Population Demography and Herbivory of Trillium Grandiflorum

Numerous pedicellate and sessile Trillium species are endemic to eastern North America, where white-tailed deer (Odocoileus virginianus) populations have been growing in recent decades. Deer feed on Trillium plants, and because they often consume all leaves and flowers, the photosynthetic capacity of browsed plants is greatly diminished. To determine if deer can influence Trillium population dynamics, we review two recent studies that applied matrix population models to understand how deer browsing affects Trillium grandijlorum. Research conducted in the Great Lakes region indicated Trillium populations in which 6-12% plants were browsed declined 3.6% per year. Simulations show that with additional browsing, the rate of population decline accelerates. Similar research conducted in the Appalachian plateau region by a different researcher yielded nearly identical results. We apply insights from these matrix population models to two additional conservation problems in Trillium: unsustainable collecting of wild plants and forest fragmentation. Because other Trillium in the eastern United States are similar morphologically and ecologically, our results from Trillium grandiflorum might be generalized to apply to other members of the genus

Wolves facilitate the recovery of browse-sensitive understory herbs in Wisconsin forests

We asked whether wolf re-colonization would facilitate increased growth and reproduction of three browse-sensitive plant species. We hypothesized plant size and the proportion of reproductive individuals would be lowest in areas with no wolves, intermediate where wolves had been present for 4-6 years, and highest where wolves had been present for 12-13 years. Two plant species exhibited significantly greater reproduction where wolves were present for 12-13 years. Mean leaf size of indicator plants was significantly greater in areas where wolves were present for 12-13 years, as compared with that in areas where wolves were not present or were present for 4-6 years, but the effect size appears small. While the return of wolves to this region is likely to benefit browse-sensitive plant species, our findings suggest that wolf recovery will not generate atrophic cascade of sufficient magnitude to halt or reverse the loss of plant diversity in the Great Lakes region in the near term

Food Limitation as a Potentially Emerging Contributor to the Asian Vulture Crisis

It was believed that the reason for decline in Asian vulture population is the drug, Diclofenac sodium (DFS), used in livestock. Even after declaring the DFS use banned by the government, apparent decrease in the population of vultures was reported. Alternate hypothesis was suggested that food limitation may be a cause of Asian vulture crisis in Pakistan. Very recent shifts in livestock utilization observed in Pakistan may present a significant barrier to vulture recovery. Increased livestock utilization is translated to fewer carcasses. Since 2005, no livestock carcasses were found in 1650 km transect in the habitat of vultures. Carcasses recorded 13 in 1999 gradually declined to almost zero in 2005 and onwards, which suggests DFS may not be the only cause of Asian Vulture Crisi

Distributed under Creative Commons CC-BY 4.0 OPEN ACCESS Deer herbivory reduces web-building spider abundance by simplifying forest vegetation structure

ABSTRACT Indirect ecological effects are a common feature of ecological systems, arising when one species affects interactions among two or more other species. We examined how browsing by white-tailed deer (Odocoileus virginianus) indirectly affected the abundance and composition of a web-building spider guild through their effects on the structure of the ground and shrub layers of northern hardwood forests. We examined paired plots consisting of deer-free and control plots in the Allegheny Plateau region Pennsylvania and Northern Highlands region of Wisconsin. We recorded the abundance of seven types of webs, each corresponding to a family of web-building spiders. We quantified vegetation structure and habitat suitability for the spiders by computing a web scaffold availability index (WSAI) at 0.5 m and 1.0 m above the ground. At Northern Highlands sites, we recorded prey availability. Spider webs were twice as abundant in deer-free plots compared to control plots, while WSAI was 7-12 times greater in deerfree plots. Prey availability was lower in deer-free plots. With the exception of funnel web-builders, all spider web types were significantly more abundant in deer-free plots. Both deer exclusion and the geographic region of plots were significant predictors of spider community structure. In closed canopy forests with high browsing pressure, the low density of tree saplings and shrubs provides few locations for web-building spiders to anchor webs. Recruitment of these spiders may become coupled with forest disturbance events that increase tree and shrub recruitment. By modifying habitat structure, deer appear to indirectly modify arthropod food web interactions. As deer populations have increased in eastern North America over the past several decades, the effects of deer on web-building spiders may be widespread

