An automated differential scanning dilatometer.

A sensitive scanning dilatometer has been constructed which continuously records the apparent partial specific volume of small biological samples (10–100 mg) as a function of temperature. Changes in volume of 0.02 μl can be resolved. Tedious calibrations with their inherent errors are eliminated by employing a differential approach in which a recording electrobalance responds to the difference in buoyancy of identical sample and reference tubes. Agreement with the literature values for the specific volume of n-eicosane and the apparent partial specific volume of KCl was excellent. Apparent partial specific volumes obtained for dipalmitoyl lecithin, egg albumin, and bovine serum albumin agreed well with published values.     

限制性酶切片段差异显示及其应用

差异显示技术(DD)-PCR是一种研究基因表达差异的重要而应用广泛的方法,传统的差异显示法由于在PCR时采用Poly（T）引物和随机引物而导致较高的假阳性率和产物的近Poly(A)非编码区的大量扩增。改进后的限制性酶切片段差异显示技术(RFDD)-PCR采用ToqI酶切双链cDNA,连上特殊设计的接头,再用经特殊设计的特异性配对于接头的引物来扩增,因此能重点扩增编码区并能极大地消除假阳性率。由于扩增时引物就带有荧光或放射性核素标记,还使得差异显示条带的检测更为方便、灵敏。本简要介绍了该法的原理、步骤、应用及其优缺点。     

A decade of differential display

It has been 10 years since the invention of differential display (DD), a conceptually simple methodology that allows the detection and identification of differentially expressed genes. In the past decade, the number of publications describing successful applications of DD has outnumbered those using any other competing methodologies, including subtractive hybridization, representational difference analysis, serial analysis of gene expression, and DNA microarrays. This review will provide a glimpse of the current progress made in DD technological development, refinement, and automation. Excellent examples of DD applications in studying a variety of biological problems, in such diverse biological systems as bacteria, yeast, flies, plants, and higher mammals, are presented to provide a roadmap for those who would like to pursue a fruitful gene "fishing" expedition. Some of the fundamental differences between DD and DNA microarrays are also discussed.     

A space-variant differential operator for visual sensitivity

All the elements of a Fourier analysis can be derived from the experiments of Graham and Robson on contrast sensitivity. Once their experiment is posed as an eigenvalue problem, a complete orthonormal set of eigenfunctions results from solving the associated differential equation. Neither sine and cosine nor Gabor functions result. Instead, the Hermite functions arise as the eigenfunctions of a space-variant differential operator used to model the contrast sensitivity of human observers. These functions, up to a constant, are their own Fourier transforms, and in principle can be used to exactly represent the Fourier transform of naturally occuring visual images.     

A unified evaluation of differential vaccine efficacy

Many infectious diseases are well prevented by proper vaccination. However, when a vaccine is not completely efficacious, there is great interest in determining how the vaccine effect differs in subgroups conditional on measured immune responses postvaccination and also according to the type of infecting agent (eg, strain of a virus). The former is often called correlate of protection (CoP) analysis, while the latter has been called sieve analysis. We propose a unified framework for simultaneously assessing CoP and sieve effects of a vaccine in a large Phase III randomized trial. We use flexible parametric models treating times to infection from different agents as competing risks and estimated maximum likelihood to fit the models. The parametric models under competing risks allow for estimation of both cumulative incidence-based contrasts and instantaneous rates. We outline the assumptions with which we can link the observable data to the causal contrasts of interest, propose hypothesis testing procedures, and evaluate our proposed methods in an extensive simulation study.     

A theory of optimal differential gene expression

We investigate a model of optimal regulation, intended to describe large-scale differential gene expression. Relations between the optimal expression patterns and the function of genes are deduced from an optimality principle: the regulators have to maximise a fitness function which they influence directly via a cost term, and indirectly via their control on important cell variables, such as metabolic fluxes. According to the model, the optimal linear response to small perturbations reflects the regulators' functions, namely their linear influences on the cell variables. The optimal behaviour can be realised by a linear feedback mechanism. Known or assumed properties of response coefficients lead to predictions about regulation patterns. A symmetry relation predicted for deletion experiments is verified with gene expression data. Where the optimality assumption is valid, our results justify the use of expression data for functional annotation and for pathway reconstruction and suggest the use of linear factor models for the analysis of gene expression data.     

A selective differential medium for Lactobacillus plantarum

The quantification of exogenous lactobacilli in faecal samples is frequently required for the evaluation of the intestinal colonization by probiotic bacteria. In this study, a selective and differential medium, designated LPSM, was developed for the culture of exogenous Lactobacillus plantarum. In quantitative assays, LPSM showed a sensitivity similar to those of enriched and Lactobacillus-adapted media. The presence of ciprofloxacin made LPSM inhibitory to most intestinal bacteria, including endogenous acid lactic bacteria, whereas exogenous L. plantarum strains grew producing a yellow color caused by acid production from sorbitol in the presence of bromocresol purple. The results showed that LPSM is suitable for detection and enumeration of L. plantarum in faecal samples.     

