| 1. |
- Allentoft, Morten E., et al.
(författare)
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Population genomics of post-glacial western Eurasia
- 2024
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 625:7994, s. 301-311
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Tidskriftsartikel (refereegranskat)abstract
- Western Eurasia witnessed several large-scale human migrations during the Holocene1–5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods—from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a ‘great divide’ genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 bp, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 bp, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a ‘Neolithic steppe’ cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.
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| 2. |
- Carvalho, Francisca C., et al.
(författare)
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Rock sponges (lithistid Demospongiae) of the Northeast Atlantic seamounts, with description of ten new species
- 2020
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Background: Lithistid demosponges, also known as rock sponges, are a polyphyletic group of sponges which are widely distributed. In the Northeast Atlantic (NEA), 17 species are known and the current knowledge on their distribution is mainly restricted to the Macaronesian islands. In the Mediterranean Sea, 14 species are recorded and generally found in marine caves.Methods: Lithistids were sampled in nine NEA seamounts during the scientific expeditions Seamount 1 (1987) and Seamount 2 (1993) organized by the MNHN of Paris. Collected specimens were identified through the analyses of external and internal morphological characters using light and scanning electron microscopy, and compared with material from various museum collections as well as literature records.Results: A total of 68 specimens were analysed and attributed to 17 species across two orders, seven families, and seven genera, representing new records of distribution. Ten of these species are new to science, viz. Neoschrammeniella inaequalis sp. nov., N. piserai sp. nov., N. pomponiae sp. nov., Discodermia arbor sp. nov., D. kellyae sp. nov., Macandrewia schusterae sp. nov., M. minima sp. nov., Exsuperantia levii sp. nov., Leiodermatium tuba sp. nov. and Siphonidium elongatus sp. nov., and are here described and illustrated. New bathymetric records were also found for D. ramifera, D. verrucosa and M. robusta. The Meteor seamount group has a higher species richness (15 species) compared to the Lusitanian seamount group (six species). The majority of the species had their distribution restricted to one seamount, and ten are only known from a single locality, but this can be a result of sample bias.Discussion: The number of species shared between the seamounts and the Macaronesian islands is very reduced. The same pattern repeats between the NEA and Mediterranean Sea. This study demonstrates that NEA seamounts are ecosystems with a higher diversity of lithistids than previously thought, increasing the number of lithistids known to occur in the NEA and Mediterranean Sea from 26 to 36 species.
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| 3. |
- Colomé, Núria, et al.
(författare)
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Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis
- 2022
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Ingår i: Journal of Proteomics. - : Elsevier. - 1874-3919 .- 1876-7737. ; 251
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Tidskriftsartikel (refereegranskat)abstract
- Global analysis of protein phosphorylation by mass spectrometry proteomic techniques has emerged in the last decades as a powerful tool in biological and biomedical research. However, there are several factors that make the global study of the phosphoproteome more challenging than measuring non-modified proteins. The low stoichiometry of the phosphorylated species and the need to retrieve residue specific information require particular attention on sample preparation, data acquisition and processing to ensure reproducibility, qualitative and quantitative robustness and ample phosphoproteome coverage in phosphoproteomic workflows. Aiming to investigate the effect of different variables in the performance of proteome wide phosphoprotein analysis protocols, ProteoRed-ISCIII and EuPA launched the Proteomics Multicentric Experiment 11 (PME11). A reference sample consisting of a yeast protein extract spiked in with different amounts of a phosphomix standard (Sigma/Merck) was distributed to 31 laboratories around the globe. Thirty-six datasets from 23 laboratories were analyzed. Our results indicate the suitability of the PME11 reference sample to benchmark and optimize phosphoproteomics strategies, weighing the influence of different factors, as well as to rank intra and inter laboratory performance.
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| 4. |
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| 5. |
- Koutsouveli, Vasiliki, et al.
(författare)
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Insights into the reproduction of some Antarctic dendroceratid, poecilosclerid, and haplosclerid demosponges
- 2018
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 13:2
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Tidskriftsartikel (refereegranskat)abstract
- Sponges are a dominant element of the Antarctic benthic communities, posing both high species richness and large population densities. Despite their importance in Antarctic ecosystems, very little is known about their reproductive patterns and strategies. In our study, we surveyed the tissue of six different species for reproductive elements, namely, Dendrilla antarctica Topsent, 1905 (order Dendroceratida), Phorbas areolatus (Thiele, 1905), Kirkpatrickia variolosa (Kirkpatrick, 1907), and Isodictya kerguelenensis (Ridley & Dendy, 1886) (order Poecilosclerida), and Hemigellius pilosus (Kirkpatrick, 1907) and Haliclona penicillata (Topsent, 1908) (Haplosclerida). Samples of these six species containing various reproductive elements were collected in Deception Island and were processed for both light and transmission electron microscopy (TEM). Even though we were not able to monitor the entire reproductive cycle, due to time and meteorological conditions, we report important aspects of the reproduction of these species. This includes oocyte and embryo morphology and cell ultrastructure, follicular structures and nurse cell activity, as well as vitellogenesis. All species were brooding their embryos within their mesohyl. Both oocytes and embryos were registered in the majority of the studied species, and a single sperm cell being carried to an egg for fertilization was observed in H. penicillata. While the reproductive periods of all species coincided temporally, some of them seemed to rely on a single spawning event, this being suggested by the synchronic oogenesis and embryogenesis occurrence of D. antarctica, P. areolatus and I. kerguelenensis. In contrast, K. variolosa had an asynchronous embryo development, which suggests several larval release events. Our results suggest that differences in the reproductive strategies and morphological traits might succeed in the coexistence of these species at the same habitat avoiding the direct competition between them.
