Proteomic analysis of colorectal cancer metastasis:stathmin-1 revealed as a player in cancer cell migration and prognostic marker

Metastasis accounts largely for the high mortality rate of colorectal cancer (CRC) patients. In this study, we performed comparative proteome analysis of primary CRC cell lines HCT-116 and its metastatic derivative E1 using 2-D DIGE. We identified 74 differentially expressed proteins, many of which function in transcription, translation, angiogenesis signal transduction, or cytoskeletal remodeling pathways, which are indispensable cellular processes involved in the metastatic cascade. Among these proteins, stathmin-1 (STMN1) was found to be highly up-regulated in E1 as compared to HCT-116 and was thus selected for further functional studies. Our results showed that perturbations in STMN1 levels resulted in significant changes in cell migration, invasion, adhesion, and colony formation. We further showed that the differential expression of STMN1 correlated with the cells' metastatic potential in other paradigms of CRC models. Using immunohistochemistry, we also showed that STMN1 was highly expressed in colorectal primary tumors and metastatic tissues as compared to the adjacent normal colorectal tissues. Furthermore, we also showed via tissue microarray analyses of 324 CRC tissues and Kaplan-Meier survival plot that CRC patients with higher expression of STMN1 have poorer prognosis.

Roles of multiple flagellins in flagellar formation and flagellar growth post bdelloplast lysis in Bdellovibrio bacteriovorus

Bdellovibrio bacteriovorus cells have a single polar flagellum whose helical pitch and diameter characteristically change near the midpoint, resulting in a tapered wave. There are six flagellin genes in the genome: fliC1 to fliC6. Accordingly, the flagellar filament is composed of several similar flagellin species. We have used knockout mutants of each gene and analyzed the mutational effects on the filament length and on the composition and localization of each flagellin species in the filament by electron microscopy and one- and two-dimensional polyacrylamide gel electrophoresis. The location and amounts of flagellins in a filament were determined to be as follows: a small amount of FliC3 at the proximal end, followed by a large amount of FliC5, a large amount of FliC1, a small amount of FliC2 in this order, and a large amount of FliC6 at the distal end. FliC4 was present at a low level, but the location was not determined. Filament lengths of newly born progeny cells increased during prolonged incubation in nutrient-deficient buffer. The newly formed part of the elongated filament was composed of mainly FliC6. Reverse transcription PCR analysis of flagellar gene expression over 5 days in buffer showed that fliC gene expression tailed off over 5 days in the wild-type cells, but in the fliC5 mutant, expression of the fliC2, fliC4, and fliC6 genes was elevated on day 5, suggesting that they may be expressed to compensate for the absence of a major component, FliC5.

Proteomics and in silico approaches to extend understanding of the glutathione transferase superfamily of the tropical liver fluke Fasciola gigantica

Fasciolosis is an important foodborne, zoonotic disease of livestock and humans, with global annual health and economic losses estimated at several billion US$. Fasciola hepatica is the major species in temperate regions, while F. gigantica dominates in the tropics. In the absence of commercially available vaccines to control fasciolosis, increasing reports of resistance to current chemotherapeutic strategies and the spread of fasciolosis into new areas, new functional genomics approaches are being used to identify potential new drug targets and vaccine candidates. The glutathione transferase (GST) superfamily is both a candidate drug and vaccine target. This study reports the identification of a putatively novel Sigma class GST, present in a water-soluble cytosol extract from the tropical liver fluke F. gigantica. The GST was cloned and expressed as an enzymically active recombinant protein. This GST shares a greater identity with the human schistosomiasis GST vaccine currently at Phase II clinical trials than previously discovered F. gigantica GSTs, stimulating interest in its immuno-protective properties. In addition, in silico analysis of the GST superfamily of both F. gigantica and F. hepatica has revealed an additional Mu class GST, Omega class GSTs, and for the first time, a Zeta class member.

Proteomic analysis of coronary sinus serum reveals leucine-rich α2-glycoprotein as a novel biomarker of ventricular dysfunction and heart failure

BACKGROUND: Heart failure (HF) prevention strategies require biomarkers that identify disease manifestation. Increases in B-type natriuretic peptide (BNP) correlate with increased risk of cardiovascular events and HF development. We hypothesize that coronary sinus serum from a high BNP hypertensive population reflects an active pathological process and can be used for biomarker exploration. Our aim was to discover differentially expressed disease-associated proteins that identify patients with ventricular dysfunction and HF.

