Use of the EM algorithm to detect QTL affecting multiple-traits in an across half-sib family analysis

QTL detection experiments in livestock species commonly use the half-sib design. Each male is mated to a number of females, each female producing a limited number of progeny. Analysis consists of attempting to detect associations between phenotype and genotype measured on the progeny. When family sizes are limiting experimenters may wish to incorporate as much information as possible into a single analysis. However, combining information across sires is problematic because of incomplete linkage disequilibrium between the markers and the QTL in the population. This study describes formulæ for obtaining MLEs via the expectation maximization (EM) algorithm for use in a multiple-trait, multiple-family analysis. A model specifying a QTL with only two alleles, and a common within sire error variance is assumed. Compared to single-family analyses, power can be improved up to fourfold with multi-family analyses. The accuracy and precision of QTL location estimates are also substantially improved. With small family sizes, the multi-family, multi-trait analyses reduce substantially, but not totally remove, biases in QTL effect estimates. In situations where multiple QTL alleles are segregating the multi-family analysis will average out the effects of the different QTL alleles.     

Evidence of Yersinia pestis DNA from fleas in an endemic plague area of Zambia

Background

Study protocols involving experimental animals often require the monitoring of different parameters not only in anesthetized, but also in free moving animals. Most animal research involves small rodents, in which continuously monitoring parameters such as temperature and heart rate is very stressful for the awake animals or simply not possible. Aim of the underlying study was to monitor heart rate, temperature and activity and to assess inflammation in the heart, lungs, liver and kidney in the early postoperative phase after experimental cardiopulmonary bypass involving 45 min of deep hypothermic circulatory arrest in rats. Besides continuous monitoring of heart rate, temperature and behavioural activity, the main focus was on avoiding uncontrolled death of an animal in the early postoperative phase in order to harvest relevant organs before autolysis would render them unsuitable for the assessment of inflammation.

Findings

We therefore set up a telemetry-based system (Data Science International, DSI?) that continuously monitored the rat's temperature, heart rate and activity in their cages. The data collection using telemetry was combined with an analysis software (Microsoft excel?), a webmail application (GMX) and a text message-service. Whenever an animal's heart rate dropped below the pre-defined threshold of 150 beats per minute (bpm), a notification in the form of a text message was automatically sent to the experimenter's mobile phone. With a positive predictive value of 93.1% and a negative predictive value of 90.5%, the designed surveillance and alarm system proved a reliable and inexpensive tool to avoid uncontrolled death in order to minimize suffering and harvest relevant organs before autolysis would set in.

Conclusions

This combination of a telemetry-based system and software tools provided us with a reliable notification system of imminent death. The system's high positive predictive value helped to avoid uncontrolled death and facilitated timely organ harvesting. Additionally we were able to markedly reduce the drop out rate of experimental animals, and therefore the total number of animals used in our study. This system can be easily adapted to different study designs and prove a helpful tool to relieve stress and more importantly help to reduce animal numbers.     

Legacy of prior host and soil selection on rhizobial fitness in planta

Measuring selection acting on microbial populations in natural or even seminatural environments is challenging because many microbial populations experience variable selection. The majority of rhizobial bacteria are found in the soil. However, they also live symbiotically inside nodules of legume hosts and each nodule can release thousands of daughter cells back into the soil. We tested how past selection (i.e., legacies) by two plant genotypes and by the soil alone affected selection and genetic diversity within a population of 101 strains of Ensifer meliloti. We also identified allelic variants most strongly associated with soil‐ and host‐dependent fitness. In addition to imposing direct selection on rhizobia populations, soil and host environments had lasting effects across host generations. Host presence and genotype during the legacy period explained 22% and 12% of the variance in the strain composition of nodule communities in the second cohort, respectively. Although strains with high host fitness in the legacy cohort tended to be enriched in the second cohort, the diversity of the strain community was greater when the second cohort was preceded by host rather than soil legacies. Our results indicate the potential importance of soil selection driving the evolution of these plant‐associated microbes.     

