Single chain force spectroscopy - Reading the sequence of HP protein models

We study the elastic properties of single A/B random copolymer chains, with a specific sequence and use them as theoretical model for so called HP proteins. HP proteins carry hydrophilic (P) and hydrophobic (H) monomers. We predict a rich structure in the force-extension relations which can be attributed to the information in the sequence. The variational method is used to probe local minima on the path of stretching and releasing for the chain molecules. At a given force, we find multiple configurations which are separated by energy barriers. A collapsed globular configuration consists of several domains which unravel cooperatively. Upon stretching, the unfolding path shows a stepwise pattern corresponding to the unfolding of each domain. While releasing, several cores can be created simultaneously in the middle of the chain, resulting in a different path of collapse. The long-range interactions and stiffness of the chain simplify the potential landscape given by the disorder in sequence. Received 5 March 2002 / Received in final form 16 May 2002 Published online 13 August 2002     

Unoccupied electronic states in adsorbate systems

Experimental work on unoccupied electronic states in adsorbate systems on metallic substrates is reviewed with emphasis on recent developments. The first part is devoted to molecular adsorbates. Weakly chemisorbed hydrocarbons are briefly discussed. An exhaustive inverse photoemission (IPE) study of the CO bond to the transition metals Ni, Pb, and Pt is presented. Adsorbed NO is taken as an example to demonstrate the persisting discrepancies in the interpretation of IPE spectra. Atomic adsorbates are discussed in the second part. The quantum well state model is applied to interpret the surface states in reconstructing and non-reconstructing adsorption systems of alkali metals and hydrogen. A recent controversy on the unoccupied electronic states of the Cu(110)/O p(2×1) surface is critically reviewed. The quantum well state model is then compared to tight binding and local-density-functional calculations of the unoccupied bands and the deficiencies of the various approaches are pointed out. Finally, the relation between the surface state model and more chemically oriented models of surface bonding is briefly discussed.     

A Feigenbaum sequence of bifurcations in the Lorenz model

For some high values of the Rayleigh numberr, the Lorenz model exhibits laminar behavior due to the presence of a stable periodic orbit. A detailed numerical study shows that, forr decreasing, the turbulent behavior is reached via an infinite sequence of bifurcations, whereas forr increasing, this is due to a collapse of the stable orbit to a hyperbolic one. The infinite sequence of bifurcations is found to be compatible with Feigenbaum's conjecture.     

Supervised Domain Adaptation for Automated Semantic Segmentation of the Atrial Cavity

Atrial fibrillation (AF) is the most common cardiac arrhythmia. At present, cardiac ablation is the main treatment procedure for AF. To guide and plan this procedure, it is essential for clinicians to obtain patient-specific 3D geometrical models of the atria. For this, there is an interest in automatic image segmentation algorithms, such as deep learning (DL) methods, as opposed to manual segmentation, an error-prone and time-consuming method. However, to optimize DL algorithms, many annotated examples are required, increasing acquisition costs. The aim of this work is to develop automatic and high-performance computational models for left and right atrium (LA and RA) segmentation from a few labelled MRI volumetric images with a 3D Dual U-Net algorithm. For this, a supervised domain adaptation (SDA) method is introduced to infer knowledge from late gadolinium enhanced (LGE) MRI volumetric training samples (80 LA annotated samples) to a network trained with balanced steady-state free precession (bSSFP) MR images of limited number of annotations (19 RA and LA annotated samples). The resulting knowledge-transferred model SDA outperformed the same network trained from scratch in both RA (Dice equals 0.9160) and LA (Dice equals 0.8813) segmentation tasks.     

Mechanistic studies of reactions catalysed by diamine oxidase using isotope effects

Diamine oxidase (DAO), the enzyme that is responsible for amine biodegradation in animals, plants and humans, catalyses the biotransformation of amines such as histamine (HA), putrescine, 1-phenylethylamine, tyrosine, tryptamine, serotonine and spermine. The kinetic and solvent isotope effects (SIEs) were applied to study the mechanism of the biotransformation using HA and its methylderivatives. The SIE for the biotransformation of HA, N^τ-methylhistamine and N^π-methylhistamine was found to be 3.58, 2.22 and 5.70 on V_max, and 1.58, 1.06 and 1.14 on V_max/K_M, respectively. On the other hand, the kinetic isotope effect for oxidation of stereospecifically deuterium-labelled [(α R)-²H]-N^τ-methylhistamine and [(α R)-²H]-N^π-methylhistamine was 0.69 and 0.62 on V_max, and 15.06 and 7.50 on V_max/K_M, respectively. These results demonstrate that DAO catalyses amine biotransformation by stereospecifically cleaving the αC\bond H bond in the pro-S position. Moreover, the oxidation of amine to aldehyde involves several transition states, including hybridisation change from sp³ (Schiff base) to sp² (imine), then back again to sp³ to give a final product with hybridisation sp² (aldehyde).     

