Optimization of DNA Extraction Methods for Sequencing of the NADH Dehydrogenase Subunit 2 (ND2) Gene in Rainbow Trout (\u3cem\u3eOncorhynchus mykiss\u3c/em\u3e)

Morphological, behavioral, and genetic variation due to broad geographic ranges is common in salmonid fishes. This variation can be attributed to the isolation of populations from natural phenomenon or human alteration to habitats, which affect gene flow and genetic drift. These changes may play a role in intraspecific genetic variation, potentially isolating them into separate subspecies or locally adapted populations. Rainbow Trout (Oncorhynchus mykiss) are one of the most widely distributed fish species in western North America but no study has identified the main evolutionary lineages from across its range. Identifying and comparing distinct evolutionary lineages can be achieved by comparing sequence data from mitochondrial genes but requires extraction of archived tissue samples of rainbow trout and amplification of selected genes. In this study, we compare different DNA extraction methods for rainbow trout tissue samples, some of which are more than 25 years old. DNA was extracted from tissue samples following a 5 or 15% Chelex method, or by following Zymo Research extraction kit instructions. Following extractions, polymerase chain reaction (PCR) for the highly conserved NADH dehydrogenase subunit 2 mtDNA gene (ND2) was completed using a BIO RAD thermal cycler and a gel electrophoresis is done to determine whether the ND2 gene was successfully amplified. Photographs of the agarose gels were taken using a ChemiDoc imaging system, and samples showing a band at 1050 base pairs are sent to the Molecular Research Core Facility at Idaho State University for sequencing. The genetic sequences are then compared and used to create a phylogeny and distribution for Rainbow trout subspecies. Sequencing of individual specimen and comparison across the species range will aid in the development of management and conservation strategies for rainbow trout across the species range

Thirty years of connectivity conservation planning : An assessment of factors influencing plan implementation

Connectivity conservation is an emergent approach to counteracting landscape fragmentation and enhancing resilience to climate change at local, national, and global scales. While policy that promotes connectivity is advancing, there has been no systematic, evidence-based study that assesses whether connectivity conservation plans (CCPs) resulted in conservation outcomes, and identifies specific plan attributes that may favor successful implementation. To fill this gap, we gathered 263 terrestrial CCPs from around the world, characterized attributes of 109 plans by surveying plan authors, and conducted semi-structured interviews with authors and implementers of 77 CCPs. The production of CCPs started around 1990 and has increased markedly in all parts of the world, most notably in the United States (led by NGOs and a few states, with little federal involvement), Europe (led by the EU and national policies and implemented at local levels), and the Republic of South Africa (where national legislation mandates each municipality to map corridors and zone all land by 2020). All of the 109 plans that we examined in detail were followed by implementation actions such as crossing structures, ecological restoration, land purchases or easements, recognition of corridors through zoning or government designation, and public engagement. Interviewees emphasized the importance of initial buy-in from key government stakeholders, stakeholder involvement beyond initial buy-in, minimizing staff turnover, and transparent and repeatable procedures. Our quantitative and qualitative analyses similarly suggested that implementation of a CCP was enhanced by enduring partnerships among stakeholders, continuity of leadership, specific recommendations in the CCP using tools appropriately selected from a large toolbox, the existence of enabling legislation and policy, a transparent and repeatable scientific approach, adequate funding, and public outreach.</p

Neutrophils are Mediators of Metastatic Prostate Cancer Progression in Bone

Bone metastatic prostate cancer (BM-PCa) significantly reduces overall patient survival and is currently incurable. Current standard immunotherapy showed promising results for PCa patients with metastatic, but less advanced, disease (i.e., fewer than 20 bone lesions) suggesting that PCa growth in bone contributes to response to immunotherapy. We found that: (1) PCa stimulates recruitment of neutrophils, the most abundant immune cell in bone, and (2) that neutrophils heavily infiltrate regions of prostate tumor in bone of BM-PCa patients. Based on these findings, we examined the impact of direct neutrophil-prostate cancer interactions on prostate cancer growth. Bone marrow neutrophils directly induced apoptosis of PCa in vitro and in vivo, such that neutrophil depletion in bone metastasis models enhanced BM-PCa growth. Neutrophil-mediated PCa killing was found to be mediated by suppression of STAT5, a transcription factor shown to promote PCa progression. However, as the tumor progressed in bone over time, neutrophils from late-stage bone tumors failed to elicit cytotoxic effector responses to PCa. These findings are the first to demonstrate that bone-resident neutrophils inhibit PCa and that BM-PCa are able to progress via evasion of neutrophil-mediated killing. Enhancing neutrophil cytotoxicity in bone may present a novel therapeutic option for bone metastatic prostate cancer

