The role of recent admixture in forming the contemporary West Eurasian genomic landscape

Over the past few years, studies of DNA isolated from human fossils and archaeological remains have generated considerable novel insight into the history of our species. Several landmark papers have described the genomes of ancient humans across West Eurasia, demonstrating the presence of large-scale, dynamic population movements over the last 10,000 years, such that ancestry across present-day populations is likely to be a mixture of several ancient groups [1-7]. While these efforts are bringing the details of West Eurasian prehistory into increasing focus, studies aimed at understanding the processes behind the generation of the current West Eurasian genetic landscape have been limited by the number of populations sampled or have been either too regional or global in their outlook [8-11]. Here, using recently described haplotype-based techniques [11], we present the results of a systematic survey of recent admixture history across Western Eurasia and show that admixture is a universal property across almost all groups. Admixture in all regions except North Western Europe involved the influx of genetic material from outside of West Eurasia, which we date to specific time periods. Within Northern, Western, and Central Europe, admixture tended to occur between local groups during the period 300 to 1200 CE. Comparisons of the genetic profiles of West Eurasians before and after admixture show that population movements within the last 1,500 years are likely to have maintained differentiation among groups. Our analysis provides a timeline of the gene flow events that have generated the contemporary genetic landscape of West Eurasia

Alpha-1 antitrypsin gene polymorphism in Chronic Obstructive Pulmonary Disease (COPD)

Alpha-1-antitrypsin (AAT) plays an important role in the pathogenesis of emphysema, the pathological lesion underlying the majority of the manifestations of Chronic Obstructive Pulmonary Disease (COPD). In this study we tested the hypothesis that common AAT polymorphisms influence the risk of developing COPDs. We investigated PiM1 (Ala213Val), PiM2 (Arg101His), PiM3 (Glu376Asp), PiS (Glu264Val) and PiZ (Glu342Lys) SERPINA1 alleles in 100 COPD patients and 200 healthy controls. No significant differences were observed in allele frequencies between COPD patients and controls, neither did haplotype analysis show significant differences between the two groups. A cross-sectional study revealed no significant relationship between common SERPINA1 polymorphisms (PiM1, PiM2, PiM3) and the emphysematous type of COPD. In addition, FEV1 annual decline, determined during a two-year follow up period, revealed no difference among carriers of the tested polymorphisms

