Peptide location fingerprinting reveals tissue region-specific differences in protein structures in an ageing human organ

In ageing tissues, long-lived extracellular matrix (ECM) proteins are susceptible to the accumulation of structural damage due to diverse mechanisms including glycation, oxidation and protease cleavage. Peptide location fingerprinting (PLF) is a new mass spectrometry (MS) analysis technique capable of identifying proteins exhibiting structural differences in complex proteomes. PLF applied to published young and aged intervertebral disc (IVD) MS datasets (posterior, lateral and anterior regions of the annulus fibrosus) identified 268 proteins with age-associated structural differences. For several ECM assemblies (collagens I, II and V and aggrecan), these differences were markedly conserved between degeneration-prone (posterior and lateral) and -resistant (anterior) regions. Significant differences in peptide yields, observed within collagen I alpha 2, collagen II alpha 1 and collagen V alpha 1, were located within their triple-helical regions and/or cleaved C-terminal propeptides, indicating potential accumulation of damage and impaired maintenance. Several proteins (collagen V alpha 1, collagen II alpha 1 and aggrecan) also exhibited tissue region (lateral)-specific differences in structure between aged and young samples, suggesting that some ageing mechanisms may act locally within tissues. This study not only reveals possible age-associated differences in ECM protein structures which are tissue-region specific, but also highlights the ability of PLF as a proteomic tool to aid in biomarker discovery

Biomineralization of dolomite and magnesite discovered in tropical coralline algae: a biological solution to the geological dolomite problem

Final revised paper can be found at Description (Link) belowDolomite is a magnesium-rich carbonate mineral abundant in fossil carbonate reef platforms but surprisingly rare in modern sedimentary environments, a conundrum known as the ''Dolomite Problem". Marine sedimentary dolomite has been interpreted to form by an unconfirmed, post-depositional diagenetic process, despite minimal experimental success at replicating this. Here we show that dolomite, accompanied by magnesite, forms within living crustose coralline alga, Hydrolithon onkodes, a prolific global tropical reef species. Chemical micro-analysis of the coralline skeleton reveals that not only are the cell walls calcitised, but that cell spaces are typically filled with magnesite, rimmed by dolomite, or both. Mineralogy was confirmed by X-ray diffraction. Thus there are at least three mineral phases present (magnesium calcite, dolomite and magnesite) rather than one or two (magnesium calcite and brucite) as previously thought. Our results are consistent with dolomite occurrences in coralline algae rich environments in fossil reefs. Instead of a theory of post-depositional dolomitisation, we present evidence revealing biomineralization that can account for the massive formations seen in the geologic record. Additionally, our findings imply that previously unrecognized dolomite and magnesite have formed throughout the Holocene. This discovery together with the scale of coralline algae dominance in past shallow carbonate environments raises the possibility that environmental factors driving this biological dolomitisation process have influenced the global marine magnesium/calcium cycle. Perhaps, most importantly, we reveal that what has been considered a geological process can be a biological process, having many implications for both disciplines.M. C. Nash, U. Troitzsch, B. N. Opdyke, J. M. Trafford, B. D. Russell and D. I. Klinehttp://hdl.handle.net/2440/6855

First discovery of dolomite and magnesite in living coralline algae and its geobiological implications

Dolomite is a magnesium-rich carbonate mineral abundant in fossil carbonate reef platforms but surprisingly rare in modern sedimentary environments, a conundrum known as the "Dolomite Problem". Marine sedimentary dolomite has been interpreted to form by an unconfirmed, post-depositional diagenetic process, despite minimal experimental success at replicating this. Here we show that dolomite, accompanied by magnesite, forms within living crustose coralline alga, Hydrolithon onkodes, a prolific global tropical reef species. Chemical micro-analysis of the coralline skeleton reveals that not only are the cell walls calcitised, but that cell spaces are typically filled with magnesite, rimmed by dolomite, or both. Mineralogy was confirmed by X-ray Diffraction. Thus there are at least three mineral phases present (magnesium calcite, dolomite and magnesite) rather than one or two (magnesium calcite and brucite) as previously thought. Our results are consistent with dolomite occurrences in coralline algae rich environments in fossil reefs of the last 60 million years. We reveal that the standard method of removing organic material prior to Xray Diffraction analysis can result in a decrease in the most obvious dolomite and magnesite diffraction patterns and this may explain why the abundant protodolomite and magnesite discovered in this study has not previously been recognized. This discovery of dolomite in living coralline algae extends the range of palaeo-environments for which biologically initiated dolomite can be considered a possible source of primary dolomite.M. C. Nash, U. Troitzsch, B. N. Opdyke, J. M. Trafford, B. D. Russell and D. I. Klin

A carbohydrate-binding protein, B-GRANULE CONTENT 1, influences starch granule size distribution in a dose-dependent manner in polyploid wheat

