Contextual organismality: Beyond pattern to process in the emergence of organisms

Biologists have taken the concept of organism largely for granted. However, advances in the study of chimerism, symbiosis, bacterial‐eukaryote associations, and microbial behavior have prompted a redefinition of organisms as biological entities exhibiting low conflict and high cooperation among their parts. This expanded view identifies organisms in evolutionary time. However, the ecological processes, mechanisms, and traits that drive the formation of organisms remain poorly understood. Recognizing that organismality can be context dependent, we advocate elucidating the ecological contexts under which entities do or do not act as organisms. Here we develop a “contextual organismality” framework and provide examples of entities, such as honey bee colonies, tumors, and bacterial swarms, that can act as organisms under specific life history, resource, or other ecological circumstances. We suggest that context dependence may be a stepping stone to the development of increased organismal unification, as the most integrated biological entities generally show little context dependence. Recognizing that organismality is contextual can identify common patterns and testable hypotheses across different entities. The contextual organismality framework can illuminate timeless as well as pressing issues in biology, including topics as disparate as cancer emergence, genomic conflict, evolution of symbiosis, and the role of the microbiota in impacting host phenotype.     

Human‐mediated extirpation of the unique Chatham Islands sea lion and implications for the conservation management of remaining New Zealand sea lion populations

While terrestrial megafaunal extinctions have been well characterized worldwide, our understanding of declines in marine megafauna remains limited. Here, we use ancient DNA analyses of prehistoric (<1450–1650 AD) sea lion specimens from New Zealand's isolated Chatham Islands to assess the demographic impacts of human settlement. These data suggest there was a large population of sea lions, unique to the Chatham Islands, at the time of Polynesian settlement. This distinct mitochondrial lineage became rapidly extinct within 200 years due to overhunting, paralleling the extirpation of a similarly large endemic mainland population. Whole mitogenomic analyses confirm substantial intraspecific diversity among prehistoric lineages. Demographic models suggest that even low harvest rates would likely have driven rapid extinction of these lineages. This study indicates that surviving Phocarctos populations are remnants of a once diverse and widespread sea lion assemblage, highlighting dramatic human impacts on endemic marine biodiversity. Our findings also suggest that Phocarctos bycatch in commercial fisheries may contribute to the ongoing population decline.     

Invader or resident? Ancient-DNA reveals rapid species turnover in New Zealand little penguins

The expansion of humans into previously unoccupied parts of the globe is thought to have driven the decline and extinction of numerous vertebrate species. In New Zealand, human settlement in the late thirteenth century AD led to the rapid demise of a distinctive vertebrate fauna, and also a number of ''turnover'' events where extinct lineages were subsequently replaced by closely related taxa. The recent genetic detection of an Australian little penguin (Eudyptula novaehollandiae) in southeastern New Zealand may potentially represent an additional ‘cryptic’ invasion. Here we use ancient-DNA (aDNA) analysis and radiocarbon dating of pre-human, archaeological and historical Eudyptula remains to reveal that the arrival of E. novaehollandiae in New Zealand probably occurred between AD 1500 and 1900, following the anthropogenic decline of its sister taxon, the endemic Eudyptula minor. This rapid turnover event, revealed by aDNA, suggests that native species decline can be masked by invasive taxa, and highlights the potential for human-mediated biodiversity shifts.     

Facility-Based Delivery during the Ebola Virus Disease Epidemic in Rural Liberia: Analysis from a Cross-Sectional,Population-Based Household Survey

BackgroundThe Ebola virus disease (EVD) epidemic has threatened access to basic health services through facility closures, resource diversion, and decreased demand due to community fear and distrust. While modeling studies have attempted to estimate the impact of these disruptions, no studies have yet utilized population-based survey data.ConclusionsWe detected a 30% decreased odds of FBD after the start of EVD in a rural Liberian county with relatively few cases. Because health facilities never closed in Rivercess County, this estimate may under-approximate the effect seen in the most heavily affected areas. These are the first population-based survey data to show collateral disruptions to facility-based delivery caused by the West African EVD epidemic, and they reinforce the need to consider the full spectrum of implications caused by public health emergencies.     

Data merging for integrated microarray and proteomic analysis.

