Medical Researchers' Ancillary Care Obligations: The Relationship‐Based Approach

In this article, I provide a new account of the basis of medical researchers' ancillary care obligations. Ancillary care in medical research, or medical care that research participants need but that is not required for the validity or safety of a study or to redress research injuries, is a topic that has drawn increasing attention in research ethics over the last ten years. My view, the relationship‐based approach, improves on the main existing theory, Richardson and Belsky's ‘partial‐entrustment model’, by avoiding its problematic restriction on the scope of health needs for which researchers could be obligated to provide ancillary care. Instead, it grounds ancillary care obligations in a wide range of morally relevant features of the researcher‐participant relationship, including the level of engagement between researchers and participants, and weighs these factors against each other. I argue that the level of engagement, that is, the duration and intensity of interactions, between researchers and participants matters for ancillary care because of its connection to the meaningfulness of a relationship, and I suggest that other morally relevant features can be grounded in researchers' role obligations.     

Canopy Carbon Gain and Water Use: Analysis of Old-growth Conifers in the Pacific Northwest

This report summarizes our current knowledge of leaf-level physiological processes that regulate carbon gain and water loss of the dominant tree species in an old-growth forest at the Wind River Canopy Crane Research Facility. Analysis includes measurements of photosynthesis, respiration, stomatal conductance, water potential, stable carbon isotope values, and biogenic hydrocarbon emissions from Douglas-fir (Pseudotsuga menziesii), western hemlock (Tsuga heterophylla), and western red cedar (Thuja plicata). Leaf-level information is used to scale fluxes up to the canopy to estimate gross primary production using a physiology-based process model. Both light-saturated and in situ photosynthesis exhibit pronounced vertical gradients through the canopy, but are consistently highest in Douglas-fir, intermediate in western hemlock, and lowest in western red cedar. Net photosynthesis and stomatal conductance are strongly dependent on vapor-pressure deficit in Douglas-fir, and decline through the course of a seasonal drought. Foliar respiration is similar for Douglas-fir and western hemlock, and lowest for western red cedar. Water-use efficiency varied with species and tree height, as indexed using stable carbon isotopes values for foliage. Leaf water potential is most negative for Douglas-fir and similar for western hemlock and western red cedar. Terpene fluxes from foliage equal approximately 1% of the net carbon loss from the forest. Modeled estimates based on physiological measurements show gross primary productivity (GPP) to be about 22 Mg C m^–2 y^–1. Physiological studies will be necessary to further refine estimates of stand-level carbon balance and to make long-term predictions of changes in carbon balance due to changes in forest structure, species composition, and climate.     

Response of the Soil Microbial Community to Changes in Precipitation in a Semiarid Ecosystem

Microbial communities regulate many belowground carbon cycling processes; thus, the impact of climate change on the structure and function of soil microbial communities could, in turn, impact the release or storage of carbon in soils. Here we used a large-scale precipitation manipulation (+18%, −50%, or ambient) in a piñon-juniper woodland (Pinus edulis-Juniperus monosperma) to investigate how changes in precipitation amounts altered soil microbial communities as well as what role seasonal variation in rainfall and plant composition played in the microbial community response. Seasonal variability in precipitation had a larger role in determining the composition of soil microbial communities in 2008 than the direct effect of the experimental precipitation treatments. Bacterial and fungal communities in the dry, relatively moisture-limited premonsoon season were compositionally distinct from communities in the monsoon season, when soil moisture levels and periodicity varied more widely across treatments. Fungal abundance in the drought plots during the dry premonsoon season was particularly low and was 4.7 times greater upon soil wet-up in the monsoon season, suggesting that soil fungi were water limited in the driest plots, which may result in a decrease in fungal degradation of carbon substrates. Additionally, we found that both bacterial and fungal communities beneath piñon pine and juniper were distinct, suggesting that microbial functions beneath these trees are different. We conclude that predicting the response of microbial communities to climate change is highly dependent on seasonal dynamics, background climatic variability, and the composition of the associated aboveground community.     

Characteristic mass spectral fragments of the organophosphorus agent FP-biotin and FP-biotinylated peptides from trypsin and bovine albumin (Tyr410)

A mass spectrometry-based method was developed for selective detection of FP-biotinylated peptides in complex mixtures. Mixtures of peptides, at the low-picomole level, were analyzed by liquid chromatography and positive ion, nanospray, triple quadrupole, linear ion trap mass spectrometry. Peptides were fragmented by collision-activated dissociation in the mass spectrometer. The free FP-biotin and peptides containing FP-biotinylated serine or FP-biotinylated tyrosine yielded characteristic fragment ions at 227, 312, and 329 m/z. FP-biotinylated serine yielded an additional characteristic fragment ion at 591 m/z. Chromatographic peaks containing FP-biotinylated peptides were indicated by these diagnostic ions. Data illustrating the selectivity of the approach are presented for tryptic digests of FP-biotinylated trypsin and FP-biotinylated serum albumin. A 16-residue peptide from bovine trypsin was biotinylated on the active site serine. A 3-residue peptide from bovine albumin, YTR, was biotinylated on Tyr410. This latter result confirms that the organophosphorus binding site of albumin is a tyrosine. This method can be used to search for new biomarkers of organophosphorus agent exposure.     

