Selection Of A Novel Aptamer Against Vitronectin Using Capillary Electrophoresis And Next Generation Sequencing

Breast cancer (BC) results in ≃40,000 deaths each year in the United States and even among survivors treatment of the disease may have devastating consequences, including increased risk for heart disease and cognitive impairment resulting from the toxic effects of chemotherapy. Aptamer-mediated drug delivery can contribute to improved treatment outcomes through the selective delivery of chemotherapy to BC cells, provided suitable cancer-specific antigens can be identified. We report here the use of capillary electrophoresis in conjunction with next generation sequencing to develop the first vitronectin (VN) binding aptamer (VBA-01; Kd 405 nmol/l, the first aptamer to vitronectin (VN; Kd = 405 nmol/l), a protein that plays an important role in wound healing and that is present at elevated levels in BC tissue and in the blood of BC patients relative to the corresponding nonmalignant tissues. We used VBA-01 to develop DVBA-01, a dimeric aptamer complex, and conjugated doxorubicin (Dox) to DVBA-01 (7:1 ratio) using pH-sensitive, covalent linkages. Dox conjugation enhanced the thermal stability of the complex (60.2 versus 46.5°C) and did not decrease affinity for the VN target. The resulting DVBA-01-Dox complex displayed increased cytotoxicity to MDA-MB-231 BC cells that were cultured on plasticware coated with VN (1.8 × 10⁻⁶mol/l) relative to uncoated plates (2.4 × 10⁻⁶ mol/l), or plates coated with the related protein fibronectin (2.1 × 10⁻⁶ mol/l). The VBA-01 aptamer was evaluated for binding to human BC tissue using immunohistochemistry and displayed tissue specific binding and apparent association with BC cells. In contrast, a monoclonal antibody that preferentially binds to multimeric VN primarily stained extracellular matrix and vessel walls of BC tissue. Our results indicate a strong potential for using VN-targeting aptamers to improve drug delivery to treat BC

Action of Molecular Switches in GPCRs - Theoretical and Experimental Studies

G protein coupled receptors (GPCRs), also called 7TM receptors, form a huge superfamily of membrane proteins that, upon activation by extracellular agonists, pass the signal to the cell interior. Ligands can bind either to extracellular N-terminus and loops (e.g. glutamate receptors) or to the binding site within transmembrane helices (Rhodopsin-like family). They are all activated by agonists although a spontaneous auto-activation of an empty receptor can also be observed. Biochemical and crystallographic methods together with molecular dynamics simulations and other theoretical techniques provided models of the receptor activation based on the action of so-called “molecular switches” buried in the receptor structure. They are changed by agonists but also by inverse agonists evoking an ensemble of activation states leading toward different activation pathways. Switches discovered so far include the ionic lock switch, the 3-7 lock switch, the tyrosine toggle switch linked with the nPxxy motif in TM7, and the transmission switch. The latter one was proposed instead of the tryptophan rotamer toggle switch because no change of the rotamer was observed in structures of activated receptors. The global toggle switch suggested earlier consisting of a vertical rigid motion of TM6, seems also to be implausible based on the recent crystal structures of GPCRs with agonists. Theoretical and experimental methods (crystallography, NMR, specific spectroscopic methods like FRET/BRET but also single-molecule-force-spectroscopy) are currently used to study the effect of ligands on the receptor structure, location of stable structural segments/domains of GPCRs, and to answer the still open question on how ligands are binding: either via ensemble of conformational receptor states or rather via induced fit mechanisms. On the other hand the structural investigations of homo- and heterodimers and higher oligomers revealed the mechanism of allosteric signal transmission and receptor activation that could lead to design highly effective and selective allosteric or ago-allosteric drugs

Seasonal succession of pollinator floral resources in four types of grasslands

Pollinators are declining globally, and this decline in ecosystem services threatens the stability of agricultural and natural systems. Pollinators depend on a diversity of floral resources that are primarily found in uncultivated areas of agro‐ecosystems such as grasslands. Seasonal succession (the seasonal changes that occur in community composition and structure) of floral resources is an essential consideration for pollinator conservation within agro‐ecosystems. Different types of grasslands common within agricultural landscapes could be expected to differ in their seasonal succession of floral resources. Here we investigated how different types of grasslands important for pollinator conservation in the tallgrass prairie ecoregion (remnant prairies, reconstructed prairies, conservation grazed cattle pastures, and old fields) differ in their seasonal succession of floral resources by sampling the plant community every two weeks from 3 May through 4 October 2013. We found remnant prairies had greater richness of inflorescences when summed over the growing season, and that remnants were least similar to the other grassland types in terms of composition. Reconstructed prairies had high richness of inflorescences and exhibited the most similarity in composition to remnant prairies only during the middle of the growing season. Conservation grazed cattle pastures had more periods where turnover in composition from one survey to the next was low, indicated by the coefficient of variation in turnover throughout the season. Old fields had the lowest richness of inflorescences and were significantly different from reconstructed and remnant prairies