Shifts in Southern Wisconsin Forest Canopy and Understory Richness, Composition, and Heterogeneity

We resurveyed the under- and overstory species composition of 94 upland forest stands in southern Wisconsin in 2002–2004 to assess shifts in canopy and understory richness, composition, and heterogeneity relative to the original surveys in 1949–1950. The canopy has shifted from mostly oaks (Quercus spp.) toward more mesic and shade-tolerant trees (primarily Acer spp.). Oak-dominated early-successional stands and those on coarse, nutrient-poor soils changed the most in canopy composition. Understories at most sites (80%) lost native species, with mean species density declining 25% at the 1-m2 scale and 23.1% at the 20-m2 scale. Woody species have increased 15% relative to herbaceous species in the understory despite declining in absolute abundance. Initial canopy composition, particularly the abundance of red oaks (Quercus rubra and Q. velutina), predicted understory changes better than the changes observed in the overstory. Overall rates of native species loss were greater in later-successional stands, a pattern driven by differential immigration rather than differential extirpation. However, understory species initially found in early-successional habitats declined the most, particularly remnant savanna taxa with narrow or thick leaves. These losses have yet to be offset by compensating increases in native shade-adapted species. Exotic species have proliferated in prevalence (from 13 to 76 stands) and relative abundance (from 1.2% to 8.4%), but these increases appear unrelated to the declines in native species richness and heterogeneity observed. Although canopy succession has clearly influenced shifts in understory composition and diversity, the magnitude of native species declines and failure to recruit more shade-adapted species suggest that other factors now act to limit the richness, heterogeneity, and composition of these communities

