Quantitative metrics of overlaps in Grinnellian niches: advances and possible drawbacks

Aim Studies of environmental niche shift/niche conservatism that are based on species distribution modelling require a quantification of niche purity and potential overlap. Although various metrics have been proposed for this task, no comparisons of their performance are available yet that express the linearity of range shifts and error‐proneness. Herein, we assess the performance of six niche overlap metrics using three sister pairs of plethodontid salamanders as well as artificial species to test for linearity of overlap curves, impacts of varying potential distribution sizes and study area sizes. Location North America, artificial environments. Methods Species distribution models for the salamanders were performed with Maxent , and artificial species were created in the R environment. Potential distributions of species with varying range sizes and extents of the study area were compared using the Bray–Curtis distance BC, Schoener's D, two different modifications of the Hellinger distance I_mod, I_cor, Pianka's O and Horn's R. Niche overlaps in ecological space were compared using linear discriminant analyses based on principal components. Results Simulations of niche overlaps revealed strong variations in the performance of the niche overlap metrics. In artificial species, BC and D performed best, followed by O, R and I_cor, but the modified Hellinger distance I_mod showed a nonlinear slope and a truncated range. Furthermore, the simulations suggest that, in proportionally small potential distributions on large grids, an inclusion of a high proportion of grid cells with low occurrence probabilities representing background noise may bias assessments of niche overlaps. Main conclusions Both the salamander examples and simulations suggest that Schoener's D and the Bray–Curtis distance BC are best suited to compute niche overlaps from potential distributions derived from species distribution models. However, like all analysed metrics, both D and BC are seriously affected by the inclusion of high numbers of grid cells where the species are probably absent, i.e. with low occurrence probabilities. Therefore, pre‐processing to eliminate background noise in the potential distribution grids is highly recommended.     

Stiffness gradients mimicking in vivo tissue variation regulate mesenchymal stem cell fate

Mesenchymal stem cell (MSC) differentiation is regulated in part by tissue stiffness, yet MSCs can often encounter stiffness gradients within tissues caused by pathological, e.g., myocardial infarction ～8.7±1.5 kPa/mm, or normal tissue variation, e.g., myocardium ～0.6±0.9 kPa/mm; since migration predominantly occurs through physiological rather than pathological gradients, it is not clear whether MSC differentiate or migrate first. MSCs cultured up to 21 days on a hydrogel containing a physiological gradient of 1.0±0.1 kPa/mm undergo directed migration, or durotaxis, up stiffness gradients rather than remain stationary. Temporal assessment of morphology and differentiation markers indicates that MSCs migrate to stiffer matrix and then differentiate into a more contractile myogenic phenotype. In those cells migrating from soft to stiff regions however, phenotype is not completely determined by the stiff hydrogel as some cells retain expression of a neural marker. These data may indicate that stiffness variation, not just stiffness alone, can be an important regulator of MSC behavior.     

Elevated [11C]-D-deprenyl uptake in chronic Whiplash Associated Disorder suggests persistent musculoskeletal inflammation

There are few diagnostic tools for chronic musculoskeletal pain as structural imaging methods seldom reveal pathological alterations. This is especially true for Whiplash Associated Disorder, for which physical signs of persistent injuries to the neck have yet to be established. Here, we sought to visualize inflammatory processes in the neck region by means Positron Emission Tomography using the tracer (11)C-D-deprenyl, a potential marker for inflammation. Twenty-two patients with enduring pain after a rear impact car accident (Whiplash Associated Disorder grade II) and 14 healthy controls were investigated. Patients displayed significantly elevated tracer uptake in the neck, particularly in regions around the spineous process of the second cervical vertebra. This suggests that whiplash patients have signs of local persistent peripheral tissue inflammation, which may potentially serve as a diagnostic biomarker. The present investigation demonstrates that painful processes in the periphery can be objectively visualized and quantified with PET and that (11)C-D-deprenyl is a promising tracer for these purposes.     

