Plant organelle proteomics: Collaborating for optimal cell function

Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear‐encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter‐plant and inter‐tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in‐depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in cell, their proper function and evolution. © 2010 Wiley Periodicals, Inc., Mass Spec Rev 30:772–853, 2011     

Cysteine tagging for MS-based proteomics

Amino acid-tagging strategies are widespread in proteomics. Because of the central role of mass spectrometry (MS) as a detection technique in protein sciences, the term "mass tagging" was coined to describe the attachment of a label, which serves MS analysis and/or adds analytical value to the measurements. These so-called mass tags can be used for separation, enrichment, detection, and quantitation of peptides and proteins. In this context, cysteine is a frequent target for modifications because the thiol function can react specifically by nucleophilic substitution or addition. Furthermore, cysteines present natural modifications of biological importance and a low occurrence in the proteome that justify the development of strategies to specifically target them in peptides or proteins. In the present review, the mass-tagging methods directed to cysteine residues are comprehensively discussed, and the advantages and drawbacks of these strategies are addressed. Some concrete applications are given to underline the relevance of cysteine-tagging techniques for MS-based proteomics.     

Modern strategies for protein quantification in proteome analysis: advantages and limitations

Over the last 3 years, a number of mass spectrometry-based methods for the simultaneous identification and quantification of individual proteins within complex mixtures have been reported. Most, if not all, of such strategies apply a two-step approach: the first for the separation of proteins or peptides, and the second uses mass spectrometry to identify and quantify the individual components. To simplify the outcome of both steps, certain chemicals and heavy-isotope-labeling are commonly used in the early stages of sample preparation (except in differential fluorescence labeling protocols). The ultimate goal of these strategies is to be able to identify every protein expressed in a cell or tissue, and to determine each protein's abundance, state of modification, and possible involvement in multi-protein complexes. In this review, an attempt is made to highlight the salient characteristics of the existing strategies with particular attention to their strengths and weaknesses.     

基于质谱的蛋白质绝对定量研究策略和建议

科学家已经研究获得了大量的蛋白质/多肽潜在生物标志物,这些生物标志物需要经过验证和确证才能进一步转化到临床应用.针对蛋白质/多肽的绝对定量研究在标志物验证和确证过程中起到关键作用.传统的蛋白质定量方法,如酶联免疫吸附试验(ELISA)技术存在蛋白质抗体难以获得、不同抗体批次之间存在差异、基于抗体的检测存在交叉反应等问题...     

Fluorescence microscopy: established and emerging methods, experimental strategies, and applications in immunology

Cutting-edge biophysical technologies including total internal reflection fluorescence microscopy, single molecule fluorescence, single channel opening events, fluorescence resonance energy transfer, high-speed exposures, two-photon imaging, fluorescence lifetime imaging, and other tools are becoming increasingly important in immunology as they link molecular events to cellular physiology, a key goal of modern immunology. The primary concern in all forms of microscopy is the generation of contrast; for fluorescence microscopy contrast can be thought of as the difference in intensity between the cell and background, the signal-to-noise ratio. High information-content images can be formed by enhancing the signal, suppressing the noise, or both. As improved tools, such as ICCD and EMCCD cameras, become available for fluorescence imaging in molecular and cellular immunology, it is important to optimize other aspects of the imaging system. Numerous practical strategies to enhance fluorescence microscopy experiments are reviewed. The use of instrumentation such as light traps, cameras, objectives, improved fluorescent labels, and image filtration routines applicable to low light level experiments are discussed. New methodologies providing resolution well beyond that given by the Rayleigh criterion are outlined. Ongoing and future developments in fluorescence microscopy instrumentation and technique are reviewed. This review is intended to address situations where the signal is weak, which is important for emerging techniques stressing super-resolution or live cell dynamics, but is less important for conventional applications such as indirect immunofluorescence. This review provides a broad integrative discussion of fluorescence microscopy with selected applications in immunology.     

