Quantitative proteomics for identifying biomarkers for Rabies

Introduction

Rabies is a fatal acute viral disease of the central nervous system, which is a serious public health problem in Asian and African countries. Based on the clinical presentation, rabies can be classified into encephalitic (furious) or paralytic (numb) rabies. Early diagnosis of this disease is particularly important as rabies is invariably fatal if adequate post exposure prophylaxis is not administered immediately following the bite.

Methods

In this study, we carried out a quantitative proteomic analysis of the human brain tissue from cases of encephalitic and paralytic rabies along with normal human brain tissues using an 8-plex isobaric tags for relative and absolute quantification (iTRAQ) strategy.

Results and conclusion

We identified 402 proteins, of which a number of proteins were differentially expressed between encephalitic and paralytic rabies, including several novel proteins. The differentially expressed molecules included karyopherin alpha 4 (KPNA4), which was overexpressed only in paralytic rabies, calcium calmodulin dependent kinase 2 alpha (CAMK2A), which was upregulated in paralytic rabies group and glutamate ammonia ligase (GLUL), which was overexpressed in paralytic as well as encephalitic rabies. We validated two of the upregulated molecules, GLUL and CAMK2A, by dot blot assays and further validated CAMK2A by immunohistochemistry. These molecules need to be further investigated in body fluids such as cerebrospinal fluid in a larger cohort of rabies cases to determine their potential use as antemortem diagnostic biomarkers in rabies. This is the first study to systematically profile clinical subtypes of human rabies using an iTRAQ quantitative proteomics approach.     

Multidimensional separation prior to mass spectrometry: Getting closer to the bottom of the iceberg

While prefractionation has previously been shown to improve results in MS analysis, a novel combination provides an additional dimension of separation: protein fractionation by SDS‐PAGE followed by IEF of tryptic peptides before separation by RP‐LC [Atanassov and Urlaub, Proteomics 2013, 13, 2947–2955]. This three‐step separation procedure prior to MS/MS substantially increases proteome coverage and represents a further step toward a more comprehensive analysis of complex proteomes.     

Evaluation of Tris–citric acid,skim milk and sodium citrate extenders for liquid storage of Punjab Urial (Ovis vignei punjabiensis) spermatozoa

The Punjab Urial (Ovis vignei punjabiensis) is an endangered subspecie of ovidae, distributed as small scattered populations in the forest belt of the Himalayan foothills of Pakistan and in the areas enclosed by the Indus and the Jhelum rivers. The present study was conducted to evaluate the liquid storage of Punjab Urial spermatozoa in different extenders for use in future in situ conservation activities. Semen was collected by electro-ejaculation from three captive Punjab Urial rams. Suitable ejaculates of individual animals were pooled and divided into three aliquots for dilution with the experimental extenders (Tris–citric acid, skim milk and sodium citrate) at 37 °C. Extended semen was cooled from 37 °C to 5 °C in 2 h, and stored for three days at 5 °C. Sperm motility (%), viability (%; live/dead), acrosome integrity (%) and plasma membrane integrity (%) were assessed on days 1, 2 and 3 of storage. On day 1, sperm motility, viability as well as acrosome and plasma membrane integrity were similar (p > 0.05) in all three experimental extenders. On day 2, sperm motility, viability, acrosome and plasma membrane integrity were higher (p < 0.05) in Tris–citric acid extender compared to sodium citrate based extender. On day 3 of storage, the values of motility, viability and acrosome integrity were higher (p < 0.05) in Tris–citric acid extender than in skim milk and sodium citrate based extenders. In conclusion, Tris–citric acid extender appears to be a better option compared with skim milk and sodium citrate extenders for liquid storage of Punjab Urial semen.     

液相杂交快速检测特异DNA

检测特异DNA片段的方法中,传统Southern blot技术由于其高度可重复性及能够显示条带大小的特性,一直是DNA检测的“黄金标准”.但是杂交时间长,步骤复杂,放射性污染等问题亟待解决.为了简化Southern blot,研究使用了一种液相杂交快速检测DNA的方法,即使用异硫氰酸荧光素(FITC)标记的dUTP掺入探针后,在溶液中与待检测DNA样本42℃下杂交,然后琼脂糖凝胶电泳检测荧光杂交信号.利用质粒为模板,优化了探针制作、杂交液组成、杂交时间和温度等参数.在FITC-dUTP∶ dTTP比例为1∶3、模板质粒浓度为50μg、1×杂交缓冲液(25 mmol/LTris,10mmol/L EDTA,8mmol/L Nacl,PH =8.0)中95℃变性5～9 min和42℃杂交3h的实验条件下,可检出1.2μg的质粒,探针灵敏度为7.3 ng/μl.这种方法不需要转膜,曝光,大大节约了时间,简化了操作,荧光检测也为该方法同时检测多色样本提供了可能,可广泛应用于核酸检测.     

