Spatio-temporal patterns of eukaryotic biodiversity in shallow hard-bottom communities from the West Antarctic Peninsula revealed by DNA metabarcoding

Aim: We studied molecular eukaryotic biodiversity patterns in shallow hard-bottom Antarctic benthic communities using community DNA metabarcoding. Polar ecosystems are extremely exposed to climate change, and benthic macroinvertebrate communities have demonstrated rapid response to a range of natural and anthropogenic pressures. However, these rich and diverse ecosystems are poorly studied, revealing how little is known about the biodiversity of the Antarctic benthos associated with hard-bottom habitats. Location: West Antarctic Peninsula and South Shetland Islands. Methods: Using data collected in seven localities along the western Antarctic Peninsula, we calculated spatial patterns of alpha and beta diversities. Furthermore, we analysed temporal changes in benthic composition in one location (Deception Island) over 3 years. We calculated the temporal alpha and beta diversities to reveal changes in this community over time. Results: We obtained a final list of 2057 molecular operational taxonomic units. We found significant differences in benthic community composition between localities and among years. Our dataset revealed a total of 10 different kingdom-level lineages and 34 different phyla in the samples. The most diverse phylum was Arthropoda, followed by Bacillariophyta, and Annelida, while the highest relative read abundances belonged to Annelida, Porifera and Echinodermata. Benthic community compositions changed between 2016 and 2018 in Deception Island, and decreasing species richness was the main component of temporal beta diversity. Main Conclusions: Direct sampling methods are required for monitoring these complex communities. Informative biodiversity patterns can be retrieved even though most of the benthic biodiversity found in Antarctic habitats is yet to be taxonomically described and barcoded. Hard-bottom assemblages exhibit high spatial variability and heterogeneity, not related to depth, which represent a huge challenge for largescale studies in the Southern Ocean. Local patchiness and structure within the communities are probably a consequence of a combination of several biotic and abiotic factors (i.e. ice disturbance, food supply and competition)

Genome-wide association analysis of dementia and its clinical endophenotypes reveal novel loci associated with Alzheimer's disease and three causality networks: The GR@ACE project

Introduction: Large variability among Alzheimer's disease (AD) cases might impact genetic discoveries and complicate dissection of underlying biological pathways. Methods: Genome Research at Fundacio ACE (GR@ACE) is a genome-wide study of dementia and its clinical endophenotypes, defined based on AD's clinical certainty and vascular burden. We assessed the impact of known AD loci across endophenotypes to generate loci categories. We incorporated gene coexpression data and conducted pathway analysis per category. Finally, to evaluate the effect of heterogeneity in genetic studies, GR@ACE series were meta-analyzed with additional genome-wide association study data sets. Results: We classified known AD loci into three categories, which might reflect the disease clinical heterogeneity. Vascular processes were only detected as a causal mechanism in probable AD. The meta-analysis strategy revealed the ANKRD31-rs4704171 and NDUFAF6-rs10098778 and confirmed SCIMP-rs7225151 and CD33-rs3865444. Discussion: The regulation of vasculature is a prominent causal component of probable AD. GR@ACE meta-analysis revealed novel AD genetic signals, strongly driven by the presence of clinical heterogeneity in the AD series

Genome-wide association analysis of dementia and its clinical endophenotypes reveal novel loci associated with Alzheimer's disease and three causality networks: The GR@ACE project

INTRODUCTION: Large variability among Alzheimer's disease (AD) cases might impact genetic discoveries and complicate dissection of underlying biological pathways. METHODS: Genome Research at Fundacio ACE (GR@ACE) is a genome-wide study of dementia and its clinical endophenotypes, defined based on AD's clinical certainty and vascular burden. We assessed the impact of known AD loci across endophenotypes to generate loci categories. We incorporated gene coexpression data and conducted pathway analysis per category. Finally, to evaluate the effect of heterogeneity in genetic studies, GR@ACE series were meta-analyzed with additional genome-wide association study data sets. RESULTS: We classified known AD loci into three categories, which might reflect the disease clinical heterogeneity. Vascular processes were only detected as a causal mechanism in probable AD. The meta-analysis strategy revealed the ANKRD31-rs4704171 and NDUFAF6-rs10098778 and confirmed SCIMP-rs7225151 and CD33-rs3865444. DISCUSSION: The regulation of vasculature is a prominent causal component of probable AD. GR@ACE meta-analysis revealed novel AD genetic signals, strongly driven by the presence of clinical heterogeneity in the AD series

