

Jack-of-all-trades effects drive biodiversity-ecosystem multifunctionality relationships in European forests.

There is considerable evidence that biodiversity promotes multiple ecosystem functions (multifunctionality), thus ensuring the delivery of ecosystem services important for human well-being. However, the mechanisms underlying this relationship are poorly understood, especially in natural ecosystems. We develop a novel approach to partition biodiversity effects on multifunctionality into three mechanisms and apply this to European forest data. We show that throughout Europe, tree diversity is positively related with multifunctionality when moderate levels of functioning are required, but negatively when very high function levels are desired. For two well-known mechanisms, 'complementarity' and 'selection', we detect only minor effects on multifunctionality. Instead a third, so far overlooked mechanism, the 'jack-of-all-trades' effect, caused by the averaging of individual species effects on function, drives observed patterns. Simulations demonstrate that jack-of-all-trades effects occur whenever species effects on different functions are not perfectly correlated, meaning they may contribute to diversity-multifunctionality relationships in many of the world's ecosystems.The research leading to these results received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 265171.This is the final version of the article. It first appeared from Nature Publishing Group via http://dx.doi.org/10.1038/ncomms1110

Biotic homogenization can decrease landscape-scale forest multifunctionality.

Many experiments have shown that local biodiversity loss impairs the ability of ecosystems to maintain multiple ecosystem functions at high levels (multifunctionality). In contrast, the role of biodiversity in driving ecosystem multifunctionality at landscape scales remains unresolved. We used a comprehensive pan-European dataset, including 16 ecosystem functions measured in 209 forest plots across six European countries, and performed simulations to investigate how local plot-scale richness of tree species (α-diversity) and their turnover between plots (β-diversity) are related to landscape-scale multifunctionality. After accounting for variation in environmental conditions, we found that relationships between α-diversity and landscape-scale multifunctionality varied from positive to negative depending on the multifunctionality metric used. In contrast, when significant, relationships between β-diversity and landscape-scale multifunctionality were always positive, because a high spatial turnover in species composition was closely related to a high spatial turnover in functions that were supported at high levels. Our findings have major implications for forest management and indicate that biotic homogenization can have previously unrecognized and negative consequences for large-scale ecosystem multifunctionality.We thank the Hainich National Park administration as well as Felix Berthold and Carsten Beinhoff for support of this study and Gerald Kaendler and the Johann Heinrich von Thünen-Institut for providing access to the German National Forest Inventory data. The research leading to these results received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under Grant Agreement 265171.This is the final version of the article. It first appeared from the National Academy of Sciences via https://doi.org//10.1073/pnas.151790311

Better peacekeepers, better protection? Troop quality of United Nations peace operations and violence against civilians

Why do similarly sized peacekeeping missions vary in their effectiveness to protect civilians in conflicts? We argue that peace operations with a large share of troops from countries with high-quality militaries are better able to deter violence from state and non-state actors, create buffer zones within conflict areas, can better reach remote locations, and have superior capabilities—including diplomatic pressure by troop contributing countries—to monitor the implementation of peace agreements. These operational advantages enable them to better protect civilians. Combining data from military expenditures of troop contributing countries together with monthly data on the composition of peace operations, we create a proxy indicator for the average troop quality of UN PKOs. Statistical evidence from an extended sample of conflicts in Africa and Asia between 1991 and 2010 supports our argument

Patterns of Sequence Divergence and Evolution of the S1 Orthologous Regions between Asian and African Cultivated Rice Species

A strong postzygotic reproductive barrier separates the recently diverged Asian and African cultivated rice species, Oryza sativa and O. glaberrima. Recently a model of genetic incompatibilities between three adjacent loci: S1A, S1 and S1B (called together the S1 regions) interacting epistatically, was postulated to cause the allelic elimination of female gametes in interspecific hybrids. Two candidate factors for the S1 locus (including a putative F-box gene) were proposed, but candidates for S1A and S1B remained undetermined. Here, to better understand the basis of the evolution of regions involved in reproductive isolation, we studied the genic and structural changes accumulated in the S1 regions between orthologous sequences. First, we established an 813 kb genomic sequence in O. glaberrima, covering completely the S1A, S1 and the majority of the S1B regions, and compared it with the orthologous regions of O. sativa. An overall strong structural conservation was observed, with the exception of three isolated regions of disturbed collinearity: (1) a local invasion of transposable elements around a putative F-box gene within S1, (2) the multiple duplication and subsequent divergence of the same F-box gene within S1A, (3) an interspecific chromosomal inversion in S1B, which restricts recombination in our O. sativa×O. glaberrima crosses. Beside these few structural variations, a uniform conservative pattern of coding sequence divergence was found all along the S1 regions. Hence, the S1 regions have undergone no drastic variation in their recent divergence and evolution between O. sativa and O. glaberrima, suggesting that a small accumulation of genic changes, following a Bateson-Dobzhansky-Muller (BDM) model, might be involved in the establishment of the sterility barrier. In this context, genetic incompatibilities involving the duplicated F-box genes as putative candidates, and a possible strengthening step involving the chromosomal inversion might participate to the reproductive barrier between Asian and African rice species

How genomics can help biodiversity conservation

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.info:eu-repo/semantics/publishedVersio