Molecular dynamics simulation of liquid water under the influence of an external electric field

Molecular dynamics simulations of liquid water were performed at 258K and a density of 1.0?g/cm³ under various applied external electric field, ranging 0～10¹⁰?V/m. The influence of external field on structural and dynamical properties of water was investigated. The simple point charge (SPC) model is used for water molecules. An enhancement of the water hydrogen bond structure with increasing strength of the electric field has been deduced from the radial distribution functions and the analysis of hydrogen bonds structure. With increasing field strength, water system has a more perfect structure, which is similar to ice structure. However, the electrofreezing phenomenon of liquid water has not been detected since the self-diffusion coefficient was very large. The self-diffusion coefficient decreases remarkably with increasing strength of electric field and the self-diffusion coefficient is anisotropic.     

Comparison of Different Three-site Interaction Potentials for Liquid Acetonitrile

Abstract

Computer simulations of liquid acetonitrile at normal room conditions are reported. Both static and dynamic properties are analysed. Special attention is paid to the dielectric properties. A three-site interaction potential has been derived from ab initio calculations on the gas phase dimer and a comparison with different three-site interaction potentials available in the literature is presented. The suitability of three-site models to reproduce the properties of the real liquid is discussed by comparing computer simulation results with experimental data.     

Nonadditive Monte Carlo Simulation of Liquid Hydrogen Chloride Difference Algorithm and Parallel Implementation

Abstract

This paper continues our Monte Carlo simulation study of liquid hydrogen chloride [1]. The importance of non-additive interactions is carefully analyzed. Computed atom pair correlation functions are compared to neutron scattering experiments [2]. A difference algorithm (“Δ—algorithm”) is developed, which makes non-additive Monte Carlo simulations practicable. We also report an implementation of this algorithm on a transputer network, taking advantage of the inherent parallelism of the Δ — algorithm.     

Angularly Resolved Density Distributions–A Starting Point for Analysis of Liquid Structure

Abstract

We propose that the angular unfolding of atomic density distributions exposes some main features of liquid structure. Examples are the mass and the angular location of major maxima. Such structural features constitute a useful starting point for the analysis of liquid structure. To demonstrate this we have analyzed a molecular dynamics trajectory of an equimolar water-acetonitrile mixture. A new method to characterize the extrema of density distributions is used for the analysis. Using this method we draw some conclusions about different types of hydrogen bonds, their lifetimes, and their associated transition probabilities. We also draw some conclusions about recurrent molecular pair configurations.     

A Monte Carlo Simulation of Nematic and Discotic Ordering in a Polymeric Liquid Crystal

A cyclic polymeric liquid crystal system is simulated using the Metropolis Monte Carlo method in the NVT ensemble. The polymeric system consists of mesogenic moieties attached by alkyl chain spacers to siloxane ring polymers. In the model, the mesogenic moieties are represented individually by an anisotropic Lennard-Jones potential and the polymer ring is represented solely as a constraint on the relative motions of the attached mesogens. A transition from calamitic ordering to discotic ordering is observed as the ring-mesogen bond is varied from full flexible to rigid.     

Identification of very long chain unsaturated fatty acids from Ximenia oil by atmospheric pressure chemical ionization liquid chromatography-mass spectroscopy

A method is described for the enrichment of very long chain unsaturated fatty acids from total fatty acids of Ximenia oil and their identification as picolinyl esters by means of liquid chromatography-mass spectrometry with atmospheric pressure chemical ionization (LC-MS/APCI). The method is based on the use of preparative reversed phase HPLC and their subsequent identification by microbore LC-MS/APCI. The combination of these two techniques was used to identify unusual unsaturated VLCFAs up to tetracontenoic acid. All four positional isomers of tetratriacontenoic acid were also synthesized to unambiguously confirm their structure.