Demographic hallmarks of an overbrowsed population state in American ginseng

Effects of high deer herbivory in North America on populations of favored plant browse species have been well-documented, however since less palatable plants now dominate the understory, we asked whether these species could be vulnerable as well, and if so, what symptoms might signal that this was occurring? Using American ginseng (Panax quinquefoliusL.) as our representative less palatable understory plant, we compared two subpopulations within a single natural population that were differentially exposed to browse; one isolated from deer by growing atop a large, flat-topped boulder, and a browse-exposed subpopulation in the surrounding low-lying area. We tested the hypothesis that deer effects would be manifested in all parts of the life history; through reduced growth, survival and reproduction. In turn, we hypothesized that browse would reduce population growth rates, and that differences in stage structure of the population would be produced. Taking advantage of a 20 year record of formal demographic censusing, we showed that browse effects were manifested primarily in reduced size-specific growth, while size-specific fertility and survival were relatively unaffected by exposure to browse. Demographically, these differences in growth were sufficient to drive population size reductions of 4.5%/y in the off rock subpopulation while the on rock plants slowly increased in number. High browse off the rock resulted in high proportions of plants in a stunted juvenile state in the off rock population relative to the on rock plants. A high proportion of juveniles is therefore a clear symptom of an understory subjected to chronic overbrowsing, providing land managers a rapid way to assess whether deer could be impacting understory biodiversity. The sharp demographic contrasts we observed between browsed and unbrowsed subpopulations also implies that promotion of refugia within managed lands will likely become increasingly important management tools for biodiversity preservation as long as unchecked deer populations persis

Demographic hallmarks of an overbrowsed population state in American ginseng

Effects of high deer herbivory in North America on populations of favored plant browse species have been well-documented, however since less palatable plants now dominate the understory, we asked whether these species could be vulnerable as well, and if so, what symptoms might signal that this was occurring? Using American ginseng (Panax quinque- foliusL.) as our representative less palatable understory plant, we compared two sub- populations within a single natural population that were differentially exposed to browse; one isolated from deer by growing atop a large, flat-topped boulder, and a browse-exposed subpopulation in the surrounding low-lying area. We tested the hypothesis that deer ef- fects would be manifested in all parts of the life history; through reduced growth, survival and reproduction. In turn, we hypothesized that browse would reduce population growth rates, and that differences in stage structure of the population would be produced. Taking advantage of a 20 year record of formal demographic censusing, we showed that browse effects were manifested primarily in reduced size-specific growth, while size-specific fertility and survival were relatively unaffected by exposure to browse. Demographically, these dif- ferences in growth were sufficient to drive population size reductions of 4.5%/y in the off rock subpopulation while the on rock plants slowly increased in number. High browse off the rock resulted in high proportions of plants in a stunted juvenile state in the off rock population relative to the on rock plants. A high proportion of juveniles is therefore a clear symptom of an understory subjected to chronic overbrowsing, providing land managers a rapid way to assess whether deer could be impacting understory biodiversity. The sharp demographic contrasts we observed between browsed and unbrowsed subpopulations also implies that promotion of refugia within managed lands will likely become increasingly important management tools for biodiversity preservation as long as unchecked deer populations persist

Preserving and Promoting Diverse Transit-Oriented Neighborhoods

This report, researched and written by staff at the Center for Neighborhood Technology, Reconnecting America, and Strategic Economics -- working together as the Center for Transit-Oriented Development -- makes a substantial new contribution to our knowledge base regarding mixed-income, mixed-race housing. We now know, via this report, that there are ample opportunities for the creation of mixed-income, mixed-race housing in transit zones. Demand for transit-oriented housing is projected to soar over the next twenty years.Locating mixed-income housing in these particular settings carries the remarkable advantage of permitting residents to stretch their budgets because transit use can lower transportation costs substantially

Service Learning with Individuals with Disabilities: Emerging Themes

In this study, 92 students, enrolled in introductory level courses at a small liberal arts university in rural central Virginia, were asked to fulfill 15 hours of service learning with individuals with disabilities. Students were required to keep journal reflections after each hour they completed. The researchers analyzed this data qualitatively by looking at themes and changes in attitude toward individuals with disabilities across the service learning activities. Data was organized into case studies representing each service learning activity. Then, common themes across the activities were discussed to assess the impact the activities had on attitudes of the college students toward individuals with disabilities

Historical ecology with real numbers: past and present extent and biomass of an imperiled estuarine habitat

