原子力显微镜拉伸吸附在金膜表面的短单链DNA分子

对单根DNA分子的操纵和拉伸可以直接研究DNA的弹性等力学性质. 首先通过将金沉积到云母表面制备了表面粗糙度小于0.3 nm的金膜,然后一段硫代的单链DNA (100 bases) 吸附到金膜表面. 利用原子力显微镜观察不同浓度的DNA吸附在金膜上的表面形貌. 进一步用原子力显微镜的力曲线模式拉伸DNA分子,在50％的情况下DNA可以被针尖拉伸,观察到了由于针尖和DNA分子间作用力的不同导致的多种不同力曲线.     

Tip loci: six Chlamydomonas nuclear suppressors that permit the translocation of proteins with mutant thylakoid signal sequences.

Mutations within the signal sequence of cytochrome f (cytf) in Chlamydomonas inhibit thylakoid membrane protein translocation and render cells nonphotosynthetic. Twenty-seven suppressors of the mutant signal sequences were selected for their ability to restore photoautotrophic growth and these describe six nuclear loci named tip1 through 6 for thylakoid insertion protein. The tip mutations restore the translocation of cytf and are not allele specific, as they suppress a number of different cytf signal sequence mutations. Tip5 and 2 may act early in cytf translocation, while Tip1, 3, 4, and 6 are engaged later. The tip mutations have no phenotype in the absence of a signal sequence mutation and there is genetic interaction between tip4, and tip5 suggesting an interaction of their encoded proteins. As there is overlap in the energetic, biochemical and genetic requirements for the translocation of nuclear and chloroplast-encoded thylakoid proteins, the tip mutations likely identify components of a general thylakoid protein translocation apparatus.     

Magnetic force microscopy of iron oxide nanoparticles and their cellular uptake

Magnetic force microscopy has the capability to detect magnetic domains from a close distance, which can provide the magnetic force gradient image of the scanned samples and also simultaneously obtain atomic force microscope (AFM) topography image as well as AFM phase image. In this work, we demonstrate the use of magnetic force microscopy together with AFM topography and phase imaging for the characterization of magnetic iron oxide nanoparticles and their cellular uptake behavior with the MCF7 carcinoma breast epithelial cells. This method can provide useful information such as the magnetic responses of nanoparticles, nanoparticle spatial localization, cell morphology, and cell surface domains at the same time for better understanding magnetic nanoparticle‐cell interaction. It would help to design magnetic‐related new imaging, diagnostic and therapeutic methods. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Atomic force microscope imaging contrast based on molecular recognition.

The contrast in atomic force microscope images arises from forces between the tip and the sample. It was shown recently that specific molecular interaction forces may be measured with the atomic force microscope; consequently, we use such forces to map the distribution of binding partners on samples. Here we demonstrate this concept by imaging a streptavidin pattern with a biotinylated tip in a novel imaging mode called affinity imaging. In this mode topography, adhesion, and sample elasticity are extracted online from local force scans. We show that this technique allows the separation of these values and that the measured binding pattern is based on specific molecular interactions.     

The intrinsic resolution limit in the atomic force microscope: implications for heights of nano-scale features

Background

Accurate mechanical characterization by the atomic force microscope at the highest spatial resolution requires that topography is deconvoluted from indentation. The measured height of nanoscale features in the atomic force microscope (AFM) is almost always smaller than the true value, which is often explained away as sample deformation, the formation of salt deposits and/or dehydration. We show that the real height of nano-objects cannot be obtained directly: a result arising as a consequence of the local probe-sample geometry.

Methods and Findings

We have modeled the tip-surface-sample interaction as the sum of the interaction between the tip and the surface and the tip and the sample. We find that the dynamics of the AFM cannot differentiate between differences in force resulting from 1) the chemical and/or mechanical characteristics of the surface or 2) a step in topography due to the size of the sample; once the size of a feature becomes smaller than the effective area of interaction between the AFM tip and sample, the measured height is compromised. This general result is a major contributor to loss of height and can amount to up to ∼90% for nanoscale features. In particular, these very large values in height loss may occur even when there is no sample deformation, and, more generally, height loss does not correlate with sample deformation. DNA and IgG antibodies have been used as model samples where experimental height measurements are shown to closely match the predicted phenomena.

