Arbuscular Mycorrhizal Fungi Associations Across Multiple Saltmarsh Plant Species Mitigating the Impacts of Sea-Level Rise

Sea level rise caused by climate change will detrimentally impact saltmarsh habitats by increasing the elevation and rate of terrestrial salt water inundation, thereby reducing effective functionality of ecosystem services provided by saltmarshes. Facilitation is key to community structuring and function in habitats characterized by abiotic stress, such as salt marshes. Halophytic plants within salt marshes can benefit from symbiotic arbuscular mycorrhizal fungi (AMF) facilitations through increased inundation tolerance, greater nutrient availability and uptake, alleviation from drought stress and relief from saline stress. Through this research, land managers developing sea-level rise mitigation plans will have data supporting which plants will be most resilient to future increases in inundation and limits to nutrient availability due to AMF association. Potential inoculation of host plants could protect estuaries from sea level rise and increased frequency and intensity of storm events in coastal regions. In identifying plants which host beneficial fungi, and thereby have greater inundation resilience and nutrient availability, fungal inoculation of plants in marshes could help plants grow further into lower marsh elevations, increasing sediment accretion and decreasing erosion and soil degradation

Frequency-Dependent Seed Dispersal by Ants of Two Deciduous Forest Herbs

Two co—occurring deciduous forest myrmecochores, Asarum canadense and Jeffersonia diphylla, release their seeds at approximately the same time, and therefore potentially compete for ants as dispersers. Within a single woodlot, we placed seeds of both species inside a dense Jeffersonia population away from Asarum plants, inside a dense Asarum population away from Jeffersonia plants, and in a site where plants of neither species occurred. No preference was exhibited by ants where natural populations were absent. Preference at the other two sites was frequency dependent: ants preferred seeds of the introduced species. Species preferred by ants have higher seed and seedling survival because by being carried into ant nests they escape predation and avoid nutrient deficiency. Implications of frequency—dependent dispersal are discussed

Multiple and Long-Term Effects of an Introduced Predatory Crab

Despite the importance of invasions, few studies have explored their long-term consequences in marine systems or examined multiple types of population-level effects. Initial effects, however, may not persist over longer time frames; effects have been shown to wane in freshwater systems. We combined 14 yr of field surveys (1993 to 2006) with manipulative experiments to examine the potential for multiple effects of a nonindigenous crab Carcinus maenas on the native shore crab Hemigrapsus oregonensis over time in central California. H. oregonensis abundance was negatively correlated with C. maenas abundance. However, H. oregonensis abundance rebounded to pre-invasion levels once C. maenas numbers declined. Other measured changes include a marked decrease in H. oregonensis body size and an increase in the proportion of H. oregonensis in the high intertidal zone since the arrival of C. maenas. These changes in body size and tidal distribution persisted nearly a decade beyond the peak abundance of C. maenas and after H. oregonensis numbers rebounded. Observed changes in the distribution of the H. oregonensis population correspond to shifts in C. maenas abundance, and experiments support a causal relationship. Stepwise regression suggests a complex and possibly nonlinear relationship between predictor variables and H. oregonensis size and distribution. Overall, our data indicate strong persistent effects on multiple attributes, with a lag in recovery with declining invader abundance, underscoring the potential for long-term effects that are decoupled from year-to-year invasion dynamics

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Sex differences in self-construal and in depressive symptoms: predictors of cross-national variation

Sex differences in aspects of independent versus interdependent self-construal and depressive symptoms were surveyed among 5,320 students from 24 nations. Men were found to perceive themselves as more self-contained whereas women perceived themselves as more connected to others. No significant sex differences were found on two further dimensions of self-construal, or on a measure of depressive symptoms. Multilevel modeling was used to test the ability of a series of predictors derived from a social identity perspective and from evolutionary theory to moderate sex differences. Contrary to most prior studies of personality, sex differences in self-construal were larger in samples from nations scoring lower on the Gender Gap Index, and the Human Development Index. Sex differences were also greater in nations with higher pathogen prevalence, higher self-reported religiosity, and in nations with high reported avoidance of settings with strong norms. The findings are discussed in terms of the interrelatedness of self-construals and the cultural contexts in which they are elicited and the distinctiveness of student samples

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London