Genome-wide association analysis of dementia and its clinical endophenotypes reveal novel loci associated with Alzheimer's disease and three causality networks : The GR@ACE project

Introduction: Large variability among Alzheimer's disease (AD) cases might impact genetic discoveries and complicate dissection of underlying biological pathways. Methods: Genome Research at Fundacio ACE (GR@ACE) is a genome-wide study of dementia and its clinical endophenotypes, defined based on AD's clinical certainty and vascular burden. We assessed the impact of known AD loci across endophenotypes to generate loci categories. We incorporated gene coexpression data and conducted pathway analysis per category. Finally, to evaluate the effect of heterogeneity in genetic studies, GR@ACE series were meta-analyzed with additional genome-wide association study data sets. Results: We classified known AD loci into three categories, which might reflect the disease clinical heterogeneity. Vascular processes were only detected as a causal mechanism in probable AD. The meta-analysis strategy revealed the ANKRD31-rs4704171 and NDUFAF6-rs10098778 and confirmed SCIMP-rs7225151 and CD33-rs3865444. Discussion: The regulation of vasculature is a prominent causal component of probable AD. GR@ACE meta-analysis revealed novel AD genetic signals, strongly driven by the presence of clinical heterogeneity in the AD series

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

Multiancestry analysis of the HLA locus in Alzheimer’s and Parkinson’s diseases uncovers a shared adaptive immune response mediated by HLA-DRB1*04 subtypes

Across multiancestry groups, we analyzed Human Leukocyte Antigen (HLA) associations in over 176,000 individuals with Parkinson’s disease (PD) and Alzheimer’s disease (AD) versus controls. We demonstrate that the two diseases share the same protective association at the HLA locus. HLA-specific fine-mapping showed that hierarchical protective effects of HLA-DRB1*04 subtypes best accounted for the association, strongest with HLA-DRB1*04:04 and HLA-DRB1*04:07, and intermediary with HLA-DRB1*04:01 and HLA-DRB1*04:03. The same signal was associated with decreased neurofibrillary tangles in postmortem brains and was associated with reduced tau levels in cerebrospinal fluid and to a lower extent with increased Aβ42. Protective HLA-DRB1*04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, however only when acetylated at a lysine (K311), a common posttranslational modification central to tau aggregation. An HLA-DRB1*04-mediated adaptive immune response decreases PD and AD risks, potentially by acting against tau, offering the possibility of therapeutic avenues

More Than Expected From Old Sponge Samples: A Natural Sampler DNA Metabarcoding Assessment of Marine Fish Diversity in Nha Trang Bay (Vietnam)