Conclusions

Being able to measure the true height of single nanoscale features is paramount in many nanotechnology applications since phenomena and properties in the nanoscale critically depend on dimensions. Our approach allows accurate predictions for the true height of nanoscale objects and will lead to reliable mechanical characterization at the highest spatial resolution.     

An internal polarity landmark is important for externally induced hyphal behaviors in Candida albicans

Directional growth is a function of polarized cells such as neurites, pollen tubes, and fungal hyphae. Correct orientation of the extending cell tip depends on signaling pathways and effectors that mediate asymmetric responses to specific environmental cues. In the hyphal form of the eukaryotic fungal pathogen Candida albicans, these responses include thigmotropism and galvanotropism (hyphal turning in response to changes in substrate topography and imposed electrical fields, respectively) and penetration into semisolid substrates. During vegetative growth in C. albicans, as in the model yeast Saccharomyces cerevisiae, the Ras-like GTPase Rsr1 mediates internal cellular cues to position new buds in a prespecified pattern on the mother cell cortex. Here, we demonstrate that Rsr1 is also important for hyphal tip orientation in response to the external environmental cues that induce thigmotropic and galvanotropic growth. In addition, Rsr1 is involved in hyphal interactions with epithelial cells in vitro and its deletion diminishes the hyphal invasion of kidney tissue during systemic infection. Thus, Rsr1, an internal polarity landmark in yeast, is also involved in polarized growth responses to asymmetric environmental signals, a paradigm that is different from that described for the homologous protein in S. cerevisiae. Rsr1 may thereby contribute to the pathogenesis of C. albicans infections by influencing hyphal tip responses triggered by interaction with host tissues.     

Atomic force microscopy of RecA--DNA complexes using a carbon nanotube tip

We report high resolution images of RecA-double stranded (ds) DNA complexes obtained by atomic force microscopy (AFM). When a carbon nanotube (CNT) tip was used, AFM images visualized the 10-nm pitch of RecA-dsDNA complexes and RecA filaments as three-dimensional surface topography without reconstruction analysis. The depth of the notch between two pitches was less than 1 nm. When adsorbed on a soft surface covered with proteins, naked DNA, RecA monomers, RecA hexamers, and short RecA filaments were all clearly resolved in one image. The high resolution images with a CNT tip provided valuable information on the initiation process of RecA-dsDNA complex formation.     

Active oxygen species in blue light mediated signal transduction in coleoptile tips

Coleoptile tip is a blue-light sensitive tissue possessing a "blue light receptor" which, upon activation, elicits a signal cascade resulting in phototropic curvature of the coleoptile. In this context, the nature of the photoreceptors and the exact mechanism through which the photoreceptors transduces the signal across the membrane are not clear. In this study, we attempted to examine whether the blue light receptor perturbs redox status of the coleoptile tip and sensitizes molecular oxygen as part of the signal reactions. Coleoptile tips of Sorghum bicolor and wheat (Triticum vulgare) grown in the dark showed pronounced ascorbate free radical signal, which diminished upon illumination with weak blue light for one minute. Concomitantly, the generation of superoxide radical by the coleoptile tip was augmented upon illumination with blue light. Various thiol blockers tested in this study caused powerful inhibition of blue light induced superoxide anion radical generation. Treatment with these thiol blockers, with the exception of NEM, resulted in marked increase in the levels of ascorbic acid free radical in the blue light irradiated coleoptiles. The blue light stimulated O*-2-generation by the coleoptile tip homogenate is also inhibited by the inhibitors of blue light responses viz phenylacetic acid, potassium iodide, and sodium azide. Based on our observations, we postulate that the activated blue light receptor present in the coleoptile tip sensitizes molecular oxygen to superoxide anion radical in the tip initializing the blue light signal cascade reactions.     

