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Abstract Colorectal cancer (CRC) is the third most common cancer worldwide. Screening programs allow early diagnosis and have improved the clinical management of this disease. Aberrant DNA methylation is increasingly being explored as potential biomarkers for many types of cancers. In this study we investigate the methylation of ten target genes in 105 CRC and paired normal adjacent colonic tissue samples using a MethylLight droplet digital PCR (ML-ddPCR) assay. Receiver operator characteristic (ROC) curves were used to determine the diagnostic performance of all target genes individually and in combination. All 515 different combinations of genes showed significantly higher levels of methylation in CRC tissue. The combination of multiple target genes into a single test generally resulted in greater diagnostic accuracy when compared to single target genes. Our data confirms that ML-ddPCR is able to reliably detect significant differences in DNA methylation between CRC tissue and normal adjacent colonic tissue in a specific selection of target genes.

During the last decades, mid-infrared (3–12 μm) laser sources using crystals with nonlinear optical properties have attracted a particular attention due to their potential applications in different fields such as optical counter-measures and remote chemical sensing. As transparency of common oxide crystals is limited to about 4 μm, many researches have been focused on chalcopyrite compounds because of their wide transparency in the mid-IR range and their strong nonlinear optical coefficients. There is a need of such crystals able to convert efficiently the near infrared wavelengths from commercially available lasers into wavelengths higher than 5 μm through Optical Parametric Oscillators (OPO) systems. This paper presents a new compound: ZnGa2Se4 (ZGSe). Measurements made on dense polycrystals show a high thermal conductivity value in comparison with other selenides (2.9 W m−1 K−1), a wide transparency from visible to beyond the band III of the mid IR (0.6 μm–17 μm) and a coefficient of thermal expansion inferior to 10−5 K−1. These results are very encouraging and improvements of the growth process are now undertaken to obtain single crystals with the required optical quality. Keywords: Crystal growth, ZnGa2Se4, Optical materials and properties, Thermomechanical properties

Relationships between native and invasive species can modify trophic interactions in food webs and the diet of native species, leading to substantial changes in their trophic niches. We quantified the stable isotope niche of native amphibians (two species of tadpoles and two species of newts) and the invasive red swamp crayfish (Procambarus clarkii) in 18 ponds of an area invaded for more than 30 years. We tested whether crayfish presence and abundance explained variation in the size and position of the amphibians’ stable isotope niches compared with proxies of pond resource availability and competition levels. Agile frog tadpoles (Rana dalmatina) had consistently low trophic positions, while tree frog tadpoles’ niches (Hyla arborea) showed signs of an opportunistic diet. Newts (palmate newt (Lissotriton helveticus) and marbled newt (Triturus marmoratus)) had high trophic positions consistent with a predatory diet. Crayfish showed a high level of trophic variability, but their trophic niche never overlapped with the trophic niche of amphibians. Amphibian niche size and position were associated with amphibian density and pond canopy cover rather than with crayfish presence or abundance. This study suggests limited changes in amphibian diets in the presence of red swamp crayfish in ponds compared with results from experimental studies, suggesting that complex environmental conditions and the long time since invasion might limit trophic interactions between these native and invasive species.

Las condiciones agroecológicas del estado Mérida, Venezuela tienen potencialidad para establecer plantaciones de árboles de navidad con fines de comercialización. Se estudió el comportamiento silvicultural de la especie Cupressus lusitánica Mill., en condiciones de la zona alto-andina, con el fin de promocionar el cultivo de árboles de navidad entre las comunidades interesadas, El ensayo se estableció en la Estación Experimental Santa Rosa, Instituto de Investigaciones Agropecuarias de la Universidad de Los Andes. Los árboles fueron monitoreados y evaluados a lo largo de 20 meses, realizando mediciones de diámetro basal, altura total; aplicando podas apicales y de formación. Se obtuvo una sobrevivencia de 82.69 % y mortalidad de 17.31 %; altura promedio de 2.56 m. y diámetro basal de 7.79 cm, con respuestas positivas a las podas apicales y de formación. El incremento anual en altura fue de 1.51 m y de 3.80 cm en diámetro. Se concluyó que Cupressus lusitanica demostró adaptación a las condiciones ambientales del estado Mérida, de acuerdo a los parámetros evaluados.

