10 research outputs found
The genetic structure of the rare lagoonal sea anemone, Nematostella vectensis (Cnidaria; Anthozoa) in the United Kingdom based on RAPD analysis
No full textThe sea anemone Nematostella vectensis occurs in lagoons in the United States and along the southern and eastern coasts of the United Kingdom. In the United Kingdom it is considered rare and is threatened, principally through the destruction of lagoonal habitat. Random amplified polymorphic DNA (RAPD) data from populations across most of the rane of N. vectensis in the United Kingdom revealed that 61% of individuals had an identical genotype, the frequency of which varied from 0.01 to 1.00. These data provide strong evidence for predominantly clonal reproduction and for the existence of a 'general-purpose genotype' in the UK populations. Alternatively, the low levels of genetic variation observed in some N. vectensis populations may have resulted if they were founded from very few successful individuals from the United States. Analysis of molecular variance (amova) showed significant genetic differentiation between lagoons with no large-scale pattern of geographical variation. This result is consistent with occasional passive or anthropogenic dispersal of low numbers of individuals between lagoons followed by asexual proliferation of immigrants. Transplantation of individuals of the predominant (general-purpose) genotype, for conservation purposes, will probably stand a good chance of survival given its prevalence throughout the United Kingdom
Isolation of polymorphic microsatellite markers for the demersal fish Helicolenus dactylopterus (Dela Roche 1809)
No full textSix microsatellite loci were identified for the demersal deep-sea fish Helicolenus dactylopterus. All loci were highly polymorphic (5–21 alleles per locus). Observed heterozygosities were from 0.378 to 0.868, while the expected heterozygosities ranged from 0.529 to 0.925. Multiplex PCR reactions were optimized. Microsatellite markers were developed for analysis of genetic structure including identification of stocks and migration patterns. The resulting data will be used to help in the establishment of scientifically based fisheries management for this species. Departures from the expected Hardy–Weinberg equilibrium were observed in three loci, and are likely to be a consequence of population structuring across the Azorean islands
Desigualdades en la longevidad de mujeres y hombres mayores de 65 años en España, 2008-2021. El papel de los ingresos por pensiones.
No full textAcknowledgments: We would like to thank the seminar participants at the Independent Authority for Fiscal Responsibility (AIReF, September 2023), and Peter Hall for his help with the English text.
Author Contributions: C.V.M. conceived the study and was in charge of overall direction and planning. M.R.C. and C.V.M. designed the model. J.M.P.S, M.R.C., M.V.M. and C.V.M. verified the analytical methods. J.M.P.S. contributed to sample preparation. J.M.P.S. M.R.C. and M.V.M. designed and performed the computational framework. All authors contributed to the interpretation of the results. M.R.C and C.V.M. wrote the paper with input from all authors. All authors have read and agreed to the published version of the manuscript.
