Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus

Clustering the difference in transcriptome response of PtQTL and PdQTL genotypes. Modulated Modularity Clustering of genes displaying a similar pattern of expression differences between genotypes from the PtQTL and PdQTL categories, at all time points. (DOCX 25 kb

Agricultural intensification can help protect the Amazon Forest and reduce global warming / Protecting the Amazon forest and reducing global warming via agricultural intensification

The Amazon basin includes 550 M ha covered with rainforests, with 60% of this area being in Brazil. Conversion of rainforest for soybean production raises concerns about the degree to which Brazil can reconcile production and environmental goals. Here we investigated the degree to which intensification could help Brazil produce more soybean without further encroachment of the Amazon Forest. Our analysis shows that continuation of current trends in soybean yield and area would lead to conversion of additional 5.7 M ha of forests and savannas during the next 15 years, with an associated 2550 Mt of CO2eq released into the atmosphere. In contrast, acceleration of yield improvement, coupled with expansion of soybean area only in areas currently used for livestock production, would allow Brazil to achieve similar economic benefits without deforestation and with substantially lower global climate warming

O risco das falsas controvérsias científicas para as políticas ambientais brasileiras

Fake controversies have influenced policy making on health and environmental issues for decades, resulting in major implementation setbacks worldwide. As a case study, in this paper we examine fake controversies produced by a small group of active Brazilian researchers that have seriously impacted environmental conservation, particularly in issues related to deforestation and climate change. Based on the literature, we develop a typology of strategies deployed in fake controversies, which include manufacturing uncertainty, misusing scientific credentials, and disregarding scientific literature. Afterwards, we examine the influence of this group of contrarians at the National Congress. We then analyze the fake controversies promoted by these contrarians and argue that, to properly understand them, we need to consider a strategy so far overlooked in the literature: the manufacture of “pseudo-facts”, namely, affirmations at odds with the established literature but that strives to appear as scientific facts. Unlike other contexts, in which contrarians have mainly sought to cast doubt on consensual issues by arguing that there are still considerable uncertainties surrounding them, in Brazil pseudo-facts on deforestation have been produced and published outside the peer-reviewed literature. We conclude the study with recommendations on how to oppose fake scientific controversies that threaten environmental conservation in general.Falsas controvérsias têm influenciado a elaboração de políticas sobre questões ambientais e de saúde há décadas, resultando em grandes retrocessos na implementação dessas políticas em todo o mundo. Utilizando um estudo de caso, neste artigo são examinadas falsas controvérsias produzidas por um pequeno grupo de pesquisadores brasileiros que têm afetado seriamente a conservação ambiental, particularmente em questões relacionadas ao desmatamento e às mudanças climáticas. Com base na literatura, foi desenvolvida uma tipologia das estratégias empregadas em falsas controvérsias, que incluem a fabricação de incertezas, o uso indevido de credenciais científicas e a desconsideração da literatura científica. Posteriormente, foi examinada a influência desse grupo de negacionistas no Congresso Nacional. Analisam-se, então, as falsas controvérsias promovidas por esses negacionistas e argumenta-se que, para entendê-las adequadamente, é necessário considerar uma estratégia até agora negligenciada na literatura: a criação de “pseudofatos”, ou seja, afirmações em desacordo com a literatura científica já estabelecida, mas que são mascaradas para parecerem fatos científicos. Ao contrário de outros contextos, nos quais os negacionistas têm procurado principalmente lançar dúvidas sobre questões já consensuais, argumentando que ainda existem incertezas consideráveis em torno delas, no Brasil foram produzidos e publicados pseudofatos sobre o desmatamento fora do âmbito da literatura revisada por pares. Concluímos o estudo com recomendações sobre como se opor às falsas controvérsias científicas que ameaçam a conservação ambiental em geral

Arthropod distribution in a tropical rainforest: tackling a four dimensional puzzle

Quantifying the spatio-temporal distribution of arthropods in tropical rainforests represents a first step towards scrutinizing the global distribution of biodiversity on Earth. To date moststudies have focused on narrow taxonomic groups or lack a design that allows partitioning of the components of diversity. Here, we consider an exceptionally large dataset (113,952 individuals representing 5,858 species), obtained from the San Lorenzo forest in Panama, where the phylogenetic breadth of arthropod taxa was surveyed using 14 protocols targeting the soil, litter, understory, lower and upper canopy habitats, replicated across seasons in 2003 and 2004. This dataset is used to explore the relative influence of horizontal, vertical and seasonal drivers of arthropod distribution in this forest. We considered arthropod abundance, observed and estimated species richness, additive decomposition of species richness, multiplicative partitioning of species diversity, variation in species composition, species turnover and guild structure as components of diversity. At the scale of our study (2km of distance, 40m in height and 400 days), the effects related to the vertical and seasonal dimensions were most important. Most adult arthropods were collected from the soil/ litter or the upper canopy and species richness was highest in the canopy. We compared the distribution of arthropods and trees within our study system. Effects related to the seasonal dimension were stronger for arthropods than for trees. We conclude that: (1) models of beta diversity developed for tropical trees are unlikely to be applicable to tropical arthropods; (2) it is imperative that estimates of global biodiversity derived from mass collecting of arthropods in tropical rainforests embrace the strong vertical and seasonal partitioning observed here; and (3) given the high species turnover observed between seasons, global climate change may have severe consequences for rainforest arthropods