Durante 2006 en Yucatán se establecieron aproximadamente, 167,000 hectáreas con agricultura migratoria, en asociaciones de maíz con frijol, calabaza y hortalizas, en tierras con diferentes periodos de barbecho que son aprovechados por tres años. El objetivo del presente trabajo fue determinar el comportamiento químico del suelo al evaluar tres coberturas y dos periodos de barbecho, así como también la fase de cultivo. Los tipos de cobertura vegetal: Leucaena leucocephala (Lam) de Wit. subespecie leucocephala, Mucuna pruriens y vegetación secundaria, con dos y cuatro años de barbecho, establecidos en un diseño de bloques al azar con cuatro repeticiones. Se determinaron los contenidos nutrimentales en tres tiempos: 1998 después de dos años de establecidos los barbechos de cuatro años, 2001 al cumplirse los barbechos de dos y cuatro años e iniciar la fase de cultivo y 2004 a tres años de uso continuo del terreno. Al final de los periodos de barbecho Leucaena mejoró en mayor medida el contenido de K, Ca y Mg, mientras que Mucuna el NO3 y la vegetación secundaria la materia orgánica. El barbecho de dos años registró valores superiores en el contenido de materia orgánica, NO3 y K, al compararlo con el de cuatro años, que superó al de dos años en el contenido de Mg.

Background: Neonates with tetralogy of Fallot and symptomatic cyanosis (sTOF) require early intervention, utilizing either a staged repair (SR) or primary repair (PR) approach. They are exposed to several sources of low-dose ionizing radiation, which may contribute to increased cancer risk. Objectives: The purpose of this study was to compare cumulative radiation exposure and associated lifetime attributable risk (LAR) of cancer between treatment strategies in sTOF. Methods: Neonates with sTOF who underwent SR or PR from 2012 to 2017 were retrospectively reviewed from the Congenital Cardiac Research Collaborative. Radiation exposure from all radiologic studies prior to 18 months of age was converted to organ-equivalent doses and projected LAR of cancer incidence using the National Cancer Institute dosimetry tools. Results: There were 242 neonates from 8 centers, including patients with 146 SR and 96 PR. Cumulative total effective dose was significantly higher for SR (median 8.3 mSv, IQR: 3.0-17.4 mSv) than PR (2.1 mSv, IQR: 0.8-8.5 mSv; P 1 mGy in females, the LAR was highest for breast in SR (mean 1.9/1,000 patients). The highest proportion of cancers attributable to radiation exposure was projected for thyroid cancer in females undergoing SR (7.3%). Conclusions: Cumulative radiation exposure and LARs were higher among those undergoing SR compared to PR. This will be an important factor to consider in determining the preferred neonatal treatment strategy and should substantiate efforts to reduce radiation exposure in this vulnerable population.

La siembra directa es un método económico para establecer programas de producción de forraje con leguminosas arbustivas, La Leucaena leucocephala (Lam.) de Wit. es una leguminosa de tipo arbustivo, utilizada en agricultura, ganadería y en la recuperación de tierras, tiene gran adaptabilidad, alto valor forrajero y se cataloga entre las principales especies de uso múltiple en agroforestería. El objetivo fue establecer un ensayo de siembra directa utilizando los métodos de siembra al voleo, surcos y hoyos con Leucaena leucocephala (Lam.) de Wit en un área del Jardín Botánico Carlos Liscano de la Facultad de Ciencias Forestales y Ambientales de la Universidad de Los Andes, Venezuela, a fin de probar su efectividad para planes futuros de establecimiento de bancos forrajeros. Se estableció el ensayo en un diseño completamente al azar en un experimento factorial (2 x 3), con 4 bloques (repeticiones). Los factores experimentales fueron: Factor A: 1) terreno arado 2) terreno no arado y Factor B: 1) siembra al voleo, 2) siembra en hoyos y 3) siembra en surcos. Se encontró que el método más exitoso de siembra es el surco, tanto en terreno arado como no arado. Se determinó que la emergencia está entre el día cuatro y dieciocho después de la siembra. Tres meses después la mayor abundancia de plantas se presentó en los bloques arados con sistema de siembra al voleo, aunque los mejores promedios de altura se encontraron en los bloques con arado y la siembra en surcos.