Loss of susceptibility as an alternative for nematode resistance

Among plant pathogens, sedentary endoparasitic nematodes are one of the most damaging pests in global agriculture. These obligate parasites interact with their hosts in a quite unique and intriguing way. They induce the redifferentiation of root cells into specialized feeding cells essential for nematode growth and reproduction; thus, nematodes have evolved the ability to exploit plant genes and hijack host functions for their own requirements. Various approaches to engineer plants with resistance to parasitic nematodes have been pursued, most focusing on the introduction of resistance genes. An alternative strategy to achieve resistance is to exploit the susceptibility of plant disease. Better knowledge of the plant response during the compatible interaction should allow the identification of targets to engineer resistance to parasitic nematodes in crop species.     

Effect of Ractopamine HCl Supplementation on Fecal Shedding of Escherichia coli O157:H7 and Salmonella in Feedlot Cattle

The effects of the β-agonist ractopamine, recently approved for use in feedlot cattle to improve carcass quality and performance, on fecal shedding Escherichia coli O157:H7 and Salmonella in feedlot cattle was examined. In the first study, 20 feedlot steers and heifers were randomly assigned to receive ractopamine or no ractopamine (control) by way of oral bolus for 28 days. Fecal samples were collected daily, and shedding of E. coli O157:H7 determined. When examined during the entire 28-day experimental period, ractopamine decreased (P = 0.0006) the percentage of cattle shedding E. coli O157:H7 (58% vs. 42% for control and ractopamine treatments, respectively). A second study was conducted in a commercial feedlot facility in the southwestern United States. Eighteen pens of cross-bred beef heifers (approximately 100 head/pen and 9 pens/treatment) were randomly assigned to receive either 0 (control) or 200 mg ractopamine/head·d^–1. Fresh fecal samples (30/pen) were collected off the pen floor before ractopamine supplementation and again after approximately 28 days of ractopamine supplementation (within a few days of slaughter); the samples were cultured for E. coli O157:H7 and Salmonella. The percentage of animals shedding E. coli O157:H7 was decreased when data were pooled across replicates (P = 0.05) in ractopamine-treated cattle compared with controls. The percentage of animals shedding Salmonella tended to be higher (P = 0.08) with the ractopamine treatment when data were pooled across replicates. Although further research is required to confirm these results, the potential food safety implications of this research are intriguing. Mention of trade name, proprietary product, or specific equipment does not constitute a guarantee or warranty by the United States Drug Administration and does not imply its approval to the exclusion of other products that may be suitable.     

Matrix elasticity directs stem cell lineage specification

Microenvironments appear important in stem cell lineage specification but can be difficult to adequately characterize or control with soft tissues. Naive mesenchymal stem cells (MSCs) are shown here to specify lineage and commit to phenotypes with extreme sensitivity to tissue-level elasticity. Soft matrices that mimic brain are neurogenic, stiffer matrices that mimic muscle are myogenic, and comparatively rigid matrices that mimic collagenous bone prove osteogenic. During the initial week in culture, reprogramming of these lineages is possible with addition of soluble induction factors, but after several weeks in culture, the cells commit to the lineage specified by matrix elasticity, consistent with the elasticity-insensitive commitment of differentiated cell types. Inhibition of nonmuscle myosin II blocks all elasticity-directed lineage specification-without strongly perturbing many other aspects of cell function and shape. The results have significant implications for understanding physical effects of the in vivo microenvironment and also for therapeutic uses of stem cells.     

