Shotgun MS proteomic analysis of bronchoalveolar lavage fluid in normal subjects

We provide a review of proteomic techniques used to characterize the bronchoalveolar lavage fluid (BALF) proteome of normal healthy subjects. Bronchoalveolar lavage (BAL) is the most common technique for sampling the components of the alveolar space. The proteomic techniques used to study normal BALF include protein separation by 2DE, whereby proteins were identified by comparison to a reference gel as well as high pressure liquid chromatography (HPLC)-MS/MS, also known as shotgun proteomics. We summarize recent progress using shotgun MS technologies to define the normal BALF proteome. Surprisingly, we find that despite advances in shotgun proteomic technologies over the course of the last 10 years, which have resulted in greater numbers of proteins being identified, the functional landscape of normal BALF proteome was similarly described by all methods examined.     

Proteomics and the lung: Analysis of bronchoalveolar lavage fluid

Our knowledge of the complex bronchoalveolar lavage fluid (BALF) proteome has increased significantly over the last decade; but still, there remain many aspects of the BALF proteome that need characterization. Current proteomic methodologies resolve proteins within limited dynamic ranges: thereby, being limited in their ability to examine important areas of the BALF proteome, such as low molecular weight, low abundance proteins. To ensure proper coverage of these proteins in the BALF proteome, a refined 2-DE standard operation protocol is presented, highlighting important issues in sample collection, sample preparation, and 2-D DIGE analysis. It is hoped that this will help advance the field of BALF proteomics, BALFomics, which has lagged behind similar biofluids such as plasma and serum.     

The human synovial fluid proteome: A key factor in the pathology of joint disease

This review aims to summarise our knowledge to date on the protein complement of the synovial fluid (SF). The tissues, structure and pathophysiology of the synovial joint are briefly described. The salient features of the SF proteome, how it is composed and the influence of arthritic disease are highlighted and discussed. The concentrations of proteins that have been detected and quantified in SF are drawn together from the literature on osteoarthritis, rheumatoid arthritis and juvenile idiopathic arthritis. The measurements are plotted to give a perspective on the dynamic range of protein levels within the SF. Approaches to proteomic analysis of SF to date are discussed along with their findings. From the recent literature reviewed within, it is becoming increasingly clear that analysis of the SF proteome as a whole, could deliver the most valuable differential diagnostic fingerprints of a number of arthritic disorders. Further development of proteomic platforms could characterise prognostic profiles to improve the clinician's ability to resolve unremitting disease by existing and novel therapeutics.     

Pre-analytical influence on the low molecular weight cerebrospinal fluid proteome

Cerebrospinal fluid (CSF) is a perfect source to search for new biomarkers to improve early diagnosis of neurological diseases. Standardization of pre‐analytical handling of the sample is, however, important to obtain acceptable analytical quality. In the present study, MALDI‐TOF MS was used to examine the influence of pre‐analytical sample procedures on the low molecular weight (MW) CSF proteome. Different storage conditions like temperature and duration or the addition of as little as 0.2 µL blood/mL neat CSF caused significant changes in the mass spectra. The performance of different types of MW cut‐off spin cartridges from different suppliers used to enrich the low MW CSF proteome showed great variance in cut‐off accuracy, stability and reproducibility. The described analytical method achieved a polypeptide discriminating limit of approximately 800 pM, two to three orders of magnitude lower than reported for plasma. Based on this study, we recommend that CSF is centrifuged immediately after sampling, prior to storage at –80ºC without addition of protease inhibitors. Guanidinium hydrochloride is preferred to break protein‐protein interactions. A spin cartridge with cut‐off limit above the intended analytical mass range is recommended. Our study contributes to the important task of developing standardized pre‐analytical protocols for the proteomic study of CSF.     

