Isolation and identification of ER associated proteins with unique expression changes specific to the V144D SPTLC1 mutations in HSN-I

Axonal degeneration is the final common path in many neurological disorders. Hereditary sensory neuropathies (HSN) are a group of neuropathies involving the sensory neurons. The most common subtype is autosomal dominant hereditary sensory neuropathy type I (HSN-I). Progressive degeneration of the dorsal root ganglion (DRG) neuron with an onset of clinical symptoms between the second or third decade of life characterises HSN-I. Mutations in the serine palmitoyltransferase (SPT) long chain subunit 1 (SPTLC1) gene cause HSN-I. The endoplasmic reticulum (ER) is a dynamic organelle that houses the SPTLC1 protein. Ultra structural analysis has shown the ER in the HSN-I mutant cells to wrap around dysfunctional mitochondria and tethers them to the perinucleus. This investigation establishes that the V144D mutant of SPTLC1 alters the expression of and potentially interacts with a set of proteins within the ER. Using ER protein lysates from HSN-I patient and control lymphoblasts: we have identified a change in regulation of five proteins; Hypoxia Up regulated Protein 1: Chloride intracellular channel protein 1: Ubiqutin-40s Ribosomal protein S27a: Coactosin and Ig Kappa chain C. The expression and regulation of these proteins may help to establish a link between the ER and the ‘dying back’ process of the DRG neuron

An accurate spline polynomial cubature formula for double integration with logarithmic singularity

The paper studied the integration of logarithmic singularity problem J(ӯ) = ∫∫Δζ(ӯ)log|ӯ - ӯ 0∗|dA, where ӯ=(α,β), y0=(α0,β0) the domain Δ is rectangle Δ = [r1, r2] × [r3, r4], the arbitrary point ӯ ϵ Δ and the fixed point ӯ0 ϵ Δ. The given density function ζ(ӯ), is smooth on the rectangular domain Δ and is in the functions class C2,τ (Δ). Cubature formula (CF) for double integration with logarithmic singularities (LS) on a rectangle Δ is constructed by applying type (0, 2) modified spline function DΓ(P). The results obtained by testing the density functions ζ(ӯ) as linear and absolute value functions shows that the constructed CF is highly accurate

Regulated exocytosis per partes

This Special Issue (SI) of Cell Calcium focuses on regulated exocytosis, a recent evolutionary invention of eukaryotic cells. This essential cellular process consists of several stages: (i) the delivery of membrane bound vesicles to specific plasma membrane sites, (ii) where the merger between the vesicle and the plasma membranes occurs, (iii) leading to the formation of an aqueous channel through which vesicle content starts to be discharged to the cell exterior, (iv) after the full incorporation of the vesicle membrane into the plasma membrane, the added vesicle membrane is retrieved back into the cytoplasm by endocytosis. (v) When a fusion pore opens it may close again, a process known as transient fusion pore opening (also kiss-and-run exocytosis). In some cell types these stages are extremely shortlived, as in some neurons, and thus relatively inaccessible to experimentation. In other cell types the transition between these stages is orders of magnitude slower and can be studied in more detail. However, despite the intense investigations of this critical biological process over the last decades, the molecular mechanisms underlying regulated exocytosis have yet to be fully resolved. We thus still lack a comprehensive physiological insight into the nature of the progressive and coupled stages of exocytosis. Such a molecular-level understanding would help to fully reconstruct this process in vitro, as well as identify potential therapeutic targets for a range of diseases and dysfunctions. There are 18 papers in this SI which have been organized into three sections: Rapid regulated exocytosis and calcium homeostasis with an introduction by Erwin Neher, Molecular mechanisms of regulated exocytosis, and Cell models for regulated exocytosis. Here we briefly outline and integrate the messages of these sections

Coomassie Blue as a near-infrared fluorescent stain : a systematic comparison with Sypro Ruby for in-gel protein detection