Unforeseen plant phenotypic diversity in a dry and grazed world

23 páginas..- 4 figuras y 7 figuras.- 50 referencias y 90 referenciasEarth harbours an extraordinary plant phenotypic diversity1 that is at risk from ongoing global changes2,3. However, it remains unknown how increasing aridity and livestock grazing pressure—two major drivers of global change4,5,6—shape the trait covariation that underlies plant phenotypic diversity1,7. Here we assessed how covariation among 20 chemical and morphological traits responds to aridity and grazing pressure within global drylands. Our analysis involved 133,769 trait measurements spanning 1,347 observations of 301 perennial plant species surveyed across 326 plots from 6 continents. Crossing an aridity threshold of approximately 0.7 (close to the transition between semi-arid and arid zones) led to an unexpected 88% increase in trait diversity. This threshold appeared in the presence of grazers, and moved toward lower aridity levels with increasing grazing pressure. Moreover, 57% of observed trait diversity occurred only in the most arid and grazed drylands, highlighting the phenotypic uniqueness of these extreme environments. Our work indicates that drylands act as a global reservoir of plant phenotypic diversity and challenge the pervasive view that harsh environmental conditions reduce plant trait diversity8,9,10. They also highlight that many alternative strategies may enable plants to cope with increases in environmental stress induced by climate change and land-use intensification.This research was funded by the European Research Council (ERC Grant agreement 647038 1004 [BIODESERT]) and Generalitat Valenciana (CIDEGENT/2018/041). N.G. was supported by CAP 20–25 (16-IDEX-0001) and the AgreenSkills+ fellowship programme which has received funding from the European Union’s Seventh Framework Programme under grant agreement FP7-609398 (AgreenSkills+ contract). F.T.M. acknowledges support from the King Abdullah University of Science and Technology (KAUST), the KAUST Climate and Livability Initiative, the University of Alicante (UADIF22-74 and VIGROB22-350), the Spanish Ministry of Science and Innovation (PID2020-116578RB-I00), and the Synthesis Center (sDiv) of the German Centre for Integrative Biodiversity Research Halle–Jena–Leipzig (iDiv). Y.L.B.-P. was supported by a Marie Sklodowska-Curie Actions Individual Fellowship (MSCA-1018 IF) within the European Program Horizon 2020 (DRYFUN Project 656035). H.S. is supported by a María Zambrano fellowship funded by the Ministry of Universities and European Union-Next Generation plan. L.W. acknowledges support from the US National Science Foundation (EAR 1554894). G.M.W. acknowledges support from the Australian Research Council (DP210102593) and TERN. M.B is supported by a Ramón y Cajal grant from Spanish Ministry of Science (RYC2021-031797-I). L.v.d.B. and K.T. were supported by the German Research Foundation (DFG) Priority Program SPP-1803 (TI388/14-1). A.F. acknowledges the financial support from ANID PIA/BASAL FB210006 and Millenium Science Initiative Program NCN2021-050. A.J. was supported by the Bavarian Research Alliance for travel and field work (BayIntAn UBT 2017 61). A.L. and L.K. acknowledge support from the German Research Foundation, DFG (grant CRC TRR228) and German Federal Government for Science and Education, BMBF (grants 01LL1802C and 01LC1821A). B.B. and S.U. were supported by the Taylor Family-Asia Foundation Endowed Chair in Ecology and Conservation Biology. P.J.R. and A.J.M. acknowledge support from Fondo Europeo de Desarrollo Regional through the FEDER Andalucía operative programme, FEDER-UJA 1261180 project. E.M.-J. and C.P. acknowledge support from the Spanish Ministry of Science and Innovation (PID2020-116578RB-I00). D.J.E. was supported by the Hermon Slade Foundation. J.D. and A.Rodríguez acknowledge support from the FCT (2020.03670.CEECIND and SFRH/BDP/108913/2015, respectively), as well as from the MCTES, FSE, UE and the CFE (UIDB/04004/2021) research unit financed by FCT/MCTES through national funds (PIDDAC). S.C.R. acknowledges support from the US Department of Energy (DE-SC-0008168), US Department of Defense (RC18-1322), and the US Geological Survey Ecosystems Mission Area. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the US government. E.H.-S. acknowledges support from Mexican National Science and Technology Council (CONACYT PN 5036 and 319059). A.N. and C. Branquinho. acknowledge the support from FCT—Fundação para a Ciência e a Tecnologia (CEECIND/02453/2018/CP1534/CT0001, PTDC/ASP-SIL/7743/ 2020, UIDB/00329/2020), from AdaptForGrazing project (PRR-C05-i03-I-000035) and from LTsER Montado platform (LTER_EU_PT_001). Field work of G.P. and J.M.Z. was supported by UNRN (PI 40-C-873).Peer reviewe

Hotspots of biogeochemical activity linked to aridity and plant traits across global drylands

