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The effects of death and post-mortem cold ischemia on human tissue transcriptomes

Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and the post-mortem interval (PMI) can significantly alter physiologically normal RNA levels. We investigate the impact of PMI on gene expression using data from multiple tissues of post-mortem donors obtained from the GTEx project. We find that many genes change expression over relatively short PMIs in a tissue-specific manner, but this potentially confounding effect in a biological analysis can be minimized by taking into account appropriate covariates. By comparing ante- and post-mortem blood samples, we identify the cascade of transcriptional events triggered by death of the organism. These events do not appear to simply reflect stochastic variation resulting from mRNA degradation, but active and ongoing regulation of transcription. Finally, we develop a model to predict the time since death from the analysis of the transcriptome of a few readily accessible tissues.This work was supported by the following grants and contracts: 1) From the US NIH: Contract HHSN261200800001E (Leidos Prime contract with NCI); Contracts 10XS170 (NDRI), 10XS171 (Roswell Park Cancer Institute), 10 × 172 (Science Care Inc.), and 12ST1039 (IDOX); Contract 10ST1035 (Van Andel Institute); Contract HHSN268201000029C (Broad Institute); R01 DA006227-17 (U Miami Brain Bank) 2) Ipatimup and i3s are partially funded by the Portuguese Foundation for Science and Technology (FCT); FEDER funds through the COMPETE 2020—Operacional Programme for Competitiveness and Internationalization (POCI), Portugal 2020, and by Portuguese funds through FCT/MCTES in the framework POCI-01-0145-FEDER-007274; 3) NORTE-01-0145-FEDER-000029, supported by NORTE 2020, under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF); 4) FCT Fellowships SFRH/BPD/89764/2012 to PO, PD/BD/128007/2016 to AS; Salary support to PGF by POPH—QREN Type 4.2, European Social Fund and MCTES, program Investigador FCT, IF/01127/2014. 5) BIO2014-57291-R from the Spanish Ministry of Economy and Competitiveness and “Plataforma de Recursos Biomoleculares y Bioinformáticos” PT13/0001/0007 from the ISCIII, and EU H2020-INFRADEV-1-2015-1 ELIXIR-EXCELERATE (ref. 6,676559) Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’ and CERCA Programme/Generalitat de Catalunya, 7) Ministerio de Educación, Cultura y Deporte, under the FPU programme (Formación de Profesorado Universitario) with pre-doctoral fellowship FPU15/03635 to MMA. 8) Award Number 1R01MH101814 and 3R01MH101814-03S1 from the National Human Genome Research Institute. European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC grant agreement RNA-MAPS_294653, Ministerio de Economía, Industria y Competitividad, referencia MEIC BIO2015-70777-P y los Fondos Estructurales de la Unión Europea (FEDER) and ISCIII del Ministerio de Economía y Competitividad, referencia PT13/0001/0021 cofinaciada por el Fondo Europeo de Desarrollo Regional (FEDER). 9) MS received funding from CNPq (grant 310132/2015-0 and 427541/2016-6), and from FAPERJ (grant E_06/2015)

Floristic and phytosociology in permanent plots of the Atlantic Rainforest along an altitudinal gradient in southeastern Brazil

This paper summarizes floristic and phytossociology data of 11, out of 14 plots of 1 ha, allocated along an altitudinal gradient in the Serra do Mar, Silo Paulo, Brazil. The study was conducted at Serra do Mar State Park and the plots start at the sea level (10 m - plot of Restinga Forest that occurs at Praia da Fazenda, Picinguaba, municipality of Ubatuba) up to 1100 m above sea level (the Montane Ombrophilous Dense occurs alongside the Itamambuca Trail, municipality of Silo Luis do Paraitinga). The Restinga Forest occurs in Pleistocenic Coastal Plain where the soil is classified as a sandy Quartzipsamment (Quartzenic Neosol), while along the slopes of the Serra do Mar, the Ombrophylus Dense Forest grows on the top of a pre-Cambrian crystalline basement with granitic rocks, where the soil is a sandy-loam Dystrophic Inceptisol (Cambisol/Latosol). In all 14 plots soils are acidic (pH 3 - 4), chemically poor, with high dilution of nutrients and high saturation of aluminum. In the Restinga and at the foot of the slope the climate is Tropical/Subtropical Humid (Af/Cfa), with no dry season, an average annual rainfall over 2,200 mm and an average annual temperature of 22 degrees C. Towards the top of the Serra do Mar there is a gradual cooling along the slope, but there is no reduction in rainfall, so at 1,100 m above sea level the climate is classified as Humid Subtropical (Cfa/Cfb), with no dry season and an average annual temperature of 17 degrees C. It is important to remark that, almost daily, from 400 m above sea level up to the top of slopes the mountains are covered by a dense fog. In the 14 plots 21,733 individuals with DBH >= 4.8 cm, including trees, palms and ferns, were marked, measured and sampled. The average number of individuals sampled in each plot was 1264 ind.ha(-1)(+/- 218 SE 95%). Within the parameters considered trees prevailed (71% in the Montane ODF to 90% in the Restinga Forest), followed by palms (10% in the RF and 25% in the Montane Ombrophilous Dense Forest/ODF) and ferns (0% % in the RF and 4% in the Montane ODF). Regarding these proportions the Exploited Lowlands ODF differs from the others with only 1.8% of palm trees and striking 10% of ferns. The forest canopy is irregular with heights ranging from 7 to 9 m, rarely emergent trees reach 18 m, and due to this irregularity of the canopy the amount of light that gets through sets conditions for the development of hundreds of epiphytic species. Aside from Montana ODF, where the number of dead trees was more than 5% of individuals sampled, in the other phytophysiognomies this value was below 2.5%. In the 11 plots where the floristic study was conducted we found 562 species in 195 genera and 68 families. Only seven species - Euterpe edulis Mart. (Arecaceae), Calyptranthes lucida Mart. ex DC. and Marlierea tomentosa Cambess (both Myrtaceae), Guapira opposita (Veil.) Reitz (Nyctaginaceae), Cupania oblongifolia Mart. (Sapindaceae), Cecropia glaziovii Snethl. and Coussapoa microcarpa (Schott) Rizzini (both Urticaceae) - occurred from Restinga to Montane ODF, while 12 other species did not occur only in the Restinga Forest. Families with the greatest number of species are Myrtaceae (133 spp), Fabaceae (47 spp), Rubiaceae (49) and Lauraceae (49) throughout the gradient and Monimiaceae (21) specifically in portions Montane ODF. Only in the F plot, where logging has occurred between 1950 and 1985, the abundance of palm trees has been replaced by Cyatheaceae. The study shows a peak of diversity and richness, Shannon-Weiner index (H') ranging from 3.96 to 4. 48 nats.ind(-1), in the intermediate altitudes (300 to 400 m) along the slope. Several explanations for this result are raised here, including the fact that these elevations are within the limits expansions and retractions of the different phytophysiognomies of the Atlantic ODF due to climate fluctuations during the Pleistocene. The results presented in this paper demonstrate the extraordinary richness of tree species of the Atlantic Rainforest from the northeastern coast of the State of Sao Paulo, reinforcing the importance of its conservation throughout the altitudinal gradient. The richness of this forest justifies a long term commitment to study its dynamics and functioning through permanent plots, and monitor the impacts of climate change in this vegetation.12112314