Historic baselines are important in developing our understanding of ecosystems in the face of rapid global change. While a number of studies have sought to determine changes in extent of exploited habitats over historic timescales, few have quantified such changes prior to late twentieth century baselines. Here, we present, to our knowledge, the first ever large-scale quantitative assessment of the extent and biomass of marine habitat-forming species over a 100-year time frame. We examined records of wild native oyster abundance in the United States from a historic, yet already exploited, baseline between 1878 and 1935 (predominantly 1885–1915), and a current baseline between 1968 and 2010 (predominantly 2000–2010). We quantified the extent of oyster grounds in 39 estuaries historically and 51 estuaries from recent times. Data from 24 estuaries allowed comparison of historic to present extent and biomass. We found evidence for a 64 per cent decline in the spatial extent of oyster habitat and an 88 per cent decline in oyster biomass over time. The difference between these two numbers illustrates that current areal extent measures may be masking significant loss of habitat through degradation

Archeological Significance Testing at 41BX17/271, the Granberg Site: A Multi-Component Site along the Salado Creek in Bexar County, Texas

The Center for Archaeological Research (CAR) of The University of Texas at San Antonio conducted archeological significance testing at 41BX17, the Granberg Site, from January to March 2006. The testing was conducted for the Texas Department of Transportation, Environmental Affairs Division (TxDOT-ENV). The Granberg Site sits on the eastern flood terrace of the Salado Creek south of Loop 410 in San Antonio, Bexar County, Texas. Planned road improvements including installation of a storm sewer line and a water main prompted the need to assess whether (1) cultural deposits including human remains still exist after previous testing and (2) if the deposits contribute to the site’s National Register of Historic Places eligibility. The archeological work was conducted under Texas Antiquities Permit No. 4010. Steve A. Tomka served as Principal Investigator and Jennifer Thompson served as Project Archeologist. Fieldwork included mechanical auger boring and backhoe trenching to determine the horizontal extent of the site boundaries within the median of Loop 410 eastbound. Sixteen 1-x-1-m units were excavated to determine the distribution and integrity of the cultural deposits and to locate any possible burials that may still exist at the site. Materials recovered included burned rock features, chipped stone artifacts, animal bone, snail and mussel shell and charred plant remains. The distribution of the artifacts, the geomorphic investigations, the radiocarbon assays, and temporally diagnostic artifacts indicate the presence of Middle and Late Archaic archeological materials with good stratigraphic integrity. The Granberg Site was determined to be ineligible for the National Register of Historic Places. Following the completion of eligibility testing efforts, the TxDOT directed the CAR to develop a research design linking the data recovered from the various excavations at the Granberg Site with research goals. The CAR developed the research design (Munoz et al. 2007) under Work Authorization No. 57513SA005 with Cynthia M. Munoz serving as Project Archeologist. At roughly the time of the research design implementation, the CAR was the recipient of a donation of a collection of commingled human skeletal remains recovered from the Granberg Site. These remains were recovered from 41BX17/271 in 1962 by Harvey Kohnitz, an avocational archeologist, without knowledge or permission from the Texas Highway Department. The remains were stored at the Kohnitz home until his son, Mark Kohnitz, donated them to the CAR in 2007. An osteological analysis was conducted at the CAR laboratory during February 2008 for TxDOT, under Work Authorization No. 57513SA005 Supplemental Work Authorization No. 4. The results of this analysis are reported in Appendix H of this report. The commingled remains will be curated the CAR and all required documents, including an inventory, will be submitted to the National Park Service National NAGPRA Program to fulfill all obligations pertaining to the NAGPRA laws. All artifacts collected during this project and all project-associated documentation are permanently curated at the CAR according to Texas Historical Commission guidelines

No Significant Role for Smooth Muscle Cell Mineralocorticoid Receptors in Atherosclerosis in the Apolipoprotein-E Knockout Mouse Model

Objective: Elevated levels of the hormone aldosterone are associated with increased risk of myocardial infarction and stroke in humans and increased progression and inflammation of atherosclerotic plaques in animal models. Aldosterone acts through the mineralocorticoid receptor (MR) which is expressed in vascular smooth muscle cells (SMCs) where it promotes SMC calcification and chemokine secretion in vitro. The objective of this study is to explore the role of the MR specifically in SMCs in the progression of atherosclerosis and the associated vascular inflammation in vivo in the apolipoprotein E knockout (ApoE−/−) mouse model.Methods and Results: Male ApoE−/− mice were bred with mice in which MR could be deleted specifically from SMCs by tamoxifen injection. The resulting atheroprone SMC-MR-KO mice were compared to their MR-Intact littermates after high fat diet (HFD) feeding for 8 or 16 weeks or normal diet for 12 months. Body weight, tail cuff blood pressure, heart and spleen weight, and serum levels of glucose, cholesterol, and aldosterone were measured for all mice at the end of the treatment period. Serial histologic sections of the aortic root were stained with Oil Red O to assess plaque size, lipid content, and necrotic core area; with PicroSirius Red for quantification of collagen content; by immunofluorescent staining with anti-Mac2/Galectin-3 and anti-smooth muscle α-actin antibodies to assess inflammation and SMC marker expression; and with Von Kossa stain to detect plaque calcification. In the 16-week HFD study, these analyses were also performed in sections from the brachiocephalic artery. Flow cytometry of cell suspensions derived from the aortic arch was also performed to quantify vascular inflammation after 8 and 16 weeks of HFD. Deletion of the MR specifically from SMCs did not significantly change plaque size, lipid content, necrotic core, collagen content, inflammatory staining, actin staining, or calcification, nor were there differences in the extent of vascular inflammation between MR-Intact and SMC-MR-KO mice in the three experiments.Conclusion: SMC-MR does not directly contribute to the formation, progression, or inflammation of atherosclerotic plaques in the ApoE−/− mouse model of atherosclerosis. This indicates that the MR in non-SMCs mediates the pro-atherogenic effects of MR activation