14 páginas.- 4 figuras.- 67 referencias.- The online version contains supplementary material available at https://doi.org/10.1038/s41477-024-01670-7Perennial plants create productive and biodiverse hotspots, known as fertile islands, beneath their canopies. These hotspots largely determine the structure and functioning of drylands worldwide. Despite their ubiquity, the factors controlling fertile islands under conditions of contrasting grazing by livestock, the most prevalent land use in drylands, remain virtually unknown. Here we evaluated the relative importance of grazing pressure and herbivore type, climate and plant functional traits on 24 soil physical and chemical attributes that represent proxies of key ecosystem services related to decomposition, soil fertility, and soil and water conservation. To do this, we conducted a standardized global survey of 288 plots at 88 sites in 25 countries worldwide. We show that aridity and plant traits are the major factors associated with the magnitude of plant effects on fertile islands in grazed drylands worldwide. Grazing pressure had little influence on the capacity of plants to support fertile islands. Taller and wider shrubs and grasses supported stronger island effects. Stable and functional soils tended to be linked to species-rich sites with taller plants. Together, our findings dispel the notion that grazing pressure or herbivore type are linked to the formation or intensification of fertile islands in drylands. Rather, our study suggests that changes in aridity, and processes that alter island identity and therefore plant traits, will have marked effects on how perennial plants support and maintain the functioning of drylands in a more arid and grazed world.This research was supported by the European Research Council (ERC grant 647038 (BIODESERT) awarded to F.T.M.) and Generalitat Valenciana (CIDEGENT/2018/041). D.J.E. was supported by the Hermon Slade Foundation (HSF21040). J. Ding was supported by the National Natural Science Foundation of China Project (41991232) and the Fundamental Research Funds for the Central Universities of China. M.D.-B. acknowledges support from TED2021-130908B-C41/AEI/10.13039/501100011033/Unión Europea Next Generation EU/PRTR and the Spanish Ministry of Science and Innovation for the I + D + i project PID2020-115813RA-I00 funded by MCIN/AEI/10.13039/501100011033. O.S. was supported by US National Science Foundation (Grants DEB 1754106, 20-25166), and Y.L.B.-P. by a Marie Sklodowska-Curie Actions Individual Fellowship (MSCA-1018 IF) within the European Program Horizon 2020 (DRYFUN Project 656035). K.G. and N.B. acknowledge support from the German Federal Ministry of Education and Research (BMBF) SPACES projects OPTIMASS (FKZ: 01LL1302A) and ORYCS (FKZ: FKZ01LL1804A). B.B. was supported by the Taylor Family-Asia Foundation Endowed Chair in Ecology and Conservation Biology, and M. Bowker by funding from the School of Forestry, Northern Arizona University. C.B. acknowledges funding from the National Natural Science Foundation of China (41971131). D.B. acknowledges support from the Hungarian Research, Development and Innovation Office (NKFI KKP 144096), and A. Fajardo support from ANID PIA/BASAL FB 210006 and the Millennium Science Initiative Program NCN2021-050. M.F. and H.E. received funding from Ferdowsi University of Mashhad (grant 39843). A.N. and M.K. acknowledge support from FCT (CEECIND/02453/2018/CP1534/CT0001, SFRH/BD/130274/2017, PTDC/ASP-SIL/7743/2020, UIDB/00329/2020), EEA (10/CALL#5), AdaptForGrazing (PRR-C05-i03-I-000035) and LTsER Montado platform (LTER_EU_PT_001) grants. O.V. acknowledges support from the Hungarian Research, Development and Innovation Office (NKFI KKP 144096). L.W. was supported by the US National Science Foundation (EAR 1554894). Y.Z. and X.Z. were supported by the National Natural Science Foundation of China (U2003214). H.S. is supported by a María Zambrano fellowship funded by the Ministry of Universities and European Union-Next Generation plan. The use of any trade, firm or product names does not imply endorsement by any agency, institution or government. Finally, we thank the many people who assisted with field work and the landowners, corporations and national bodies that allowed us access to their land.Peer reviewe

Rapid genotyping of alpha 1 antitrypsin deletion mutation (PI*Mmalton) using Bi-directional PCR allele-specific amplification