L’aquaculture intensive est considérée comme une source de pollution. Les interactions étroites entre le milieu d’élevage et l’écosystème où est implanté l’élevage confèrent des caractères particuliers à cette pollution. Les formes de pollution par l’aquaculture sont variées : pollutions organique, chimique, bactériologique, génétique etc. Les flux polluants peuvent être importants localement et géographiquement. On estime que la production d’une tonne de saumons implique 1 km2 marin, et que les élevages norvégiens contribuent pour 8 % et 14 % de l’azote et du phosphore respectivement rejetés en mer du Nord. La législation n’est pas adaptée aux problèmes tels qu’ils se posent en pisciculture. Une législation européenne plutôt axée sur le contrôle des intrants dans l’aliment semble se profiler avec l’exemple danois. Le moyen le plus rapide de réduire la pollution générée par l’aquaculture semble être, pour l’instant, d’abaisser la quantité d’aliments déversés par augmentation de la valeur énergétique de ceux-ci (ce qui diminuera la quantité de matières en suspension), et de remplacer une partie des protéines par des lipides. La mise en oeuvre de ce type d’aliment demande toutefois une technicité élevée. L’avenir des traitements en aval semble limité par le caractère très dilué des polluants et les grands volumes d’eau à traiter. L’aquaculture en tant que production dépendante de l’Environnement peut être un lien privilégié pour des études sur le coût de l’Environnement.

Abstract Key message In arboriculture, the number and diversity of pollen donors can have a major impact on fruit production. We studied pollination insurance in hybrid chestnut orchards (C. sativa × C. crenata) provided by nearby wild European chestnuts (C. sativa) in southwestern France. Most fruits were sired by hybrid pollenizers rather than by wild chestnuts. When these hybrid pollenizers were too scarce, a frequent situation, pollen produced by wild chestnut trees did not compensate for the lack of compatible pollen and fertilization rates and fruit production collapsed. Context The demand for chestnuts has been increasing in recent years in many European countries, but fruit production is not sufficient to meet this demand. Improving pollination service in chestnut orchards could increase fruit production. Aims Investigate pollination service in chestnut orchards. Evaluate the contribution to pollination of trees growing in chestnut woods and forests. Methods We investigated five orchards planted with hybrid chestnuts (C. sativa × C. crenata) cultivars in southwestern France. We combined fruit set data, which provide information about pollination rate, with genetic data, which provide information about pollen origin. We used this information to estimate the contribution of nearby C. sativa forest stands to the pollination of each orchard. Results Pollination rates vary considerably, being fivefold higher in orchards comprising numerous pollen donors than in monovarietal orchards. Because of asymmetric hybridization barriers between hybrid and purebred cultivars, the surrounding chestnut forests provide very limited pollination insurance: less than 14% of the flowers in these monovarietal orchards had been pollinated by forest trees. Conclusion Because chestnut orchards are now increasingly relying on hybrid cultivars, surrounding wild European chestnut trees are no longer a reliable pollen source. To achieve maximal fruit set, efforts must therefore concentrate on orchard design, which should include enough cultivar diversity.

Abstract Key message Appropriate silvicultural practices combined with the use of resistant Central European provenances can reduce the prevalence of larch canker caused by Lachnellula willkommii (R. Hartig) Dennis, a major disease affecting larch plantations in France. However, cascading translocations have resulted in frequent admixture in European larch (Larix decidua Mill.) and subsequent certification errors regarding the origin of plant material. Our study highlights the urgent need to improve the certification process of seed orchards. Context The recent history of European larch has been marked by translocations of plant stock within and beyond its native range. In order to increase stand resistance to larch canker disease, it is strongly recommended by French authorities to plant Central European provenances. However, a recent disease outbreak questioned the resistance of Central European provenances and the origin of the forest material used in these plantations. Aims Our goal was to assess the effects of cascading translocations and mixing between larch gene pools on genetic composition of plantations and on their vulnerability to the disease. Methods In the outbreak area, we checked the genetic origin of the trees and we estimated the percentage of Central European trees, disease prevalence and severity. Results Intra-site genetic diversity was high. Genetic composition did not match with geographic origin certificates. A high proportion of trees could not be assigned to either the Alpine or Central European gene pools. These admixed trees were as resistant as Central European trees. Geographic origin turned out to be one of the main drivers of canker prevalence, along with abiotic factors. Conclusion We need a precise knowledge of the origin of material used in seed orchards to mitigate canker disease and adapt forests through assisted migration.