The functioning of even a simple biological system is much more complicated than the sum of its genes, proteins and metabolites. A premise of systems biology is that molecular profiling will facilitate the discovery and characterization of important disease pathways. However, as multiple levels of effector pathway regulation appear to be the norm rather than the exception, a significant challenge presented by high-throughput genomics and proteomics technologies is the extraction of the biological implications of complex data. Thus, integration of heterogeneous types of data generated from diverse global technology platforms represents the first challenge in developing the necessary foundational databases needed for predictive modelling of cell and tissue responses. Given the apparent difficulty in defining the correspondence between gene expression and protein abundance measured in several systems to date, how do we make sense of these data and design the next experiment? In this review, we highlight current approaches and challenges associated with integration and analysis of heterogeneous data sets, focusing on global analysis obtained from high-throughput technologies.     

Long‐term changes in the feeding of Pollachius virens on the Scotian Shelf: responses to a dynamic ecosystem

The diet and feeding ecology of pollock Pollachius virens from the Scotian Shelf and Bay of Fundy in the north‐west Atlantic changed over the last few decades, which was associated with decreases in euphausiid abundance. Stomach contents data for 2078 pollock collected during the 1958–1967 period and for 1230 pollock collected during the 1996–2002 period indicated that pollock diet contained fewer euphausiids and feeding activity decreased. During the early period, euphausiids were present in 65% of the pollock stomachs that contained food and only 9% of these stomachs in the recent period. The decrease of euphausiids was not wholly offset by an increase in piscivory, since there was little increase in the frequency of fish prey in the diet or in the fullness index for this prey type. Empty stomachs were significantly more common in the recent period during both the winter and summer. The decreased occurrence of euphausiids in stomach samples coincided with a significantly decreased abundance of this prey, suggesting that the near‐absence of euphausiids in recently collected pollock stomachs reflected prey abundance. Concurrent with changes in diet and feeding intensity, the condition or 'plumpness' of pollock significantly declined from the early to the late sampling periods.     

Approaches for Integrated Risk Assessment

Recognizing the need to enhance the effectiveness and efficiency of risk assessments globally, the World Health Organization's International Programme on Chemical Safety, the U.S. Environmental Protection Agency, the European Commission, and the Organization for Economic Cooperation and Development developed a collaborative partnership to foster integration of assessment approaches used to evaluate human health and ecological risks. The objectives of this effort included: improving understanding of the benefits of integration, identifying obstacles to the integration process, and engaging key agencies, organizations, and scientific societies to promote integration. A framework with supporting documentation was developed to describe an approach for integration. Four case studies were constructed to illustrate how integrated risk assessments might be conducted for chemical and nonchemical stressors. The concepts and approaches developed in the project were evaluated in an international workshop. The goal of this effort was international acceptance of guidance for integrated risk assessment.     

Tissue factor activity is increased in human endothelial cells cultured under elevated static pressure

We tested the hypothesis that elevated blood pressure, a knownstimulus for vascular remodeling and an independent risk factor for thedevelopment of atherosclerotic disease, can modulate basal andcytokine-induced tissue factor (TF; CD 142) expression in culturedhuman endothelial cells (EC). Using a chromogenic enzymatic assay, wemeasured basal and tumor necrosis factor- (TNF-; 10 ng/ml, 5 h)-induced TF activities in human aortic EC (HAEC) and vena cava EC(HVCEC) cultured at atmospheric pressure and at 170 mmHg imposedpressure for up to 48 h. Basal TF activities were 22 ± 10 U/mgprotein for HAEC and 14 ± 9 U/mg protein for HVCEC and wereupregulated in both cell types >10-fold by TNF-. Exposure topressure for 5 h induced additional elevation of basal TF activity by47 ± 16% (P < 0.05, n = 6) for HAEC and 17 ± 5%(P < 0.05, n = 3) for HVCEC. Pressurization alsoenhanced TF activity in TNF--treated cells from 240 ± 28 to 319 ± 32 U/mg protein in HAEC (P < 0.05, n = 4) and from 148 ± 25 to179 ± 0.8 U/mg protein (P < 0.05, n = 3) in HVCEC. Cytokinestimulation caused an ~100-fold increase in steady-state TF mRNAlevels in HAEC, whereas pressurization did not alter either TF mRNA orcell surface antigen expression, as determined by quantitative RT-PCRmethodology and ELISA. Elevated pressure, however, modulated the ECplasma membrane organization and/or permeability as inferred from theincreased cellular uptake of the fluorescent amphipathic dyemerocyanine 540 (33 ± 7%, P < 0.05). Our data suggest that elevated static pressure modulates thehemostatic potential of vascular cells by modifying the molecular organization of the plasma membrane.