The chemical genomic portrait of yeast: uncovering a phenotype for all genes

Genetics aims to understand the relation between genotype and phenotype. However, because complete deletion of most yeast genes ( approximately 80%) has no obvious phenotypic consequence in rich medium, it is difficult to study their functions. To uncover phenotypes for this nonessential fraction of the genome, we performed 1144 chemical genomic assays on the yeast whole-genome heterozygous and homozygous deletion collections and quantified the growth fitness of each deletion strain in the presence of chemical or environmental stress conditions. We found that 97% of gene deletions exhibited a measurable growth phenotype, suggesting that nearly all genes are essential for optimal growth in at least one condition.     

Does adding microbial mechanisms of decomposition improve soil organic matter models? A comparison of four models using data from a pulsed rewetting experiment

Contemporary soil organic matter (SOM) models have been successful at simulating decomposition across a range of spatial and temporal scales using first-order kinetics to represent the decomposition process; however, recent work suggests the simplicity of the first-order representation of decomposition is not adequate to capture the microbially-driven dynamics of SOM decomposition over short timescales. For example, the response of soils to drying-rewetting events may best be explained by microbial and/or exoenzyme controls on decomposition. To test if adding these microbial mechanisms improves the ability of SOM models to simulate the response of soils to short-term environmental changes, we developed four different SOM decomposition models with varying mechanistic complexity and compared their ability to simulate soil respiration from a pulsed drying-rewetting laboratory-based experiment. Specifically, we tested the ability of the models to capture the timing and magnitude of soil CO₂ efflux in response to rewetting or constant moisture conditions. The results of the comparison suggest that the inclusion of exoenzyme and microbial controls on decomposition can improve the ability to simulate pulsed rewetting dynamics; however, less mechanistic first-order models prevail under steady-state moisture conditions. These modeling results may have implications for understanding the long-term response of soil carbon stocks in response to local and regional climate change.     

Main stem movement of Atlantic salmon parr in response to high river temperature

Atlantic salmon become thermally stressed when water temperatures exceed 23 °C. To alleviate this stress, they behaviourally thermoregulate by moving to patches of cold water, often forming large aggregations. These patches are known as thermal refuges. Given the consensus that climate change will increase temperatures in Atlantic salmon catchments, thermal refuges will become increasingly important in minimising summer mortalities. While the behaviour of salmonids within thermal refuges is fairly well understood, less is known about their main stem movement in search of thermal refuges or its thermal and temporal cues. We detail the results of a PIT telemetry study to investigate the main stem movement behaviour of thermally stressed Atlantic salmon parr in a temperature‐impacted river. PIT antennas placed around two thermal refuges and at the upstream and downstream limits of their surrounding reach were used to record the movement of salmonids during a heatwave. We observed parr movement at the upstream and downstream antennas 135 min prior to the occurrence of the midpoint of aggregations in the thermal refuges, indicating that Atlantic salmon parr make reach‐scale movements in search of cool water prior to aggregating. Logistic regression showed that the number of degree hours >28 °C predicted the occurrence of main stem movement with a good degree of accuracy, indicating that this temperature represents a fundamental threshold causing Atlantic salmon parr to move towards cool water. Such data could be instrumental in allowing river managers to place limits on human activity within rivers, allowing salmon populations time to recover following heat stress events.     

Michigan Mute Swan Management: A Case Study to Understand Contentious Natural Resource Management Issues

U.S. state fish and wildlife agencies have responded to perceived ecological and social threats posed by mute swans by implementing population control strategies. In Michigan, some stakeholder groups have vocally opposed particular control activities. To better understand and characterize key aspects of the underlying media dialogue about mute swan management in Michigan, one factor in the development of public perceptions about wildlife issues, we conducted a qualitative content analysis of Michigan-specific online news articles. Results revealed tensions between stakeholder groups about management priorities were rooted in differing ideas about healthy social and ecological systems, appropriate wildlife behavior, and the acceptability of lethal control (i.e., shooting living birds). Characterizing which stakeholder groups aligned with particular arguments might allow managers to tailor and direct messaging to specific audiences.     

Intake of Salt Cedar by Two Different Breeds of Sheep

Salt cedar (Tamarix spp.) readily invades and dominates riparian areas and lake basins throughout the western United States. Traditional control efforts (chemical and mechanical control) are expensive and provide limited long-term control. The salt cedar leaf beetle (Diorhabda elongata) provides a method of biological control through reduction in cover. However, population establishment of leaf beetles in some locations is often difficult because of environmental conditions. In previous research, goats readily consumed salt cedar, offering an alternative method of reducing salt cedar cover. For this study, we determined if sheep would consume salt cedar and consume a similar amount as goats. Twelve Rambouillet and 12 Suffolks lambs were fed salt cedar once daily (Trial 1) and three times daily (Trial 2). Intake of salt cedar by sheep was compared between breeds and with intake of salt cedar by goats (n = 10). Salt cedar was fed once a day in Trial 1 for 30 min over 15 d. Intake was recorded daily for individual animals. In Trial 2, salt cedar was offered three times daily for 13 d with intake recorded. There were no differences (P > 0.05) between breeds of sheep. In addition, sheep consumed more salt cedar than goats except on the last day of the study. When salt cedar was offered three times daily, both breeds of sheep increased intake and gained weight over the 13 d of feeding in Trial 2. By the end of the study, intake appeared to still be increasing. Collectively, these results illustrate that both Rambouillet and Suffolk sheep will consume a similar amount of salt cedar as goats and will provide another species of livestock that can be potentially used to reduce salt cedar cover.     