Abstract Extra‐organismal DNA (eoDNA) from material left behind by organisms (noninvasive DNA, e.g., feces, hair) or from environmental samples (eDNA, e.g., water, soil) is a valuable source of genetic information. However, the relatively low quality and quantity of eoDNA, which can be further degraded by environmental factors, results in reduced amplification and sequencing success. This is often compensated for through cost‐ and time‐intensive replications of genotyping/sequencing procedures. Therefore, system‐ and site‐specific quantifications of environmental degradation are needed to maximize sampling efficiency (e.g., fewer replicates, shorter sampling durations), and to improve species detection and abundance estimates. Using 10 environmentally diverse bat roosts as a case study, we developed a robust modeling pipeline to quantify the environmental factors degrading eoDNA, predict eoDNA quality, and estimate sampling‐site‐specific ideal exposure duration. Maximum humidity was the strongest eoDNA‐degrading factor, followed by exposure duration and then maximum temperature. We also found a positive effect when hottest days occurred later. The strength of this effect fell between the strength of the effects of exposure duration and maximum temperature. With those predictors and information on sampling period (before or after offspring were born), we reliably predicted mean eoDNA quality per sampling visit at new sites with a mean squared error of 0.0349. Site‐specific simulations revealed that reducing exposure duration to 2–8 days could substantially improve eoDNA quality for future sampling. Our pipeline identified high humidity and temperature as strong drivers of eoDNA degradation even in the absence of rain and direct sunlight. Furthermore, we outline the pipeline's utility for other systems and study goals, such as estimating sample age, improving eDNA‐based species detection, and increasing the accuracy of abundance estimates.

Abstract Background Sitting at the interface of gene expression and host-pathogen interaction, polymerase associated factor 1 complex (PAF1C) is a rising player in the innate immune response. The complex localizes to the nucleus and associates with chromatin to modulate RNA polymerase II (RNAPII) elongation of gene transcripts. Performing this function at both proximal and distal regulatory elements, PAF1C interacts with many host factors across such sites, along with several microbial proteins during infection. Therefore, translating the ubiquity of PAF1C into specific impacts on immune gene expression remains especially relevant. Results Advancing past work, we treat PAF1 knockout cells with a slate of immune stimuli to identify key trends in PAF1-dependent gene expression with broad analytical depth. From our transcriptomic data, we confirm PAF1 is an activator of traditional immune response pathways as well as other cellular pathways correlated with pathogen defense. With this model, we employ computational approaches to refine how PAF1 may contribute to both gene activation and suppression. Specifically focusing on transcriptional motifs and regulons, we predict gene regulatory elements strongly associated with PAF1, including those implicated in an immune response. Overall, our results suggest PAF1 is involved in innate immunity at several distinct axes of regulation. Conclusions By identifying PAF1-dependent gene expression across several pathogenic contexts, we confirm PAF1C to be a key mediator of innate immunity. Combining these transcriptomic profiles with potential regulatory networks corroborates the previously identified functions of PAF1C. With this, we foster new avenues for its study as a regulator of innate immunity, and our results will serve as a basis for targeted study of PAF1C in future validation studies.

Metabolism is key to cellular processes that underlie the ability of a virus to productively infect. Polyamines are small metabolites vital for many host cell processes including proliferation, transcription, and translation. Polyamine depletion also inhibits virus infection via diverse mechanisms, including inhibiting polymerase activity and viral translation. We showed that Coxsackievirus B3 (CVB3) attachment requires polyamines; however, the mechanism was unknown. Here, we report polyamines' involvement in translation, through a process called hypusination, promotes expression of cholesterol synthesis genes by supporting SREBP2 synthesis, the master transcriptional regulator of cholesterol synthesis genes. Measuring bulk transcription, we find polyamines support expression of cholesterol synthesis genes, regulated by SREBP2. Thus, polyamine depletion inhibits CVB3 by depleting cellular cholesterol. Exogenous cholesterol rescues CVB3 attachment, and mutant CVB3 resistant to polyamine depletion exhibits resistance to cholesterol perturbation. This study provides a novel link between polyamine and cholesterol homeostasis, a mechanism through which polyamines impact CVB3 infection.

