Highlights d Pan-cancer analysis reveals heterogeneity in tumorinfiltrating myeloid cell composition d The ratio of TNF + versus VEGFA + mast cells underlines their cancer-type-specific functions d LAMP3 + cDCs are widely present, with diverse developmental origins and functions d Pro-angiogenic TAMs exhibit distinct expression profiles across different cancer types

An atlas of cancer-associated T cells The tumor microenvironment contains many different kinds of immune cells, the composition, function, and roles of which are unclear. Using single-cell RNA sequencing of T cells in 21 cancer types from more than 300 patients, Zheng et al . identified differences in transcript composition that could be used to catalog different T cell types (see the Perspective by van der Leun and Schumacher). These annotations identified the different roles of specific types of CD4 + and CD8 + T cells among the different tumor types. Some of these clusters revealed evidence for two developmental paths for T cells, one of which shows a trajectory toward the “exhausted” T cell state, knowledge of which may be useful in developing future cancer immunotherapies. —LMZ

Protected areas are intended to safeguard biodiversity in perpetuity, yet evidence suggests that widespread legal changes undermine protected area durability and efficacy. We documented these legal changes—protected area downgrading, downsizing, and degazettement (PADDD) events—in the United States and Amazonian countries and compiled available data globally. Governments of the United States and Amazonian countries enacted 269 and 440 PADDD events, respectively. Between 1892 and 2018, 73 countries enacted 3749 PADDD events, removing 519,857 square kilometers from protection and tempering regulations in an additional 1,659,972 square kilometers; 78% of events were enacted since 2000. Most PADDD events (62%) are associated with industrial-scale resource extraction and development, suggesting that PADDD may compromise biodiversity conservation objectives. Strategic policy responses are needed to address PADDD and sustain effective protected areas.

Single-cell RNA-seq technologies require library preparation prior to sequencing. Here, we present the first report to compare the cheaper BGISEQ-500 platform to the Illumina HiSeq platform for scRNA-seq. We generate a resource of 468 single cells and 1297 matched single cDNA samples, performing SMARTer and Smart-seq2 protocols on two cell lines with RNA spike-ins. We sequence these libraries on both platforms using single- and paired-end reads. The platforms have comparable sensitivity and accuracy in terms of quantification of gene expression, and low technical variability. Our study provides a standardized scRNA-seq resource to benchmark new scRNA-seq library preparation protocols and sequencing platforms. Electronic supplementary material The online version of this article (10.1186/s13059-019-1676-5) contains supplementary material, which is available to authorized users.

Protected areas (PAs) remain the dominant policy to protect biodiversity and ecosystem services but have been shown to have limited impact when development interests force them to locations with lower deforestation pressure. Far less known is that such interests also cause widespread tempering, reduction, or removal of protection [i.e., PA downgrading, downsizing, and degazettement (PADDD)]. We inform responses to PADDD by proposing and testing a bargaining explanation for PADDD risks and deforestation impacts. We examine recent degazettements for hydropower development and rural settlements in the state of Rondônia in the Brazilian Amazon. Results support two hypotheses: () ineffective PAs (i.e., those where internal deforestation was similar to nearby rates) were more likely to be degazetted and () degazettement of ineffective PAs caused limited, if any, additional deforestation. We also report on cases in which ineffective portions were upgraded. Overall our results suggest that enhancing PAs' ecological impacts enhances their legal durability.

The genetic paradox of biological invasions is complex and multifaceted. In particular, the relative role of disparate propagule sources and genetic adaptation through postintroduction hybridization has remained largely unexplored. To add resolution to this paradox, we investigate the genetic architecture responsible for the invasion of two invasive Asian carp species, bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) (bigheaded carps) that experience extensive hybridization in the Mississippi River Basin (MRB). We sequenced the genomes of bighead and silver carps (~1.08G bp and ~1.15G bp, respectively) and their hybrids collected from the MRB. We found moderate-to-high heterozygosity in bighead (0.0021) and silver (0.0036) carps, detected significantly higher dN/dS ratios of single-copy orthologous genes in bigheaded carps versus 10 other species of fish, and identified genes in both species potentially associated with environmental adaptation and other invasion-related traits. Additionally, we observed a high genomic similarity (96.3% in all syntenic blocks) between bighead and silver carps and over 90% embryonic viability in their experimentally induced hybrids. Our results suggest intrinsic genomic features of bigheaded carps, likely associated with life history traits that presumably evolved within their native ranges, might have facilitated their initial establishment of invasion,

We study harmonically trapped two-species Bose-Einstein condensates within the Gross-Pitaevskii formalism. By invoking the Thomas-Fermi approximation, we derive an analytical solution for the miscible ground state in a particular region of the system's parameter space. This solution furnishes a simple formula that relates the interspecies interaction strength to the second spatial moments of the density distribution of the minority condensate species. Accompanying numerical simulations confirm the accuracy of the solution and the interaction-strength formula for sufficiently large numbers of condensed particles. The introduced formula may provide an additional scheme for determining interspecies scattering lengths that complements existing methods, such as those based on collective-excitation spectroscopy of the two-species condensates or on collisional measurements on thermal samples.

Protected areas (PAs) are expected to conserve nature and provide ecosystem services in perpetuity, yet widespread protected area downgrading, downsizing, and degazettement (PADDD) may compromise these objectives. Even iconic protected areas are vulnerable to PADDD, although these PADDD events are often unrecognized. We identified 23 enacted and proposed PADDD events within World Natural Heritage Sites and examined the history, context, and consequences of PADDD events in 4 iconic PAs (Yosemite National Park, Arabian Oryx Sanctuary, Yasuní National Park, and Virunga National Park). Based on insights from published research and international workshops, these 4 cases revealed the diverse pressures brought on by competing interests to develop or exploit natural landscapes and the variety of mechanisms that enables PADDD. Knowledge gaps exist in understanding of the conditions through which development pressures translate to PADDD events and their impacts, partially due to a lack of comprehensive PADDD records. Future research priorities should include comprehensive regional and country‐level profiles and analysis of risks, impacts, and contextual factors related to PADDD. Policy options to better govern PADDD include improving tracking and reporting of PADDD events, establishing transparent PADDD policy processes, coordinating among legal frameworks, and mitigating negative impacts of PADDD. To support PADDD research and policy reforms, enhanced human and financial capacities are needed to train local researchers and to host publicly accessible data. As the conservation community considers the achievements of Aichi Target 11 and moves toward new biodiversity targets beyond 2020, researchers, practitioners, and policy makers need to work together to better track, assess, and govern PADDD globally.