Predation Risk, Elk, and Aspen: Comment

With the exception of humans, gray wolves (Canis lupus) are perhaps the most significant predator of cervids in the northern hemisphere, mainly due to the group-hunting, year-round activity, and widespread geographic distribution (Peterson et al. 2003). Thus, interactions between wolves and large herbivore prey, such as elk (Cervus elaphus) and moose (Alces alces), have long been of interest to biologists (Peterson 1995, Jęodrzejewska et al. 2000, Mech and Boitani 2003). The potential ecological role this apex predator may have, via trophic cascades, has also received attention in recent years by researchers (e.g., Callan et al. 2013, Kuijper et al. 2013, 2014), wildlife management agencies (e.g., state wolf management plans), as well as the general public. Perhaps nowhere in the western United States has a heightened examination of this large predator been more focused than in Yellowstone National Park (YNP; Laundré et al. 2001, Smith et al. 2003, 2013, Fortin et al. 2005). Here, wolves were reintroduced in the mid-1990s, again completing the park\u27s large predator guild after approximately seven decades of absence, thus providing a long-term, landscape-scale, natural experiment (Diamond 1983). The Gallatin winter range is one of two that occur along the northern portion of YNP, the other is the northern ungulate winter range, or “northern range,” located some 25 km or more to the east. Of these, the Gallatin has been less studied. Nevertheless, the Gallatin winter range, like the northern range, experienced high levels of elk herbivory following the extirpation of wolves in the early 1900s. Over a period of approximately seven decades, intensive herbivory by elk led to the long-term decline in aspen (Populus tremuloides) and willow (Salix spp.) recruitment (i.e., growth of young plants above the browse level of elk) in the Gallatin winter range, leaving these plant communities in an impoverished condition (Lovaas 1967, Patten 1968, Kay 2001, Ripple and Beschta 2004, Halofsky and Ripple 2008). Accelerated soil and channel erosion also occurred (Lovaas 1967, Beschta and Ripple 2006). Thus, when wolves were reintroduced into Yellowstone in the mid-1990s, aspen recruitment within the Gallatin elk winter range, had been largely absent for several decades (Kay 2001, Halofsky and Ripple 2008). In 2010, Winnie (2012) sampled 65 aspen stands in the northwestern corner of YNP, within the Gallatin elk winter range, to determine if a behaviorally mediated trophic cascade (BMTC) was occurring. As background information Winnie (2012:2600) included only a single sentence about wolves in the Greater Yellowstone Ecosystem and the remainder of the paragraph briefly discussed elk numbers, with most of the emphasis on elk in YNP\u27s northern range where there has been a pronounced redistribution of elk since the reintroduction of wolves (White et al. 2012). A more complete summary regarding the status and dynamics of wolves and elk over the last 15 years (i.e., 1995–2010) in the Gallatin elk winter range, as well as in the Daly Creek sub-drainage where Winnie\u27s study occurred, would have helped readers better understand the context of his study. Furthermore, information regarding human harvest of elk in the Gallatin winter range since the return of wolves, or whether such hunting has been affecting elk numbers or distribution in recent years was not provided. As part of his 2010 field study, Winnie (2012) characterized the presence or absence of several hypothesized risk factors (independent variables) for each aspen stand, including escape impediments, visual impediments, distance to conifer forest edge, and presence of deadfall trees. For dependent variables, Winnie (2012) recorded the presence or absence of browsing on aspen suckers (ramets \u3c2 m in height) and the number of aspen juveniles (plants \u3e2 m in height but \u3c6 cm in diameter at breast height). A height of 2 m generally represents the upper browse level of elk, and young aspen exceeding this height are considered to have successfully recruited. Such recruitment would represent a major departure from the browsing suppression that occurred in his study area over recent decades (Kay 2001, Halofsky and Ripple 2008) and an indication that a tri-trophic cascade involving wolves, elk, and aspen may be underway. From the results of his analyses, Winnie (2012:2600) concluded that “aspen were not responding to hypothesized fine-scale risk factors in ways consistent with the current BMTC hypothesis.” We respectfully submit that the design and analysis used to support such a conclusion may be deficient for two reasons, the first based on conceptual concerns and the second on statistical concerns. (1) Unfortunately, some aspen stands Winnie (2012) sampled contained juveniles associated with “physical barriers,” barriers that could prevent elk from browsing young aspen. To be scientifically valid, a risk assessment using young aspen as the dependent variable must inherently assure that all evaluated plants were accessible to elk browsing. (2) The inclusion of 10 aspen stands containing some physically protected aspen likely confounded results from his predation risk analyses (i.e., Figs. 5, 6, and 7 in Winnie 2012). While the inclusion of stands with protected aspen may increase the variance associated with his dependent variables (i.e., browsing rate, number of juveniles), the fallacy of doing so is revealed by inspecting these variables for the 85% of his stands (n = 55 stands) that did not have physically protected aspen. Here, a browsing rate of ∼99% and an average of \u3c1 juvenile per stand occurred (back-transformed means from Fig. 8b and a, respectively [Winnie 2012:2609]), indicating a general lack of variance in the dependent variables associated with these stands and little likelihood of a statistically significant outcome. Thus, we suspect that the “statistically significant” results Winnie (2012) found in Figs. 5, 6, and 7, whether contrary to or in support of a BMTC hypothesis, are primarily influenced by the occurrence of risk factors associated with those stands where some of the young aspen were physically protected. A reanalysis by Winnie of browsing rate and number of juveniles vs. his risk factors, using just the 55 stands accessible to elk, could clarify this issue. Because of the above concerns, we would offer that results of Winnie\u27s (2012) analyses of “proportion of sprouts browsed” or “number of juveniles per stand” relative to his hypothesized risk factors may well be spurious. If so, any discussions and conclusions based on those results are in question. A 2004 field study of aspen stands in the Gallatin winter range found aspen recruitment had declined precipitously following the extirpation of wolves in the 1920s and remained essentially absent through the late 1990s (Halofsky and Ripple 2008). Thus, when Winnie (2012) undertook his field study in 2010, a wolf–elk–aspen trophic cascade had not yet been confirmed. While the occurrence of juvenile aspen would be important to the long-term survival of aspen stands, the data for elk-accessible stands continue to show exceptionally high browse rates and little or no recruitment (Winnie 2012). This situation contrasts with YNP\u27s northern range where decreased browsing and increased heights of young aspen in portions of that range have been observed some 6–10 years after the occurrence of increased willow growth, although this recruitment has been spatially patchy (e.g., Ripple and Beschta 2012, Painter 2013; also see northern range photos of aspen recruitment available online).5 It should be noted that decreased browsing and increased heights of willows in the Gallatin winter range (at the base of the Daly Creek watershed) following the return of wolves, and consistent with the occurrence of a trophic cascade, were documented as early as 1999–2000 (Ripple and Beschta 2004), with heights continuing to increase in more recent years (Beschta and Ripple 2010). Also consistent with a trophic cascade, various northern range studies have found increased willow growth/canopy cover, sometimes interacting with climatic fluctuations, following wolf reintroduction (e.g., Groshong 2004, Beschta and Ripple 2007, Beyer et al. 2007, Baril 2009, Tercek et al. 2010, Marshall 2012). The occurrence of 192 juvenile aspen within Winnie\u27s (2012) study area would seem to indicate the beginnings of a tri-trophic cascade, particularly when compared to the lack of juvenile production in the decades immediately before wolf reintroduction (Halofsky and Ripple 2008). However, most of the 192 juveniles were associated with aspen stands characterized as having some degree of physical protection from elk (Fig. 8a in Winnie 2012), making it difficult to confirm if they represent a wolf–elk–aspen trophic cascade involving density and/or behavioral mediation. A trophic cascade involving aspen can be complex and context dependent (e.g., linked to bottom-up factors such as fire [Eisenberg et al. 2013]). Furthermore, undertaking risk assessments associated with large mammalian predators and ungulates in mountainous terrain, where human hunting is also occurring across part of the landscape, can be especially challenging. While we commend Winnie (2012) for attempting such an assessment, without a reanalysis of only those young aspen accessible to elk it would appear that his evaluation may not have been sufficiently rigorous to evaluate the presence or absence of a potential BMTC in the Gallatin winter range