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DECLARATIONS
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Competing interests: The authors declare that they have no competing interests.Studies using pensions and/or pensionable income as proxies for life expectancy are few and far between. This paper looks at Spain, a country for which until recently very little was known about the life expectancy of pensioners by pension income (PI) level. We use a large administrative data set to estimate inequalities in longevity among pensioners grouped according to their PI levels. We present the results for mortality trends among retirement pensioners aged 65 and over for nine rolling windows covering six years each for the period 2008-2021. We find that life expectancy by PI level at ages 65 (LE65) has a positive link with the PI level for both males and females, and this is true for all the periods analysed. The absolute differences in LE65 between pensioners in the highest and the lowest PI groups fluctuate across the nine rolling windows examined. For males, the differences increase from the beginning (2.67 years) until 4.06 years and then tend to decrease (2.83 years). For females there are also fluctuations (between 1.84 and 2.67 years), but the absolute differences are always smaller than those observed for males. Another finding is that socioeconomic inequality in longevity by PI group is lower when measured with M65 than LE65. We also find that the pensioner population seems to have been more affected by the COVID-19 pandemic than the general population and that two groups of pensioners – the lowest PI group of males and the highest PI group of females – appear to have improved their longevity during the pandemic.Los estudios que utilizan la cuantía de la pensión y/o la base reguladora como indicadores de la esperanza de vida son escasos. Este trabajo se centra en España, un país del que hasta hace poco se sabía muy poco sobre la esperanza de vida de los pensionistas según la cuantía de la pensión de jubilación (IP). Se utiliza un amplio conjunto de datos administrativos para estimar las desigualdades en longevidad entre pensionistas agrupados según cuantía de pensión (IP). Se presentan resultados de las tendencias de la mortalidad entre los pensionistas de 65 años o más para nueve ventanas móviles de seis años cada una para el periodo 2008-2021. Se encuentra que la esperanza de vida por cuantía de pensión (IP) a los 65 años (LE65) tiene una relación positiva tanto para hombres como para mujeres, y esto es así para todos los periodos analizados. Las diferencias absolutas en la LE65 entre los pensionistas con mayor y menor cuantía fluctúan a lo largo de las nueve ventanas móviles examinadas. En el caso de los hombres, las diferencias aumentan desde el principio (2,67 años) hasta los 4,06 años y luego tienden a disminuir (2,83 años). En el caso de las mujeres también hay fluctuaciones (entre 1,84 y 2,67 años), pero las diferencias absolutas son siempre menores que las observadas en los hombres. Otra conclusión es que la desigualdad socioeconómica en la longevidad por cuantía (IP) es menor cuando se mide con la moda (M65) que con LE65. También observamos que la población de pensionistas parece haberse visto más afectada por la pandemia de COVID-19 que la población general y que dos grupos de pensionistas -el grupo de varones con menor cuantía y el grupo de mujeres con mayor - parecen haber mejorado su longevidad durante la pandemia.Ministerio de Ciencia, Innovación y Universidades (España)Eusko JaurlaritzaDepto. de Análisis Económico y Economía CuantitativaInstituto Complutense de Análisis Económico (ICAE)TRUEpu
Galaxolide and tonalide modulate neuroendocrine activity in marine species from two taxonomic groups
No full textGalaxolide (HHCB) and tonalide (AHTN) are polycyclic musk compounds (PMCs) used in household and personal care products that have been included on the list as emerging contaminants of environmental concern due to their ubiquity in aquatic and terrestrial environments. There still exists a dearth of information on the neurotoxicity and endocrine disrupting effects of these contaminants, especially for marine and estuarine species. Here, we assessed the neuroendocrine effects of HHCB and AHTN using adult clams, Ruditapes philippinarum, and yolk-sac larvae of sheepshead minnow, Cyprinodon variegatus. The clams were treated with concentrations (0.005–50 μg/L) of each compound for 21 days. Meanwhile, sheepshead minnow