Geometrical principles for analysing hypoidal gears in Coordinate Measuring Machines: Involutometry,protocols, data interpretation

The design of hypoidal gears has many degrees of freedom; some external such as eccentricity, diameters, surfaces of pitch; and others internal such as pressure angle, helix angle, or involute. All parameters are linked producing teeth which are continuously variable in their shape. Apart from indexing, Coordinate Measuring Machines are required for quality control, reverse engineering, analysis of faults, or for setting up manufacturing processes. To design measurement protocols with Coordinate Machines, it is necessary to define: involutometry, boundaries of teeth and paths for touching. To interpret the data from Coordinate Machines, mathematical tools are proposed as complementary to those proposed by previous authors in this field. Since couples of crown–pinion may differ from theoretical designs, it is necessary to define universal frames to aid the analysis of geometrical quality. Both mathematical tools and CAD tools are considered as part of the Coordinate Machines for these applications.     

Challenges for measurement science and measurement practice: the collection and interpretation of home-monitored blood glucose data

In insulin-dependent diabetes mellitus, home monitoring of blood glucose was a major breakthrough in the empowerment of patients and for the first time provided raw data of sufficient accuracy from which to infer insulin therapy adjustments. Typically recorded on paper, such data are often illegible, lack details of measurement times and insulin doses and omit contextual information on diet, behaviour and general health. Home meter technology is offering improved access to patient data and allowing a more flexible range of variables to be recorded. Psychometric questionnaires give a broader view of individual and patient group perceptions of the disease and its treatment. This paper reports on early studies of home data collection using the Accutrend DM meter and the Diabetes Quality of Life and Treatment Satisfaction Questionnaires. It also describes a prototype computer system for interpreting data collected with such meters and advising on insulin dosage adjustment, based primarily on principles of time series analysis together with mathematical models of insulin profiles and search algorithms.     

Stereo vision for 3D measurement: accuracy analysis, calibration and industrial applications

This paper evaluates the accuracy of different camera calibration and measurement methods used in 3D stereo vision with CCD cameras. These methods are evaluated by means of several precision tests, determining their error limits under specified conditions of operation. To check the precision of such systems, a CMM and some calibration objects, such as grids, plates, spheres, etc. are used. Two practical applications are described: a cost-effective system for the measurement of free-form surfaces, able to generate CAD models and measuring programs for CMMs. The system aims to reduce some difficulties associated with stereo vision and to speed up the traditional digitizing process. The other application involves car frame measurement. A new automatic measuring system has been developed, allowing contactless car frame measurement through two rotating CCD cameras.     

Relative labelling index: a novel stereological approach to test for non-random immunogold labelling of organelles and membranes on transmission electron microscopy thin sections

Simple and efficient protocols for quantifying immunogold labelling of antigens localized in different cellular compartments (organelles or membranes) and statistically evaluating resulting labelling distributions are presented. Two key questions are addressed: (a) is compartmental labelling within an experimental group (e.g. control or treated) consistent with a random distribution? and (b) do labelling patterns vary between groups (e.g. control vs. treated)? Protocols rely on random sampling of cells and compartments. Numbers of gold particles lying on specified organelle compartments provide an observed frequency distribution. By superimposing test‐point lattices on cell profiles, design‐based stereology is used to determine numbers of points lying on those same compartments. Random points hit compartments with probabilities determined by their relative sizes and so provide a convenient internal standard, namely, the expected distribution if labelling is purely random. By applying test‐line lattices, and counting sites at which these intersect membrane traces, analogous procedures provide observed and expected labelling distributions for different classes of membranes. Dividing observed golds by expected golds provides a relative labelling index (RLI) for each compartment and, for random labelling, the predicted RLI = 1. In contrast to labelling densities of organelles (golds µm^?2) or membranes (golds µm^?1), RLI values are estimated without needing to know lattice constants (area per point or length per intersection) or specimen magnification. Gold distributions within a group are compared by chi‐squared analysis to test if the observed distribution differs significantly from random and, if it is non‐random, to identify compartments which are preferentially labelled (RLI > 1). Contingency table analysis allows labelling distributions in different groups of cells to be compared. Protocols are described and illustrated using worked specimen examples and real data.     

