DNA microarray study of genes differentiating acute myocardial infarction patients from healthy persons

Objective: Using oligonucleotide microarrays HG-U133A, we here studied the expression levels of genes that could differentiate between patients with myocardial infarction (MI) from healthy subjects, as well as to select among such genes those that seem crucial for manifestation of cardiovascular diseases.

Materials and methods: The microarray study was conducted using material derived from blood samples collected in 17 individuals.

Results: Analysis of gene expression data from 17 microarrays allowed identification of 28 genes strongly differentiating the examined groups.

Conclusion: The differentiating genes that we tracked down indicate possible linkage with atherosclerotis and could be a prognostic marker for development of cardiovascular diseases.     

Evaluation of hybridization conditions for spotted oligonucleotide-based DNA microarrays

We compared different hybridization conditions of oligonucleotide-based DNA microarray to acquire optimized and reliable microarray data. Several parameters were evaluated at different hybridization conditions, including signal-to-background (S:B) ratios, signal dynamic range, usable spots, and reproducibility. Statistical analysis showed that better results were obtained when spotted, presynthesized long oligonucleotide arrays were blocked with succinic anhydride and hybridized at 42°C in the presence of 50% formamide.     

Target concentration dependence of DNA melting temperature on oligonucleotide microarrays

The design of microarrays is currently based on studies focusing on DNA hybridization reaction in bulk solution. However, the presence of a surface to which the probe strand is attached can make the solution‐based approximations invalid, resulting in sub‐optimum hybridization conditions. To determine the effect of surfaces on DNA duplex formation, the authors studied the dependence of DNA melting temperature (T_m) on target concentration. An automated system was developed to capture the melting profiles of a 25‐mer perfect‐match probe–target pair initially hybridized at 23°C. Target concentrations ranged from 0.0165 to 15 nM with different probe amounts (0.03–0.82 pmol on a surface area of 10¹⁸ Ų), a constant probe density (5 × 10¹² molecules/cm²) and spacer length (15 dT). The authors found that T_m for duplexes anchored to a surface is lower than in‐solution, and this difference increases with increasing target concentration. In a representative set, a target concentration increase from 0.5 to 15 nM with 0.82 pmol of probe on the surface resulted in a T_m decrease of 6°C when compared with a 4°C increase in solution. At very low target concentrations, a multi‐melting process was observed in low temperature domains of the curves. This was attributed to the presence of truncated or mismatch probes. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012     

Explicit-solvent molecular dynamics simulations of a DNA tetradecanucleotide duplex: lattice-sum versus reaction-field electrostatics

Five long-timescale (10 ns) explicit-solvent molecular dynamics simulations of a DNA tetradecanucleotide dimer are performed using the GROMOS 45A4 force field and the simple-point-charge water model, in order to investigate the effect of the treatment of long-range electrostatic interactions as well as of the box shape and size on the structure and dynamics of the molecule (starting from an idealised B-DNA conformation). Long-range electrostatic interactions are handled using either a lattice-sum (LS) method (particle–particle–particle–mesh; one simulation performed within a cubic box) or a cutoff-based reaction-field (RF) method (four simulations, with long-range cutoff distances of 1.4 or 2.0 nm and performed within cubic or truncated octahedral periodic boxes). The overall double-helical structure, including Watson–Crick (WC) base-pairing, is well conserved in the simulation employing the LS scheme. In contrast, the WC base-pairing is nearly completely disrupted in the four simulations employing the RF scheme. These four simulations result in highly distorted compact (cutoff distance of 1.4 nm) or extended (cutoff distance of 2 nm) structures, irrespective of the shape and size of the computational box. These differences observed between the two schemes seem correlated with large differences in the radial distribution function between charged entities (backbone phosphate groups and sodium counterions) within the system.     

Oligonucleotide microarrays: widely applied--poorly understood.