larvae were exposed to 0.5, 5 and 50 μg/L of HHCB and AHTN for 3 days. Enzyme activities related to neurotoxicity (acetylcholinesterase - AChE), neuroendocrine function (cyclooxygenase - COX), and energy reserves (total lipids - TL) were assessed in R. philippinarum. Gene expression levels of cyp19 and vtg1 were measured in C. variegatus using qPCR. Our results indicated induction of AChE and COX in the clams exposed to HHCB while AHTN exposure significantly inhibited AChE and COX. Gene expression of cyp19 and vtg1 in yolk-sac C. variegatus larvae exposed to 50 μg/L AHTN was significantly downregulated versus the control. The results of this study demonstrate that HHCB and AHTN might pose neurotoxic and endocrine disrupting effects in coastal ecosystems.This research was supported by the Spanish Ministry of Economy and Competitiveness (Ref. CTM2012-37591), FEDER Funds from the European Union. The first author sincerely appreciates the Erasmus + KA 107 UCA grant for the research stay at the University of Southern Mississippi. C.V.M. Araújo is grateful to the Spanish Ministry of Science and Innovation for the Ramón y Cajal (RYC-2017-22324) contract
Avoidance responses by Danio rerio reveal interactive effects of warming, pesticides and their mixtures
No full textTemperature variations and thermal extremes events caused by climate change can have profound implications for the toxicity of pesticides in aquatic organisms. Using an innovative system (Heterogeneous Multi-Habitat Test System - HeMHAS) that allows the simulation of different scenarios within a spatially heterogeneous landscape, the effects on the habitat selection of Danio rerio fish caused by the pesticides fipronil and 2,4-D were studied as single compounds and in mixture and integrated with air temperature variation (20, 24 and 28 °C). As a result, D. rerio detected and avoided both pesticides at air temperatures of 20 and 24 °C; however, at 28 °C no significant difference was observed in habitat choice by fish. Additionally, when pesticides were mixed in a heterogeneously contaminated landscape, it was observed that D. rerio detected contamination and preferred the clean zone at 20 and 24 °C; however, at 28 °C the potential to escape from the most contaminated areas was impaired. Thus, contamination by both pesticides made the habitat selection behavior of fish at 20 and 24 °C more noticeable. In addition, the association between pesticides and temperature showed negative effects on the response of fish to detect and escape from contaminated environments, suggesting the influence of temperature in altering the ability of the organism to provide an efficient response to stress.R.A. Moreira would like to thank the São Paulo Research Foundation “Fundação de Amparo à Pesquisa do Estado de São Paulo” (FAPESP) for the post doctorate grant to the first author (Process number: 2020/16131-0 and 2017/24126-4). Financial support was also provided by FAPESP (2015/18790-3). C.V.M. Araújo is grateful to the grant (Ramón y Cajal contract: RYC-2017-22324) funded by MCIN/AEI/10.13039/501100011033 and by “ESF Investing in your future”. This research was funded by MCIN/AEI/10.13039/501100011033 (BrEStress project: PID2019-105868RA-I00) and i-COOP2019 program from CSIC (MultiCecotox project: #COOPB20444).Peer reviewe
Robust BRCA1-like classification of copy number profiles of samples repeated across different datasets and platforms
No full textBreast cancers with BRCA1 germline mutation have a characteristic DNA copy number (CN) pattern. We developed a test that assigns CN profiles to be ‘BRCA1-like’ or ‘non-BRCA1-like’, which refers to resembling a BRCA1-mutated tumor or resembling a tumor without a BRCA1 mutation, respectively. Approximately one third of the BRCA1-like breast cancers have a BRCA1 mutation, one third has hypermethylation of the BRCA1 promoter and one third has an unknown reason for being BRCA1-like. This classification is indicative of patients' response to high dose alkylating and platinum containing chemotherapy regimens, which targets the inability of BRCA1 deficient cells to repair DNA double strand breaks. We investigated whether this classification can be reliably obtained with next generation sequencing and copy number platforms other than the bacterial artificial chromosome (BAC) array Comparative Genomic Hybridization (aCGH) on which it was originally developed. We investigated samples from 230 breast cancer patients for which a CN profile had been generated on two