We describe the use of direct percutaneous cardiac access to recanalize an atretic right pulmonary artery in an adolescent with complex congenital heart disease and right heart failure. This case highlights the problems associated with loss of central venous access and potential advantages of a direct cardiac approach to catheterization. (Level of Difficulty: Intermediate.)

We describe an adolescent with long-standing atresia of the head/neck arteries and severe aortic coarctation. Because of progressive symptoms, a series of interventions was undertaken to provide direct aorta–to–carotid artery flow and coarctation treatment. This case highlights the unusual physiological features associated with atresia of all head and neck arteries. (Level of Difficulty: Advanced.)

Dengue virus (DENV) disruption of the innate immune response is critical to establish infection. DENV non-structural protein 5 (NS5) plays a central role in this disruption, such as antagonism of STAT2. We recently found that DENV serotype 2 (DENV2) NS5 interacts with Polymerase associated factor 1 complex (PAF1C). The primary members of PAF1C are PAF1, LEO1, CTR9, and CDC73. This nuclear complex is an emerging player in the immune response. It promotes the expression of many genes, including genes related to the antiviral, antimicrobial and inflammatory responses, through close association with the chromatin of these genes. Our previous work demonstrated that NS5 antagonizes PAF1C recruitment to immune response genes. However, it remains unknown if NS5 antagonism of PAF1C is complementary to its antagonism of STAT2. Here, we show that knockout of PAF1 enhances DENV2 infectious virion production. By comparing gene expression profiles in PAF1 and STAT2 knockout cells, we find that PAF1 is necessary to express immune response genes that are STAT2-independent. Finally, we mapped the viral determinants for the NS5-PAF1C protein interaction. We found that NS5 nuclear localization and the C-terminal region of the methyltransferase domain are required for its interaction with PAF1C. Mutation of these regions rescued the expression of PAF1-dependent immune response genes that are antagonized by NS5. In sum, our results support a role for PAF1C in restricting DENV2 replication that NS5 antagonizes through its protein interaction with PAF1C.

Pulmonary vein stenosis (PVS) has emerged as a critical problem in premature infants with persistent respiratory diseases, particularly bronchopulmonary dysplasia (BPD). As a parenchymal lung disease, BPD also influences vascular development with associated pulmonary hypertension recognized as an important comorbidity of both BPD and PVS. PVS is commonly detected later in infancy, suggesting additional postnatal factors that contribute to disease development, progression, and severity. The same processes that result in BPD, some of which are inflammatory-mediated, may also contribute to the postnatal development of PVS. Although both PVS and BPD are recognized as diseases of inflammation, the link between them is less well-described. In this review, we explore the relationship between parenchymal lung diseases, BPD, and PVS, with a specific focus on the epidemiology, clinical presentation, risk factors, and plausible biological mechanisms in premature infants. We offer an algorithm for early detection and prevention and provide suggestions for research priorities.

Marine organisms show population structure at a relatively fine spatial scale, even in open habitats. The tools commonly used to assess subtle patterns of connectivity have diverse levels of resolution and can complement each other to inform on population structure. We assessed and compared the discriminatory power of genetic markers and otolith shape to reveal the population structure on evolutionary and ecological time scales of the common sole (Solea solea), living in the Eastern English Channel (EEC) stock off France and the UK. First, we genotyped fish with Single Nucleotide Polymorphisms to assess population structure at an evolutionary scale. Then, we tested for spatial segregation of the subunits using otolith shape as an integrative tracer of life history. Finally, a supervised machine learning framework was applied to genotypes and otolith phenotypes to probabilistically assign adults to subunits and assess the discriminatory power of each approach. Low but significant genetic differentiation was found among subunits. Moreover, otolith shape appeared to vary spatially, suggesting spatial population structure at fine spatial scale. However, results of the supervised discriminant analyses failed to discriminate among subunits, especially for otolith shape. We suggest that the degree of population segregation may not be strong enough to allow for robust fish assignments. Finally, this study revealed a weak yet existing metapopulation structure of common sole at the fine spatial scale of the EEC based on genotypes and otolith shape, with one subunit being more isolated. Our study argues for the use of complementary tracers to investigate marine population structure.