In Triticeae endosperm (e.g. wheat and barley), starch granules have a bimodal size distribution (with A- and B-type granules) whereas in other grasses the endosperm contains starch granules with a unimodal size distribution. Here, we identify the gene, BGC1 (B-GRANULE CONTENT 1), responsible for B-type starch granule content in Aegilops and wheat. Orthologues of this gene are known to influence starch synthesis in diploids such as rice, Arabidopsis, and barley. However, using polyploid Triticeae species, we uncovered a more complex biological role for BGC1 in starch granule initiation: BGC1 represses the initiation of A-granules in early grain development but promotes the initiation of B-granules in mid grain development. We provide evidence that the influence of BGC1 on starch synthesis is dose dependent and show that three very different starch phenotypes are conditioned by the gene dose of BGC1 in polyploid wheat: normal bimodal starch granule morphology; A-granules with few or no B-granules; or polymorphous starch with few normal A- or B-granules. We conclude from this work that BGC1 participates in controlling B-type starch granule initiation in Triticeae endosperm and that its precise effect on granule size and number varies with gene dose and stage of development

Groundwater geochemistry, hydrogeology and potash mineral potential of the Lake Woods region, Northern Territory, Australia

We collected 38 groundwater and two surface-water samples in the semi-arid Lake Woods region of the Northern Territory to better understand the hydrogeochemistry of this system, which straddles the Wiso, Tennant Creek and Georgina geological regions. Lake Woods is presently a losing waterbody feeding the underlying groundwater system. The main aquifers comprise mainly carbonate (limestone and dolostone), siliciclastic (sandstone and siltstone) and evaporitic units. The water composition was determined in terms of bulk properties (pH, electrical conductivity, temperature, dissolved oxygen, redox potential), 40 major, minor and trace elements, and six isotopes (δ18Owater, δ2Hwater, δ13CDIC, δ34SSO42–, δ18OSO42–, 87Sr/86Sr). The groundwater is recharged through infiltration in the catchment from monsoonal rainfall (annual average rainfall ∼600 mm) and runoff. It evolves geochemically mainly through evapotranspiration and water–mineral interaction (dissolution of carbonates, silicates and to a lesser extent sulfates). The two surface waters (one from the main creek feeding the lake, the other from the lake itself) are extraordinarily enriched in 18O and 2H isotopes (δ18O of +10.9 and +16.4‰ VSMOW, and δ2H of +41 and +93‰ VSMOW, respectively), which is interpreted to reflect evaporation during the dry season (annual average evaporation ∼3000 mm) under low humidity conditions (annual average relative humidity ∼40%). This interpretation is supported by modelling results. The potassium (K) relative enrichment (K/Cl– mass ratio over 50 times that of sea water) is similar to that observed in salt-lake systems worldwide that are prospective for potash resources. Potassium enrichment is believed to derive partly from dust during atmospheric transport/deposition, but mostly from weathering of K-silicates in the aquifer materials (and possibly underlying formations). Further studies of Australian salt-lake systems are required to reach evidence-based conclusions on their mineral potential for potash, lithium, boron and other low-temperature mineral system commodities such as uranium.This project was undertaken as part of the salt-lake mineral prospectivity project at Geoscience Australia during 2012–2013, which was supported by appropriation funding from the Commonwealth of Australi

Responsible management: Engaging moral reflexive practice through threshold concepts

YesIn this conceptual paper we argue that, to date, principles of responsible management have not impacted practice as anticipated because of a disconnect between knowledge and practice. This disconnect means that an awareness of ethical concerns, by itself, does not help students take personal responsibility for their actions. We suggest that an abstract knowledge of principles has to be supplemented by an engaged understanding of the responsibility of managers and leaders to actively challenge irresponsible practices. We argue that a form of moral reflexive practice drawing on an understanding of threshold concepts is central to responsible management, and provides a gateway to transformative learning. Our conceptual argument leads to implications for management and professional education

Examination of the Effects of Heterogeneous Organization of RyR Clusters, Myofibrils and Mitochondria on Ca2+ Release Patterns in Cardiomyocytes

Spatio-temporal dynamics of intracellular calcium, [Ca2+]i, regulate the contractile function of cardiac muscle cells. Measuring [Ca2+]i flux is central to the study of mechanisms that underlie both normal cardiac function and calcium-dependent etiologies in heart disease. However, current imaging techniques are limited in the spatial resolution to which changes in [Ca2+]i can be detected. Using spatial point process statistics techniques we developed a novel method to simulate the spatial distribution of RyR clusters, which act as the major mediators of contractile Ca2+ release, upon a physiologically-realistic cellular landscape composed of tightly-packed mitochondria and myofibrils.We applied this method to computationally combine confocal-scale (~ 200 nm) data of RyR clusters with 3D electron microscopy data (~ 30 nm) of myofibrils and mitochondria, both collected from adult rat left ventricular myocytes. Using this hybrid-scale spatial model, we simulated reaction-diffusion of [Ca2+]i during the rising phase of the transient (first 30 ms after initiation). At 30 ms, the average peak of the simulated [Ca2+]i transient and of the simulated fluorescence intensity signal, F/F0, reached values similar to that found in the literature ([Ca2+]i 1 μM; F/F0 5.5). However, our model predicted the variation in [Ca2+]i to be between 0.3 and 12.7 μM (~3 to 100 fold from resting value of 0.1 μM) and the corresponding F/F0 signal ranging from 3 to 9.5. We demonstrate in this study that: (i) heterogeneities in the [Ca2+]i transient are due not only to heterogeneous distribution and clustering of mitochondria; (ii) but also to heterogeneous local densities of RyR clusters. Further, we show that: (iii) these structureinduced heterogeneities in [Ca2+]i can appear in line scan data. Finally, using our unique method for generating RyR cluster distributions, we demonstrate the robustness in the [Ca2+]i transient to differences in RyR cluster distributions measured between rat and human cardiomyocytes