Arthropod distribution in a tropical rainforest: tackling a four dimensional puzzle

Quantifying the spatio-temporal distribution of arthropods in tropical rainforests represents a first step towards scrutinizing the global distribution of biodiversity on Earth. To date most studies have focused on narrow taxonomic groups or lack a design that allows partitioning of the components of diversity. Here, we consider an exceptionally large dataset (113,952 individuals representing 5,858 species), obtained from the San Lorenzo forest in Panama, where the phylogenetic breadth of arthropod taxa was surveyed using 14 protocols targeting the soil, litter, understory, lower and upper canopy habitats, replicated across seasons in 2003 and 2004. This dataset is used to explore the relative influence of horizontal, vertical and seasonal drivers of arthropod distribution in this forest. We considered arthropod abundance, observed and estimated species richness, additive decomposition of species richness, multiplicative partitioning of species diversity, variation in species composition, species turnover and guild structure as components of diversity. At the scale of our study (2km of distance, 40m in height and 400 days), the effects related to the vertical and seasonal dimensions were most important. Most adult arthropods were collected from the soil/litter or the upper canopy and species richness was highest in the canopy. We compared the distribution of arthropods and trees within our study system. Effects related to the seasonal dimension were stronger for arthropods than for trees. We conclude that: (1) models of beta diversity developed for tropical trees are unlikely to be applicable to tropical arthropods; (2) it is imperative that estimates of global biodiversity derived from mass collecting of arthropods in tropical rainforests embrace the strong vertical and seasonal partitioning observed here; and (3) given the high species turnover observed between seasons, global climate change may have severe consequences for rainforest arthropods1012CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQSolVin-Solvay SA; Smithsonian Institution; Smithsonian Tropical Research Institute; United Nations Environment Programme; Smithsonian Institution; Smithsonian National Museum of Natural History; European Science Foundation (ESF); Global Canopy Programme; Czech Science foundation GACR grant; European Social Fund (ESF); Ministry of Education, Youth & Sports - Czech Republic; French National Research Agency (ANR); Research Council of Norway; Grant Agency of the Czech Republi

Reduced SLIT2 is Associated with Increased Cell Proliferation and Arsenic Trioxide Resistance in Acute Promyelocytic Leukemia

Simple Summary In solid tumors, the altered expression of embryonic genes such as the SLIT-ROBO family has been associated with poor prognosis, while little is known about their role in acute myeloid leukemia (AML). Previous studies reported frequent hypermethylation of SLIT2 mediated by the methyltransferase enzyme EZH2 and more recently the PML protein, which are commonly found to be aberrantly expressed in AML. Here, we aim to assess retrospectively the clinical relevance of the SLIT2 gene in acute promyelocytic leukemia, a homogenous subtype of AML. We demonstrated that reduced SLIT2 expression was associated with high leukocyte counts and reduced overall survival in different APL cohorts. STLI2 treatment decreased APL growth, while SLIT2 knockdown accelerated cell cycle progression and proliferation. Finally, reduced expression of SLIT2 in murine APL blasts resulted in fatal leukemia associated with increased leukocyte counts in vivo. These findings demonstrate that SLIT2 can be considered as a prognostic marker in APL, and a potential candidate for clinical studies of a more heterogeneous disease, such as AML. The SLIT-ROBO axis plays an important role in normal stem-cell biology, with possible repercussions on cancer stem cell emergence. Although the Promyelocytic Leukemia (PML) protein can regulate SLIT2 expression in the central nervous system, little is known about SLIT2 in acute promyelocytic leukemia. Hence, we aimed to investigate the levels of SLIT2 in acute promyelocytic leukemia (APL) and assess its biological activity in vitro and in vivo. Our analysis indicated that blasts with SLIT2(high) transcript levels were associated with cell cycle arrest, while SLIT2(low) APL blasts displayed a more stem-cell like phenotype. In a retrospective analysis using a cohort of patients treated with all-trans retinoic acid (ATRA) and anthracyclines, high SLIT2 expression was correlated with reduced leukocyte count (p = 0.024), and independently associated with improved overall survival (hazard ratio: 0.94; 95% confidence interval: 0.92-0.97; p <0.001). Functionally, SLIT2-knockdown in primary APL blasts and cell lines led to increased cell proliferation and resistance to arsenic trioxide induced apoptosis. Finally, in vivo transplant of Slit2-silenced primary APL blasts promoted increased leukocyte count (p = 0.001) and decreased overall survival (p = 0.002) compared with the control. In summary, our data highlight the tumor suppressive function of SLIT2 in APL and its deteriorating effects on disease progression when downregulated