Background In infants with ductal‐dependent pulmonary blood flow, the impact of palliation strategy on interstage growth and feeding regimen is unknown. Methods and Results This was a retrospective multicenter study of infants with ductal‐dependent pulmonary blood flow palliated with patent ductus arteriosus (PDA) stent or Blalock‐Taussig shunt (BTS) from 2008 to 2015. Subjects with a defined interstage, the time between initial palliation and subsequent palliation or repair, were included. Primary outcome was change in weight‐for‐age Z‐score. Secondary outcomes included % of patients on: all oral feeds, feeding‐related medications, higher calorie feeds, and feeding‐related readmission. Propensity score was used to account for baseline differences. Subgroup analysis was performed in 1‐ (1V) and 2‐ventricle (2V) groups. The cohort included 66 PDA stent (43.9% 1V) and 195 BTS (54.4% 1V) subjects. Prematurity was more common in the PDA stent group (P=0.051). After adjustment, change in weight‐for‐age Z‐score did not differ between groups over the entire interstage. However, change in weight‐for‐age Z‐score favored PDA stent during the inpatient interstage (P=0.005) and BTS during the outpatient interstage (P=0.032). At initial hospital discharge, PDA stent treatment was associated with all oral feeds (P

Abstract Background The distinction between lineages of neotropical bats from the Pteronotus parnellii species complex has been previously made according to mitochondrial DNA, and especially morphology and acoustics, in order to separate them into two species. In these studies, either sample sizes were too low when genetic and acoustic or morphological data were gathered on the same individuals, or genetic and other data were collected on different individuals. In this study, we intensively sampled bats in 4 caves and combined all approaches in order to analyse genetic, morphologic, and acoustic divergence between these lineages that live in the same caves in French Guiana. Results A multiplex of 20 polymorphic microsatellite markers was developed using the 454-pyrosequencing technique to investigate for the first time the extent of reproductive isolation between the two lineages and the population genetic structure within lineages. We genotyped 748 individuals sampled between 2010 and 2015 at the 20 nuclear microsatellite loci and sequenced a portion of the cytochrome c oxydase I gene in a subset of these. Two distinct, non-overlapping haplogroups corresponding to cryptic species P. alitonus and P. rubiginosus were revealed, in accordance with previous findings. No spatial genetic structure between caves was detected for both species. Hybridization appeared to be quite limited (0.1–4%) using microsatellite markers whereas introgression was more common (7.5%) and asymmetric for mitochondrial DNA (mtDNA). Conclusions The extremely low rate of hybridization could be explained by differences in life cycle phenology between species as well as morphological and acoustical distinction between sexes in one or the other species. Taken together, these results add to our growing understanding of the nature of species boundaries in Pteronotus parnelli, but deserve more in-depth studies to understand the evolutionary processes underlying asymmetric mtDNA introgression in this group of cryptic species.

Abstract Ecological manipulative experiments conducted in marine coastal ecosystems have substantially improved ecological theory during the last decades and have provided useful knowledge for the management and conservation of coastal ecosystems. Although different studies report global trends in ecological patterns worldwide, Southeastern Pacific coastal ecosystems have been poorly considered. Given that the SE Pacific coast encompasses diverse coastal ecosystems, consideration of studies conducted along this range can shed light on the heterogeneity of processes regulating coastal communities. We reviewed the biotic interactions and habitat type considered, as well as the complexity in terms of spatial and temporal extent of manipulative field experimental studies conducted along the SE Pacific coast from 0°S to 56°S (Ecuador to Chile). We test the effect of funding reported by different studies as a main factor limiting experimental complexity. From field ecological studies published from 1970 to 2016, we found that 81 studies were truly manipulative, in which one or multiple factors were “manipulated.” Around 77% of these studies were located between 21°S and 40°S, and conducted in intertidal rocky habitats. An increase in experimental studies was observed between 2010 and 2015, especially focused on herbivore–alga interactions, although we found that both the temporal extent and spatial extent of these studies have shown a decrease in recent decades. Funding grant amount reported had a positive effect on elapsed time of field experiments, but no effect was observed on spatial extent or in the biotic interactions considered. Elapsed time of experiments was different among the main biotic interactions considered, that is, herbivory, predation, and competition. We suggest that to further progress in applied ecological knowledge, it will be necessary to consider pollution and urbanization processes explicitly using a field experimental framework. This information could improve our understanding of how ecosystems present along the SE Pacific coast respond to climate change and increased levels of human interventions.