Alpha 1 antitrypsin deficiency (AATD) is a well recognized genetic risk factor for pulmonary disease and less common liver disease. The two most common deficiency alleles worldwide PI*S and PI*Z can be easily detected using several molecular methods. However, there are at least 30 other AATD variants, which are only detectable by alpha 1 antitrypsin (AAT) gene sequencing and, therefore, seem to be more under-recognized than the PI*S and PI*Z alleles. PI*Mmalton is the most frequent AATD variant in different regions of the Southern Mediterranean basin countries, where its prevalence seems to prevail over PI*S and PI*Z. In this work, we report the development of a simple PCR-based analysis designed for the detection of the PI*Mmalton deficiency alleles using two specific primers. A one-tube reaction enables the distinction between the different genotypes. This reliable, easy, fast, and low-cost technique might be useful for laboratories involved in the study of AATD-related diseases, especially those of the Southern Mediterranean basin area with modest budget or where sophisticated equipment is not available. This will allow larger targeted screening for PI*Mmalton in order to better understand this mutation epidemiology and its origin. \ua9 Springer Science+Business Media, LLC 2010

Glycemia balance impact on oxidant-antioxidant status balance in Tunisian patients with type 2 diabetesL\u27impact de l\u27\ue9quilibre glyc\ue9mique sur le statut oxydant-antioxydant dans un \ue9chantillon de diab\ue9tiques de type 2 tunisiens

The aim of this study was to investigate glycemia balance impact on oxidant-antioxidant status. Patients and methods: The study was carried out on 200 patients with type 2 diabetes and 200 healthy subjects. Glycemia, glycated hemoglobin, insulin, hydrogen peroxide, homocysteine, total antioxidant status, superoxide dismutase, glutathione peroxidase and zinc were assayed using colorimetric methods. Thiobarbituric acid reactive substances in LDL were measured by fluoremetric method. LDL polyunsaturated fatty acids quantification was measured by gas chromatography and vitamins A-E was by high-performance liquid chromatography. Quantitative insulin check index was calculated by Perseghin et al.\u27s equation. Results: Thiobarbituric acid reactive substances in LDL, hydrogen peroxide and homocysteine significantly increased whereas LDL polyunsaturated fatty acids, total antioxidant status, vitamins A-E, zinc, insulin and quantitative insulin check index significantly decreased in diabetes compared to controls. Total antioxidant status and superoxide dismutase activity depended on glycated hemoglobin and hydrogen peroxide. Diabetes group presenting glycated hemoglobin greater than 9% had the smallest insulin concentration and quantitative insulin check index value and the highest oxidant stress parameters. Conclusion: Unbalanced glycaemia produces an oxidant stress which is implicated in insulin sensitivity decrease in type 2 diabetes. \ua9 2012

Glutathione-s-transferases GSTM1 and GSTT1 genetic polymorphisms and colorectal cancer onset in a sample of Tunisian population / Polymorphisme g\ue9n\ue9tique des glutathion-s-transf\ue9rases GSTM1 et GSTT1 et survenue d\u27un cancer colorectal dans un \ue9chantillon de la population tunisienne

Individual susceptibility to colorectal cancer (CRC) may be partly due to genetic differences in detoxification and/or activation of xenobiotics. This study was carried out pointing GSTT1 and GSTM1 polymorphisms on the risk of CRC development. Taking into account the important impact of diet in CRC development and prevention, this study explored the correlation of certain foods (fast food, fish, salami, red meat and poultry) with CRC occurrence. Ninety-one patients and 127 controls from the Tunisian population, all from the Sahel region, were enrolled in this study. No association between the GSTM1 gene polymorphism and the CRC was found. However, an association between the GSTT1 gene polymorphism and the risk of CRC was encountered (P=0.039, OR = 0.53, CI: 0.29-0.97). Our results revealed a significant correlation between fast food consumption and CRC occurrence (P=0.00015; correlation coefficient = 0.258), whereas fish consumption was inversely correlated to CRC incidence (P=0.049; correlation coefficient = -0.136). In conclusion, the homozygous null GSTT1 gene may be considered as a protective factor CRC onset. Unlike fast food consumption, fish consumption appeared to be a protector factor. \ua9 2012 Elsevier Masson SAS