Grazing by manatees excludes both new and established wild celery transplants: Implications for restoration in Kings Bay, FL, USA

We conducted a field experiment between August 2001 and February 2002 in Kings Bay, FL, USA, designed to determine whether the amount of time allowed for wild celery (Vallisneria americana Michx) transplants to establish altered the effect of herbivorous manatees (Trichechus manatus L.)on their survival

Production and carbonate dynamics of Halimeda incrassata (Ellis)Lamouroux altered by Thalassia testudinum Banks and Soland ex König

Ocean acidification poses a serious threat to a broad suite of calcifying organisms. Scleractinian corals and cal- careous algae that occupy shallow, tropical waters are vulnerable to global changes in ocean chemistry be- cause they already are subject to stressful and variable carbon dynamics at the local scale. For example, net heterotrophy increases carbon dioxide concentrations, and pH varies with diurnal fluctuations in photosyn- thesis and respiration. Few researchers, however, have investigated the possibility that carbon dioxide con- sumption during photosynthesis by non-calcifying photoautotrophs, such as seagrasses, can ameliorate deleterious effects of ocean acidi fi cation on sympatric calcareous algae. Naturally occurring variations in the density of seagrasses and associated calcareous algae provide an ecologically relevant test of the hypoth- esis that diel fl uctuations in water chemistry driven by cycles of photosynthesis and respiration within seagrass beds create microenvironments that enhance macroalgal calci fi cation. In Grape Tree Bay off Little Cayman Island BWI, we quanti fi ed net production and characterized calci fi cation for thalli of the calcareous green alga Halimeda incrassata growing within beds of Thalassia testudinum with varying shoot densities. Re- sults indicated that individual H . incrassata thalli were ~6% more calci fi ed in dense seagrass beds. On an areal basis, however, far more calcium carbonate was produced by H . incrassata in areas where seagrasses were less dense due to higher rates of production. In addition, diel pH regimes in vegetated and unvegetated areas within the lagoon were not signi fi cantly different, suggesting a high degree of water exchange and mixing throughout the lagoon. These results suggest that, especially in well-mixed lagoons, carbonate pro- duction by calcareous algae may be more related to biotic interactions between seagrasses and calcareous algae than to seagrass-mediated changes in local water chemistry

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

Renal cell carcinoma(RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers. Somatic alteration of BAP1, PBRM1, and PTEN and altered metabolic pathways correlated with subtype-specific decreased survival, while CDKN2A alteration, increased DNA hypermethylation, and increases in the immune-related Th2 gene expression signature correlated with decreased survival within all major histologic subtypes. CIMP-RCC demonstrated an increased immune signature, and a uniform and distinct metabolic expression pattern identified a subset of metabolically divergent (MD) ChRCC that associated with extremely poor survival

The Immune Landscape of Cancer

We performed an extensive immunogenomic anal-ysis of more than 10,000 tumors comprising 33diverse cancer types by utilizing data compiled byTCGA. Across cancer types, we identified six im-mune subtypes\u2014wound healing, IFN-gdominant,inflammatory, lymphocyte depleted, immunologi-cally quiet, and TGF-bdominant\u2014characterized bydifferences in macrophage or lymphocyte signa-tures, Th1:Th2 cell ratio, extent of intratumoral het-erogeneity, aneuploidy, extent of neoantigen load,overall cell proliferation, expression of immunomod-ulatory genes, and prognosis. Specific drivermutations correlated with lower (CTNNB1,NRAS,orIDH1) or higher (BRAF,TP53,orCASP8) leukocytelevels across all cancers. Multiple control modalitiesof the intracellular and extracellular networks (tran-scription, microRNAs, copy number, and epigeneticprocesses) were involved in tumor-immune cell inter-actions, both across and within immune subtypes.Our immunogenomics pipeline to characterize theseheterogeneous tumors and the resulting data areintended to serve as a resource for future targetedstudies to further advance the field