Tracking individual membrane proteins and their biochemistry: The power of direct observation

The advent of single molecule fluorescence microscopy has allowed experimental molecular biophysics and biochemistry to transcend traditional ensemble measurements, where the behavior of individual proteins could not be precisely sampled. The recent explosion in popularity of new super-resolution and super-localization techniques coupled with technical advances in optical designs and fast highly sensitive cameras with single photon sensitivity and millisecond time resolution have made it possible to track key motions, reactions, and interactions of individual proteins with high temporal resolution and spatial resolution well beyond the diffraction limit. Within the purview of membrane proteins and ligand gated ion channels (LGICs), these outstanding advances in single molecule microscopy allow for the direct observation of discrete biochemical states and their fluctuation dynamics. Such observations are fundamentally important for understanding molecular-level mechanisms governing these systems. Examples reviewed here include the effects of allostery on the stoichiometry of ligand binding in the presence of fluorescent ligands; the observation of subdomain partitioning of membrane proteins due to microenvironment effects; and the use of single particle tracking experiments to elucidate characteristics of membrane protein diffusion and the direct measurement of thermodynamic properties, which govern the free energy landscape of protein dimerization. The review of such characteristic topics represents a snapshot of efforts to push the boundaries of fluorescence microscopy of membrane proteins to the absolute limit.

Pollen dispersal properties of Poaceae and Cyperaceae: First estimates of their absolute pollen productivities

Pollen-trap results from the Swiss Alps 1996–2009 were used to assess the pollen dispersal–deposition properties of Poaceae (grasses) and Cyperaceae (sedges). Dispersal parameter values were investigated for a modified version of the Prentice–Sugita pollen dispersal–deposition model. Appropriate values (i.e. realistic in the field and allowing realistic modelling results) for wind speed are suggested to be in the range of 3–7 m s− 1 and for pollen an injection height of 0.03–0.1 m above the ground. The appropriate range of pollen injection height values for grasses and sedges differs from that of trees in the same area, suggesting different pollen dispersal properties between herbs and trees. In addition, logarithmic weighting of the vegetation was tested as an alternative to the modified Prentice–Sugita model. This yielded very similar results, suggesting that the use of such much simpler approximations of the pollen–vegetation relationship is a plausible alternative. Based on the modified Prentice–Sugita model, absolute pollen productivity for Poaceae was estimated to 7300 ± 400 grains cm− 2 year− 1 (1 SE). The data basis for Cyperaceae is smaller than for Poaceae, but the dispersal parameter values determined as appropriate for Poaceae yield good results. Absolute pollen productivity for Cyperaceae was estimated to 6300 ± 1100 grains cm− 2 year− 1 (1 SE).

Detection of the pan neuronal marker PGP9.5 by immuno-histochemistry and quantitative PCR in eutopic endometrium from women with and without endometriosis.

PURPOSE To assess endometrial gene as well as protein expression of neuroendocrine and supposedly endometriosis-associated product PGP9.5 and pain symptoms in women with endometriosis and controls undergoing laparoscopy, using molecular biological and immuno-histochemical approaches in the same patients. METHODS Biopsy of eutopic endometrium from 29 patients by sharp curettage, and preparation of paraffin blocks. Determination of PGP9.5 gene expression and protein abundance using qPCR and immuno-histochemistry. RESULTS qPCR; The PGP9.5 mRNA expression level between women with (N = 16) and without (N = 13) endometriosis was not different, regardless of pain symptoms or menstrual cycle phase. PGP9.5 expression was higher in women who reported pain compared to those who did not; however, this association was not statistically significant. The expression of PGP9.5 mRNA was higher in women with endometriosis and pain during the proliferative than in the secretory phase (P = 0.03). Furthermore, in the first half of the cycle, the abundance of the PGP9.5 transcript was also significantly higher in endometriosis patients compared to those without (P = 0.03). Immuno-histochemistry; Thirteen of the 16 endometriosis patients showed positive PGP9.5 immuno-reactivity in the endometrium, whereas no such signal was observed in women without endometriosis. The absolute number of nerve fibres per mm(2) in women with endometriosis was similar, regardless of the pain symptoms. CONCLUSIONS PGP9.5 mRNA expression is increased in the proliferative phase of endometriotic women with pain. The presence of nerve fibres was demonstrated by a PGP9.5 protein signal in immuno-histochemistry and restricted to patients with endometriosis. Based on these results, however, there did not appear to be a direct association between the gene expression and protein abundance in women with and without endometriosis or those that experienced pain.

