Next generation sequencing for diagnosis of hereditary anemia: Experience in a Spanish reference center.

BACKGROUND AND AIMS: Hereditary anemia (HA) encloses a wide group of rare inherited disorders with clinical and hematologic overlaps that complicate diagnosis. MATERIALS AND METHODS: A 48-gene panel was developed to diagnose HA by Next Generation Sequencing (NGS) in a large cohort of 165 patients from 160 unrelated families. RESULTS: Patients were divided in: A) patients who had a suspicion of a specific type of HA (n = 109), and B) patients who had a suspicion of HA but with no clear type (n = 56). Diagnostic performance was 83.5% in group A and a change of the initial diagnosis occurred in 11% of these patients. In group B, 35.7% of patients achieved a genetic diagnosis. NGS identified 6 cases of xerocytosis, 6 of pyruvate kinase (PK) deficiency, 4 of G6PD, and 1 case of phytosterolemia with no initial suspicion of these pathologies, which is clinically relevant since they have specific treatment. Five patients were found to carry variants associated to two different pathologies (4 of them combining a metabolic deficiency and a membrane defect), and 44 new variants were identified in 41 patients. CONCLUSION: The use of NGS is a sensitive technique to diagnose HA and it shows better performance when patients are better characterized.

Effects of howler monkey reintroduction on ecological interactions and processes.

Rewilding has been an increasingly popular tool to restore plant-animal interactions and ecological processes impaired by defaunation. However, the reestablishment of such processes has seldom been assessed. We investigated the restoration of ecological interactions following the reintroduction of the brown howler monkey (Alouatta guariba) to a defaunated Atlantic forest site. We expected the reintroduction to restore plant-animal interactions and interactions between howlers and dung beetles, which promote secondary seed dispersal. We estimated the number of interactions expected to be restored by the reintroduction to provide the baseline interaction richness that could be restored. We followed the reintroduced howler monkeys twice a week for 24 months (337 hours total) to assess their diet. We used howler monkey dung in secondary seed dispersal experiments with 2484 seed mimics to estimate the removal rates by dung beetles and collected the beetles to assess community attributes. We compared the potential future contribution of howler monkeys and other frugivores to seed dispersal based on the seed sizes they disperse in other areas where they occur. In 2 years, howler monkeys consumed 60 animal-dispersed plant species out of the 330 estimated. Twenty-one dung beetle species were attracted to experimentally provided dung; most of them were tunnelers, nocturnal, and large-sized (>10 mm). On average 30% (range 0-100%) of the large seed mimics (14 mm) were moved by dung beetles. About 91% of the species consumed by howlers (size range 0.3-34.3 mm) overlapped in seed size with those removed by dung beetles. In our study area, howler monkeys may consume more large-seeded fruit species than most other frugivores, highlighting their potential to affect forest regeneration. Our results show reintroductions may effectively restore ecological links and enhance ecological processes.

Estimating interaction credit for trophic rewilding in tropical forests.

Trophic rewilding has been suggested as a restoration tool to restore ecological interactions and reverse defaunation and its cascading effects on ecosystem functioning. One of the ecological processes that has been jeopardized by defaunation is animal-mediated seed dispersal. Here, we propose an approach that combines joint species distribution models with occurrence data and species interaction records to quantify the potential to restore seed-dispersal interactions through rewilding and apply it to the Atlantic Forest, a global biodiversity hotspot. Using this approach, we identify areas that should benefit the most from trophic rewilding and candidate species that could contribute to cash the credit of seed-dispersal interactions in a given site. We found that sites within large fragments bearing a great diversity of trees may have about 20 times as many interactions to be cashed through rewilding as small fragments in regions where deforestation has been pervasive. We also ranked mammal and bird species according to their potential to restore seed-dispersal interactions if reintroduced while considering the biome as a whole and at finer scales. The suggested approach can aid future conservation efforts in rewilding projects in defaunated tropical rainforests.This article is part of the theme issue 'Trophic rewilding: consequences for ecosystems under global change'.

