Does mesocosm validation of environmental DNA methods translate to natural environment monitoring applications? A case study detecting a high-profile invader; the red eared slider turtle, Trachemys scripta elegans, in Australia

Environmental DNA (eDNA) surveys have gained popularity as a highly sensitive detection tool that generally outperform traditional detection techniques. eDNA surveys can provide a cost-effective means to identify species’ distributions and recent incursions, informing the control or containment of invasive species. The red-eared slider turtle, Trachemys scripta elegans, is one of the world’s most invasive species and is listed as a priority pest species for management in Australia. In this study, we validate two eDNA assays to detect this invasive turtle in Australia. We demonstrate high sensitivity in a laboratory setting and perfect detection rates in mesocosms for one of these eDNA assays but show that this does not translate to high detection rates in urban waterbodies at sites of known occupancy. In fact, our results suggest eDNA surveys provide sub-optimal performance compared to traditional detection methods for T.s. elegans. We suggest the capacity for eDNA surveys to provide a highly sensitive detection tool must be evaluated in natural environments on a species-by-species basis to understand any limitations and to avoid high error rates from eDNA surveys leading to wasted resources or inappropriate management decisions. For management of T.s. elegans in Australia, clearly defining the utility of certain eDNA based approaches to detect T.s. elegans and their incursions is vital for effective management of this pest species.</p

Management of sensitive data on NoSQL databases

Nowadays, NoSQL databases are winning popularity through all the e-commerce related sites and it is becoming a tendency to migrate from a relational model to others without schema. NoSQL databases are more flexible since they allow an easier adaptation of the database structure and the capability of refactoring the schema on the fly for any project without having to stop the database service and evolving the database schema. Finally, the query optimization is designed to manage large amounts of data, whereas on relational databases it is more focused on operations rather than on data. In this paper, we intend to make a demonstration on how security can be implemented on the database layer focusing on the permissions of users, this could be applied to databases where some fields can contain sensitive data that certain users should not have access to. We also test the capability of trimming determined fields of a database to have a more secure environment. For this implementation, we have chosen MongoDB for its schema less property and the lack of internal mechanisms to automatically apply Access Control Rules. In this paper, the user restrictions are implemented using a Role-Based Access Control model on MongoDB. This means that a user can be granted one or more roles previously defined, where each role would have authorizations defined to make operations in specific databases, collections or documents.This work is partially funded by the funded projects SEQUOIA-UA (TIN2015-63502-C3-3-R) and the SEQUOIA-UCLM (TIN2015-63502-C3-1-R) from the MINECO

Red LED Light Acts on the Mitochondrial Electron Chain of Mammalian Sperm via Light-Time Exposure-Dependent Mechanisms

This work analyzes the effects of red LED light on mammalian sperm mitochondrial function, using the pig as an animal model. Liquid-stored pig semen was stimulated with red-light for 1, 5 and 10 min in the presence or absence of oligomycin A, a specific inhibitor of mitochondrial ATP synthase, or carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP), a specific disruptor of mitochondrial electron chain. Whereas exposure for 1 and 5 min significantly (p < 0.05) decreased total motility and intracellular ATP levels, irradiation for 10 min induced the opposite effect. Oligomycin A abolished the light-effects on intracellular ATP levels, O2 consumption and mitochondrial membrane potential, whereas compared to non-irradiated samples, FCCP significantly (p < 0.05) increased O2 consumption when sperm were irradiated for 1 min. Both oligomycin A and FCCP significantly (p < 0.05) decreased total motility. Red-light increased cytochrome c oxidase activity with a maximal effect after 5 min of irradiation, which was abolished by both oligomycin A and FCCP. In conclusion, red-light modulates sperm mitochondrial function via electron chain activity in an exposition, time-dependent manner