Identification, quantification, spatiotemporal distribution and genetic variation of major latex secondary metabolites in the common dandelion (Taraxacum officinale agg.)

The secondary metabolites in the roots, leaves and flowers of the common dandelion (Taraxacum officinale agg.) have been studied in detail. However, little is known about the specific constituents of the plant’s highly specialized laticifer cells. Using a combination of liquid and gas chromatography, mass spectrometry and nuclear magnetic resonance spectrometry, we identified and quantified the major secondary metabolites in the latex of different organs across different growth stages in three genotypes, and tested the activity of the metabolites against the generalist root herbivore Diabrotica balteata. We found that common dandelion latex is dominated by three classes of secondary metabolites: phenolic inositol esters (PIEs), triterpene acetates (TritAc) and the sesquiterpene lactone taraxinic acid β-d-glucopyranosyl ester (TA-G). Purification and absolute quantification revealed concentrations in the upper mg g−1 range for all compound classes with up to 6% PIEs, 5% TritAc and 7% TA-G per gram latex fresh weight. Contrary to typical secondary metabolite patterns, concentrations of all three classes increased with plant age. The highest concentrations were measured in the main root. PIE profiles differed both quantitatively and qualitatively between plant genotypes, whereas TritAc and TA-G differed only quantitatively. Metabolite concentrations were positively correlated within and between the different compound classes, indicating tight biosynthetic co-regulation. Latex metabolite extracts strongly repelled D. balteata larvae, suggesting that the latex constituents are biologically active.

Quaternary uplift rates of the Central Anatolian Plateau, Turkey: insights from cosmogenic isochron-burial nuclide dating of the Kızılırmak River terraces

The Central Anatolian Plateau (CAP) in Turkey is a relatively small plateau (300 × 400 km) with moderate average elevations of ∼1 km situated between the Pontide and Tauride orogenic mountain belts. Kızılırmak, which is the longest river (1355 km) within the borders of Turkey, flows within the CAP and slowly incises into lacustrine and volcaniclastic units before finally reaching the Black Sea. We dated the Cappadocia section of the Kızılırmak terraces in the CAP by using cosmogenic burial and isochron-burial dating methods with 10Be and 26Al as their absolute dating can provide insight into long-term incision rates, uplift and climatic changes. Terraces at 13, 20, 75 and 100 m above the current river indicate an average incision rate of 0.051 ± 0.01 mm/yr (51 ± 1 m/Ma) since ∼1.9 Ma. Using the base of a basalt fill above the modern course of the Kızılırmak, we also calculated 0.05–0.06 mm/yr mean incision and hence rock uplift rate for the last 2 Ma. Although this rate might be underestimated due to normal faulting along the valley sides, it perfectly matches our results obtained from the Kızılırmak terraces. Although up to 5–10 times slower, the Quaternary uplift of the CAP is closely related to the uplift of the northern and southern plateau margins respectively.

The effective Planck mass and the scale of inflation

Observable quantities in cosmology are dimensionless, and therefore independent of the units in which they are measured. This is true of all physical quantities associated with the primordial perturbations that source cosmic microwave background anisotropies such as their amplitude and spectral properties. However, if one were to try and infer an absolute energy scale for inflation—a priori, one of the more immediate corollaries of detecting primordial tensor modes—one necessarily makes reference to a particular choice of units, the natural choice for which is Planck units. In this note, we discuss various aspects of how inferring the energy scale of inflation is complicated by the fact that the effective strength of gravity as seen by inflationary quanta necessarily differs from that seen by gravitational experiments at presently accessible scales. The uncertainty in the former relative to the latter has to do with the unknown spectrum of universally coupled particles between laboratory scales and the putative scale of inflation. These intermediate particles could be in hidden as well as visible sectors or could also be associated with Kaluza–Klein resonances associated with a compactification scale below the scale of inflation. We discuss various implications for cosmological observables.