Climate change resilience of a globally important sea turtle nesting population

Few studies have looked into climate change resilience of populations of wild animals. We use a model higher vertebrate, the green sea turtle, as its life history is fundamentally affected by climatic conditions, including temperature‐dependent sex determination and obligate use of beaches subject to sea level rise (SLR). We use empirical data from a globally important population in West Africa to assess resistance to climate change within a quantitative framework. We project 200 years of primary sex ratios (1900–2100) and create a digital elevation model of the nesting beach to estimate impacts of projected SLR. Primary sex ratio is currently almost balanced, with 52% of hatchlings produced being female. Under IPCC models, we predict: (a) an increase in the proportion of females by 2100 to 76%–93%, but cooler temperatures, both at the end of the nesting season and in shaded areas, will guarantee male hatchling production; (b) IPCC SLR scenarios will lead to 33.4%–43.0% loss of the current nesting area; (c) climate change will contribute to population growth through population feminization, with 32%–64% more nesting females expected by 2120; (d) as incubation temperatures approach lethal levels, however, the population will cease growing and start to decline. Taken together with other factors (degree of foraging plasticity, rookery size and trajectory, and prevailing threats), this nesting population should resist climate change until 2100, and the availability of spatial and temporal microrefugia indicates potential for resilience to predicted impacts, through the evolution of nest site selection or changes in nesting phenology. This represents the most comprehensive assessment to date of climate change resilience of a marine reptile using the most up‐to‐date IPCC models, appraising the impacts of temperature and SLR, integrated with additional ecological and demographic parameters. We suggest this as a framework for other populations, species and taxa.     

Collecting and Measuring Nociceptive and Inflammatory Mediators in Surgical Wounds

The objectives of this study were to test the feasibility of collecting and measuring inflammatory and nociceptive biochemical mediators at the surgical site; to evaluate the relationship between wound and serum levels; and to determine any associations between mediator release, pain and analgesic consumption post-cesarean delivery. Twenty healthy women undergoing elective cesarean delivery with spinal anesthesia were enrolled. Wound exudate and serum mediators, pain scores and analgesics consumption were measured at 1, 6, 24, and 48 hours post-cesarean. In wound exudate, 19 out of 20 mediators were reliably detected including IL-1β, IL-2, IL-4, IL-6, IL-7, IL-8, IL-10, IL-12, IL-13, IL-17, TNFα, INFγ, G-CSF, GM-CSF, MCP-1 and MIP-1β, nerve growth factor (NGF), prostaglandin E2 (PG-E2) and substance P. Wound PG-E2 and various cytokines peaked early, whereas NGF showed a more delayed release. There were no correlations between the concentration versus time profile of wound and serum cytokines. This study demonstrates the feasibility of collecting and measuring nociceptive and inflammatory mediators in surgical wounds at specific time points. The lack of significant correlations between wound and serum levels emphasizes the importance of determining site-specific release if localized pathologies are to be studied. Download video file.^{(61M, mp4)}     

Fine structure of the mineralized teeth of the chiton Acanthopleura echinata (Mollusca: Polyplacophora)

The major lateral teeth of the chiton Acanthopleura echinata are composite structures composed of three distinct mineral zones: a posterior layer of magnetite; a thin band of lepidocrocite just anterior to this; and apatite throughout the core and anterior regions of the cusp. Biomineralization in these teeth is a matrix-mediated process, in which the minerals are deposited around fibers, with the different biominerals described as occupying architecturally discrete compartments. In this study, a range of scanning electron microscopes was utilized to undertake a detailed in situ investigation of the fine structure of the major lateral teeth. The arrangement of the organic and biomineral components of the tooth is similar throughout the three zones, having no discrete borders between them, and with crystallites of each mineral phase extending into the adjacent mineral zone. Along the posterior surface of the tooth, the organic fibers are arranged in a series of fine parallel lines, but just within the periphery their appearance takes on a "fish scale"-like pattern, reflective of the cross section of a series of units that are overlaid, and offset from each other, in adjacent rows. The units are approximately 2 microm wide and 0.6 microm thick and comprise biomineral plates separated by organic fibers. Two types of subunits make up each "fish scale": one is elongate and curved and forms a trough, in which the other, rod-like unit, is nestled. Adjacent rod and trough units are aligned into large sheets that define the fracture plane of the tooth. The alignment of the plates of rod-trough units is complex and exhibits extreme spatial variation within the tooth cusp. Close to the posterior surface the plates are essentially horizontal and lie in a lateromedial plane, while anteriorly they are almost vertical and lie in the posteroanterior plane. An understanding of the fine structure of the mineralized teeth of chitons, and of the relationship between the organic and mineral components, provides a new insight into biomineralization mechanisms and controls.     