The missing light of the Hubble Ultra Deep Field

Context. The Hubble Ultra Deep field (HUDF) is the deepest region ever observed with the Hubble Space Telescope. With the main objective of unveiling the nature of galaxies up to z ∼ 7−8, the observing and reduction strategy have focused on the properties of small and unresolved objects, rather than the outskirts of the largest objects, which are usually over-subtracted. Aims. We aim to create a new set of WFC3 IR mosaics of the HUDF using novel techniques to preserve the properties of the low surface brightness regions. Methods. We created ABYSS: a pipeline that optimises the estimate and modelling of low-level systematic effects to obtain a robust background subtraction. We have improved four key points in the reduction: 1) creation of new absolute sky flat fields, 2) extended persistence models, 3) dedicated sky background subtraction and 4) robust co-adding. Results. The new mosaics successfully recover the low surface brightness structure removed on the previous HUDF published reductions. The amount of light recovered with a mean surface brightness dimmer than µ = 26 mag arcsec^(−2) is equivalent to a m = 19 mag source when compared to the XDF and a m = 20 mag compared to the HUDF12. Conclusions. We present a set of techniques to reduce ultra-deep images ( µ > 32.5 mag arcsec^(−2) , 3σ in 10 × 10 arcsec boxes), that successfully allow us to detect the low surface brightness structure of extended sources on ultra deep surveys. The developed procedures are applicable to HST, JWST, EUCLID and many other space and ground-based observatories

Human imprinted retrogenes exhibit non-canonical imprint chromatin signatures and reside in non-imprinted host genes

Imprinted retrotransposed genes share a common genomic organization including a promoter-associated differentially methylated region (DMR) and a position within the intron of a multi-exonic ‘host’ gene. In the mouse, at least one transcript of the host gene is also subject to genomic imprinting. Human retrogene orthologues are imprinted and we reveal that human host genes are not imprinted. This coincides with genomic rearrangements that occurred during primate evolution, which increase the separation between the retrogene DMRs and the host genes. To address the mechanisms governing imprinted retrogene expression, histone modifications were assayed at the DMRs. For the mouse retrogenes, the active mark H3K4me2 was associated with the unmethylated paternal allele, while the methylated maternal allele was enriched in repressive marks including H3K9me3 and H4K20me3. Two human retrogenes showed monoallelic enrichment of active, but not of repressive marks suggesting a partial uncoupling of the relationship between DNA methylation and repressive histone methylation, possibly due to the smaller size and lower CpG density of these DMRs. Finally, we show that the genes immediately flanking the host genes in mouse and human are biallelically expressed in a range of tissues, suggesting that these loci are distinct from large imprinted clusters

Model of enteric methane emissions supports climate change mitigation in Colombia’s cattle sector

Key messages ◼ The RUMINANT model qualifies as an advanced or “Tier 3” method for estimating emissions from enteric fermentation in ruminant livestock. ◼ The RUMINANT model was validated for enteric methane emissions from cattle in the tropical lowlands (Cauca Valley) of Colombia using six different diets given to feeder steers in 2017. ◼ There was a good correlation between field measurements of enteric fermentation using the polytunnel technique and estimates made using the RUMINANT model. ◼ Based on findings from the validation process, RUMINANT has been used to improve Colombia’s National Greenhouse Gas Inventory to the United Nations Framework Convention on Climate Change (UNFCCC) and the preparation of the sustainable bovine livestock Nationally Appropriate Mitigation Actions (NAMA) information note. ◼ The RUMINANT model could support the measurement, reporting and verification (MRV) phase of the NDCs of Colombia and other countries

Vacuna tetravalente de influenza en los programas nacionales de inmunización para los países de América Latina

Since 2012-2013 influenza season, World Health Organization (who) recommends the formulation of tetravalent vaccines. Globally, many countries already use tetravalent vaccines in their national immunization programs, while in Latin America only a small number. Two Influenza b lineages co-circulate, their epidemiological behavior is unpredictable. On average they represent 22.6% of influenza cases and more than 50% in predominant seasons. The lack of concordance between recommended and circulating strains was 25 and 32% in the 2010-2017 and 2000-2013 seasons, respectively. There are no clinical differences between influenza A and B. It occurs more frequently from five to 19 years of age. Influenza b has a higher proportion of attributable deaths than influenza a (1.1 vs. 0.4%), or 2.65 (95% ci 1.18-5.94). A greater number of hospitalizations when the strains mismatch (46.3 vs. 28.5%; p <.0001). Different evaluations have demonstrated its cost effectiveness. The compilation of this information supports the use of quadrivalent vaccines in Latin American countries.Revisión por pare