Bronchoalveolar lavage fluid proteomic patterns of sulfur mustard-exposed patients

Sulfur mustard is an alkylating agent that reacts with ocular, respiratory, cutaneous, and bone marrow tissues. Main late respiratory complications are chronic obstructive pulmonary disease, bronchiectasis, asthma, and bronchiolitis obliterans. The aim of the present study was to identify differentially expressed proteins in bronchoalveolar lavage (BAL) fluid of control healthy and sulfur mustard-exposed lung disease patients. The BAL protein profile of ten healthy and 30 exposed patients with mild, moderate, and severe conditions (ten males in each group) were separated with 2-D SDS-PAGE and differentially expressed protein spots were successfully identified with MALDI TOF TOF MS. Among the differentially expressed proteins we observed a significant increase in vitamin D binding protein isoforms, haptoglobin isoforms, and fibrinogen especially in exposed moderate and severe lung diseases patients (p<0.01). Moreover, compared with healthy controls, significant decreases was noted in calcyphosine, surfactant protein A, and transthyretin in these patients (p<0.01). Apolipoprotein A1 was detected in all patients' BAL fluid but none of the healthy controls. Furthermore, S100 calcium-binding protein A8 was only detected in BAL fluid of moderate and severe groups. These findings will be useful to improve current methods of monitoring and helps to identify new therapeutic targets for treatment of this complicated illness.     

机械法向接触特性参数的实验方法

针对实验的方法获取机械结合面法向接触特性参数,首先将结合面间的接触状态等效成刚度和阻尼,建立了结合面法向接触的动力学数学模型,以该动力学模型为依据设计了实验试件结构和传感器安装结构。其次设计了实验数据采集与处理系统,获取机械结合面法向接触实验参数。     

On the relation between small-time local controllability and normal self-reachability

We introduce a local property of nonlinear systems called the nontangency property and we show that, in the presence of this nontangency property, small-time local controllability by measurable controls implies small-time local controllability by piecewise-constant controls; furthermore, the initial state is normally reachable from itself in arbitrarily small time. The class of systems that are small-time locally controllable and satisfy the nontangency property is shown to contain all real-analytic systems, all smooth systems with the Lie-algebra rank condition, and all locally boundedC ¹ systems. Some consequences of small-time normal self-reachability are also discussed.     

A normal form for spider diagrams of order

We develop a reasoning system for an Euler diagram based visual logic, called spider diagrams of order. We define a normal form for spider diagrams of order and provide an algorithm, based on the reasoning system, for producing diagrams in our normal form. Normal forms for visual logics have been shown to assist in proving completeness of associated reasoning systems. We wish to use the reasoning system to allow future direct comparison of spider diagrams of order and linear temporal logic.     

Algorithm to calculate the Minkowski sums of 3-polytopes based on normal fans

Prompted by the development of algorithms for analysing geometric tolerancing, this article describes a method to determine the Minkowski sum for 3-dimensional polytopes. This method is based exclusively on intersection operations on normal cones, using the properties of the normal fan of a Minkowski sum obtained by common refinement of the normal fans of the operands. It can be used to determine from which vertices of the operands the vertices of the Minkowski sum derive. It is also possible to determine to which facets of the operands each facet of the Minkowski sum is oriented. The basic properties of the algorithms can be applied to n-polytopes.First, the main properties of the duality of normal cones and primal cones associated with the vertices of a polytope are described. Next, the properties of normal fans are applied to define the vertices and facets of the Minkowski sum of two polytopes. An algorithm is proposed, which generalises the method. Lastly, there is a discussion of the features of this algorithm, developed using the OpenCascade environment.     

An alternative way to test the criteria ensuring the existence of discrete-time normal form

In this paper an alternative version of existence condition of discrete-time normal form is derived for MIMO nonlinear systems. The proposed condition for non-singular discrete-time systems is formulated in a compact form. The theoretical results of the new condition are further investigated through examples.     