Quantitative proteome analyses suggest that the wellestablished stain colloidal Coomassie Blue, when used as an infrared dye, may provide sensitive, post-electrophoretic in-gel protein detection that can rival even Sypro Ruby. Considering the central role of two-dimensional gel electrophoresis in top-down proteomic analyses, a more cost effective alternative such as Coomassie Blue could prove an important tool in ongoing refinements of this important analytical technique. To date, no systematic characterization of Coomassie Blue infrared fluorescence detection relative to detection with SR has been reported. Here, seven commercial Coomassie stain reagents and seven stain formulations described in the literature were systematically compared. The selectivity, threshold sensitivity, inter-protein variability, and linear-dynamic range of Coomassie Blue infrared fluorescence detection were assessed in parallel with Sypro Ruby. Notably, several of the Coomassie stain formulations provided infrared fluorescence detection sensitivity to <1 ng of protein in-gel, slightly exceeding the performance of Sypro Ruby. The linear dynamic range of Coomassie Blue infrared fluorescence detection was found to significantly exceed that ofSypro Ruby. However, in two-dimensional gel analyses, because of a blunted fluorescence response, Sypro Ruby was able to detect a few additional protein spots, amounting to 0.6% of the detected proteome. Thus, althoughboth detection methods have their advantages and disadvantages, differences between the two appear to be small. Coomassie Blue infrared fluorescence detection is thus a viable alternative for gel-based proteomics, offering detection comparable to Sypro Ruby, and more reliable quantitative assessments, but at a fraction of the cost

Proteomics is analytical chemistry : fitness-for-purpose in the application of top-down and bottom-up analyses

Molecular mechanisms underlying health and disease function at least in part based on the flexibility and fine-tuning afforded by protein isoforms and post-translational modifications. The ability to effectively and consistently resolve these protein species or proteoforms, as well as assess quantitative changes is therefore central to proteomic analyses. Here we discuss the pros and cons of currently available and developing analytical techniques from the perspective of the full spectrum of available tools and their current applications, emphasizing the concept of fitness-for-purpose in experimental design based on consideration of sample size and complexity; this necessarily also addresses analytical reproducibility and its variance. Data quality is considered the primary criterion, and we thus emphasize that the standards of Analytical Chemistry must apply throughout any proteomic analysis

The role of phospholipase D in regulated exocytosis

Background: Phospholipase D (PLD)-derived phosphatidic acid (PA) is suggested to function in exocytosis. Results: PLD activity on the plasma membrane was higher than on vesicles. PLD inhibitors suppressed some fusion parameters, but blockade of PA did not affect fusion. Conclusion: PLD-derived PA has modulatory rather than direct effects on fusion. Significance: Identifying critical mechanistic components may enable interventions to target diseases affecting exocytosis

Anionic lipids in Ca²+ -triggered fusion

Anionic lipids are native membrane components that have a profound impact on many cellular processes, including regulated exocytosis. Nonetheless, the full nature of their contribution to the fast, Ca 2+-triggered fusion pathway remains poorly defined. Here we utilize the tightly coupled quantitative molecular and functional analyses enabled by the cortical vesicle model system to elucidate the roles of specific anionic lipids in the docking, priming and fusion steps of regulated release. Studies with cholesterol sulfate established that effectively localized anionic lipids could contribute to Ca 2+-sensing and even bind Ca 2+ directly as effectors of necessary membrane rearrangements. The data thus support a role for phosphatidylserine in Ca 2+ sensing. In contrast, phosphatidylinositol would appear to serve regulatory functions in the physiological fusion machine, contributing to priming and thus the modulation and tuning of the fusion process. We note the complexities associated with establishing the specific roles of (anionic) lipids in the native fusion mechanism, including their localization and interactions with other critical components that also remain to be more clearly and quantitatively defined

Dissecting the mechanism of Ca2+-triggered membrane fusion : probing protein function using thiol reactivity