Living and lost mammals of Rio de Janeiro's largest biological reserve: an updated species list of Tinguá / Mamíferos atuais e extintos na maior Reserva Biológica do Rio de Janeiro: uma lista atualizada de espécies do Tinguá

Abstract: The Tinguá Biological Reserve (TBR) is the largest protected area of this category in Rio de Janeiro state. Here, for the first time, we present the historical composition of terrestrial mammals' assemblage of TBR region. An inventory was conducted using transect surveys, nonstandard transects, survey of museum specimens and informal reports. Considering all the data, eighty-five species were recorded, placing TBR as the second one in the number of mammals recorded in "Serra do Mar" ecoregion of Atlantic Forest and in the Rio de Janeiro state. Among the species with historical records are the jaguar (Panthera onca) and the golden-lion-tamarin (Leontopithecus rosalia) while the current presence of the maned wolf (Chrysocyon brachyurus) was recorded for the first time. Priority studies should focus on Chiroptera, Rodentia and Didelphimorphia orders, especially in the most remote areas of the reserve, and long-term surveys of endangered species. Besides hunting, fragmentation of its interior by roads, pipelines and transmission lines and exotic species, TBR is also threatened by the urban growth around it and the pressure to reduce its area and its protection category, demanding greater attention by the high levels of governance of protected areas in Brazil.

Resumo: A Reserva Biológica Tinguá (RBT) é a maior área protegida desta categoria no estado do Rio de Janeiro. Aqui, pela primeira vez, apresentamos a composição histórica da assembleia de mamíferos terrestres da região da RBT. Um inventário foi realizado utilizando amostragem por transectos, transectos não padronizados, busca por espécimes em museu e relatos. Considerando todos os dados, foram registradas oitenta e cinco espécies, colocando a RBT como a segunda no número de mamíferos registrados na ecorregião "Serra do Mar" da Mata Atlântica e no estado do Rio de Janeiro. Entre as espécies com registros históricos estão a onça-pintada (Panthera onca) e o mico-leão-dourado (Leontopithecus rosalia), enquanto a presença atual do lobo-guará (Chrysocyon brachyurus) foi registrada pela primeira vez. Estudos prioritários devem se concentrar nas ordens de Chiroptera, Rodentia e Didelphimorphia, especialmente nas áreas mais remotas da reserva, e pesquisas de longo prazo sobre espécies ameaçadas de extinção. Além da caça, a fragmentação em seu interior por estradas, gasodutos e linhas de transmissão e a presença de espécies exóticas, a TBR é ameaçada também pelo crescimento urbano no entorno e pela pressão para reduzir sua área e categoria de proteção, exigindo maior atenção dos altos níveis de gestão de áreas protegidas no Brasil.

Credit of ecological interactions: A new conceptual framework to support conservation in a defaunated world.

As defaunation spreads through the world, there is an urgent need for restoring ecological interactions, thus assuring ecosystem processes. Here, we define the new concept of credit of ecological interactions, as the number of interactions that can be restored in a focal area by species colonization or reintroduction. We also define rewiring time, as the time span until all the links that build the credit of ecological interactions of a focal area have become functional again. We expect that the credit will be gradually cashed following refaunation in rates that are proportional to (1) the abundance of the reintroduced species (that is expected to increase in time since release), (2) the abundance of the local species that interact with them, and (3) the traits of reintroduced species. We illustrated this approach using a theoretical model and an empirical case study where the credit of ecological interactions was estimated. This new conceptual framework is useful for setting reintroduction priorities and for evaluating the success of conservation initiatives that aim to restore ecosystem services.

HB Puerta del Sol [HBA1:c.148A>C], HB Valdecilla [HBA2:c.3G>T], HB Gran Vía [HBA2:c.98T>G], HB Macarena [HBA2:c.358C>T] and HB El Retiro [HBA2:c.364_366dupGTG]: description of five new hemoglobinopathies.