to five platforms, comprising low coverage CN sequencing, CN extraction from targeted sequencing panels (CopywriteR), Affymetrix SNP6.0, 135K/720K oligonucleotide aCGH, Affymetrix Oncoscan FFPE (MIP) technology, 3K BAC and 32K BAC aCGH. Pairwise comparison of genomic position-mapped profiles from the original aCGH platform and other platforms revealed concordance. For most cases, biological differences between samples exceeded the differences between platforms within one sample. We observed the same classification across different platforms in over 80% of the patients and kappa values of at least 0.36. Differential classification could be attributed to CN profiles that were not strongly associated to one class. In conclusion, we have shown that the genomic regions that define our BRCA1-like classifier are robustly measured by different CN profiling technologies, providing the possibility to retro- and prospectively investigate BRCA1-like classification across a wide range of CN platforms.Intelligent SystemsElectrical Engineering, Mathematics and Computer Scienc
Genetic factors associated with a poor outcome in head and neck cancer patients receiving definitive chemoradiotherapy
No full textAbout half of advanced stage head and neck squamous cell carcinoma (HNSCC) patients can be cured by chemoradiotherapy. Patient outcome may be partially determined by the genetic alterations in HNSCC, rendering these alterations promising candidate prognostic factors and/or therapeutic targets. However, their relevance in patient outcome prognosis remains to be assessed in patients that receive standard-of-care chemoradiotherapy. We therefore tested whether frequent genetic alterations were associated with progression free survival (PFS) in advanced stage HNSCC patients who were uniformly treated with definitive platinum-based chemoradiotherapy. To this end, we performed targeted DNA sequencing on frozen pre-treatment tumor biopsy material from 77 patients with advanced stage oro- and hypopharyngeal carcinoma. This provided somatic point mutation and copy number aberration data of 556 genes. The most frequently mutated genes, TP53 (62%), CCND1 (51%), CDKN2A (30%) and PIK3CA (21%), were not associated with PFS. However, co-occurring CCND1 and CDKN2A mutations were associated with short PFS (HR 2.24, p = 0.028) in HPV-negative tumors. Furthermore, tumor mutational burden (sum of somatic point mutations) showed a trend towards decreased PFS (HR 1.9, p = 0.089), and chromosomal instability (CIN) was associated with shorter PFS (HR 2.3, p = 0.023), independent of HPV status. Our results show that tumor mutational burden, CIN markers, and co-occurring CCND1 and CDKN2A mutations are associated with chemoradiotherapy outcomes in advanced stage oro- and hypopharyngeal HNSCC patients, thereby highlighting their prognostic potential. Given their poor prognosis association and link to biological targets, they may also identify patients for novel targeted therapies and immunotherapie
Role of variant allele fraction and rare SNP filtering to improve cellular DNA repair endpoint association
No full textBackground Large cancer genome studies continue to reveal new players in treatment response and tumorigenesis. The discrimination of functional alterations from the abundance of passenger genetic alterations still poses challenges and determines DNA sequence variant selection procedures. Here we evaluate variant selection strategies that select homozygous variants and rare SNPs and assess its value in detecting tumor cells with DNA repair defects. Methods To this end we employed a panel of 29 patient-derived head and neck squamous cell carcinoma (HNSCC) cell lines, of which a subset harbors DNA repair defects. Mitomycin C (MMC) sensitivity was used as functional endpoint of DNA crosslink repair deficiency. 556 genes including the Fanconi anemia (FA) and homologous recombination (HR) genes, whose products strongly determine MMC response, were capture-sequenced. Results We show a strong association between MMC sensitivity, thus loss of DNA repair function, and the presence of homozygous and rare SNPs in the relevant FA/HR genes. Excluding such selection criteria impedes the discrimination of crosslink repair status by mutation analysis. Applied to all KEGG pathways, we find that the association with MMC sensitivity is strongest in the KEGG FA pathway, therefore also demonstrating the value of such selection strategies for exploratory analyses. Variant analyses in 56 clinical samples demonstrate that homozygous variants occur more frequently in tumor suppressor genes than oncogenes further supporting the role of a homozygosity criterion to improve gene function association or tumor suppressor gene identification studies. Conclusion Together our data show that the detection of relevant genes or of repair pathway defected tumor cells can be improved by the consideration of allele zygosity and SNP allele frequencies.Pattern Recognition and Bioinformatic