Ignoring heterozygous sites biases phylogenomic estimates of divergence times: implications for the evolutionary history of Microtus voles

Phylogenetic reconstruction of the evolutionary history of closely related organisms may be difficult because of the presence of unsorted lineages and of a relatively high proportion of heterozygous sites that are usually not handled well by phylogenetic programs. Genomic data may provide enough fixed polymorphisms to resolve phylogenetic trees, but the diploid nature of sequence data remains analytically challenging. Here, we performed a phylogenomic reconstruction of the evolutionary history of the common vole (Microtus arvalis) with a focus on the influence of heterozygosity on the estimation of intraspecific divergence times. We used genome-wide sequence information from 15 voles distributed across the European range. We provide a novel approach to integrate heterozygous information in existing phylogenetic programs by repeated random haplotype sampling from sequences with multiple unphased heterozygous sites. We evaluated the impact of the use of full, partial, or no heterozygous information for tree reconstructions on divergence time estimates. All results consistently showed four deep and strongly supported evolutionary lineages in the vole data. These lineages undergoing divergence processes split only at the end or after the last glacial maximum based on calibration with radiocarbon-dated paleontological material. However, the incorporation of information from heterozygous sites had a significant impact on absolute and relative branch length estimations. Ignoring heterozygous information led to an overestimation of divergence times between the evolutionary lineages of M. arvalis. We conclude that the exclusion of heterozygous sites from evolutionary analyses may cause biased and misleading divergence time estimates in closely related taxa.

Modeling absolute differences in life expectancy with a censored skew-normal regression approach.

Parameter estimates from commonly used multivariable parametric survival regression models do not directly quantify differences in years of life expectancy. Gaussian linear regression models give results in terms of absolute mean differences, but are not appropriate in modeling life expectancy, because in many situations time to death has a negative skewed distribution. A regression approach using a skew-normal distribution would be an alternative to parametric survival models in the modeling of life expectancy, because parameter estimates can be interpreted in terms of survival time differences while allowing for skewness of the distribution. In this paper we show how to use the skew-normal regression so that censored and left-truncated observations are accounted for. With this we model differences in life expectancy using data from the Swiss National Cohort Study and from official life expectancy estimates and compare the results with those derived from commonly used survival regression models. We conclude that a censored skew-normal survival regression approach for left-truncated observations can be used to model differences in life expectancy across covariates of interest.

The role of seasonality of mineral dust concentration and size on glacial/interglacial dust changes in the EPICA Dronning Maud Land ice core

We present a record of particulate dust concentration and size distribution in subannual resolution measured on the European Project for Ice Coring in Antarctica (EPICA) Dronning Maud Land (EDML) ice core drilled in the Atlantic sector of the East Antarctic plateau. The record reaches from present day back to the penultimate glacial until 145,000 years B.P. with subannual resolution from 60,000 years B.P. to the present. Mean dust concentrations are a factor of 46 higher during the glacial (~850–4600 ng/mL) compared to the Holocene (~16–112 ng/mL) with slightly smaller dust particles during the glacial comparedto the Holocene and with an absolute minimum in the dust size at 16,000 years B.P. The changes in dust concentration are mainly attributed to changes in source conditions in southern South America. An increase in the modal value of the dust size suggests that at 16,000 years B.P. a major change in atmospheric circulation apparently allowed more direct transport of dust particles to the EDML drill site. We find a clear in-phase relation of the seasonal variation in dust mass concentration and dust size during the glacial (r(conc,size) = 0.8) but no clear phase relationship during the Holocene (0 the transport of the dust to the ice sheet using the size as an indicator for transport intensity, we find that the effect of the changes in the seasonality of the source emission strength and the transport intensity on the dust decrease over Transition 1 can significantly contribute to the large decrease of dust concentration from the glacial to the Holocene.