BACKGROUND: Structural hemoglobinopathies do not usually have a clinical impact, but they can interfere with the analytical determination of some parameters, such as the glycated hemoglobin in diabetic patients. Thalassemias represent a serious health problem in areas where their incidence is high. The defects in the post-translational modifications produce hyper-unstable hemoglobin that is not detected by most of electrophoretic or chromatographic methods that are available so far. METHODS: We studied seven patients who belong to six unrelated families. The first two families were studied because they had peak abnormal hemoglobin (Hb) during routine analytical assays. The other four families were studied because they had microcytosis and hypochromia with normal HbA2 and HbF without iron deficiency. HbA2 and F quantification and abnormal Hb separation were performed by chromatographic and electrophoretic methods. The molecular characterization was performed using specific sequencing. RESULTS: The Hb Puerta del Sol presents electrophoretic mobility and elution in HPLC that is different from HbA and similar to HbS. The electrophoretic and chromatographic profiles of the four other variants are normal and do not show any anomalies, and their identification was only possible with sequencing. CONCLUSIONS: Some variants, such as Hb Valdecilla, Hb Gran Vía, Hb Macarena and Hb El Retiro, have significant clinical impact when they are associated with other forms of α-thalassemia, which could lead to more serious forms of this group of pathologies as for HbH disease. Therefore, it is important to maintain an adequate program for screening these diseases in countries where the prevalence is high to prevent the occurrence of severe forms.

Incorporating animal spatial memory in step selection functions.

Memory is among the most important and neglected forces that shapes animal movement patterns. Research on the movement-memory interface is crucial to understand how animals use spatial learning to navigate across space because memory-based navigation is directly linked to animals' space use and home range behaviour; however, because memory cannot be measured directly, it is difficult to account for. Here, we incorporated spatial memory into step selection functions (SSF) to understand how resource selection and spatial memory affect space use of feral hogs (Sus scrofa). We used Biased Random Bridge kernel estimates linked to residence time as a surrogate for memory and tested four conceptually different dynamic maps of spatial memory. We applied this memory-based SSF to a data set of hog relocations to evaluate the importance of land cover type, time of day and spatial memory on the animals' space use. Our approach has shown how the incorporation of spatial memory into animal movement models can improve estimates of habitat selection. Memory-based SSF provided a feasible way to gain insight into how animals use spatial learning to guide their movement decisions. We found that while hogs selected forested areas and water bodies and avoided grasslands during the day (primarily at noon), they had a strong tendency to select previously visited areas, mainly those held in recent memory. Beyond actively updating their memory with recent experiences, hogs were able to discriminate among spatial memories encoded at different circadian phases of their activity. Even though hogs are thought to have long memory retention, they likely relied on recent experiences because the local food resources are quickly depleted and slowly renewed, yielding an uncertain spatial distribution of resources.

Hemoglobin Seville [α2 ß2 81(EF5) Leu→Phe] a silent phenotypic variant that interferes in hemoglobin A1c measurement by ion-exchange HPLC method.

OBJECTIVES: The aim of the study was to investigate hemoglobin (Hb) species in a 61 year-old male with diabetes mellitus type II and a low value of Hb A(1c). DESIGN AND METHODS: Hb species were analyzed by electrophoresis and chromatography methods. Functional properties were determined by oxygen equilibrium studies. ß-globin gene was amplified by PCR and sequenced. RESULTS AND CONCLUSIONS: A novel clinically silent Hb (Hb Seville), that results in falsely low Hb A(1c) measurement, was detected. This Hb variant presented a single base mutation at codon 81 (C→T) of the ß-globin gene. This case points out the necessity of careful inspection of the chromatograms and the use of additional methods to Hb A(1c) measurement when the presence of aberrant peaks is detected.