FKBP12 Activates the Cardiac Ryanodine Receptor Ca2+-Release Channel and Is Antagonised by FKBP12.6

Changes in FKBP12.6 binding to cardiac ryanodine receptors (RyR2) are implicated in mediating disturbances in Ca2+-homeostasis in heart failure but there is controversy over the functional effects of FKBP12.6 on RyR2 channel gating. We have therefore investigated the effects of FKBP12.6 and another structurally similar molecule, FKBP12, which is far more abundant in heart, on the gating of single sheep RyR2 channels incorporated into planar phospholipid bilayers and on spontaneous waves of Ca2+-induced Ca2+-release in rat isolated permeabilised cardiac cells. We demonstrate that FKBP12 is a high affinity activator of RyR2, sensitising the channel to cytosolic Ca2+, whereas FKBP12.6 has very low efficacy, but can antagonise the effects of FKBP12. Mathematical modelling of the data shows the importance of the relative concentrations of FKBP12 and FKBP12.6 in determining RyR2 activity. Consistent with the single-channel results, physiological concentrations of FKBP12 (3 µM) increased Ca2+-wave frequency and decreased the SR Ca2+-content in cardiac cells. FKBP12.6, itself, had no effect on wave frequency but antagonised the effects of FKBP12

Modeling CICR in rat ventricular myocytes: voltage clamp studies

<p>Abstract</p> <p>Background</p> <p>The past thirty-five years have seen an intense search for the molecular mechanisms underlying calcium-induced calcium-release (CICR) in cardiac myocytes, with voltage clamp (VC) studies being the leading tool employed. Several VC protocols including lowering of extracellular calcium to affect <it>Ca</it>²⁺loading of the sarcoplasmic reticulum (SR), and administration of blockers caffeine and thapsigargin have been utilized to probe the phenomena surrounding SR <it>Ca</it>²⁺release. Here, we develop a deterministic mathematical model of a rat ventricular myocyte under VC conditions, to better understand mechanisms underlying the response of an isolated cell to calcium perturbation. Motivation for the study was to pinpoint key control variables influencing CICR and examine the role of CICR in the context of a physiological control system regulating cytosolic <it>Ca</it>²⁺concentration ([<it>Ca</it>²⁺]<it>_myo</it>).</p> <p>Methods</p> <p>The cell model consists of an electrical-equivalent model for the cell membrane and a fluid-compartment model describing the flux of ionic species between the extracellular and several intracellular compartments (cell cytosol, SR and the dyadic coupling unit (DCU), in which resides the mechanistic basis of CICR). The DCU is described as a controller-actuator mechanism, internally stabilized by negative feedback control of the unit's two diametrically-opposed <it>Ca</it>²⁺channels (trigger-channel and release-channel). It releases <it>Ca</it>²⁺flux into the cyto-plasm and is in turn enclosed within a negative feedback loop involving the SERCA pump, regulating[<it>Ca</it>²⁺]<it>_myo</it>.</p> <p>Results</p> <p>Our model reproduces measured VC data published by several laboratories, and generates graded <it>Ca</it>²⁺release at high <it>Ca</it>²⁺gain in a homeostatically-controlled environment where [<it>Ca</it>²⁺]<it>_myo</it>is precisely regulated. We elucidate the importance of the DCU elements in this process, particularly the role of the ryanodine receptor in controlling SR <it>Ca</it>²⁺release, its activation by trigger <it>Ca</it>²⁺, and its refractory characteristics mediated by the luminal SR <it>Ca</it>²⁺sensor. Proper functioning of the DCU, sodium-calcium exchangers and SERCA pump are important in achieving negative feedback control and hence <it>Ca</it>²⁺homeostasis.</p> <p>Conclusions</p> <p>We examine the role of the above <it>Ca</it>²⁺regulating mechanisms in handling various types of induced disturbances in <it>Ca</it>²⁺levels by quantifying cellular <it>Ca</it>²⁺balance. Our model provides biophysically-based explanations of phenomena associated with CICR generating useful and testable hypotheses.</p