Este artículo contiene 15 páginas, 8 figuras, 1 tabla.Sponges have recently been proposed as ideal candidates to act as natural samplers for environmental DNA due to their efficiency in filtering water. However, validation of the usefulness of DNA recovered from sponges to reveal vertebrate biodiversity patterns in Marine Protected Areas is still needed. Additionally, nothing is known about how different sponge species and morphologies influence the capture of environmental DNA and whether biodiversity patterns obtained from sponges are best described by quantitative or qualitative measures. In this study, we amplified and sequenced a vertebrate specific 12S barcode with a set of universal PCR primers (MiFish) for metabarcoding environmental DNA from fishes, to unveil fine-scale patterns of fish communities from natural-sampler DNA retrieved from 64 sponges (16 species) located in eutrophic and well-preserved coral reefs in Nha Trang Bay (central Vietnam). Ninety tropical fish species were identified from the sponges, corresponding to one third of the total local ichthyofauna reported from previous extensive conventional surveys. Significant differentiation in fish communities between eutrophic and well-preserved environments was observed, albeit eutrophication only explained a modest proportion of the variation between fish communities. Differences in efficiency of capturing fish environmental DNA among sponge species or morphologies were not observed. Overall, the majority of detected fish species corresponded to reef-associated small-sized species, as expected in coral reefs environments. Remarkably, pelagic, migratory, and deep-sea fish species were also recovered from sponge tissues, pointing out the ability of sponge natural sampled DNA to detect fishes that were not permanently associated to the biomes where the sponges were sampled. These results highlight the suitability of natural samplers as a cost-effective way to assess vertebrate diversity in hyper-diverse environments.This research was partially funded by the project MArSymbiOmics (CTM2013-43287-P) from the Spanish MINECO and by a small research grant from UiT the Arctic University of Norway to KP.Peer reviewe

Effects of ocean acidification on acid-base physiology, skeleton properties, andmetal contamination in two echinoderms fromvent sites in Deception Island, Antarctica

Antarctic surface waters are expected to be the first to experience severe ocean acidification (OA) with carbonate undersaturation and large decreases in pH forecasted before the end of this century. Due to the long stability in environmental conditions and the relatively low daily and seasonal variations to which they are exposed, Antarctic marine organisms, especially those with a supposedly poor machinery to eliminate CO2 and protons and with a heavily calcified skeleton like echinoderms, are hypothesized as highly vulnerable to these environmental shifts. The opportunities offered by the natural pH gradient generated by vent activities in Deception Island caldera, Western Antarctic Peninsula, were used to investigate for the first time the acid-base physiologies, the impact of OA on the skeleton and the impact of pH on metal accumulation in the Antarctic sea star Odontaster validus and sea urchin Sterechinus neumayeri. The two species were sampled in four stations within the caldera, two at pH (total scale) 8.0-8.1 and two at reduced pH 7.8. Measured variables were pH, alkalinity, and dissolved inorganic carbon of the coelomic fluid; characteristic fracture force, stress and Young's modulus using Weibull statistics and Cd, Cu, Fe, Pb and Zn concentrations in the integument, gonads and digestive system. Recorded acid-base characteristics of both studied species fit in the general picture deduced from temperate and tropical sea stars and sea urchins but conditions and possibly confounding factors, principally food availability and quality, in the studied stations prevented definitive conclusions. Reduced seawater pH 7.8 and metals had almost no impact on the skeleton mechanical properties of the two investigated species despite very high Cd concentrations in O. validus integument. Reduced pH was correlated to increased contamination by most metals but this relation was weak. Translocation and caging experiments taking into account food parameters are proposed to better understand future processes linked to ocean acidification and metal contamination in Antarctic echinoderms

A review of wildlife camera trapping trends across Africa

Camera traps (CTs) are used for wildlife monitoring globally. How CTs are used in wildlife studies across Africa, however, remains unknown. We provide the first literature review of CT studies conducted across Africa, to describe where, to what end, and by whom CTs are used, and to identify apparent gaps in the use of CTs. We found 172 CT studies published across 60 scientific journals, conducted in 30 of 55 African countries from 2005 to 2017. Most studies were conducted over a single year/season (74%) and primarily addressed habitat use/species distribution (43%), species presence/richness (38.4%), behaviour (35.5%) or demographics (29.7%). Most studies took place in forest (52%), woodland (33%) and grassland (33%) habitat types, and focused on a single species (45.3%). Carnivores were the most commonly studied species group (86%), followed by large herbivores (58%) and primates (38%). Our results suggest that camera trapping is rapidly increasing in use across Africa and potentially driven by country-based economic factors; however, there is room for improvement. CTs could be expanded in use for studies on underrepresented taxa (i.e. small mammals, reptiles and birds), investigations of human-wildlife conflict and understudied ecoregions (i.e. Sahara Desert)