Automated pre-processing strategies for species occurrence data used in biodiversity modelling

To construct Biodiversity richness maps from Environmental Niche Models (ENMs) of thousands of species is time consuming. A separate species occurrence data pre-processing phase enables the experimenter to control test AUC score variance due to species dataset size. Besides, removing duplicate occurrences and points with missing environmental data, we discuss the need for coordinate precision, wide dispersion, temporal and synonymity filters. After species data filtering, the final task of a pre-processing phase should be the automatic generation of species occurrence datasets which can then be directly ’plugged-in’ to the ENM. A software application capable of carrying out all these tasks will be a valuable time-saver particularly for large scale biodiversity studies

Can the Iberian floristic diversity withstand near-future climate change?

We assess how effectively the current network of protected areas (PAs) across the Iberian Peninsula will conserve plant diversity under near-future (2020) climate change. We computed 3267 MAXENT environmental niche models (ENMs) at 1-km spatial resolution for known Iberian plant species under two climate scenarios (1950-2000 baseline & 2020). To predict near-future species distributions across the network of Iberian and Balearics PAs, we combined projections of species’ ENMs with simulations of propagule dispersal by using six scenarios of annual dispersal rates (no dispersal, 0.1 km, 0.5 km, 1 km, 2 km and unlimited). Mined PA grid cell values for each species were then analyzed. We forecast 3% overall floristic diversity richness loss by 2020. The habitat of regionally extant species will contract on average by 13.14%. Niche movement exceeds 1 km per annum for 30% of extant species. While the southerly range margin of northern plant species retracts northward at 8.9 km per decade, overall niche movement is more easterly and westerly than northerly. There is little expansion of the northern range margin of southern plant species even under unlimited dispersal. Regardless of propagule dispersal rate, altitudinal niche movement of +25 m per decade is strongest for northern species. Pyrenees flora is most vulnerable to near-future climate change with many northern plant species responding by shifting their range westerly and easterly rather than northerly. Northern humid habitats will be particularly vulnerable to near-future climate change. Andalusian National Parks will become important southern biodiversity refuges. With limited human intervention (particularly in the Pyrenees), we conclude that floristic diversity in Iberian PAs should withstand near-future climate change

Democratic localism and the implementation of the Community Remedy in England and Wales

This article assesses the development and implementation of the Community Remedy anti-social behaviour policy by Police and Crime Commissioners (PCCs) in England and Wales. The Community Remedy, introduced by the Anti-Social Behaviour, Crime and Policing Act (2014), allows victims of ‘low-level’ anti-social behaviour to select an informal action for their offender from a list designed by their local PCC via consultation with the public. This article reports the results of a benchmarking exercise that investigates how PCCs have translated this policy into practice by examining: public consultation procedures; the contents of the Community Remedy documents; and police usage. The findings indicate an uneven implementation across regions with variable levels of engagement from PCCs, police forces and members of the public. We assess the enactment and adoption of this new power alongside its potential to stimulate democratic localism

Conjugative Botulinum Neurotoxin-Encoding Plasmids in Clostridium botulinum

Clostridium botulinum produces seven distinct serotypes of botulinum neurotoxins (BoNTs). The genes encoding different subtype neurotoxins of serotypes A, B, F and several dual neurotoxin-producing strains have been shown to reside on plasmids, suggesting that intra- and interspecies transfer of BoNT-encoding plasmids may occur. The objective of the present study was to determine whether these C. botulinum BoNT-encoding plasmids are conjugative.C. botulinum BoNT-encoding plasmids pBotCDC-A3 (strain CDC-A3), pCLJ (strain 657Ba) and pCLL (strain Eklund 17B) were tagged with the erythromycin resistance marker (Erm) using the ClosTron mutagenesis system by inserting a group II intron into the neurotoxin genes carried on these plasmids. Transfer of the tagged plasmids from the donor strains CDC-A3, 657Ba and Eklund 17B to tetracycline-resistant recipient C. botulinum strains was evaluated in mating experiments. Erythromycin and tetracycline resistant transconjugants were isolated from donor:recipient mating pairs tested. Transfer of the plasmids to the transconjugants was confirmed by pulsed-field gel electrophoresis (PFGE) and Southern hybridizations. Transfer required cell-to-cell contact and was DNase resistant. This indicates that transfer of these plasmids occurs via a conjugation mechanism.This is the first evidence supporting conjugal transfer of native botulinum neurotoxin-encoding plasmids in C. botulinum, and provides a probable mechanism for the lateral distribution of BoNT-encoding plasmids to other C. botulinum strains. The potential transfer of C. botulinum BoNT-encoding plasmids to other bacterial hosts in the environment or within the human intestine is of great concern for human pathogenicity and necessitates further characterization of these plasmids