The fate of carbon in a mature forest under carbon dioxide enrichment
No full textAtmospheric carbon dioxide enrichment (eCO2) can enhance plant carbon uptake and growth1 5, thereby providing an important negative feedback to climate change by slowing the rate of increase of the atmospheric CO2 concentration6. Although evidence gathered from young aggrading forests has generally indicated a strong CO2 fertilization effect on biomass growth3 5, it is unclear whether mature forests respond to eCO2 in a similar way. In mature trees and forest stands7 10, photosynthetic uptake has been found to increase under eCO2 without any apparent accompanying growth response, leaving the fate of additional carbon fixed under eCO2 unclear4,5,7 11. Here using data from the first ecosystem-scale Free-Air CO2 Enrichment (FACE) experiment in a mature forest, we constructed a comprehensive ecosystem carbon budget to track the fate of carbon as the forest responded to four years of eCO2 exposure. We show that, although the eCO2 treatment of +150 parts per million (+38 per cent) above ambient levels induced a 12 per cent (+247 grams of carbon per square metre per year) increase in carbon uptake through gross primary production, this additional carbon uptake did not lead to increased carbon sequestration at the ecosystem level. Instead, the majority of the extra carbon was emitted back into the atmosphere via several respiratory fluxes, with increased soil respiration alone accounting for half of the total uptake surplus. Our results call into question the predominant thinking that the capacity of forests to act as carbon sinks will be generally enhanced under eCO2, and challenge the efficacy of climate mitigation strategies that rely on ubiquitous CO2 fertilization as a driver of increased carbon sinks in global forests. © 2020, The Author(s), under exclusive licence to Springer Nature Limited
Australian Individual Tree Biomass Library- v4
No full textBiomass sampling: Various methods were used. But all involved harvesting individual trees or shrubs and measuring the fresh weight of the above-ground biomass. Sub-sampling was used to determine moisture content. Then dry weight of the above-ground biomass was calculated.<p><b>Credit</b><br/>We at TERN acknowledge the Traditional Owners and Custodians throughout Australia, New Zealand and all nations. We honour their profound connections to land, water, biodiversity and culture and pay our respects to their Elders past, present and emerging.<br/>We thank the Australian Government's Department of the Environment for funding this work. Assistance with data collation was also provided by Coral Allan, Grant Allan, John Bartle, Jason Barnetson, Rick Bennett, Coline Bourru, Mark Brammar, Steven Bray, Mila Bristow, Don Butler, Rob Chambers, Vanessa Chewings, Robin Cromer, Mike Cully, Eve Damm, Micah Davies, Alex Drew, Robert Eager, Tom Fairman, Ben Finn, David Freudenberger, Sean Gleason, Bob Hingston, Mark Hunt, Bruce Hogg, Laura Kmoch, Rob Law, Hamish Luck, Tracey May, Rick Giles, Gordon McLachlan, Geoff Minchin, Simon Murphy, Matt Nicholson, Jaymie Norris, Len Norris, Craig Neumann, Anthony O'Connell, David Osborne, Dailiang Peng, John Raison, Sandra Roberts, Harry Roberts, Ben Rose, Katelyn Ryan, Tim Smith, Adam Smith, Scott Swift, Mervyn Tucker, Brendan Vollemaere, Paul Warburton, Peter Walsh, Ray Wilson, Stephanie Wilson, Alex Winter, Ralph Woodford, Fabinao Ximenes, and Byron Yeo. We also thank the property owners and managers who allowed us to sample their trees for above-ground biomass. In addition to the organisations of the contributing authors, we also acknowledge Oil Mallee Association of Australia Inc, Carbon Neutral, Northern Agricultural Catchments Council, Cooperative Research Centre for Greenhouse Accounting, RIRDC, University of New England, Queensland Forestry Department, and WA Plantation Resources. Older datasets of D. Ashton, J. Lewis, W. Forrest, J. Dargavel, W. Westman, R. Rogers, P. Baldwin, H. Stewart, F. Hingston, M. Lambert, R. Cromer