Androgen Receptor Inhibition Suppresses Anti-Tumor Neutrophil Response Against Bone Metastatic Prostate Cancer via Regulation of TβRI Expression

Bone metastatic disease of prostate cancer (PCa) is incurable and progression in bone is largely dictated by tumor-stromal interactions in the bone microenvironment. We showed previously that bone neutrophils initially inhibit bone metastatic PCa growth yet metastatic PCa becomes resistant to neutrophil response. Further, neutrophils isolated from tumor-bone lost their ability to suppress tumor growth through unknown mechanisms. With this study, our goal was to define the impact of metastatic PCa on neutrophil function throughout tumor progression and to determine the potential of neutrophils as predictive biomarkers of metastatic disease. Using patient peripheral blood polymorphonuclear neutrophils (PMNs), we identified that PCa progression dictates PMN cell surface markers and gene expression, but not cytotoxicity against PCa. Importantly, we also identified a novel phenomenon in which second generation androgen deprivation therapy (ADT) suppresses PMN cytotoxicity via increased transforming growth factor beta receptor I (TβRI). High dose testosterone and genetic or pharmacologic TβRI inhibition rescued androgen receptor-mediated neutrophil suppression and restored neutrophil anti-tumor immune response. These studies highlight the ability to leverage standard-care ADT to generate neutrophil anti-tumor responses against bone metastatic PCa

Core outcome domains for early-phase clinical trials of sound-, psychology-, and pharmacology-based interventions to manage chronic subjective tinnitus in adults: the COMIT'ID study protocol for using a Delphi process and face-to-face meetings to establish consensus

Background: The reporting of outcomes in clinical trials of subjective tinnitus indicates that many different tinnitus-related complaints are of interest to investigators, from perceptual attributes of the sound (e.g. loudness) to psychosocial impacts (e.g. quality of life). Even when considering one type of intervention strategy for subjective tinnitus, there is no agreement about what is critically important for deciding whether a treatment is effective. The main purpose of this observational study is therefore to develop Core Outcome Domain Sets for the three different intervention strategies (sound, psychological, and pharmacological) for adults with chronic subjective tinnitus that should be measured and reported in every clinical trial of these interventions. Secondary objectives are to identify the strengths and limitations of our study design for recruiting and reducing attrition of participants, and to explore uptake of the core outcomes. Methods: The ‘Core Outcome Measures in Tinnitus: International Delphi’ (COMIT’ID) study will use a mixed methods approach that incorporates input from healthcare users at the pre-Delphi stage, a modified three round Delphi survey and final consensus meetings (one for each intervention). The meetings will generate recommendations by stakeholder representatives on agreed Core Outcome Domain Sets specific to each intervention. A subsequent step will establish a common cross-cutting Core Outcome Domain Set by identifying the common outcome domains included in all three intervention-specific Core Outcome Domain Sets. To address the secondary objectives, we will gather feedback from participants about their experience of taking part in the Delphi process. We aspire to conduct an observational cohort study to evaluate uptake of the core outcomes in published studies at 7 years following core outcome set publication. Discussion: The COMIT’ID study aims to develop a Core Outcome Domain Set that are agreed as critically important for deciding whether a treatment for subjective tinnitus is effective. Such a recommendation would help to standardise future clinical trials worldwide and so we will determine if participation increases use of the core outcome set in the long term. Trial registration: This project has been registered in the database of the Core Outcome Measures in Effectiveness Trials (COMET) initiative

The C-Terminus of Toxoplasma RON2 Provides the Crucial Link between AMA1 and the Host-Associated Invasion Complex

Host cell invasion by apicomplexan parasites requires formation of the moving junction (MJ), a ring-like apposition between the parasite and host plasma membranes that the parasite migrates through during entry. The Toxoplasma MJ is a secreted complex including TgAMA1, a transmembrane protein on the parasite surface, and a complex of rhoptry neck proteins (TgRON2/4/5/8) described as host cell-associated. How these proteins connect the parasite and host cell has not previously been described. Here we show that TgRON2 localizes to the MJ and that two short segments flanking a hydrophobic stretch near its C-terminus (D3 and D4) independently associate with the ectodomain of TgAMA1. Pre-incubation of parasites with D3 (fused to glutathione S-transferase) dramatically reduces invasion but does not prevent injection of rhoptry bulb proteins. Hence, the entire C-terminal region of TgRON2 forms the crucial bridge between TgAMA1 and the rest of the MJ complex but this association is not required for rhoptry protein injection