Symbolic modeling of epistasis

The workhorse of modern genetic analysis is the parametric linear model. The advantages of the linear modeling framework are many and include a mathematical understanding of the model fitting process and ease of interpretation. However, an important limitation is that linear models make assumptions about the nature of the data being modeled. This assumption may not be realistic for complex biological systems such as disease susceptibility where nonlinearities in the genotype to phenotype mapping relationship that result from epistasis, plastic reaction norms, locus heterogeneity, and phenocopy, for example, are the norm rather than the exception. We have previously developed a flexible modeling approach called symbolic discriminant analysis (SDA) that makes no assumptions about the patterns in the data. Rather, SDA lets the data dictate the size, shape, and complexity of a symbolic discriminant function that could include any set of mathematical functions from a list of candidates supplied by the user. Here, we outline a new five step process for symbolic model discovery that uses genetic programming (GP) for coarse-grained stochastic searching, experimental design for parameter optimization, graphical modeling for generating expert knowledge, and estimation of distribution algorithms for fine-grained stochastic searching. Finally, we introduce function mapping as a new method for interpreting symbolic discriminant functions. We show that function mapping when combined with measures of interaction information facilitates statistical interpretation by providing a graphical approach to decomposing complex models to highlight synergistic, redundant, and independent effects of polymorphisms and their composite functions. We illustrate this five step SDA modeling process with a real case-control dataset.     

A new measurement technique reveals rapid post-illumination changes in the carbon isotope composition of leaf-respired CO2

We describe an open leaf gas exchange system coupled to a tunable diode laser (TDL) spectroscopy system enabling measurement of the leaf respiratory CO(2) flux and its associated carbon isotope composition (delta(13)C(Rl)) every 3 min. The precision of delta(13)C(Rl) measurement is comparable to that of traditional mass spectrometry techniques. delta(13)C(Rl) from castor bean (Ricinus communis L.) leaves tended to be positively related to the ratio of CO(2) produced to O(2) consumed [respiratory quotient (RQ)] after 24-48 h of prolonged darkness, in support of existing models. Further, the apparent fractionation between respiratory substrates and respired CO(2) within 1-8 h after the start of the dark period was similar to previous observations. In subsequent experiments, R. communis plants were grown under variable water availability to provide a range in delta(13)C of recently fixed carbohydrate. In leaves exposed to high light levels prior to the start of the dark period, CO(2) respired by leaves was up to 11 per thousand more enriched than phloem sap sugars within the first 10-15 min after plants had been moved from the light into the dark. The (13)C enrichment in respired CO(2) then decreased rapidly to within 3-7 per thousand of phloem sap after 30-60 min in the dark. This strong enrichment was not observed if light levels were low prior to the start of the dark period. Measurements of RQ confirmed that carbohydrates were the likely respiratory substrate for plants (RQ > 0.8) within the first 60 min after illumination. The strong (13)C enrichment that followed a high light-to-dark transition coincided with high respiration rates, suggesting that so-called light-enhanced dark respiration (LEDR) is fed by (13)C-enriched metabolites.     

Bacteria induce skin regeneration via IL-1β signaling

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An update to Hippocampome.org by integrating single-cell phenotypes with circuit function in vivo

Understanding brain operation demands linking basic behavioral traits to cell-type specific dynamics of different brain-wide subcircuits. This requires a system to classify the basic operational modes of neurons and circuits. Single-cell phenotyping of firing behavior during ongoing oscillations in vivo has provided a large body of evidence on entorhinal–hippocampal function, but data are dispersed and diverse. Here, we mined literature to search for information regarding the phase-timing dynamics of over 100 hippocampal/entorhinal neuron types defined in Hippocampome.org. We identified missing and unresolved pieces of knowledge (e.g., the preferred theta phase for a specific neuron type) and complemented the dataset with our own new data. By confronting the effect of brain state and recording methods, we highlight the equivalences and differences across conditions and offer a number of novel observations. We show how a heuristic approach based on oscillatory features of morphologically identified neurons can aid in classifying extracellular recordings of single cells and discuss future opportunities and challenges towards integrating single-cell phenotypes with circuit function.

By integrating single-cell firing behavior during in vivo oscillations with morphological and molecular neuron classification in vitro, this study standardizes a framework for interpreting the functional roles of distinct circuit modules and ascribing extracellular recordings to identified neuron types.     

Declining carbohydrate content of Sitka-spruce treesdying from seawater exposure

Increasing sea levels associated with climate change threaten the survival of coastal forests, yet the mechanisms by which seawater exposure causes tree death remain poorly understood. Despite the potentially crucial role of nonstructural carbohydrate (NSC) reserves in tree survival, their dynamics in the process of death under seawater exposure are unknown. Here we monitored progressive tree mortality and associated NSC storage in Sitka-spruce (Picea sitchensis) trees dying under ecosystem-scale increases in seawater exposure in western Washington, USA. All trees exposed to seawater, because of monthly tidal intrusion, experienced declining crown foliage during the sampling period, and individuals with a lower percentage of live foliated crown (PLFC) died faster. Tree PLFC was strongly correlated with subsurface salinity and needle ion contents. Total NSC concentrations in trees declined remarkably with crown decline, and reached extremely low levels at tree death (2.4% and 1.6% in leaves and branches, respectively, and 0.4% in stems and roots). Starch in all tissues was almost completely consumed, while sugars remained at a homeostatic level in foliage. The decreasing NSC with closer proximity to death and near zero starch at death are evidences that carbon starvation occurred during Sitka-spruce mortality during seawater exposure. Our results highlight the importance of carbon storage as an indicator of tree mortality risks under seawater exposure.

Decline in carbohydrate storage is strongly associated with progressive mortality of trees under frequent seawater exposure, and starch is almost completely consumed at crown death.