using provenance data and DNA

Re-examination of the historical range of the greater prairie chicke

Australian scallops do not recognise the introduced predatory seastar Asterias amurensis

Copyright © 2005 Inter-Research.Escape responses of Australian scallops (Pecten fumatus and Chlamys asperrima) to native and introduced predatory seastars were compared in laboratory and field trials. The native seastar Coscinasterias muricata elicited an almost immediate escape response by scallops in all trials. In contrast, there was a low frequency of escape response exhibited by scallops when held in contact with the introduced seastar Asterias amurensis. These results are consistent with the hypothesis that escape response in invertebrates has evolved relative to predation risk. The absence of predator recognition in marine invertebrates may have serious implications for wild and farmed populations in southern Australia where introduced predators are prevalent.Kate S. Hutson, D. Jeff Ross, Rob W. Day, John J. Aher

2010 YCAP Needs Assessment Report

This report outlines the Yamhill Community Action Partnership (YCAP) areas of need, strength, and improvement. Low income and unemployed individuals receive significant support through YCAP programs, including transportation, housing, and bill pay assistance. YCAP programs were assessed during the spring of 2010 through a client survey

Achieving an Optimal Childhood Vaccine Policy

Policies to remove parents' ability to opt-out from school immunization requirements on the basis of religious or personal beliefs (ie, nonmedical exemptions) may be a useful strategy to increase immunization rates and prevent outbreaks of vaccine-preventable disease. However, there is uncertainty about the effectiveness of this strategy and the range of possible outcomes. We advocate for a more deliberative process through which a broad range of outcomes is scrutinized and the balance of values underlying the policy decision to eliminate nonmedical exemptions is clearly articulated. We identify 3 outcomes that require particular consideration before policies to eliminate nonmedical exemptions are implemented widely and outline a process for making the values underlying such policies more explicit

Re-examination of the historical range of the greater prairie chickenusing provenance data and DNA analysis of museum collections

The extent to which a species has declined within its historical range is commonly used as an important criterion in categorizing the conservation status of wild populations. The greater prairie chicken ( Tympanuchus cupido ) has been extirpated from much of the area it once inhabited. However, within a large part of this area the species is not considered to be native, warranting no recovery effort or special protection. Demographic analysis based on provenance data from 238 specimens from museum collections in addition to genetic analyses of 100 mtDNA sequences suggest this species was native to the northern prairies, extending from central Minnesota to Alberta, Canada. Provenance data from 1879 to 1935 indicate that T. cupido would have required colonization and establishment of populations on an average 11,905 km 2 every year, with an estimated per capita growth rate of 8.9% per year. These rates seem unrealistic given the limited dispersal and high mortality rates reported for this species. A survey of mtDNA sequences from “original” and “expanded” ranges revealed no differences in levels of sequence diversity within ranges (π=0.018; SE=0.004) but significant levels of genetic differentiation ( F ST =0.034; P =0.013), which suggest that these populations have been relatively isolated for significant evolutionary time periods. DNA mismatch distributions fit a sudden expansion model consistent with a post-Pleistocene expansion of the species, which coincides with the expansion of prairies into the Canadian plains about 9000 years before present. This study demonstrates the value of museum collections as stores of ecological and genetic information fundamental for the conservation of natural populations, and suggests that the current status of the greater prairie chicken should be re-evaluated within all areas where this species may occur, but is now considered non-native.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/41268/1/10592_2005_Article_9110.pd

Perceptions of the crowded sky as assessed through response to aerial infrastructure

Ever increasing numbers of wind turbines, communication towers, power lines, and aerial vehicles are clear evidence of our growing reliance on infrastructure in the lower aerosphere. As this infrastructure expands, it is important to understand public perceptions of an increasingly crowded sky. To gauge tolerance for aerial crowding, 251 participants from across the US completed a survey where they rated tolerance for a series of aerial infrastructure images (i.e., towers, turbines, and airborne vehicles) in four landscapes with varying degrees of pre-existing ground-level infrastructure that approximated rural, suburban, and urban settings. We predicted lower tolerance for aerial infrastructure 1) in more natural scenes and 2) among rural residents. In general, participants preferred an open aesthetic with relatively little aerial infrastructure across all landscape types. No clear association was found between infrastructure tolerance and natural scenes nor rural residency, with participants slightly less tolerant of infrastructure in the suburban scene. Tolerance scores were generally similar across age, income levels, and political affiliations. Women indicated less crowding tolerance than men, with this effect driven by a disproportionate number of women with zero tolerance for aerial infrastructure. African Americans and Asians had higher tolerance scores than other racial/ethnic groups, but these trends may have been affected by low sample sizes of non-white participants. Our survey revealed fewer differences in crowding tolerance across demographic groups than might be expected given widely reported political and geographic polarization in the U.S. Attitudes toward aerial infrastructure were varied with few associations with demographic parameters suggesting that public opinion has not yet solidified with regard to this issue, making possible opportunities for consensus building with regard to responsible development of aerial infrastructure

Engineering protein processing of the mammary gland to produce abundant hemophilia B therapy in milk