Effects of fire and grazing on grasshopper sparrow nest survival

ABSTRACT Patch-burn grazing is a management framework designed to promote heterogeneity in grasslands, creating more diverse grassland structure to accommodate the habitat requirements of many grassland species, particularly grassland birds. Published studies on the effects of patch-burn grazing on passerines have been conducted on relatively large (430-980 ha pastures), contiguous grasslands, and only 1 of these studies has investigated the reproductive success of grassland birds. We assessed the effects of the patch-burn grazing and a more traditional treatment on the nesting ecology of grasshopper sparrows (Ammodramus savannarum) in small (<37 ha pastures) grasslands located in southern Iowa from May to August of 2008 and 2009. The study pastures were grazed from May to September and prescribed burns were conducted in the spring. We investigated the effects of treatments on clutch size and modeled grasshopper sparrow nest survival as a function of multiple biological and ecological factors. We found no difference in clutch size between treatments; however, we did find a reduction in clutch size for nests that were parasitized by brown-headed cowbirds (Molothrus ater). Constant daily survival rates were greater in patch-burn grazed pastures than in grazed-and-burned pastures (patch-burn grazed rate x ¼ 0:930 and grazed-and-burned rate x ¼ 0:907). Competitive survival models included year, stage of nest, nest age, and cool-season grass (csg) abundance within 5 m of the nest. Overall, csg abundance had the greatest effect on survival and had a negative influence. Although survival rates were highest in patch-burn grazed pastures, multiple factors influenced grasshopper sparrow survival. Nest survival rates for both treatments were relatively low, and variables other than treatment were more instrumental in predicting grasshopper sparrow survival. We recommend decreasing overall vegetation cover if increasing nesting habitat for grasshopper sparrows is a management goal. In addition, we recommend further investigation of heterogeneity management in fragmented landscapes to better understand how it affects biodiversity in relatively small management units that typify grassland habitats in the Midwest. ß 2011 The Wildlife Society

Biodiversity Loss and the Taxonomic Bottleneck: Emerging Biodiversity Science

Human domination of the Earth has resulted in dramatic changes to global and local patterns of biodiversity. Biodiversity is critical to human sustainability because it drives the ecosystem services that provide the core of our life-support system. As we, the human species, are the primary factor leading to the decline in biodiversity, we need detailed information about the biodiversity and species composition of specific locations in order to understand how different species contribute to ecosystem services and how humans can sustainably conserve and manage biodiversity. Taxonomy and ecology, two fundamental sciences that generate the knowledge about biodiversity, are associated with a number of limitations that prevent them from providing the information needed to fully understand the relevance of biodiversity in its entirety for human sustainability: (1) biodiversity conservation strategies that tend to be overly focused on research and policy on a global scale with little impact on local biodiversity; (2) the small knowledge base of extant global biodiversity; (3) a lack of much-needed site-specific data on the species composition of communities in human-dominated landscapes, which hinders ecosystem management and biodiversity conservation; (4) biodiversity studies with a lack of taxonomic precision; (5) a lack of taxonomic expertise and trained taxonomists; (6) a taxonomic bottleneck in biodiversity inventory and assessment; and (7) neglect of taxonomic resources and a lack of taxonomic service infrastructure for biodiversity science. These limitations are directly related to contemporary trends in research, conservation strategies, environmental stewardship, environmental education, sustainable development, and local site-specific conservation. Today’s biological knowledge is built on the known global biodiversity, which represents barely 20% of what is currently extant (commonly accepted estimate of 10 million species) on planet Earth. Much remains unexplored and unknown, particularly in hotspots regions of Africa, South Eastern Asia, and South and Central America, including many developing or underdeveloped countries, where localized biodiversity is scarcely studied or described. ‘‘Backyard biodiversity’’, defined as local biodiversity near human habitation, refers to the natural resources and capital for ecosystem services at the grassroots level, which urgently needs to be explored, documented, and conserved as it is the backbone of sustainable economic development in these countries. Beginning with early identification and documentation of local flora and fauna, taxonomy has documented global biodiversity and natural history based on the collection of ‘‘backyard biodiversity’’ specimens worldwide. However, this branch of science suffered a continuous decline in the latter half of the twentieth century, and has now reached a point of potential demise. At present there are very few professional taxonomists and trained local parataxonomists worldwide, while the need for, and demands on, taxonomic services by conservation and resource management communities are rapidly increasing. Systematic collections, the material basis of biodiversity information, have been neglected and abandoned, particularly at institutions of higher learning. Considering the rapid increase in the human population and urbanization, human sustainability requires new conceptual and practical approaches to refocusing and energizing the study of the biodiversity that is the core of natural resources for sustainable development and biotic capital for sustaining our life-support system. In this paper we aim to document and extrapolate the essence of biodiversity, discuss the state and nature of taxonomic demise, the trends of recent biodiversity studies, and suggest reasonable approaches to a biodiversity science to facilitate the expansion of global biodiversity knowledge and to create useful data on backyard biodiversity worldwide towards human sustainability