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| 6. |
- Mancebo, Francisco J., et al.
(författare)
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Deciphering the Potential Coding of Human Cytomegalovirus: New Predicted Transmembrane Proteome
- 2022
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Ingår i: International Journal of Molecular Sciences. - : MDPI AG. - 1661-6596 .- 1422-0067. ; 23:5
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Tidskriftsartikel (refereegranskat)abstract
- CMV is a major cause of morbidity and mortality in immunocompromised individuals that will benefit from the availability of a vaccine. Despite the efforts made during the last decade, no CMV vaccine is available. An ideal CMV vaccine should elicit a broad immune response against multiple viral antigens including proteins involved in virus-cell interaction and entry. However, the therapeutic use of neutralizing antibodies targeting glycoproteins involved in viral entry achieved only partial protection against infection. In this scenario, a better understanding of the CMV prote-ome potentially involved in viral entry may provide novel candidates to include in new potential vaccine design. In this study, we aimed to explore the CMV genome to identify proteins with puta-tive transmembrane domains to identify new potential viral envelope proteins. We have performed in silico analysis using the genome sequences of nine different CMV strains to predict the trans-membrane domains of the encoded proteins. We have identified 77 proteins with transmembrane domains, 39 of which were present in all the strains and were highly conserved. Among the core proteins, 17 of them such as UL10, UL139 or US33A have no ascribed function and may be good candidates for further mechanistic studies.
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| 7. |
- Nishi, Stephanie K., et al.
(författare)
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Mediterranean, DASH, and MIND Dietary Patterns and Cognitive Function : The 2-Year Longitudinal Changes in an Older Spanish Cohort
- 2021
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Ingår i: Frontiers in Aging Neuroscience. - : Frontiers Media SA. - 1663-4365. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Background and Aims: Plant-forward dietary patterns have been associated with cardiometabolic health benefits, which, in turn, have been related to cognitive performance with inconsistent findings. The objective of this study was to examine the relationship between baseline adherence to three a priori dietary patterns (Mediterranean, DASH, and MIND diets) with 2-year changes in cognitive performance in older adults with overweight or obesity and high cardiovascular disease risk. Methods: A prospective cohort analysis was conducted within the PREDIMED-Plus trial, involving 6,647 men and women aged 55–75 years with overweight or obesity and metabolic syndrome. Using a validated, semiquantitative 143-item food frequency questionnaire completed at baseline, the dietary pattern adherence scores were calculated. An extensive neuropsychological test battery was administered at baseline and 2-year follow-up. Multivariable-adjusted linear regression models were used to assess associations between 2-year changes in cognitive function z-scores across tertiles of baseline adherence to the a priori dietary patterns. Results: Adherence to the Mediterranean diet at baseline was associated with 2-year changes in the general cognitive screening Mini-Mental State Examination (MMSE, β: 0.070; 95% CI: 0.014, 0.175, P-trend = 0.011), and two executive function-related assessments: the Trail Making Tests Part A (TMT-A, β: −0.054; 95% CI: −0.110, − 0.002, P-trend = 0.047) and Part B (TMT-B, β: −0.079; 95% CI: −0.134, −0.024, P-trend = 0.004). Adherence to the MIND diet was associated with the backward recall Digit Span Test assessment of working memory (DST-B, β: 0.058; 95% CI: 0.002, 0.114, P-trend = 0.045). However, higher adherence to the DASH dietary pattern was not associated with better cognitive function over a period of 2 years. Conclusion: In older Spanish individuals with overweight or obesity and at high cardiovascular disease risk, higher baseline adherence to the Mediterranean dietary pattern may be associated with better cognitive performance than lower adherence over a period of 2 years.
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| 8. |
- Palmer, Nicholette D, et al.
(författare)
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A genome-wide association search for type 2 diabetes genes in African Americans.