Both the low animal cell density of bioreactors and their ability to post-translationally process recombinant factor IX (rFIX) limit hemophilia B therapy to transgenic pigs to make rFIX in milk at about 3,000-fold higher output than provided by industrial bioreactors. However, this resulted in incomplete γ-carboxylation and propeptide cleavage where both processes are transmembrane mediated. We then bioengineered the co-expression of truncated, soluble human furin (rFurin) with pro-rFIX at a favorable enzyme to substrate ratio. This resulted in the complete conversion of pro-rFIX to rFIX while yielding a normal lactation. Importantly, these high levels of propeptide processing by soluble rFurin did not preempt γ-carboxylation in the ER and therefore was compartmentalized to the Trans-Golgi Network (TGN) and also to milk. The Golgi specific engineering demonstrated here segues the ER targeted enhancement of γ-carboxylation needed to biomanufacture coagulation proteins like rFIX using transgenic livestock

Engineering protein processing of the mammary gland to produce abundant hemophilia B therapy in milk

Both the low animal cell density of bioreactors and their ability to post-translationally process recombinant factor IX (rFIX) limit hemophilia B therapy to transgenic pigs to make rFIX in milk at about 3,000-fold higher output than provided by industrial bioreactors. However, this resulted in incomplete γ-carboxylation and propeptide cleavage where both processes are transmembrane mediated. We then bioengineered the co-expression of truncated, soluble human furin (rFurin) with pro-rFIX at a favorable enzyme to substrate ratio. This resulted in the complete conversion of pro-rFIX to rFIX while yielding a normal lactation. Importantly, these high levels of propeptide processing by soluble rFurin did not preempt γ-carboxylation in the ER and therefore was compartmentalized to the Trans-Golgi Network (TGN) and also to milk. The Golgi specific engineering demonstrated here segues the ER targeted enhancement of γ-carboxylation needed to biomanufacture coagulation proteins like rFIX using transgenic livestock

Rapid nanopore sequencing and predictive susceptibility testing of positive blood cultures from intensive care patients with sepsis

ABSTRACT We aimed to evaluate the performance of Oxford Nanopore Technologies (ONT) sequencing from positive blood culture (BC) broths for bacterial identification and antimicrobial susceptibility prediction. Patients with suspected sepsis in four intensive care units were prospectively enrolled. Human-depleted DNA was extracted from positive BC broths and sequenced using ONT (MinION). Species abundance was estimated using Kraken2, and a cloud-based system (AREScloud) provided in silico predictive antimicrobial susceptibility testing (AST) from assembled contigs. Results were compared to conventional identification and phenotypic AST. Species-level agreement between conventional methods and AST predicted from sequencing was 94.2% (49/52), increasing to 100% in monomicrobial infections. In 262 high-quality AREScloud AST predictions across 24 samples, categorical agreement (CA) was 89.3%, with major error (ME) and very major error (VME) rates of 10.5% and 12.1%, respectively. Over 90% CA was achieved for some taxa (e.g.,Staphylococcus aureus) but was suboptimal for Pseudomonas aeruginosa. In 470 AST predictions across 42 samples, with both high quality and exploratory-only predictions, overall CA, ME, and VME rates were 87.7%, 8.3%, and 28.4%. VME rates were inflated by false susceptibility calls in a small number of species/antibiotic combinations with few representative resistant isolates. Time to reporting from sequencing could be achieved within 8–16 h from BC positivity. Direct sequencing from positive BC broths is feasible and can provide accurate predictive AST for some species. ONT-based approaches may be faster but significant improvements in accuracy are required before it can be considered for clinical use. IMPORTANCE Sepsis and bloodstream infections carry a high risk of morbidity and mortality. Rapid identification and susceptibility prediction of causative pathogens, using Nanopore sequencing direct from blood cultures, may offer clinical benefit. We assessed this approach in comparison to conventional phenotypic methods and determined the accuracy of species identification and susceptibility prediction from genomic data. While this workflow holds promise, and performed well for some common bacterial species, improvements in sequencing accuracy and more robust predictive algorithms across a diverse range of organisms are required before this can be considered for clinical use. However, results could be achieved in timeframes that are faster than conventional phenotypic methods

Seagrass restoration is possible:Insights and lessons from Australia and New Zealand

Seagrasses are important marine ecosystems situated throughout the world’s coastlines. They are facing declines around the world due to global and local threats such as rising ocean temperatures, coastal development and pollution from sewage outfalls and agriculture. Efforts have been made to reduce seagrass loss through reducing local and regional stressors, and through active restoration. Seagrass restoration is a rapidly maturing discipline, but improved restoration practices are needed to enhance the success of future programs. Major gaps in knowledge remain, however, prior research efforts have provided valuable insights into factors influencing the outcomes of restoration and there are now several examples of successful large-scale restoration programs. A variety of tools and techniques have recently been developed that will improve the efficiency, cost effectiveness, and scalability of restoration programs. This review describes several restoration successes in Australia and New Zealand, with a focus on emerging techniques for restoration, key considerations for future programs, and highlights the benefits of increased collaboration, Traditional Owner (First Nation) and stakeholder engagement. Combined, these lessons and emerging approaches show that seagrass restoration is possible, and efforts should be directed at upscaling seagrass restoration into the future. This is critical for the future conservation of this important ecosystem and the ecological and coastal communities they support