White-Tailed Deer are a Biotic Filter During Community Assembly, Reducing Species and Phylogenetic Diversity

Community assembly entails a filtering process, where species found in a local community are those that can pass through environmental (abiotic) and biotic filters and successfully compete. Previous research has demonstrated the ability of white-tailed deer (Odocoileus virginianus) to reduce species diversity and favour browse-tolerant plant communities. In this study, we expand on our previous work by investigating deer as a possible biotic filter altering local plant community assembly. We used replicated 23-year-old deer exclosures to experimentally assess the effects of deer on species diversity (H′), richness (SR), phylogenetic community structure and phylogenetic diversity in paired browsed (control) and unbrowsed (exclosed) plots. Additionally, we developed a deer-browsing susceptibility index (DBSI) to assess the vulnerability of local species to deer. Deer browsing caused a 12 % reduction in H′ and 17 % reduction in SR, consistent with previous studies. Furthermore, browsing reduced phylogenetic diversity by 63 %, causing significant phylogenetic clustering. Overall, graminoids were the least vulnerable to deer browsing based on DBSI calculations. These findings demonstrate that deer are a significant driver of plant community assembly due to their role as a selective browser, or more generally, as a biotic filter. This study highlights the importance of knowledge about the plant tree of life in assessing the effects of biotic filters on plant communities. Application of such knowledge has considerable potential to advance our understanding of plant community assembly

Decellularization of human donor aortic and pulmonary valved conduits using low concentration sodium dodecyl sulfate

The clinical use of decellularised cardiac valve allografts is increasing. Long term data will be required to determine whether they outperform conventional cryopreserved allografts. Valves decellularised using different processes may show varied long-term outcomes. It is therefore important to understand the effects of specific decellularisation technologies on the characteristics of donor heart valves. Human cryopreserved aortic and pulmonary valved conduits were decellularised using hypotonic buffer, 0.1% (w/v) SDS and nuclease digestion. The decellularised tissues were compared to cellular cryopreserved valve tissues using histology, immunohistochemistry, quantitation of total DNA, collagen and glycosaminoglycan content, in vitro cytotoxicity assays, uniaxial tensile testing and subcutaneous implantation in mice. The decellularised tissues showed no histological evidence of cells or cell remnants and over 97% DNA removal in all regions (arterial wall, muscle, leaflet and junction). The decellularised tissues retained collagen IV and von Willebrand factor staining with some loss of fibronectin, laminin and chondroitin sulphate staining. There was an absence of MHC Class I staining in decellularised pulmonary valve tissues, with only residual staining in isolated areas of decellularised aortic valve tissues. The collagen content of the tissues was not decreased following decellularisation however the glycosaminoglycan content was reduced. Only moderate changes in the maximum load to failure of the tissues were recorded post-decellularisation. The decellularised tissues were non-cytotoxic in vitro, and were biocompatible in vivo in a mouse subcutaneous implant model. The decellularisation process will now be translated into a GMP compatible process for donor cryopreserved valves with a view to future clinical use