METHODS AND RESULTS: Coronary sinus serum from 11 asymptomatic, hypertensive patients underwent quantitative differential protein expression analysis by 2-dimensional difference gel electrophoresis. Proteins were identified using mass spectrometry and then studied by enzyme-linked immunosorbent assay in sera from 40 asymptomatic, hypertensive patients and 105 patients across the spectrum of ventricular dysfunction (32 asymptomatic left ventricular diastolic dysfunction, 26 diastolic HF, and 47 systolic HF patients). Leucine-rich α2-glycoprotein (LRG) was consistently overexpressed in high BNP serum. LRG levels correlate significantly with BNP in hypertensive, asymptomatic left ventricular diastolic dysfunction, diastolic HF, and systolic HF patient groups (P≤0.05). LRG levels were able to identify HF independent of BNP. LRG correlates with coronary sinus serum levels of tumor necrosis factor-α (P=0.009) and interleukin-6 (P=0.021). LRG is expressed in myocardial tissue and correlates with transforming growth factor-βR1 (P<0.001) and α-smooth muscle actin (P=0.025) expression.

CONCLUSIONS: LRG was identified as a serum biomarker that accurately identifies patients with HF. Multivariable modeling confirmed that LRG is a stronger identifier of HF than BNP and this is independent of age, sex, creatinine, ischemia, β-blocker therapy, and BNP.

Profiling excretory/secretory proteins of Trichinella spiralis muscle larvae by two-dimensional gel electrophoresis and mass spectrometry

Infection of mammalian skeletal muscle with the intracellular parasite Trichinella spiralis results in profound alterations in the host cell and a realignment of host cell gene expression. The role of parasite excretory/secretory (E/S) products in mediating these effects is unknown, largely due to the difficulty in identifying and assigning function to individual proteins. In this study, we have used two-dimensional electrophoresis to analyse the profile of muscle larva excreted/secreted proteins and have coupled this to protein identification using MALDI-TOF mass spectrometry. Interpretation of the peptide mass fingerprint data has relied primarily on the interrogation of a custom-made Trichinella EST database and the NemaGene cluster database for T. spiralis. Our results suggest that this proteomic approach is a useful tool to study protein expression in Trichinella spp. and will contribute to the identification of excreted/secreted proteins.

Two-dimensional images of dissolved sulfide and metals in anoxic sediments by a novel diffusive gradients in thin film probe and optical scanning techniques

A novel diffusive gradients in thin film probe developed comprises diffusive gel layer of silver iodide (AgI) and a back-up Microchelex resin gel layer. 2D high-resolution images of sulfide and trace metals were determined respectively on the AgI gel by densitometric analysis and on the Microchelex resin layer with laser-ablation-inductively-coupled plasma mass spectrometry (LA-ICP-MS).We investigated the validity of the analytical procedures used for the determination of sulfide and trace metals. We found low relative standard deviations on replicate measurements, linear trace-metal calibration curves between the LA-ICP-MS signal and the true trace-metal concentration in the resin gel, and a good agreement of the sulfide results obtained with the AgI resin gel and with other analytical methods. The method was applied on anoxic sediment pore waters in an estuarine and marine system. Simultaneous remobilization of sulfide and trace metals was observed in the marine sediment.

The Development of a Two-Dimensional Transient Catalyst Model for Direct Injection Two-Stroke Applications.

This paper describes the development of a two-dimensional transient catalyst model. Although designed primarily for two-stroke direct injection engines, the model is also applicable to four-stroke lean burn and diesel applications. The first section describes the geometries, properties and chemical processes simulated by the model and discusses the limitations and assumptions applied. A review of the modeling techniques adopted by other researchers is also included. The mathematical relationships which are used to represent the system are then described, together with the finite volume method used in the computer program. The need for a two-dimensional approach is explained and the methods used to model effects such as flow and temperature distribution are presented. The problems associated with developing surface reaction rates are discussed in detail and compared with published research. Validation and calibration of the model is achieved by comparing predictions with measurements from a flow reactor. While an extensive validation process, involving detailed measurements of gas composition and thermal gradients, has been completed, the analysis is too detailed for publication here and is the subject of a separate technical paper.