Bedload composition, transport and modification in rivers of Westland, New Zealand, with implications for the distribution of alluvial pounamu (jade)

River bedload surveyed at 50 sites in Westland is dominated by Alpine Schist or Torlesse Greywacke from the Alpine Fault hanging wall, with subordinate Pounamu Ultramafics or footwall-derived Western Province rocks. Tumbling experiments found ultramafics to have the lowest attrition rates, compared with greywacke sandstone and granite (which abrade to produce silt to medium-sand), or incompetent schist (which fragments). Arahura has greater total concentrations (103–105 t/km2) and proportions (5–40%) of ultramafic bedload compared with Hokitika and Taramakau catchments (101–104 t/km2, mostly <10%), matching relative areas of mapped Pounamu Ultramafic bedrock, but enriched relative to absolute areal proportions. Western Province rocks downthrown by the Alpine Fault are under-represented in the bedload. Enriched concentrations of ultramafic bedload decrease rapidly with distance downstream from source rock outcrops, changing near prominent ice-limit moraines. Bedload evolution with transport involves both downstream fining and dilution from tributaries, in a sediment supply regime more strongly influenced by tectonics and the imprint of past glaciation. Treasured New Zealand pounamu (jade) is associated with ultramafic rocks. Chances of discovery vary between catchments, are increased near glacial moraines, and are highest near source-rock outcrops in remote mountain headwaters.

TICI and Age: What's the Score?

BACKGROUND AND PURPOSE Previous studies have suggested that advanced age predicts worse outcome following mechanical thrombectomy. We assessed outcomes from 2 recent large prospective studies to determine the association among TICI, age, and outcome. MATERIALS AND METHODS Data from the Solitaire FR Thrombectomy for Acute Revascularization (STAR) trial, an international multicenter prospective single-arm thrombectomy study and the Solitaire arm of the Solitaire FR With the Intention For Thrombectomy (SWIFT) trial were pooled. TICI was determined by core laboratory review. Good outcome was defined as an mRS score of 0-2 at 90 days. We analyzed the association among clinical outcome, successful-versus-unsuccessful reperfusion (TICI 2b-3 versus TICI 0-2a), and age (dichotomized across the median). RESULTS Two hundred sixty-nine of 291 patients treated with Solitaire in the STAR and SWIFT data bases for whom TICI and 90-day outcome data were available were included. The median age was 70 years (interquartile range, 60-76 years) with an age range of 25-88 years. The mean age of patients 70 years of age or younger was 59 years, and it was 77 years for patients older than 70 years. There was no significant difference between baseline NIHSS scores or procedure time metrics. Hemorrhage and device-related complications were more common in the younger age group but did not reach statistical significance. In absolute terms, the rate of good outcome was higher in the younger population (64% versus 44%, P < .001). However, the magnitude of benefit from successful reperfusion was higher in the 70 years of age and older group (OR, 4.82; 95% CI, 1.32-17.63 versus OR 7.32; 95% CI, 1.73-30.99). CONCLUSIONS Successful reperfusion is the strongest predictor of good outcome following mechanical thrombectomy, and the magnitude of benefit is highest in the patient population older than 70 years of age.

Humanitarian intervention and the issue of state sovereignty in the discourse of legal experts between the 1830s and the First World War

This article discusses the tensions between the principle of state sovereignty and the idea of a "humanitarian intervention" (or a intervention on humanitarian grounds) as they resulted from the debate of leading legal scholars in the 19th and early 20th century. While prominent scholars such as Johann Caspar Bluntschli, Gustave Rolin Jaequemyns or Aegidius Arntz spoke out in favour of a form of "humanitarian interventions", others such as August Wilhelm Heffter or Pasquale Fiore were much more critical and in many cases spoke out in favour of absolute state sovereignty.

Absolute polarity determination of teeth cementum by phase sensitive second harmonic generation microscopy

The absolute sign of local polarity in relation to the biological growth direction has been investigated for teeth cementum using phase sensitive second harmonic generation microscopy (PS-SHGM) and a crystal of 2-cyclooctylamino-5-nitropyridine (COANP) as a nonlinear optic (NLO) reference material. A second harmonic generation (SHG) response was found in two directions of cementum: radial (acellular extrinsic fibers that are oriented more or less perpendicular to the root surface) and circumferential (cellular intrinsic fibers that are oriented more or less parallel to the surface). A mono-polar state was demonstrated for acellular extrinsic cementum. However, along the different parts of cementum in circumferential direction, two corresponding domains were observed featuring an opposite sign of polarity indicative for a bi-polar microscopic state of cellular intrinsic cementum. The phase information showed that the orientation of radial collagen fibrils of cementum is regularly organized with the donor (D) groups pointing to the surface. Circumferential collagen molecules feature orientational disorder and are oriented up and down in random manner showing acceptor or donor groups at the surface of cementum. Considering that the cementum continues to grow in thickness throughout life, we can conclude that the cementum is growing circumferentially in two opposite directions and radially in one direction. A Markov chain type model for polarity formation in the direction of growth predicts D-groups preferably appearing at the fiber front.