Genomic predictors of patterns of progression in glioblastoma and possible influences on radiation field design

We present a retrospective investigation of the role of genomics in the prediction of central versus marginal disease progression patterns for glioblastoma (GBM). Between August 2000 and May 2010, 41 patients with GBM and gene expression and methylation data available were treated with radiotherapy with or without concurrent temozolomide. Location of disease progression was categorized as within the high dose (60 Gy) or low dose (46 Gy) volume. Samples were grouped into previously described TCGA genomic groupings: Mesenchymal (m), classical (c), proneural (pn), and neural (n); and were also classified by MGMT-Methylation status and G-Cimp methylation phenotype. Genomic groupings and methylation status were investigated as a possible predictor of disease progression in the high dose region, progression in the low dose region, and time to progression. Based on TCGA category there was no difference in OS (p = 0.26), 60 Gy progression (PN: 71 %, N: 60 %, M: 89 %, C: 83 %, p = 0.19), 46 Gy progression (PN: 57 %, N: 40 %, M: 61 %, C: 50 %, p = 0.8) or time to progression (PN: 9 months, N:15 months, M: 9 months, C: 7 months, p = 0.58). MGMT methylation predicted for improved OS (median 25 vs. 13 months, p = 0.01), improved DFS (median 13 vs. 8 months, p = 0.007) and decreased 60 Gy (p = 0.003) and 46 Gy (p = 0.006) progression. There was a cohort of MGMT methylated patients with late marginal disease progression (4/22 patients, 18 %). TCGA groups demonstrated no difference in survival or progression patterns. MGMT methylation predicted for a statistically significant decrease in in-field and marginal disease progression. There was a cohort of MGMT methylated patients with late marginal progression. Validations of these findings would have implications that could affect radiation field size

Subgroup Economic Analysis for Glioblastoma in a Health Resource-Limited Setting

BACKGROUND: The aim of this research was to evaluate the economic outcomes of radiotherapy (RT), temozolomide (TMZ) and nitrosourea (NT) strategies for glioblastoma patients with different prognostic factors. METHODOLOGY/PRINCIPAL FINDINGS: A Markov model was developed to track monthly patient transitions. Transition probabilities and utilities were derived primarily from published reports. Costs were estimated from the perspective of the Chinese healthcare system. The survival data with different prognostic factors were simulated using Weibull survival models. Costs over a 5-year period and quality-adjusted life years (QALYs) were estimated. Probabilistic sensitivity and one-way analyses were performed. The baseline analysis in the overall cohort showed that the TMZ strategy increased the cost and QALY relative to the RT strategy by $25,328.4 and 0.29, respectively; and the TMZ strategy increased the cost and QALY relative to the NT strategy by$23,906.5 and 0.25, respectively. Therefore, the incremental cost effectiveness ratio (ICER) per additional QALY of the TMZ strategy, relative to the RT strategy and the NT strategy, amounts to $87,940.6 and$94,968.3, respectively. Subgroups with more favorable prognostic factors achieved more health benefits with improved ICERs. Probabilistic sensitivity analyses confirmed that the TMZ strategy was not cost-effective. In general, the results were most sensitive to the cost of TMZ, which indicates that better outcomes could be achieved by decreasing the cost of TMZ. CONCLUSIONS/SIGNIFICANCE: In health resource-limited settings, TMZ is not a cost-effective option for glioblastoma patients. Selecting patients with more favorable prognostic factors increases the likelihood of cost-effectiveness

Extinction Debt in Source-Sink Metacommunities

In an increasingly modified world, understanding and predicting the consequences of landscape alteration on biodiversity is a challenge for ecologists. To this end, metacommunity theory has developed to better understand the complexity of local and regional interactions that occur across larger landscapes. While metacommunity ecology has now provided several alternative models of species coexistence at different spatial scales, predictions regarding the consequences of landscape alteration have been done exclusively for the competition-colonization trade off model (CC). In this paper we investigate the effects of landscape perturbation on source-sink metacommunities. We show that habitat destruction perturbs the equilibria among species competitive effects within the metacommunity, driving both direct extinctions and an indirect extinction debt. As in CC models, we found a time lag for extinction following habitat destruction that varied in length depending upon the relative importance of direct and indirect effects. However, in contrast to CC models, we found that the less competitive species are more affected by habitat destruction. The best competitors can sometimes even be positively affected by habitat destruction, which corresponds well with the results of field studies. Our results are complementary to those results found in CC models of metacommunity dynamics. From a conservation perspective, our results illustrate that landscape alteration jeopardizes species coexistence in patchy landscapes through complex indirect effects and delayed extinctions patterns