Abstract Background Human population growth since the mid-1900s has been accompanied by an unsustainable use of natural resources and a corresponding impact on terrestrial and marine biota. In response, most states have established protected areas as tools to decrease biodiversity loss, being Chile one of the signatories of international conservation agreements such as the Convention on Biological Diversity (CBD) and the 2010 Aichi Targets. This study reviews the Chilean protected areas that have been created to date, with an emphasis on the existence and effectiveness of management plans for all terrestrial and marine protected areas. Effectiveness was individually evaluated using two filters: 1) the age of the management plan and 2) the first four steps of the Protected Areas Management Effectiveness (PAME) methodology recommended by the IUCN. Results We show that 84 out of a total of 145 protected areas (PAs), and only five out of a total of 20 marine protected areas (MPAs), have management plans. Only 12% (N = 16) of PAs are effectively managed; while in the marine realm, no MPA has an effective plan. Conclusions Our results show the lack of both the effectiveness of and updates to the management plans for the vast majority of the national territory and raise the following question: is it sustainable to continue adding protected areas to the national system even though it is clear that the existing support is insufficient to meet the minimum requirements for full implementation?

Pulmonary vein stenosis (PVS) is a difficult condition to treat due to recurrence and progression. In 2017, we developed a comprehensive PVS Program at our center to address the multidisciplinary needs of these patients. We discuss the components of our program and our approach to these patients, using a combination of primary (medical) therapy in addition to anatomic therapy to preserve vessel patency. A multidisciplinary approach to treating these challenging patients is critical.

Studying how arthropod-borne viruses interact with their arthropod vectors is critical to understanding how these viruses replicate and are transmitted. Until recently, these types of studies were limited in scale because of the lack of classical tools available to study virus-host interaction for non-model viruses and non-model organisms. Advances in systems biology “-omics”-based techniques such as next-generation sequencing (NGS) and mass spectrometry can rapidly provide an unbiased view of arbovirus-vector interaction landscapes. In this mini-review, we discuss how arbovirus-vector interaction studies have been advanced by systems biology. We review studies of arbovirus-vector interactions that occur at multiple time and length scales, including intracellular interactions, interactions at the level of the organism, viral and vector populations, and how new techniques can integrate systems-level data across these different scales.

In contrast to biological invasions, translocations of individuals within a species range are understudied, due to difficulties in systematically detecting them. This results in limited knowledge about the corresponding processes and uncertainties regarding the status of extant populations. European larch, a forest tree whose fragmented native distribution is restricted to the Alps and to other Central European mountains, has been massively planted for at least 300 years. Here we focus on the genetic characterization of translocations having taken place within its native range. Microsatellite variation at 13 nuclear loci and sequence data of two mitochondrial DNA fragments were analyzed on the basis of a comprehensive range-wide population sample. Two complementary methods (Geneclass and Structure) were used to infer translocation events based on nuclear data whereas mitochondrial data were used for validation of these inferences. Using Geneclass, we found translocation events in a majority of populations. Additional cases of translocation and many instances of admixture were identified using Structure, thanks to the clear-cut ancestral genetic structure detected in this species. In particular, a strong divide between Alpine and Central European populations, also apparent at mitochondrial markers, helped uncover details on translocation events and related processes. Translocations and associated admixture events were found to be heterogeneously distributed across the species range, with a particularly high frequency in Central Europe. Furthermore, translocations frequently involved multiple geographic sources, some of which were over-represented. Our study illustrates the importance of range-wide investigations for tracing translocations back to their origins and for revealing some of their consequences. It provides some first clues for developing suitable conservation and management strategies.

Although interfertility is the key criterion upon which Mayr's biological species concept is based, it has never been applied directly to delimit species under natural conditions. Our study fills this gap. We used the interfertility criterion to delimit two closely related oak species in a forest stand by analyzing the network of natural mating events between individuals. The results reveal two groups of interfertile individuals connected by only few mating events. These two groups were largely congruent with those determined using other criteria (morphological similarity, genotypic similarity and individual relatedness). Our study, therefore, shows that the analysis of mating networks is an effective method to delimit species based on the interfertility criterion, provided that adequate network data can be assembled. Our study also shows that although species boundaries are highly congruent across methods of species delimitation, they are not exactly the same. Most of the differences stem from assignment of individuals to an intermediate category. The discrepancies between methods may reflect a biological reality. Indeed, the interfertility criterion is an environment-dependant criterion as species abundances typically affect rates of hybridization under natural conditions. Thus, the methods of species delimitation based on the interfertility criterion are expected to give results slightly different from those based on environment-independent criteria (such as the genotypic similarity criteria). However, whatever the criterion chosen, the challenge we face when delimiting species is to summarize continuous but non-uniform variations in biological diversity. The grade of membership model that we use in this study appears as an appropriate tool.