A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses

ABSTRACT Several biosafety level 3 and/or 4 (BSL-3/4) pathogens are high-consequence, single-stranded RNA viruses, and their genomes, when introduced into permissive cells, are infectious. Moreover, many of these viruses are select agents (SAs), and their genomes are also considered SAs. For this reason, cDNAs and/or their derivatives must be tested to ensure the absence of infectious virus and/or viral RNA before transfer out of the BSL-3/4 and/or SA laboratory. This tremendously limits the capacity to conduct viral genomic research, particularly the application of next-generation sequencing (NGS). Here, we present a sequence-independent method to rapidly amplify viral genomic RNA while simultaneously abolishing both viral and genomic RNA infectivity across multiple single-stranded positive-sense RNA (ssRNA+) virus families. The process generates barcoded DNA amplicons that range in length from 300 to 1,000 bp, which cannot be used to rescue a virus and are stable to transport at room temperature. Our barcoding approach allows for up to 288 barcoded samples to be pooled into a single library and run across various NGS platforms without potential reconstitution of the viral genome. Our data demonstrate that this approach provides full-length genomic sequence information not only from high-titer virion preparations but it can also recover specific viral sequence from samples with limited starting material in the background of cellular RNA, and it can be used to identify pathogens from unknown samples. In summary, we describe a rapid, universal standard operating procedure that generates high-quality NGS libraries free of infectious virus and infectious viral RNA. IMPORTANCE This report establishes and validates a standard operating procedure (SOP) for select agents (SAs) and other biosafety level 3 and/or 4 (BSL-3/4) RNA viruses to rapidly generate noninfectious, barcoded cDNA amenable for next-generation sequencing (NGS). This eliminates the burden of testing all processed samples derived from high-consequence pathogens prior to transfer from high-containment laboratories to lower-containment facilities for sequencing. Our established protocol can be scaled up for high-throughput sequencing of hundreds of samples simultaneously, which can dramatically reduce the cost and effort required for NGS library construction. NGS data from this SOP can provide complete genome coverage from viral stocks and can also detect virus-specific reads from limited starting material. Our data suggest that the procedure can be implemented and easily validated by institutional biosafety committees across research laboratories

Is the NEI-VFQ-25 a useful tool in identifying visual impairment in an elderly population?

BACKGROUND: The use of self-report questionnaires to substitute for visual acuity measurement has been limited. We examined the association between visual impairment and self reported visual function in a population sample of older people in the UK. METHODS: Cross sectional study of people aged more than 75 years who initially participated in a trial of health screening. The association between 25-item National Eye Institute Visual Function Questionnaire (NEI-VFQ) scores and visual impairment (defined as an acuity of less than 6/18 in the better eye) was examined using logistic regression. RESULTS: Visual acuity and NEI-VFQ scores were obtained from 1807 participants (aged 77 to 101 years, 36% male), from 20 general practices throughout the UK. After adjustment for age, gender, practice and NEI-VFQ sub-scale scores, those complaining of poor vision in general were 4.77 times (95% CI 3.03 to 7.53) more likely to be visually impaired compared to those who did not report difficulty. Self-reported limitations with social functioning and dependency on others due to poor vision were also associated with visual impairment (odds ratios, 2.52, 95% CI 1.55 to 4.11; 1.73, 95% CI 1.05 to 2.86 respectively). Those reporting difficulties with near vision and colour vision were more likely to be visually impaired (odds ratios, 2.32, 95% CI 1.30 to 4.15; 2.25, 95% CI 1.35 to 3.73 respectively). Other NEI-VFQ sub-scale scores were unrelated to measures of acuity. Similar but weaker odds ratios were found with reduced visual acuity (defined as less than 6/12 in the better eye). Although differences in NEI-VFQ scores were small, scores were strongly associated with visual acuity, binocular status, and difference in acuity between eyes. CONCLUSION: NEI-VFQ questions regarding the quality of general vision, social functioning, visual dependency, near vision and colour vision are strongly and independently associated with an objective measure of visual impairment in an elderly population

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