Dieback of riparian alder caused by the Phytophthora alni complex: projected consequences for stream ecosystems

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Not all droughts are created equal: the impacts of interannual drought pattern and magnitude on grassland carbon cycling

Climate extremes, such as drought, may have immediate and potentially prolonged effects on carbon cycling. Grasslands store approximately one‐third of all terrestrial carbon and may become carbon sources during droughts. However, the magnitude and duration of drought‐induced disruptions to the carbon cycle, as well as the mechanisms responsible, remain poorly understood. Over the next century, global climate models predict an increase in two types of drought: chronic but subtle ‘press‐droughts’, and shorter term but extreme ‘pulse‐droughts’. Much of our current understanding of the ecological impacts of drought comes from experimental rainfall manipulations. These studies have been highly valuable, but are often short term and rarely quantify carbon feedbacks. To address this knowledge gap, we used the Community Land Model 4.0 to examine the individual and interactive effects of pulse‐ and press‐droughts on carbon cycling in a mesic grassland of the US Great Plains. A series of modeling experiments were imposed by varying drought magnitude (precipitation amount) and interannual pattern (press‐ vs. pulse‐droughts) to examine the effects on carbon storage and cycling at annual to century timescales. We present three main findings. First, a single‐year pulse‐drought had immediate and prolonged effects on carbon storage due to differential sensitivities of ecosystem respiration and gross primary production. Second, short‐term pulse‐droughts caused greater carbon loss than chronic press‐droughts when total precipitation reductions over a 20‐year period were equivalent. Third, combining pulse‐ and press‐droughts had intermediate effects on carbon loss compared to the independent drought types, except at high drought levels. Overall, these results suggest that interannual drought pattern may be as important for carbon dynamics as drought magnitude and that extreme droughts may have long‐lasting carbon feedbacks in grassland ecosystems.     

Platelet adhesion and degranulation induce pro-survival and pro-angiogenic signalling in ovarian cancer cells

Thrombosis is common in ovarian cancer. However, the interaction of platelets with ovarian cancer cells has not been critically examined. To address this, we investigated platelet interactions in a range of ovarian cancer cell lines with different metastatic potentials [HIO-80, 59M, SK-OV-3, A2780, A2780cis]. Platelets adhered to ovarian cancer cells with the most significant adhesion to the 59M cell line. Ovarian cancer cells induced platelet activation [P-selectin expression] in a dose dependent manner, with the most significant activation seen in response to the 59M cell line. The platelet antagonists [cangrelor, MRS2179, and apyrase] inhibited 59M cell induced activation suggesting a P2Y12 and P2Y1 receptor mediated mechanism of platelet activation dependent on the release of ADP by 59M cells. A2780 and 59M cells potentiated PAR-1, PAR-4, and TxA2 receptor mediated platelet activation, but had no effect on ADP, epinephrine, or collagen induced activation. Analysis of gene expression changes in ovarian cancer cells following treatment with washed platelets or platelet releasate showed a subtle but valid upregulation of anti-apoptotic, anti-autophagy pro-angiogenic, pro-cell cycle and metabolic genes. Thus, ovarian cancer cells with different metastatic potential adhere and activate platelets differentially while both platelets and platelet releasate mediate pro-survival and pro-angiogenic signals in ovarian cancer cells.