The Validation of a Two-Dimensional Transient Catalyst Model for Direct Injection Two-Stroke Applications

This paper describes the detailed validation of a computer model designed to simulate the transient light-off in a two-stroke oxidation catalyst. A plug flow reactor is employed to provide measurements of temperature and gas concentration at various radial and axial locations inside the catalyst. These measurements are recorded at discrete intervals during a transient light-off in which the inlet temperature is increased from ambient to 300oC at rates of up to 6oC/sec. The catalyst formulation used in the flow reactor, and its associated test procedures, are then simulated by the computer and a comparison made between experimental readings and model predictions. The design of the computer model to which this validation exercise relates is described in detail in a separate technical paper. The first section of the paper investigates the warm-up characteristics of the substrate and examines the validity of the heat transfer predictions between the wall and the gas in the absence of chemical reactions. The predictions from a typical single-component CO transient light-off test are discussed in the second section and are compared with experimental data. In particular the effect of the temperature ramp on the light-off curve and reaction zone development is examined. An analysis of the C3H6 conversion is given in the third section while the final section examines the accuracy of the light-off curves which are produced when both CO and C3H6 are present in the feed gas. The analysis shows that the heat and mass transfer calculations provided reliable predictions of the warm-up behaviour and post light-off gas concentration profiles. The self-inhibition and cross-inhibition terms in the global rate expressions were also found to be reasonably reliable although the surface reaction rates required calibration with experimental data.

Path-integral study of a two-dimensional Lennard-Jones glass

The glass transition in a quantum Lennard-Jones mixture is investigated by constant-volume path-integral simulations. Particles are assumed to be distinguishable, and the strength of quantum effects is varied by changing h from zero (the classical case) to one (corresponding to a highly quantum-mechanical regime). Quantum delocalization and zero point energy drastically reduce the sensitivity of structural and thermodynamic properties to the glass transition. Nevertheless, the glass transition temperature T-g can be determined by analyzing the phase space mobility of path-integral centroids. At constant volume, the T-g of the simulated model increases monotonically with increasing h. Low temperature tunneling centers are identified, and the quantum versus thermal character of each center is analyzed. The relation between these centers and soft quasilocalized harmonic vibrations is investigated. Periodic minimizations of the potential energy with respect to the positions of the particles are performed to determine the inherent structure of classical and quantum glassy samples. The geometries corresponding to these energy minima are found to be qualitatively similar in all cases. Systematic comparisons for ordered and disordered structures, harmonic and anharmonic dynamics, classical and quantum systems show that disorder, anharmonicity, and quantum effects are closely interlinked.

Parametric study of nonlinear electrostatic waves in two-dimensional quantum dusty plasmas

The nonlinear properties of two-dimensional cylindrical quantum dust-ion-acoustic (QDIA) and quantum dust-acoustic (QDA) waves are studied in a collisionless, unmagnetized and dense (quantum) dusty plasma. For this purpose, the reductive perturbation technique is employed to the quantum hydrodynamical equations and the Poisson equation, obtaining the cylindrical Kadomtsev–Petviashvili (CKP) equations. The effects of quantum diffraction, as well as quantum statistical and geometric effects on the profiles of QDIA and QDA solitary waves are examined. It is found that the amplitudes and widths of the nonplanar QDIA and QDA waves are significantly affected by the quantum electron tunneling effect. The addition of a dust component to a quantum plasma is seen to affect the propagation characteristics of localized QDIA excitations. In the case of low-frequency QDA waves, this effect is even stronger, since the actual form of the potential solitary waves, in fact, depends on the dust charge polarity (positive/negative) itself (allowing for positive/negative potential forms, respectively). The relevance of the present investigation to metallic nanostructures is highlighted.

2DRMP: A suite of two-dimensional R-matrix propagation codes

The R-matrix method has proved to be a remarkably stable, robust and efficient technique for solving the close-coupling equations that arise in electron and photon collisions with atoms, ions and molecules. During the last thirty-four years a series of related R-matrix program packages have been published periodically in CPC. These packages are primarily concerned with low-energy scattering where the incident energy is insufficient to ionize the target. In this paper we describe previous term2DRMP,next term a suite of two-dimensional R-matrix propagation programs aimed at creating virtual experiments on high performance and grid architectures to enable the study of electron scattering from H-like atoms and ions at intermediate energies.

Two-dimensional Banach spaces with polynomial numerical index zero

We study two-dimensional Banach spaces with polynomial numerical indices equal to zero.