Systematics of the genus Chaetosphaeria and its allied genera: morphological and phylogenetic diversity in north temperate and neotropical taxa.

Chaetosphaeria is a common saprobic pyrenomycete genus with simple, homogeneous teleomorphs and complex, diverse anamorphs. As currently circumscribed in the literature, the genus encompasses 30 species distributed in four 'natural groups', and includes morphological entities in 11 anamorphic genera. Species frequently have been defined primarily based on characters of the anamorphs resulting in species with almost indistinguishable teleomorphs. This study aimed to assess the value and significance of morphological characters in resolving phylogenetic relationships in Chaetosphaeria and its allied genera. Phylogenetic relationships of 42 taxa, representing 29 species distributed in Chaetosphaeria and five related genera, were estimated with partial sequences of the nuclear LSU rDNA and beta-tubulin genes. Sequences were analyzed with maximum parsimony, maximum likelihood and Bayesian methods. Phylogenetic analyses of these two genes combined revealed two major lineages. The Chaetosphaeria lineage includes 21 species possessing both typical and new sexual and asexual morphologies. The lineage contains a strongly supported monophyletic clade of 13 species and eight paraphyletic taxa; the latter includes C. innumera, the type species of the genus. The second major lineage includes groupings concordant with the morphological circumscriptions of the genera Melanochaeta, Melanopsammella, Striatosphaeria, Zignoëlla and the new genus Tainosphaeria.

Distribución geográfica de las mutaciones del gen HFE en España / Geographical distribution of HFE C282Y and H63D mutation in Spain

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Molecular systematics of the Coronophorales and new species of Bertia, Lasiobertia and Nitschkia.

The Nitschkiaceae has been placed in the Coronophorales or the Sordariales in recent years. Most recently it was accepted in the Coronophorales and placed in the Hypocreomycetidae based on sequence data from large subunit nrDNA. To confirm and corroborate the taxonomic placement and monophyly of the Coronophorales, additional taxa representing the diversity of the group were targeted for phylogenetic analysis using partial sequences of the large subunit nrDNA (LSU). Based on molecular data, the Coronophorales is found to be monophyletic and its placement in the Hypocreomycetidae is maintained. The order is a coherent group with morphologies that include superficial, often turbinate, often collabent ascomata that may or may not contain a quellkorper and asci that are often stipitate and at times polysporous. Three species with accepted Nitschkia names, together with Fracchiaea broomeiana and Acanthonitschkea argentinensis, comprise the paraphyletic nitschkiaceous complex. Two new families, Chaetosphaerellaceae and Scortechiniaceae fams nov., are described for the clades containing Chaetosphaerella and Crassochaeta and the taxa having a quellkorper (Euacanthe, Neofracchiaea and Scortechinia) respectively. The Bertiaceae is accepted for the clade containing Bertia species. Three new species are described: Bertia tropicalis, Lasiobertia portoricensis, and Nitschkia meniscoidea spp. nov.

Ophiorosellinia costaricensis gen. et sp. nov., a xylariaceous fungus with scolecosporous ascospores.

A pyrenomycete featuring uniperitheciate stromata embedded in a subiculum and asci with iodine-positive apical ascal rings that bear scolecosporous ascospores is described as new. The fungus, Ophiorosellinia costaricensis, is known only from the type location in Costa Rica. It has been cultured, but no anamorph was discovered.

Paramphisphaeria costaricensis gen. et sp. nov. and Pachytrype rimosa sp. nov. from Costa Rica.

Paramphisphaeria is described as a new genus on the basis of the single species, P. costaricensis. It differs from Amphisphaeria spp. primarily in having bicellular ascospores with a germ slit and in having an ascus apical ring that does not become blue in iodine. It resembles Amphisphaeria in its brown color and lack of constriction at the septum of the ascospore. An anamorph is unknown. It tentatively is placed in the Xylariaceae for reasons discussed. Pachytrype rimosa is described as a new species.