are acknowledged. See sources below. Forrest WG (1969) Variations in the accumulation, distribution and movement of mineral nutrients in radiata pine plantations. Ph.D. Thesis. Australian National University, Canberra. Dargavel JB (1970) Provisional tree weight tables for radiata pine. Australian Forestry, 34: 131-140. Forrest W, Ovington J (1970) Organic Matter Changes in an Age Series of Pinus radiata Plantations. Journal of Applied Ecology, 7, 177-186. Ashton D (1976) Phosphorus in Forest Ecosystems at Beenak, Victoria. Journal of Ecology, 64, 171-186. Westman, WE, Rogers RW (1977) Biomass and structure of a subtropical eucalypt forest, north Stradbroke Island. Australian Journal of Botany, 25, 171-191. Lewis JW (1978) Ecological studies of coastal forests and its regeneration after mining. PhD Thesis, University of Queensland, Brisbane. Lambert MJ (1979) Sulphur relationships of native and exotic species. MSc(Hons) thesis, Macquarie Uni. 170pp. Cromer R, Williams E (1982) Biomass and Nutrient Accumulation in a Planted E. globulus (Labill.) Fertilizer Trial. Australian Journal of Botany, 30, 265-278. Baldwin PJ, Stewart HTL (1987) Distribution, length and weight of roots in young plantations of Eucalyptus grandis W. Hill ex. Maiden irrigated with recycled water. Plant Soil, 97, 243-252 Cromer RN, Cameron DM, Rance SJ, Ryan PA, Brown M (1993). Response to nutrients in Eucalyptus grandis. 1. Biomass accumulation. Forest Ecology and Management, 62, 211-230. Hingston F, Galbraith J (1998) Application of the process-based model BIOMASS to Eucalyptus globulus ssp. globulus plantations on ex-farmland in south western Australia. Forest Ecology and Management, 106, 157-168. Hingston F, Galabraith J, Jones M (1990) Dimensional data for trees at several sites in northern Jarrah (Eucalyptus marginata) forest. DFFP Division of Forestry and Forestry Products User Series. No. 11.<b>Purpose</b><br/>The data on individual tree or shrub biomass were derived from numerous projects over the last five decades. Support was given to collate these datasets under the Complex Woody Systems Project (MDP-CWS) funded by the Australian Department of the Environment's Methodology Development Program and CSIRO. The objective of the MDP-CWS project was to develop tools and information to underpin increased land manager participation in the domestic carbon market; the Emissions Reduction Fund (ERF). However, the intention is that this database will be expanded over time and have broader use beyond supporting carbon accounting methodologies.Progress Code: completedMaintenance and Update Frequency: notPlannedThis data set is a compilation of individual tree and shrub above-ground biomass (dry weight), stem diameter, height, and associated auxiliary information about the sites from which the trees or shrubs were sampled. The data were derived from numerous different projects over the last 5 decades. However, the project under which support was given to collate these datasets was Australia's Department of the Environments Methodology Development Program's Complex Wood System Project (MDP-CWS). The objective of the MDP-CWS project was to develop tools and information to underpin increased land manager participation in the domestic carbon market; the Emissions Reduction Fund (ERF). However, the intention is that this database will be expanded over time and have much greater use than just supporting carbon accounting methodologies.
See publication for details: "Keryn I. Paul, John Larmour, Alison Specht, Ayalsew Zerihun, Peter Ritson, Stephen H. Roxburgh, Stan Sochacki, Tom Lewis, Craig V.M. Barton, Jacqueline R. England, Michael Battaglia, Anthony O'Grady, Elizabeth Pinkard, Grahame Applegate, Justin Jonson, Kim Brooksbank, Rob Sudmeyer, Dan Wildy, Kelvin D. Montagu, Matt Bradford, Don Butler, Trevor Hobbs, Testing the generality of below-ground biomass allometry across plant functional types, Forest Ecology and Management. 432: 102-114. https://doi.org/10.1016/j.foreco.2018.08.043.
Paul, K.I., Larmour, J., Specht, A., Zerihun, A., Ritson, P., Roxburgh, S.H., Sochacki, S., Lewis, T., Barton, C.V.M., England, J.R., Battaglia, M., O’Grady, A., Pinkard, E., Applegate, G., Jonson, J., Brooksbank, K., Sudmeyer, R., Wildy, D., Montagu, K.D., Bradford, M., Butler, D., Hobbs, T., 2019. Testing the generality of below-ground biomass allometry across plant functional types. Forest Ecology and Management 432, 102–114. https://doi.org/10.1016/j.foreco.2018.08.04