Evaluation of the efficacy of tulathromycin as a metaphylactic antimicrobial in feedlot calves

The purpose of this study was to determine the efficacy and cost-effectiveness of tulathromycin (DRAX) versus tilmicosin (MIC) or oxytetracycline (TET) as a metaphylactic antimicrobial in feedlot calves. Calves that received DRAX had significantly (P<.05) lower initial undifferentiated fever (UF) treatment and relapse rates; lower overall chronicity, overall mortality, and cause-specific mortality rates; higher average daily gains; and improved quality grades. However, calves that received DRAX also had poorer (P<.05) yield grades compared with calves that received MIC or TET and worse feed conversion compared with calves that received MIC. Net advantages in the DRAX group were 3.79CanDollars/animal and 16.96CanDollars/animal compared with the MIC and TET groups, respectively. Based on these results, DRAX is a more efficacious and cost-effective metaphylactic antimicrobial than MIC or TET in feedlot calves at ultra-high risk of developing UF. In addition, this study presents a comparison between two methods ("deads out" and "deads in") of calculating feedlot performance variables.     

Evaluation of a commercially available hyperimmune plasma product for prevention of naturally acquired pneumonia caused by Rhodococcus equi in foals

OBJECTIVE: To determine efficacy of a commercially available hyperimmune plasma product for prevention of naturally acquired pneumonia caused by Rhodococcus equi in foals. DESIGN: Randomized clinical trial. ANIMALS: 165 foals. PROCEDURE: Foals were randomly assigned to 1 of 2 groups (hyperimmune plasma or nontreated controls). Foals with failure of passive transfer (FPT) of immunity were treated with hyperimmune plasma and evaluated as a third group. Foals that received plasma were given 950 ml between 1 and 10 days of age and between 30 and 50 days of age. A tracheobronchial aspirate was obtained from foals with clinical signs of respiratory tract disease for bacteriologic culture. RESULTS: A significant difference in incidence of pneumonia caused by R equi in foals with adequate passive transfer was not detected between foals that received plasma (19.1%) and nontreated foals (30%). Of 13 foals without FPT that received plasma and developed pneumonia caused by R equi, 12 developed disease prior to administration of the second dose of hyperimmune plasma. Incidence of undifferentiated pneumonia of all causes was not different between groups. CONCLUSION AND CLINICAL RELEVANCE: Intravenous administration of the commercially available hyperimmune plasma was safe, and the product contained high concentrations of anti-R equi antibodies. However, within this limited foal population, the difference in incidence of pneumonia caused by R equi observed between foals that received plasma and control foals was not significant.     

Pragmatic population viability targets in a rapidly changing world

To ensure both long-term persistence and evolutionary potential, the required number of individuals in a population often greatly exceeds the targets proposed by conservation management. We critically review minimum population size requirements for species based on empirical and theoretical estimates made over the past few decades. This literature collectively shows that thousands (not hundreds) of individuals are required for a population to have an acceptable probability of riding-out environmental fluctuation and catastrophic events, and ensuring the continuation of evolutionary processes. The evidence is clear, yet conservation policy does not appear to reflect these findings, with pragmatic concerns on feasibility over-riding biological risk assessment. As such, we argue that conservation biology faces a dilemma akin to those working on the physical basis of climate change, where scientific recommendations on carbon emission reductions are compromised by policy makers. There is no obvious resolution other than a more explicit acceptance of the trade-offs implied when population viability requirements are ignored. We recommend that conservation planners include demographic and genetic thresholds in their assessments, and recognise implicit triage where these are not met.     

Hydrothermal Assessment of Temporal Variability in Seedbed Microclimate

The microclimatic requirements for successful seedling establishment are much more restrictive than those required for adult plant survival. The purpose of the current study was to use hydrothermal germination models and a soil energy and water flux model to evaluate intra- and interannual variability in seedbed microclimate relative to potential germination response of six perennial grasses and cheatgrass. We used a 44-yr weather record to parameterize a seedbed microclimate model for estimation of hourly temperature and moisture at seeding depth for a sandy loam soil type at the Orchard Field Test Site in southwestern Ada County, Idaho. Hydrothermal germination response was measured in the laboratory for two seed lots of cheatgrass (Bromus tectorum L.), four seed lots of bluebunch wheatgrass (Pseudoroegneria spicata [Pursh] Löve), three seed lots of bottlebrush squirreltail (Elymus elymoides [Raf] Swezey), and one seed lot each of Sandberg bluegrass (Poa secunda J. Presl.), big squirreltail (Elymus multisetus [J.G. Smith] M.E. Jones), thickspike wheatgrass (Elymus lanceolatus [Scribn. And J.G. Smith] Gould) and Idaho fescue (Festuca idahoensis Elmer). Germination response models were developed to estimate potential germination rate for 13 subpopulations of each seed lot for every hour of the 44-yr simulation. Seedbed microclimate was assessed seasonally and for each day, month, and year, and germination rate-sum estimates integrated for a numerical index of relative site favorability for germination for each time period. The rate-sum favorability index showed a consistent pattern among seed lots for different years, and provides a relatively sensitive indicator of annual and seasonal variability in seedbed microclimate. This index could be used with field data to define minimum weather thresholds for successful establishment of alternative plant materials, in conjunction with weather forecast models for making restoration and fire-rehabilitation management decisions in the fall season, for evaluation of potential climate-change impacts on plant community trajectories, and in optimization schemes for selecting among alternative restoration/rehabilitation management scenarios.