A differential scanning calorimetric study of brain clathrin

The thermal denaturation of clathrin-coated vesicles isolated from bovine brain tissue has been studied by differential scanning calorimetry and has been compared to basket structures reformed from isolated triskelion trimers of clathrin and to isolated triskelions. The coated vesicles and reformed baskets displayed similar, yet distinct, thermal behavior. Calorimetric data of the coated vesicles exhibited a single denaturation transition peak at 55.9 +/- 0.1 degrees C, skewed to low temperatures whereas the thermograms for the reformed baskets exhibited a broad transition peak at 53.1 +/- 0.1 degrees C and a peak at 56.3 +/- 0.1 degrees C. Neither transition was reversible. The specific transition enthalpy was 11.5 +/- 1.0 J g-1 for the coated vesicles and the total transition enthalpy was 9.1 +/- 0.3 J g-1 for the reformed baskets. In contrast, isolated triskelions showed no thermal transition between 15 and 90 degrees C. Although the coated vesicles and the reformed baskets have similar stability reflecting their similar structures, the coated vesicles appear to be marginally more stable than the reformed baskets. The complexity of the transition profiles and their lack of symmetry suggest the existence of several, somewhat independent, domains unique to the cage-like structure of the coated vesicles and reformed baskets.     

A delay differential equation model for tumor growth

We present a competition model of tumor growth that includes the immune system response and a cycle-phase-specific drug. The model considers three populations: Immune system, population of tumor cells during interphase and population of tumor during mitosis. Delay differential equations are used to model the system to take into account the phases of the cell cycle. We analyze the stability of the system and prove a theorem based on the argument principle to determine the stability of a fixed point and show that the stability may depend on the delay. We show theoretically and through numerical simulations that periodic solutions may arise through Hopf Bifurcations.Send offprint requests to:Minaya Villasana     

A new approach to high sensitivity differential hybridization

We describe a new approach to differential hybridization, designed to identify cDNA clones representing rare mRNA species. Duplicate filters carrying a library of cDNA from phorbolmyristate acetate (PMA)-induced EL-4 cells in λgt11 were hybridized with high concentrations of unlabeled, cloned, single-stranded cDNA from induced and control EL-4 cells, respectively. Plaques binding single-stranded cDNA were revealed by a second round of hybridization with ³⁵S-labeled DNA complementary to the vector moiety of the single-stranded cDNA. Plaques corresponding to PMA-induced mRNAs occurring at a level of about 1 part in 15000 were isolated. We believe the method is at least ten times more sensitive than conventional differential hybridization.     

A differential geometry approach for biomedical image processing

We show in this paper how simple considerations about bio-arrays images lead to a peak segmentation allowing the genes activity analysis. Bio-arrays images have a particular structure and the aim of the paper is to present a mathematical method allowing their automatic processing. The differential geometry approach used here can be also employed for other types of images presenting grey level peaks corresponding to a functional activity or to a chemical concentration. The mathematical method is based on elementary techniques of differential geometry and dynamical systems theory and provides a simple efficient algorithm when the peaks to segment are isolated.     

A differential geometric treatment of protein structure comparison

The technique of model-building a protein of known sequence but unknown tertiary structure from the structures of homologous proteins is probably so far the most reliable means of mapping from primary to tertiary structure. A key step towards the realization of the aim is to develop ways of aligning three-dimensional structures of homologus proteins, thereby deriving the rules useful for protein modelling. We have developed a generalized differential-geometric representation of protein local conformation for use in a protein comparison program which aligns protein sequences on the basis of their sequence and conformational knowledge. Because the differetial-geometric distance measure between local conformations is independent of the coordinate frame and remains chirality information, the comparison program is easily implemented, relatively rational and reasonably fast. The utility of this program for aligning closely and distantly related homologous proteins is demonstrated by multiple alignment of globins, serine proteinases and aspartic proteinase domains. Particularly, the method has reached the rational alignment between the mammalian and microbial serine proteinases as compared with many published alignment programs.     

A novel strategy for identifying differential gene expression: An improved method of differential display analysis.

We propose a novel alternative approach, an advanced method for recently developed strategies, for identifying differentially expressed genes. Firstly, double-stranded cDNAs were digested using Sau3AI and the 3'-end restriction fragments of the cDNA were ligated to a double-stranded adapter. Next, the restriction fragments were directly amplified using several combinations of adapter-specific primers and FITC-labeled oligo dT primers. The selected cDNA fragments were displayed on a polyacrylamide gel. Neither nested PCR nor purification of 3'-end fragments are necessary. We examined the validity of this approach by evaluating gene expression changes during granulocytic differentiation of HL-60 cells. This method can theoretically detect almost all gene expression changes more rapidly and through simpler manipulations than by any other approach.     

A differential scanning calorimetry study of tetracycline repressor.

Tetracycline repressor (TetR), which constitutes the most common mechanism of bacterial resistance to an antibiotic, is a homodimeric protein composed of two identical subunits, each of which contains a domain possessing a helix-turn-helix motif and a domain responsible for binding tetracycline. Binding of tetracycline in the protein pocket is accompanied by conformational changes in TetR, which abolish the specific interaction between the protein and DNA. Differential scanning calorimetry (DSC) and CD measurements, performed at pH 8.0, were used to observe the thermal denaturation of TetR in the absence and presence of tetracycline. The DSC results show that, in the absence of tetracycline, the thermally induced transitions of TetR can be described as an irreversible process, strongly dependent on scan rate and indicating that the protein denaturation is under kinetic control described by the simple kinetic scheme: N(2)--->D(2), where k is a first-order kinetic constant, N is the native state, and D is the denatured state. On the other hand, analysis of the scan rate effect on the transitions of TetR in the presence of tetracycline shows that thermal unfolding of the protein can be described by the two-state model: N(2)<--->U(2)--->D. In the proposed model, TetR in the presence of tetracycline undergoes co-operative unfolding, characterized by an enthalpy change (DeltaH(cal) = 1067 kJ x mol(-1)) and an entropy change (DeltaS = 3.1 kJ x mol(-1)).