Policy climates and climate policies: Analysing the politics of building urban climate change resilience

This paper examines the process of building resilience to climate change in urban areas by scrutinising the manner in which initiatives to build resilience interact with the urban policy environments in which they unfold. The urban policy environment is broken into three analytical areas of actors, spaces and discourses. This illustrates the influence of actor networks, epistemic communities and policy entrepreneurs in helping climate change resilience gain traction in urban settings, how discourses attached to Resilience urban resilience are dissonant with those prevailing in ossified Discourses urban policy environments, and the dynamic interaction of interest, agendas and power in decision making that accompanies resilience building processes. The paper applies this framework to case studies of two Indian cities within a major international urban climate change resilience initiative. Using data gathered through a variety of rigorous qualitative research methods, the paper provides insights into the politics of policy processes around urban climate change initiatives. Findings from this study can inform urban development policies and allow resilience project planners to calibrate their efforts to better suit urban policy environments. The paper highlights how issues of politics and power are more significant determinants of such policy processes than conventional, science-led analyses would suggest

Biological flora of Central Europe: Cyperus esculentus L

This paper presents information on all aspects of the biology of Cyperus esculentus L. (yellow nutsedge) and deals with its taxonomy, morphology, genetic diversity, distribution, habitat requirements, ecology and life cycle, with special emphasis on uses and cultivation, history of introduction, impact and management in Europe. C. esculentus is a tuber geophyte and most likely originates from the Mediterranean and Southwest Asia. It is a variable plant and four wild-type varieties are presently recognized, in addition to a cultivated form. C. esculentus reproduces primarily by its underground tubers, although abundant seeds are produced. In temperate climates, tubers usually sprout in late spring and the plant withers at the beginning of the winter. C. esculentus is only cultivated in the València region in Spain. Invasion foci emerged across Europe at the beginning of the 1980s and at present, C. esculentus is most abundant on arable land and in ruderal habitats, followed by riverine vegetation. In heavily infested regions of Europe, C. esculentus causes substantial yield losses in field crops and although different management strategies are available, C. esculentus remains difficult to control.Follak, S.; Belz, R.; Bohren, C.; Castro, OD.; Guacchio, ED.; Pascual-Seva, N.; Schwarz, M.... (2016). Biological flora of Central Europe: Cyperus esculentus L. Perspectives in Plant Ecology, Evolution and Systematics. 23:33-51. doi:10.1016/j.ppees.2016.09.003S33512

Seed Bank Changes with Time-Since-Fire In Florida Rosemary Scrub

The soil seed bank plays a central role in the regeneration of obligate seeding species in fire-prone habitats. We evaluated how seed density and species composition changed with time-since-fire in the Florida, USA, rosemary scrub community. Because fire affects habitat availability and plant demographic variation, we predicted that soil seed density would be low in recently burned and long-unburned stands and high at intermediate time-since-fire. Seed bank soil samples were collected from a chronosequence of time-since-fire composited from two trials conducted in 1992-1993 and 2008-2009: two sites each of 3, 6, 10, and 24 years post-fire, and 3 long-unburned (similar to 67 years) sites. The seedling emergence method was used to determine species composition of the seed bank. Across all time-since-fire age classes, herbaceous species dominated the seed bank, while long-lived subshrubs and shrubs were present in low densities. Seed banks from sites three years post-fire were distinct from the other sites. When species were sorted as functional groups, seed density was related with time-since-fire for subshrubs and ruderal herbs, but not for scrub herbs and graminoids. Subshrubs and ruderal herbs had highest seed densities in recently burned stands. Seed densities of Florida rosemary (Ceratiola ericoides Michx.) (the major obligate seeding shrub in this community) were associated with time-since-fire and showed highest densities at recently burned and long-unburned sites. The seed banks of two scrub herb species, paper nailwort (Paronychia chartacea Fernald) and nodding pinweed (Lechea cernua Small), were associated with time-since-fire. They reached peaks in density in the first ten years post-fire, corresponding with similar changes in their aboveground abundances with time-since-fire. Soil seed densities of several species and functional groups were associated with time-since-fire, but timing of peak seed density varied depending on species\u27 life span and age of reproductive maturity