Ca2+-triggered membrane fusion involves the coordinated actions of both lipids and proteins, but the specific mechanisms remain poorly understood. The urchin cortical vesicle model is a stage-specific native preparation fully enabling the directly coupled functional-molecular analyses necessary to identify critical components of fast triggered membrane fusion. 2. Recent work on lipidic components has established a direct role for cholesterol in the fusion mechanism via local contribution of negative curvature to readily enable the formation of transient lipidic fusion intermediates. In addition, cholesterol- and sphingomyelin-enriched domains regulate the efficiency of fusion by focally organizing other components to ensure an optimized response to the triggering Ca2+ transient. 3. There is less known about the identity of proteins involved in the Ca2+-triggering steps of membrane fusion. Thiol reagents can be used as unbiased tools to probe protein functions. Comparisons of several thiol-reactive reagents have identified different effects on Ca2+ sensitivity and the extent of fusion, suggesting that there are at least two distinct thiol sites that participate in the fusion mechanism: one that regulates the efficiency of Ca2+ sensing/triggering and one that may function during the membrane merger event itself. 4. To identify the proteins that regulate Ca2+ sensitivity, the fluorescent thiol reagent Lucifer yellow iodoacetamide was used to potentiate fusion and simultaneously tag the proteins involved. Ongoing work involves the isolation of cholesterol-enriched membrane fractions to reduce the complexity of the labelled proteome, narrowing the number of candidate proteins

A routine 'top-down' approach to analysis of the human serum proteome

Serum provides a rich source of potential biomarker proteoforms. One of the major obstacles in analysing serum proteomes is detecting lower abundance proteins owing to the presence of hyper- abundant species (e.g., serum albumin and immunoglobulins). Although depletion methods have been used to address this, these can lead to the concomitant removal of non-targeted protein species, and thus raise issues of specificity, reproducibility, and the capacity for meaningful quantitative analyses. Altering the native stoichiometry of the proteome components may thus yield a more complex series of issues than dealing directly with the inherent complexity of the sample. Hence, here we targeted method refinements so as to ensure optimum resolution of serum proteomes via a top down two-dimensional gel electrophoresis (2DE) approach that enables the routine assessment of proteoforms and is fully compatible with subsequent mass spectrometric analyses. Testing included various fractionation and non-fractionation approaches. The data show that resolving 500 mu g protein on 17 cm 3-10 non-linear immobilised pH gradient strips in the first dimension followed by second dimension resolution on 7-20% gradient gels with a combination of lithium dodecyl sulfate (LDS) and sodium dodecyl sulfate (SDS) detergents markedly improves the resolution and detection of proteoforms in serum. In addition, well established third dimension electrophoretic separations in combination with deep imaging further contributed to the best available resolution, detection, and thus quantitative top-down analysis of serum proteomes

Coomassie blue staining for high sensitivity gel-based proteomics

Gel electrophoresis, particularly one- (1DE) and two-dimensional electrophoresis (2DE), remain among the most widely used top-down methods for resolving and analysing proteomes. Detection of the resulting protein maps relies on staining (i.e. colloidal coomassie blue (CCB) or SYPRO Ruby (SR), in addition to many others). Fluorescent in-gel protein stains are generally preferred for higher sensitivity, reduced background, and wider dynamic range. Although traditionally used for densitometry, CBB has fluorescent properties. Indeed, infrared detection of CCB stained protein was comparable to SR, with BioSafe (Bio-Rad) and the Neuhoff formulation (NCCB) identified as potentially superior to SR; a minor sensitivity issue encountered in gel-resolved proteomes; might have been due to the unified staining protocol used. Here the staining protocol for both CCB formulations was optimised, yielding improved selectivity without affecting sensitivity; the resulting linear dynamic range was similar for BioSafe and NCCB and somewhat better than SR. 2D gel-based analyses of mouse brain and Arabidopsis thaliana (leaf) proteomes indicated markedly superior spot detection using the NCCB formulation. Thus more sensitive, quantitative in-gel protein analyses can be achieved using NCCB, at a fraction of the cost. This article is part of a Special Issue entitled: From Genome to Proteome: Open Innovations