A genome-wide deletion mutant screen identifies pathways affected by nickel sulfate in Saccharomyces cerevisiae

<p>Abstract</p> <p>Background</p> <p>The understanding of the biological function, regulation, and cellular interactions of the yeast genome and proteome, along with the high conservation in gene function found between yeast genes and their human homologues, has allowed for <it>Saccharomyces cerevisiae </it>to be used as a model organism to deduce biological processes in human cells. Here, we have completed a systematic screen of the entire set of 4,733 haploid <it>S. cerevisiae </it>gene deletion strains (the entire set of nonessential genes for this organism) to identify gene products that modulate cellular toxicity to nickel sulfate (NiSO₄).</p> <p>Results</p> <p>We have identified 149 genes whose gene deletion causes sensitivity to NiSO₄and 119 genes whose gene deletion confers resistance. Pathways analysis with proteins whose absence renders cells sensitive and resistant to nickel identified a wide range of cellular processes engaged in the toxicity of <it>S. cerevisiae </it>to NiSO₄. Functional categories overrepresented with proteins whose absence renders cells sensitive to NiSO₄include homeostasis of protons, cation transport, transport ATPases, endocytosis, siderophore-iron transport, homeostasis of metal ions, and the diphthamide biosynthesis pathway. Functional categories overrepresented with proteins whose absence renders cells resistant to nickel include functioning and transport of the vacuole and lysosome, protein targeting, sorting, and translocation, intra-Golgi transport, regulation of C-compound and carbohydrate metabolism, transcriptional repression, and chromosome segregation/division. Interactome analysis mapped seven nickel toxicity modulating and ten nickel-resistance networks. Additionally, we studied the degree of sensitivity or resistance of the 111 nickel-sensitive and 72 -resistant strains whose gene deletion product has a similar protein in human cells.</p> <p>Conclusion</p> <p>We have undertaken a whole genome approach in order to further understand the mechanism(s) regulating the cell's toxicity to nickel compounds. We have used computational methods to integrate the data and generate global models of the yeast's cellular response to NiSO₄. The results of our study shed light on molecular pathways associated with the cellular response of eukaryotic cells to nickel compounds and provide potential implications for further understanding the toxic effects of nickel compounds to human cells.</p

Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response

S-phase and DNA damage promote increased ribonucleotide reductase (RNR) activity. Translation of RNR1 has been linked to the wobble uridine modifying enzyme tRNA methyltransferase 9 (Trm9). We predicted that changes in tRNA modification would translationally regulate RNR1 after DNA damage to promote cell cycle progression. In support, we demonstrate that the Trm9-dependent tRNA modification 5-methoxycarbonylmethyluridine (mcm⁵U) is increased in hydroxyurea (HU)-induced S-phase cells, relative to G₁ and G₂, and that mcm⁵U is one of 16 tRNA modifications whose levels oscillate during the cell cycle. Codon-reporter data matches the mcm⁵U increase to Trm9 and the efficient translation of AGA codons and RNR1. Further, we show that in trm9Δ cells reduced Rnr1 protein levels cause delayed transition into S-phase after damage. Codon re-engineering of RNR1 increased the number of trm9Δ cells that have transitioned into S-phase 1 h after DNA damage and that have increased Rnr1 protein levels, similar to that of wild-type cells expressing native RNR1. Our data supports a model in which codon usage and tRNA modification are regulatory components of the DNA damage response, with both playing vital roles in cell cycle progression.National Institute of Environmental Health Sciences (R01 ES015037)National Institute of Environmental Health Sciences (R01 ES017010)National Institute of Environmental Health Sciences (P30 ES002109)Massachusetts Institute of Technology (Westaway Fund)Singapore-MIT Alliance for Research and Technolog