Group II Intron-Based Gene Targeting Reactions in Eukaryotes

Mobile group II introns insert site-specifically into DNA target sites by a mechanism termed retrohoming in which the excised intron RNA reverse splices into a DNA strand and is reverse transcribed by the intron-encoded protein. Retrohoming is mediated by a ribonucleoprotein particle that contains the intron-encoded protein and excised intron RNA, with target specificity determined largely by base pairing of the intron RNA to the DNA target sequence. This feature enabled the development of mobile group II introns into bacterial gene targeting vectors ("targetrons") with programmable target specificity. Thus far, however, efficient group II intron-based gene targeting reactions have not been demonstrated in eukaryotes.By using a plasmid-based Xenopus laevis oocyte microinjection assay, we show that group II intron RNPs can integrate efficiently into target DNAs in a eukaryotic nucleus, but the reaction is limited by low Mg(2+) concentrations. By supplying additional Mg(2+), site-specific integration occurs in up to 38% of plasmid target sites. The integration products isolated from X. laevis nuclei are sensitive to restriction enzymes specific for double-stranded DNA, indicating second-strand synthesis via host enzymes. We also show that group II intron RNPs containing either lariat or linear intron RNA can introduce a double-strand break into a plasmid target site, thereby stimulating homologous recombination with a co-transformed DNA fragment at frequencies up to 4.8% of target sites. Chromatinization of the target DNA inhibits both types of targeting reactions, presumably by impeding RNP access. However, by using similar RNP microinjection methods, we show efficient Mg(2+)-dependent group II intron integration into plasmid target sites in zebrafish (Danio rerio) embryos and into plasmid and chromosomal target sites in Drosophila melanogster embryos, indicating that DNA replication can mitigate effects of chromatinization.Our results provide an experimental foundation for the development of group II intron-based gene targeting methods for higher organisms

Base molecular para resistência a fluazifop-p-butyl em capim-camalote (rottboellia cochinchinensis) da Costa Rica

Rottboellia cochinchinensis is an annual grass weed species known as itchgrass, or “caminadora” in America´s Spanish speaking countries, and has become a major and troublesome weed in several crops. The application of fluazifop-P-butyl at recommended rates (125 g a.i. ha-1) was observed to be failing to control itchgrass in a field in San José, Upala county, Alajuela province, Costa Rica. Plants from the putative resistant R. cochinchinensis population survived fluazifop-P-butyl when treated with 250 g a.i. ha-1 (2X label rate) at the three- to four-leaf stage under greenhouse conditions. PCR amplification and sequencing of partial carboxyl transferase domain (CT) of the acetyl-CoA carboxylase (ACCase) gene were used to determine the molecular mechanism of resistance. A single non-synonymous point mutation from TGG (susceptible plants) to TGC (putative resistant plants) that leads to a Trp-2027-Cys substitution was found. This Trp-2027-Cys mutation is known to confer resistance to all aryloxyphenoxyproprionate (APP) herbicides to which fluazifop-P-butyl belongs. To the best of our knowledge, this is the first report of fluazifop-P-butyl resistance and a mutation at position 2027 for a Costa Rican R. cochinchinensis population.Rottboellia cochinchinensis, espécie de planta daninha anual conhecida como capim-camalote, ou “caminadora”, em países de língua espanhola das Américas, tornou-se uma planta daninha significativa e problemática em diversas culturas. Observou-se que a aplicação de fluazifop-p-butyl nas doses recomendadas (125 g i.a. ha-1) não conseguiu controlar capim-camalote em uma região em San José, condado de Upala, província de Alajuela, Costa Rica. As plantas da população supostamente resistente de R. cochinchinensis sobreviveram a fluazifop-p-butyl quando tratadas com 250 g i.a. ha-1 (2X a dose do rótulo) na fase de três a quatro folhas em condições de estufa. Amplificação e sequenciamento de reação em cadeia da polimerase de domínio de transferase de ácido carboxílico parcial (TC) do gene acetil-CoA carboxilase (ACCase) foram utilizados para determinar o mecanismo molecular de resistência. Foi encontrada uma mutação de ponto não sinônimo individual de TGG (plantas suscetíveis) para TGC (plantas supostamente resistentes) que conduz a uma substituição de Trp-2027-Cys. Sabe-se que essa mutação de Trp-2027-Cys confere resistência a todos os herbicidas ariloxifenoxipropionatos (AFP) a que fluazifop-p-butyl pertence. Pelo visto, este é o primeiro relato de resistência a fluazifop-p-butyl de uma mutação na posição 2027 para uma população costarriquenha de R. cochinchinensisWest Florida Research and Education Center, University of Florida/[]//United States of AmericaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Estación Experimental Agrícola Fabio Baudrit Moreno (EEAFBM

New insights into the genetic etiology of Alzheimer's disease and related dementias

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele

Evidence-based Kernels: Fundamental Units of Behavioral Influence

This paper describes evidence-based kernels, fundamental units of behavioral influence that appear to underlie effective prevention and treatment for children, adults, and families. A kernel is a behavior–influence procedure shown through experimental analysis to affect a specific behavior and that is indivisible in the sense that removing any of its components would render it inert. Existing evidence shows that a variety of kernels can influence behavior in context, and some evidence suggests that frequent use or sufficient use of some kernels may produce longer lasting behavioral shifts. The analysis of kernels could contribute to an empirically based theory of behavioral influence, augment existing prevention or treatment efforts, facilitate the dissemination of effective prevention and treatment practices, clarify the active ingredients in existing interventions, and contribute to efficiently developing interventions that are more effective. Kernels involve one or more of the following mechanisms of behavior influence: reinforcement, altering antecedents, changing verbal relational responding, or changing physiological states directly. The paper describes 52 of these kernels, and details practical, theoretical, and research implications, including calling for a national database of kernels that influence human behavior