Palynostratigraphy of the last centuries in Switzerland based on 23 lake and mire deposits: chronostratigraphic pollen markers, regional patterns, and local histories

A total of 23 pollen diagrams [stored in the Alpine Palynological Data-Base (ALPADABA), Geobotanical Institute, Bern] cover the last 100 to over 1000 years. The sites include 15 lakes, seven mires, and one soil profile distributed in the Jura Mts (three sites), Swiss Plateau (two sites), northern Pre-Alps and Alps (six sites), central Alps (five sites), southern Alps (three sites), and southern Pre-Alps (four sites) in the western and southern part of Switzerland or just outside the national borders. The pollen diagrams have both a high taxonomic resolution and a high temporal resolution, with sampling distances of 0.5–3 cm, equivalent to 1 to 11 years for the last 100 years and 8 to 130 years for earlier periods. The chronology is based on absolute dating (14 sites: 210Pb 11 sites; 14C six sites; varve counting two sites) or on biostratigraphic correlation among pollen diagrams. The latter relies mainly on trends in Cannabis sativa, Ambrosia, Mercurialis annua, and Ostrya-type pollen. Individual pollen stratigraphies are discussed and sites are compared within each region. The principle of designating local, extra-local, and regional pollen signals and vegetation is exemplified by two pairs of sites lying close together. Trends in biostratigraphies shared by a major part of the pollen diagrams allow the following generalisations. Forest declined in phases since medieval times up to the late 19th century. Abies and Fagus declined consistently, whereas the behaviour of short-lived trees and trees of moist habitats differed among sites (Alnus glutinosa-type, Alnus viridis, Betula, Corylus avellana). In the present century, however, Picea and Pinus increased, followed by Fraxinus excelsior in the second half of this century. Grassland (traced by Gramineae and Plantago lanceolata-type pollen) increased, replacing much of the forest, and declined again in the second half of this century. Nitrate enrichment of the vegetation (traced by Urtica) took place in the first half of this century. These trends reflect the intensification of forest use and the expansion of grassland from medieval times up to the end of the last century, whereas subsequently parts of the grassland became used more intensively and the marginal parts were abandoned for forest regrowth. In most pollen diagrams human impact is the dominant factor in explaining inferred changes in vegetation, but climatic change plays a role at three sites.

Trends and characteristics of attendance at the emergency department of a Swiss university hospital: 2002-2012.

BACKGROUND The numbers of people attending emergency departments (EDs) at hospitals are increasing. We aimed to analyse trends in ED attendance at a Swiss university hospital between 2002 and 2012, focussing on age-related differences and hospital admission criteria. METHODS We used hospital administrative data for all patients aged ≥16 years who attended the ED (n=298,306) at this university hospital between 1 January 2002, and 31 December 2012. We descriptively analysed the numbers of ED visits according to the admission year and stratified by age (≥65 vs <65 years). RESULTS People attending the ED were on average 46.6 years old (standard deviation 20 years, maximum range 16‒99 years). The annual number of ED attendances grew by n=6,639 (27.6%) from 24,080 in 2002 to 30,719 in 2012. In the subgroup of patients aged ≥65 the relative increase was 42.3%, which is significantly higher (Pearson's χ2=350.046, df=10; p=0.000) than the relative increase of 23.4% among patients<65 years. The subgroup of patients≥65 years attended the ED more often because of diseases (n=56,307; 85%) than accidents (n=9,844; 14.9%). This subgroup (patients≥65 years) was also more often admitted to hospital (Pearson's χ2=23,377.190; df=1; p=0.000) than patients<65 years. CONCLUSIONS ED attendance of patients≥65 years increased in absolute and relative terms. The study findings suggest that staff of this ED may want to assess the needs of patients≥65 years and, if necessary, adjust the services (e.g., adapted triage scales, adapted geriatric screenings, and adapted hospital admission criteria).