Analysis of the human testis proteome by mass spectrometry and bioinformatics

The testis is a unique organ responsible for sperm production and androgen secretion in men. To analyze the human testis proteome on a large scale, 1-D SDS-PAGE and RP-LC-MS/MS were applied and 1430 proteins in the human testis were identified. Both the false-positive rate of peptides and protein identification confidence scores were calculated in the present study. Subsequent bioinformatics analysis of the human testis proteome revealed 39 testis-specific proteins which may be important for testis functions. And a large family of proteins were identified possibly involved in alternative splicing, which may also be involved in testis-specific splicing events and explain why splicing is so prevalent in the testis. Compared with the studies on brain proteome, researches on the testis proteome is still very limited. Studies of these proteins will give a better understanding on the function of the testis. Moreover, this large-scale identification of testis proteins in humans could serve as a reference for future studies on the mechanisms underlying male infertility, searching for potential contraceptive targets, and developing new treatments for testis cancer.     

Asymptotic non-linear normal modes for large-amplitude vibrations of continuous structures

Non-linear normal modes (NNMs) are used in order to derive accurate reduced-order models for large amplitude vibrations of structural systems displaying geometrical non-linearities. This is achieved through real normal form theory, recovering the definition of a NNM as an invariant manifold in phase space, and allowing definition of new co-ordinates non-linearly related to the initial, modal ones. Two examples are studied: a linear beam resting on a non-linear elastic foundation, and a non-linear clamped–clamped beam. Throughout these examples, the main features of the NNM formulation will be illustrated: prediction of the correct trend of non-linearity for the amplitude-frequency relationship, as well as amplitude-dependent mode shapes. Comparisons between different models—using linear and non-linear modes, different number of degrees of freedom, increasing accuracy in the asymptotic developments—are also provided, in order to quantify the gain in using NNMs instead of linear modes.     

Anthropometric characteristics of disabled and normal Indian men

This paper describes a preliminary study of the anthropometric characteristics of disabled Indian men, undertaken in order to facilitate the design of mobility aids. Fourteen anthropometric measurements were made in 61 men with disabilities of the lower extremities caused by poliomyelitis or spinal cord injury, and in 140 normal men. The study reports reduced growth of the affected parts and also some acquired deformity in the upper limbs. Inter-correlations between the body dimensions were different in the disabled and normal groups.     

Bias from misspecification of the component variances in a normal mixture

Bias in parameter estimates can be substantial when heteroscedastic normal mixtures are misspecified as homoscedastic normal mixtures, and vice versa. We show through simulations that the maximum likelihood estimators under the false assumption of equal variances are inconsistent and bias in parameter estimates is appreciable and even substantial when the mixture components are not well-separated. Finite sample bias in parameter estimates is close to the asymptotic bias even for a sample size of 200 or less. When homoscedastic normal mixtures are misspecified as heteroscedastic normal mixtures, the maximum likelihood estimators are consistent. However, the maximum likelihood estimators under a correctly specified homoscedastic mixture model converge to the true parameter values faster than those under a misspecified heteroscedastic mixture model. The bias of the maximum likelihood estimators is less dependent on the lower bound imposed on the component variances to ensure that the likelihood is bounded under the false assumption of unequal variances when the sample size is 500 or more and the component distributions are well-separated. An example is given to demonstrate the effects of a misspecification of the component variances on estimates of the prevalence of hypertension using normal mixtures.     

Differences in the proteome profile in placenta from normal term and preeclamptic preterm pregnancies

The aim of this study was to use proteomic approaches to examine differences in protein expression in placentae from normal term and preterm preeclamptic pregnancies and to validate the data thus obtained by other independent methods. Using 2-DE we found that 80% of the proteins were present in both normal and preeclamptic placentae. However, 26 proteins in the normal term placentae were not matched in the preterm preeclamptic group. Six proteins showed increased intensity and one protein was down-regulated in preeclampsia. Four of the seven proteins that were altered in preeclampsia were further analyzed by Western blot and immunohistochemistry. Identification by MS techniques revealed these proteins to be involved in regulatory pathways activated by stress. This is significant because preeclampsia is a multisystem disorder in human pregnancies that results in considerable oxidative and nitrative stress. Three proteins identified by MS to be Hsp27, catalase, and glucose-regulated protein were confirmed by Western blot analysis to be significantly up-regulated in preeclampsia. Endothelial monocyte-activating polypeptide was shown to be down-regulated in preeclampsia by 2-DE and MS.