The diagnonal multivariate natural exponential families and their classification

A natural exponential family (NEF)F in ? ⁿ ,n>1, is said to be diagonal if there existn functions,a ₁,...,a _n , on some intervals of ?, such that the covariance matrixV _F (m) ofF has diagonal (a ₁(m ₁),...,a _n (m _n )), for allm=(m ₁,...,m _n ) in the mean domain ofF. The familyF is also said to be irreducible if it is not the product of two independent NEFs in ? ^k and ? ^n-k , for somek=1,...,n?1. This paper shows that there are only six types of irreducible diagonal NEFs in ? ⁿ , that we call normal, Poisson, multinomial, negative multinomial, gamma, and hybrid. These types, with the exception of the latter two, correspond to distributions well established in the literature. This study is motivated by the following question: IfF is an NEF in ? ⁿ , under what conditions is its projectionp(F) in ? ^k , underp(x ₁,...,x _n )∶=(x ₁,...,x _k ),k=1,...,n?1, still an NEF in ? ^k ? The answer turns out to be rather predictable. It is the case if, and only if, the principalk×k submatrix ofV _F (m ₁,...,m _n ) does not depend on (m _k+1,...,m _n ).     

B组轮状病毒WH-1株nsp2基因的原核表达与抗体制备

根据B组轮状病毒(GBRV)WH-1株nsp2基因的全序列,设计引物,用PCR的方法扩增得到nsp2基因的编码区.将其片段克隆到原核表达载体pGEX-KG上,经IPTG诱导,在E.coliDH5α菌株中得到高效表达.表达的GST融合蛋白大小为61×103,经SDS-PAGE分离纯化,免疫小白鼠制备了多克隆抗体.抗体经1∶3 000倍稀释后用于Western Blot分析,获得特异性显色信号.所表达的蛋白和制备的抗体可用于蛋白结构和功能的进一步研究.     

介导GAD基因的人泡沫病毒载体的构建及其应用

构建了两种新的重组人泡沫病毒载体pGPSNI—hGAD67和pGPSNI—hGAD65，分别携带人符氨酸脱羧酶（GAD）的两种同工酶GAD65和GAD67基因，并研究其在帕金森病（PD）模刭鼠丘脑底核中的表达及对帕金森病的治疗作用．RT—PCR结果表明，人泡沫病毒载体成功地介导了GAD65基因和GAD67基因在PD模型鼠丘脑底核中有效表达．动物行为检测表明，GAD65基因导入组PD模型鼠行为与对照组相比得到明显的改善（n=12，由〈0．01）．     

基质刚性影响声孔效应介导的单细胞基因转染

实验研究了基质刚性对单细胞质粒DNA转染效果的影响。实验采用高声压短脉冲(0.45MPa,10μs)条件的超声对培养在不同硬度凝胶基质(软的凝胶基质：0.2kPa,硬的凝胶基质：40kPa)上的力学敏感细胞NIH 3T3进行质粒DNA转染实验。实验结果表明,培养在硬的凝胶基质上的细胞,质粒DNA转染效率明显高于培养在软的凝胶基质上的细胞。进一步对质粒DNA进行荧光示踪可知培养在不同刚性基质上的细胞导入质粒DNA的方式不同。当细胞被培养在硬的凝胶基质上时,通过声致穿孔产生的小孔进入细胞内的质粒DNA更多,而培养在软的凝胶基质上的细胞,更多的质粒DNA可以通过非声致穿孔作用,例如内吞方式导入细胞。 细胞骨架蛋白分布规律表明,硬的凝胶基质上培养的细胞内有更多的F肌动蛋白微丝,可以更好地支撑起细胞的铺展形态,相对不容易发生内吞作用。而软的凝胶基质上培养的细胞内F肌动蛋白则更多以球形状态存在,细胞形貌骗向圆形,此时更容易发生胞吞作用。