Wetlands and coastal water quality: Should wetland size matter?

Generally, wetlands are thought to perform water purification functions, removing contaminants as water flows through sediment and vegetation. This paradigm was challenged when Grant et al. (2001) reported that Talbert Salt Marsh (Figure 1.) increased fecal indicator bacteria (FIB) output to coastal waters, contributing to poor coastal water quality. Like most southern California wetlands, Talbert Salt Marsh has been severely degraded. It is a small (10 ha), restored wetland, only 1/100th its original size, and located at the base of a highly urbanized watershed. Is it reasonable to expect that this or any severely altered wetland will perform the same water purification benefits as a natural wetland? To determine how a more pristine southern California coastal wetland attenuated bacterial contaminants, we investigated FIB concentrations entering and exiting Carpinteria Salt Marsh (Figure 2.), a 93 ha, moderate-sized, relatively natural wetland.(PDF contains 4 pages

A multidisciplinary coastal vulnerability assessment for local government focused on ecosystems, Santa Barbara area, California

Incorporating coastal ecosystems in climate adaptation planning is needed to maintain the well-being of both natural and human systems. Our vulnerability study uses a multidisciplinary approach to evaluate climate change vulnerability of an urbanized coastal community that could serve as a model approach for communities worldwide, particularly in similar Mediterranean climates. We synthesize projected changes in climate, coastal erosion and flooding, watershed runoff and impacts to two important coastal ecosystems, sandy beaches and coastal salt marshes. Using downscaled climate models along with other regional models, we find that temperature, extreme heat events, and sea level are expected to increase in the future, along with more intense rainfall events, despite a negligible change in annual rainfall. Consequently, more droughts are expected but the magnitude of larger flood events will increase. Associated with the continuing rise of mean sea level, extreme coastal water levels will occur with increasingly greater magnitudes and frequency. Severe flooding will occur for both natural (wetlands, beaches) and built environments (airport, harbor, freeway, and residential areas). Adaptation actions can reduce the impact of rising sea level, which will cause losses of sandy beach zones and salt marsh habitats that support the highest biodiversity in these ecosystems, including regionally rare and endangered species, with substantial impacts occurring by 2050. Providing for inland transgression of coastal habitats, effective sediment management, reduced beach grooming and removal of shoreline armoring are adaptations that would help maintain coastal ecosystems and the beneficial services they provide

Salt Marsh Reduces Fecal Indicator Bacteria Input to Coastal Waters in Southern California

We investigated fecal indicator bacteria (FIB) concentrations in water and sediment from Carpinteria Salt Marsh, a medium-sized (93 ha), mostly natural southern California coastal wetland. High FIB concentrations, exceeding recreational water quality standards, were found at inlet sites after winter storm events and during a summer dry weather sampling event. Runoff entering the wetland had the highest concentrations of FIB after large rain events and after rain events following extended periods without rain. The watersheds with the greatest agricultural and urban development draining into the wetland generally contributed the highest loads of FIB, while the largest and least developed watershed contributed the lowest FIB concentrations. Surface water exiting the wetland at the ocean contained relatively low concentrations of FIB and only exceeded recreational water quality standards after the largest rain event of the year. Bacterial concentrations in sediment were only elevated after rain events, suggesting wetland sediment was not a reservoir for bacteria. Our results provide evidence that moderate-sized tidal wetlands at the base of moderately urbanized watersheds can attenuate FIB, improving coastal water quality

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

Paternal and Maternal History of Myocardial Infarction and Cardiovascular Diseases Incidence in a Dutch Cohort of Middle-Aged Persons

Background - A positive parental history of myocardial infarction (MI) is an independent risk factor for cardiovascular diseases (CVD). However, different definitions of parental history have been used. We evaluated the impact of parental gender and age of onset of MI on CVD incidence. Methods - Baseline data were collected between 1993 and 1997 in 10¿524 respondents aged 40–65 years. CVD events were obtained from the National Hospital Discharge Register and Statistics Netherlands. We used proportional hazard models to calculate hazard ratios (HR) and 95% confidence intervals (CI) for CVD incidence and adjusted for lifestyle and biological risk factors. Results - At baseline, 36% had a parental history of MI. During 10-year follow-up, 914 CVD events occurred. The age and gender adjusted HR was 1.3 (95% CI 1.1–1.5) for those with a paternal MI, 1.5 (1.2–1.8) for those with a maternal MI and 1.6 (1.2–2.2) for those with both parents with an MI. With decreasing parental age of MI, HR increased from 1.2 (1.0–1.6) for age =70 years to 1.5 (1.2–1.8) for ag

Circum-Arctic distribution of chemical anti-herbivore compounds suggests biome-wide trade-off in defence strategies in Arctic shrubs

Spatial variation in plant chemical defence towards herbivores can help us understand variation in herbivore top-down control of shrubs in the Arctic and possibly also shrub responses to global warming. Less defended, non-resinous shrubs could be more influenced by herbivores than more defended, resinous shrubs. However, sparse field measurements limit our current understanding of how much of the circum-Arctic variation in defence compounds is explained by taxa or defence functional groups (resinous/non-resinous). We measured circum-Arctic chemical defence and leaf digestibility in resinous (Betula glandulosa, B. nana ssp. exilis) and non-resinous (B. nana ssp. nana, B. pumila) shrub birches to see how they vary among and within taxa and functional groups. Using liquid chromatography-mass spectrometry (LC-MS) metabolomic analyses and in vitro leaf digestibility via incubation in cattle rumen fluid, we analysed defence composition and leaf digestibility in 128 samples from 44 tundra locations. We found biogeographical patterns in anti-herbivore defence where mean leaf triterpene concentrations and twig resin gland density were greater in resinous taxa and mean concentrations of condensing tannins were greater in non-resinous taxa. This indicates a biome-wide trade-off between triterpene- or tannin-dominated defences. However, we also found variations in chemical defence composition and resin gland density both within and among functional groups (resinous/non-resinous) and taxa, suggesting these categorisations only partly predict chemical herbivore defence. Complex tannins were the only defence compounds negatively related to in vitro digestibility, identifying this previously neglected tannin group as having a potential key role in birch anti-herbivore defence. We conclude that circum-Arctic variation in birch anti-herbivore defence can be partly derived from biogeographical distributions of birch taxa, although our detailed mapping of plant defence provides more information on this variation and can be used for better predictions of herbivore effects on Arctic vegetation