A novel parallel-kinematics mechanism for integrated, multi-axis nanopositioning: Part 2: Dynamics, control and performance analysis

In this paper, we discuss the dynamics, controls and performance of a parallel-kinematics, integrated, multi-axis nanopositioner, the PKXYZNP [Yao Q, Dong J, Ferreira PM. A novel parallel-kinematics mechanisms for integrated, multi-axis nano-positioning. Part 1: Kinematics and design for fabrications]. The paper focuses on computing the workspace of the stage, characterization of its dynamic behavior, synthesis of a controller for it, and the testing of its contour tracking and positioning performance. For this system, because of the coupled nature of the axes, a MIMO control scheme is adopted to directly close the loop around the kinematics of the stage, i.e., the position of the table/end-effector is fed back to control the actuators. This scheme has the added advantage of not requiring complex and fragile kinematic calibration of the stage as the accuracy becomes a function of only the accuracy of the sensing system and the servo performance. To make the MIMO control scheme tractable by reducing its order, the controller design is performed in the modal space of the system. A resolution of 2–4 nm is achieved from this stage. Linear and circular tests were performed to evaluate the contouring performance of the PKXYZ stage. In spite of a relatively heavy load condition (the weight of a solid target), the linear and circular contouring errors are less than 40 and 150 nm, respectively, with contouring speeds ranging up to 40 μm/s.     

Low‐temperature glycol methacrylate resin embedding method: A protocol suitable for bone marrow immunohistochemistry,PCR, and fish analysis

Molecular analyses such as fluorescence in situ hybridization (FISH) and polymerase chain reaction (PCR) are demanded to improve diagnostic accuracy in addition to immunohistopathology of bone marrow (BM) trephine specimens. Conventional BM embedding method needs decalcification, and its procedure may impair tissue morphology and DNA quality. Here, we report an undecalcified method by which glycol methacrylate resin is polymerized at low temperature (4°C). Using this method, BM enzyme activity and antigenic determinants are well preserved, and moreover, DNA extracted from plastic embedding sections is suitable for PCR amplification and sequencing, FISH analysis can be well done because of the DNA integrity of BM sections. If working with BM trephine specimen, our protocol offers the possibility to combine superior morphology with modern molecular analysis. Microsc. Res. Tech. 73:1067–1071, 2010. © 2010 Wiley‐Liss, Inc.     

A novel parallel-kinematics mechanisms for integrated, multi-axis nanopositioning: Part 1. Kinematics and design for fabrication

Multi-axis micro and nanopositioning systems are increasingly used in much of the metrology and process equipment related to the field of nanotechnology. This, the first of a two-part series of papers on a novel piezo-driven, parallel-kinematics XYZ nanopositioning (PKXYZNP) stage, concentrates on the development of a viable scheme to achieve pure spatial translation. First, the mechanism is shown to admit closed-form solutions to both; the forward and reverse kinematic problems. The Jacobian and the dynamics of the system indicate that the mechanical structure produces a relatively large work volume, and is capable of high bandwidth and uniform performance across it. The fabrication of the system is described along with some basic testing of its Jacobian and its modal frequencies. Using capacitive gages, the stage is capable of about 85 μm of motion along each axis with a resolution of about 2–4 nm. The controls, testing and performance are discussed in detail in the companion paper [Dong J, Yao Q, Ferreira PM. A novel parallel-kinematics mechanism for integrated, multi-axis nanopositioning. Part 2. Dynamics, control and performance analysis. Precis Eng].     

RETRACTED: A likely role for a novel PH-domain containing protein,PEPP2, in connecting membrane and cytoskeleton

The published article titled “A likely role for a novel PH-domain containing protein, PEPP2, in connecting membrane and cytoskeleton” has been retracted from the BIOCELL, Vol. 36, Issue 3, 2012. Title: A likely role for a novel PH-domain containing protein, PEPP2, in connecting membrane and cytoskeleton Authors: Yi Zou and Wenping Zhong URL: http://150.109.118.215/uploads/attached/file/20190102/20190102065508_87612.pdf The article “A likely role for a novel PH-domain containing protein, PEPP2, in connecting membrane and cytoskeleton” (Biocell 36, 127-132, 2012) has been retracted after publication by decision of the Editor-in-Chief, after he received compelling evidence indicating that the article’s content was part of a doctoral thesis and that the supervisor had not been included as an author. Also, the published work is the legal property of the University of Adelaide, and the author has not properly recognized the origin of the actual funding but, instead, has falsely attributed the funding to Jinan University and the Science Foundation (Ministry of Education of the People’s Republic of China). Tech Science Press is fully committed to enforce strict ethical policies and follow the COPE Retraction Guidelines. The essential condition of submission of a paper for publication in BIOCELL is that authors must declare explicitly that their works are original and have not been previously published elsewhere. Re-use of any data should be appropriately cited. To set the record straight, we hereby announce the retraction of the paper, and would like to sincerely apologize to our readers for any inconvenience this may have caused.