Microarray technology, which has been around for almost two decades, now provides an indispensable service to the biomedical research community. Soaring demand for high-throughput screening of genes potentially associated with cancer and other diseases, as well as the increased need for identifying microorganisms, have substantially opened up the application of this technology to many fields of science, including new ones such as array-based comparisons of whole genomes. Yet, despite this significant progress, the fundamental understanding of the pillars of this technology, have been largely unexplored, in particular for oligonucleotide-based microarrays. In fact, most of the current approaches for the design of microarrays are based on 'common-sense' parameters, such as guanine-cytosine content, secondary structure, melting temperature or possibility of minimizing the effects of nonspecific hybridization. However, recent experiments suggest that these are inadequate. Here we discuss these results, which challenge the basic principles and assumptions of oligonucleotide microarray technology. It is clear that more systematic physicochemical studies will be required to better understand the hybridization and dissociation behaviour of oligonucleotides.     

DNA methylation profiling in cancer: From single nucleotides towards the methylome

The genomic DNA methylation pattern (methylome) is a cell epigenetic program that controls the expression of genetic information. The methylation pattern substantially changes in early carcinogenesis. A detailed survey of the methylcytosine distribution in the genome in norm and pathology is of immense importance for a better understanding of the etiology of cancer and its early diagnosis. The techniques available make it possible to simultaneously examine many samples (high-throughput analysis) and to examine large genome loci or even the total methylome (large-scale analysis). The review considers the main trends in the development of new approaches to DNA methylation and describes the techniques most commonly used in the field, their application, and results. Emphasis is placed on the use of various DNA microarrays (oligonucleotide microarrays, BAC arrays, etc.) as a method of choice for epigenetic analysis of tumors. Alternative sequence-based techniques of methylation analysis are discussed. The use of large-scale analysis to identify new epigenetic markers and to develop an epigenetic classification of neoplasms is considered.     

Interactions between two sheets of a bilayer membrane and its internal lateral pressure

We have modelled a phospholipid bilayer as two monolayer sheets which interact with each other by a coupling which depends upon the states of the lipid hydrocarbon chains in each sheet. We make use of a model (Georgallas and Pink 1982a) and its parameters, already used to study monolayer phase changes at the LC-LE transition, in order to study the lipid main transition. Although the monolayer coexistence curve can be calculated exactly, we have made use of high-temperature series expansions to calculate the critical point of the bilayer. We also present the results of computer simulations on triangular lattices for the pressure-area isotherms. We find: (i) the interaction between the sheets of a DPPC bilayer is about 1.5–2% of the maximum interaction within the plane of each sheet; (ii) the internal lateral pressure of a DPPC bilayer is about 30.5 dyne/cm; (iii) the bilayer transition enthalpy depends sensitively upon the coupling between the sheets. Should this coupling vary from sample to sample (due, possibly, to its preparation) then very different values of transition enthalpy may be measured. (iv) We present a rough rule-of-thumb for estimating the internal lateral pressure of a bilayer from a knowledge of the corresponding monolayer pressure-area isotherms.Abbreviations LC-LE liquid condensed — liquid expanded - DPPC dipalmitoylphosphatidylcholine - Q transition enthalpy Work supported in part by the Natural Sciences and Engineering Research Council of Canada     

蛋白质的糖组学研究进展

蛋白质的糖组学主要研究单个个体所包含的所有糖蛋白上聚糖的结构、功能等生物学作用。糖组学的出现使人类可以更深刻理解第三类生物信息大分子——聚糖在生命活动中的作用。目前,糖组学的发展仍处于初步阶段,基于DNA测序仪的荧光糖电泳、糖芯片等新技术的出现和质谱技术的应用对糖组学研究起到了很大的推动作用。     

脱落酸对植物线粒体膜生物物理特性的影响

采用１,６－二苯基－１,３,５－已三乙烯（ＤＰＨ）荧光偏振法和中性红法分别研究了脱落酸（ＡＢＡ）对玉米黄化芽及大豆子叶离体线粒体膜的微粘度（η）、表面电位（ψ）等生物物理特性的影响。结果表明：ＡＢＡ有降低线粒体膜的微粘度及提高线粒体膜的表面电位作用,并导致呼吸速率升高,呼吸控制和氧化磷酸化偶联下降。ＡＢＡ对线粒体膜微粘度的作用具有浓度饱和效应;ＡＢＡ对线粒体膜表面电位的提高作用,因植物不同而有差异,对玉米的作用要大于对大豆的。追踪线粒体Ａ（３５０）值的变化,还证实,ＡＢＡ提高了大豆线粒体的Ａ（３５０）值,即导致大豆线粒体的相互聚集（ａｇｇｒｅｇａｔｉｏｎ）。