Alveolar macrophages (AM) are thought to have a key role in the immunopathogenesis of respiratory diseases. We sought to test the hypothesis that human AM exhibit an anti-inflammatory bias by making genome-wide comparisons with monocyte derived macrophages (MDM). Adherent AM obtained by bronchoalveolar lavage of patients under investigation for haemoptysis, but found to have no respiratory pathology, were compared to MDM from healthy volunteers by whole genome transcriptional profiling before and after innate immune stimulation. We found that freshly isolated AM exhibited a marked pro-inflammatory transcriptional signature. High levels of basal pro-inflammatory gene expression gave the impression of attenuated responses to lipopolysaccharide (LPS) and the RNA analogue, poly IC, but in rested cells pro-inflammatory gene expression declined and transcriptional responsiveness to these stimuli was restored. In comparison to MDM, both freshly isolated and rested AM showed upregulation of MHC class II molecules. In most experimental paradigms ex vivo adherent AM are used immediately after isolation. Therefore, the confounding effects of their pro-inflammatory profile at baseline need careful consideration. Moreover, despite the prevailing view that AM have an anti-inflammatory bias, our data clearly show that they can adopt a striking pro-inflammatory phenotype, and may have greater capacity for presentation of exogenous antigens than MDM.

The species status of two closely related Chinese oaks, Quercus liaotungensis and Q. mongolica, has been called into question. The objective of this study was to investigate the species status and to estimate the degree of introgression between the two taxa using different approaches.Using SSR (simple sequence repeat) and AFLP (amplified fragment length polymorphism) markers, we found that interspecific genetic differentiation is significant and higher than the differentiation among populations within taxa. Bayesian clusters, principal coordinate analysis and population genetic distance trees all classified the oaks into two main groups consistent with the morphological differentiation of the two taxa rather than with geographic locations using both types of markers. Nevertheless, a few individuals in Northeast China and many individuals in North China have hybrid ancestry according to Bayesian assignment. One SSR locus and five AFLPs are significant outliers against neutral expectations in the interspecific FST simulation analysis, suggesting a role for divergent selection in differentiating species.All results based on SSRS and AFLPS reached the same conclusion: Q. liaotungensis and Q. mongolica maintain distinct gene pools in most areas of sympatry. They should therefore be considered as discrete taxonomic units. Yet, the degree of introgression varies between the two species in different contact zones, which might be caused by different population history or by local environmental factors.

BACKGROUND:Emerging infectious diseases in wildlife are major threats for both human health and biodiversity conservation. Infectious diseases can have serious consequences for the genetic diversity of populations, which could enhance the species' extinction probability. The Ebola epizootic in western and central Africa induced more than 90% mortality in Western lowland gorilla population. Although mortality rates are very high, the impacts of Ebola on genetic diversity of Western lowland gorilla have never been assessed. METHODOLOGY/PRINCIPAL FINDINGS:We carried out long term studies of three populations of Western lowland gorilla in the Republic of the Congo (Odzala-Kokoua National Park, Lossi gorilla sanctuary both affected by Ebola and Lossi's periphery not affected). Using 17 microsatellite loci, we compared genetic diversity and structure of the populations and estimate their effective size before and after Ebola outbreaks. Despite the effective size decline in both populations, we did not detect loss in genetic diversity after the epizootic. We revealed temporal changes in allele frequencies in the smallest population. CONCLUSIONS/SIGNIFICANCE:Immigration and short time elapsed since outbreaks could explain the conservation of genetic diversity after the demographic crash. Temporal changes in allele frequencies could not be explained by genetic drift or random sampling. Immigration from genetically differentiated populations and a non random mortality induced by Ebola, i.e., selective pressure and cost of sociality, are alternative hypotheses. Understanding the influence of Ebola on gorilla genetic dynamics is of paramount importance for human health, primate evolution and conservation biology.