- 2012
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Ingår i: PloS one. - San Francisco : Public Library of Science (PLoS). - 1932-6203. ; 7:1, s. e29202-
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Tidskriftsartikel (refereegranskat)abstract
- African Americans are disproportionately affected by type 2 diabetes (T2DM) yet few studies have examined T2DM using genome-wide association approaches in this ethnicity. The aim of this study was to identify genes associated with T2DM in the African American population. We performed a Genome Wide Association Study (GWAS) using the Affymetrix 6.0 array in 965 African-American cases with T2DM and end-stage renal disease (T2DM-ESRD) and 1029 population-based controls. The most significant SNPs (n = 550 independent loci) were genotyped in a replication cohort and 122 SNPs (n = 98 independent loci) were further tested through genotyping three additional validation cohorts followed by meta-analysis in all five cohorts totaling 3,132 cases and 3,317 controls. Twelve SNPs had evidence of association in the GWAS (P<0.0071), were directionally consistent in the Replication cohort and were associated with T2DM in subjects without nephropathy (P<0.05). Meta-analysis in all cases and controls revealed a single SNP reaching genome-wide significance (P<2.5×10(-8)). SNP rs7560163 (P = 7.0×10(-9), OR (95% CI) = 0.75 (0.67-0.84)) is located intergenically between RND3 and RBM43. Four additional loci (rs7542900, rs4659485, rs2722769 and rs7107217) were associated with T2DM (P<0.05) and reached more nominal levels of significance (P<2.5×10(-5)) in the overall analysis and may represent novel loci that contribute to T2DM. We have identified novel T2DM-susceptibility variants in the African-American population. Notably, T2DM risk was associated with the major allele and implies an interesting genetic architecture in this population. These results suggest that multiple loci underlie T2DM susceptibility in the African-American population and that these loci are distinct from those identified in other ethnic populations.
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| 9. |
- Rios, Pilar, et al.
(författare)
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Aviles Canyon System : Increasing the benthic biodiversity knowledge
- 2022
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Ingår i: Estuarine, Coastal and Shelf Science. - : Elsevier. - 0272-7714 .- 1096-0015. ; 274
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Tidskriftsartikel (refereegranskat)abstract
- Macro and megafauna were studied in the Avile acute accent s Canyon System (ACS), southern Bay of Biscay (Cantabrian Sea), during several oceanographic cruises carried out from 2009 to 2017. The biodiversity of ACS is summarized and its description is herein updated after sampling surveys of several programmes (ECOMARG, INDEMARES, SponGES, INTEMARES) conducted by the Spanish Institute of Oceanography (IEO).This study has updated previous knowledge in the canyon area from past national and international projects, their reports and publications as well as data collected in the context of regional projects designed to gain new insight into the diversity of marine invertebrates and fishes from the ACS. Samples were taken using a range of sampling gears (Rock dredge, Beam trawl, Trawl gear GOC-73, Suprabenthic sledge, Box corer and Remoted operated vehicle), from 55 to 2291 m in depth. A total of 1015 species were identified at the ACS: 98 Porifera, 153 Cnidaria, 14 Brachiopoda, 22 Bryozoa, 97 Mollusca, 151 Annelida, 315 Arthropoda, 74 Echinodermata and 91 Chordata. New records for the Bay of Biscay fauna include 13 Porifera species, 17 Cnidaria, 7 Mollusca, Arthopoda, 3 Echinodermata and 4 Chordata. Also the bathymetric range of some species has been extended. As a result of the research projects carried out in the area in the last fifteen years, important information is now available which suggests that the ACS houses a large number of species with a high ecological value, that represents a biodiversity hotspot in terms of the presence of sponge aggregations and coral reefs in certain regions, and that it sustains important fisheries due to the abundance of comercial species. Given the relevance of the species and habitats occurring in the ACS, there is a need to implement a conservation and management plan of the area in order to maintain habitats in good state of preservation.
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| 10. |
- Taboada, Sergi, et al.
(författare)
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Genetic diversity, gene flow and hybridization in fan-shaped sponges (Phakellia spp.) in the North-East Atlantic deep sea
- 2022
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Ingår i: Deep Sea Research Part I. - : Elsevier. - 0967-0637 .- 1879-0119. ; 181
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Tidskriftsartikel (refereegranskat)abstract
- Deep-sea North Atlantic sponge grounds are crucial components of the marine fauna providing a key role in ecosystem functioning. To properly develop effective conservation and management plans, it is crucial to understand the genetic diversity, molecular connectivity patterns and turnover at the population level of the species involved. Here we present the study of two congeneric sponges, Phakellia robusta and Phakellia hirondellei, using multiple sources of evidence. Our phylogenetic study using a fragment of COI placed these two species as sister. Haplotype network analysis using COI revealed no genetic structure for P. hirondellei in samples from the Cantabrian Sea (<100 km). Contrastingly, P. robusta showed a clear genetic structure separating deep-water samples from the Cantabrian Sea and the Hatton-Rockall Basin, from samples from shallower waters from Kerry Head Reefs, NW of Orkney, and Norway. ddRADseq-derived SNPs for P. robusta also segregated samples by bathymetry rather than by geographical distances, and detected a predominant northwards migration for shallow-water specimens connecting sites separated ca. 2,000 km, probably thanks to prevalent oceanographic currents. Importantly, our analysis using SNPs combining the datasets of the two species revealed the presence of potential hybrids, which was corroborated by morphological (spicule) and microbial (16S amplicon sequencing) analyses. Our data suggest that hybridization between these two species occurred at least two times in the past. We discuss the importance of using next-generation techniques to unveil hybridization and the implications of our results for conservation.
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