Structural and thermodynamic strategies for site-specific DNA binding proteins

BACKGROUND: Site-specific protein-DNA complexes vary greatly in structural properties and in the thermodynamic strategy for achieving an appropriate binding free energy. A better understanding of the structural and energetic engineering principles might lead to rational methods for modification or design of such proteins. RESULTS: A novel analysis of ten site-specific protein-DNA complexes reveals a striking correspondence between the degree of imposed DNA distortion and the thermodynamic parameters of each system. For complexes with relatively undistorted DNA, favorable enthalpy change drives unfavorable entropy change, whereas for complexes with highly distorted DNA, unfavorable DeltaH degrees is driven by favorable DeltaS degrees. We show for the first time that protein-DNA associations have isothermal enthalpy-entropy compensation, distinct from temperature-dependent compensation, so DeltaH degrees and DeltaS degrees do not vary independently. All complexes have favorable DeltaH degrees from direct protein-DNA recognition interactions and favorable DeltaS degrees from water release. Systems that strongly distort the DNA nevertheless have net unfavorable DeltaH degrees as the result of molecular strain, primarily associated with the base pair destacking. These systems have little coupled protein folding and the strained interface suffers less immobilization, so DeltaS degrees is net favorable. By contrast, systems with little DNA distortion have net favorable DeltaH degrees, which must be counterbalanced by net unfavorable DeltaS degrees, derived from loss of vibrational entropy (a result of isothermal enthalpy-entropy compensation) and from coupling between DNA binding and protein folding. CONCLUSIONS: Isothermal enthalpy-entropy compensation implies that a structurally optimal, unstrained fit is achieved only at the cost of entropically unfavorable immobilization, whereas an enthalpically weaker, strained interface entails smaller entropic penalties.     

The use of PIB-PET as a dual pathological and functional biomarker in AD

Amyloid imaging with positron emission tomography (PET) is presently used in Alzheimer's disease (AD) research. In this study we investigated the possibility to use early frames (ePIB) of the PIB scans as a rough index of CBF by comparing normalised early PIB values with cerebral glucose metabolism (rCMRglc). PIB-PET and FDG-PET were performed in 37 AD patients, 21 subjects with mild cognitive impairment (MCI) and 6 healthy controls (HC). The patients were divided based on their PIB retention (amyloid load) as either PIB positive (PIB+) or PIB negative (PIB−). Data of the unidirectional influx K₁ from a subset of the subjects including 7 AD patients and 3 HC was used for correlative analysis. Data was analysed using regions of interest (ROI) analysis. A strong, positive correlation was observed across brain regions between K₁ and ePIB (r = 0.70; p ≤ 0.001). The ePIB values were significantly lower in the posterior cingulate (p ≤ 0.001) and the parietal cortices (p = 0.002) in PIB+ subjects compared to PIB−, although the group difference were stronger for rCMRglc in cortical areas (p ≤ 0.001). Strong positive correlations between ePIB and rCMRglc were observed in all cortical regions analysed, especially in the posterior cingulate and parietal cortices (p ≤ 0.001). A single dynamic PIB-PET scan may provide information about pathological and functional changes (amyloidosis and impaired blood flow). This might be important for diagnosis of AD, enrichment of patients in clinical trials and evaluation of treatment effects. This article is part of a Special Issue entitled: Imaging Brain Aging and Neurodegenerative disease.     

Continuous and long-term volume measurements with a commercial Coulter counter

We demonstrate a method to enhance the time resolution of a commercial Coulter counter and enable continuous and long-term cell size measurements for growth rate analyses essential to understanding basic cellular processes, such as cell size regulation and cell cycle progression. Our simple modifications to a commercial Coulter counter create controllable cell culture conditions within the sample compartment and combine temperature control with necessary adaptations to achieve measurement stability over several hours. We also wrote custom software, detailed here, to analyze instrument data files collected by either this continuous method or standard, periodic sampling. We use the continuous method to measure the growth rate of yeast in G1 during a prolonged arrest and, in different samples, the dependency of growth rate on cell size and cell cycle position in arrested and proliferating cells. We also quantify with high time resolution the response of mouse lymphoblast cell culture to drug treatment. This method provides a technique for continuous measurement of cell size that is applicable to a large variety of cell types and greatly expands the set of analysis tools available for the Coulter counter.