Cell-cell interactions prevent a potential inductive interaction between soma and germline in C. elegans

In each gonadal arm of wild-type C. elegans hermaphrodites, the somatic distal tip cell (DTC) maintains distal germline nuclei in mitosis, while proximal nuclei enter meiosis. We have identified two conditions under which a proximal somatic cell, the anchor cell (AC), inappropriately maintains proximal germline nuclei in mitosis: when defined somatic gonadal cells have been ablated in wild type, and in lin-12 null mutants. Laser ablations and mosaic analysis indicate that somatic gonadal cells neighboring the AC normally require lin-12 activity to prevent the inappropriate AC-germline interaction. The AC-germline interaction, like the DTC-germline interaction, requires glp-1 activity. In one model, we propose that the AC sends an intercellular signal intended to interact with the lin-12 product in somatic gonadal cells; when lin-12 activity is absent, the signal interacts instead with the related glp-1 product in germline. Our data illustrate the importance of mechanisms that prevent inappropriate interactions during development.     

Flowering response of day-neutral and short-day cultivars of Nicotiana tabacum L. interactions among roots,genotype, leaf ontogenic position and growth conditions

The interaction between roots and leaves as a function of the capacity of differently positioned leaves to induce flowering of four cultivars of Nicotiana tabacum L. was assessed under long-and short-day growth conditions with three types of manipulations: 1) repeated rooting of the shoot tip, 2) removal of apical leaves, and 3) removal of basal leaves. Repeated rooting of the shoot tip increased the number of nodes produced by all cultivars; however, a substantial extension of vegetative growth was only caused by rerooting in conditions where apical leaves exhibited little or no inductive capacity. The simplest and most consistent interpretation of these data is that floral initiation in tobacco results from an interaction of inputs from the leaves and the roots and that the root influence can be overridden by a strong leaf signal.     

Atomic Force Microscopy of Biological Membranes

Atomic force microscopy (AFM) is an ideal method to study the surface topography of biological membranes. It allows membranes that are adsorbed to flat solid supports to be raster-scanned in physiological solutions with an atomically sharp tip. Therefore, AFM is capable of observing biological molecular machines at work. In addition, the tip can be tethered to the end of a single membrane protein, and forces acting on the tip upon its retraction indicate barriers that occur during the process of protein unfolding. Here we discuss the fundamental limitations of AFM determined by the properties of cantilevers, present aspects of sample preparation, and review results achieved on reconstituted and native biological membranes.     

复杂度脑电地形图研究

脑电地形图是近年脑电分析的热点之一。通过对各种复杂度算法的分析得出,近似熵由于所需要的时间序列长度较短,大大减少了脑电非平稳性所带来的困难,且无需粗粒化,在对生物医学信号的复杂度分析中有其一定的优点,采用近似熵对多道脑电信号的复杂度运算结果,通过空间插值,构建复杂性动态脑地形图,以便于观察大脑各部ＥＥＧ信号复杂度在同一时刻的相对强弱关系和这种关系随时间的变化。并通过对一些脑疾病患者脑电数据的分析,     

Ultrastructural and physico-chemical heterogeneities of yeast surfaces revealed by mapping lateral-friction and normal-adhesion forces using an atomic force microscope

Scanning force microscopy has been used to probe the surface of the emerging pathogenic yeast Candida parapsilosis, in order to get insight into its surface structure and properties at submicrometer scales. AFM friction images eventually show patches with a very strong contrast, showing high lateral interaction with the tip. Adhesion force measurement also reveals a high normal interaction with the tip, and patches show extraordinarily high pull off values. The tip eventually sticks completely at the center of the patches. While an extraordinarily high interaction is measured by the tip at those zones, topographic images show extraordinarily flat topography over those zones, both of which characteristics are consistent with a liquid-like area. High resolution friction images show those zones to be surrounded by microfibrillar structures, concentrically oriented, of a mean width of about 25 nm, structures that become progressively less defined as we move away from the center of the patches. No structure can be appreciated inside the zones of maximum contrast. Also some helical or ribbon-like structure can be resolved from friction images. There is not only an ordered disposition of the microfibrillar structures, but also the adhesion force increases radially in the direction towards the center of the patches. These structures responsible for the high adhesion are thought to be incipient-emerging budding zones. Microfibrillar structures are thought to represent the first steps of chitin biosynthesis and cell wall digestion, with chitin polymers being biosynthesized, associated with other macromolecules of the yeast cell wall. They can be also beta glucan helical structures, made visible in the zone of yeast division due to the action of autolysins. The observed gradient in surface adhesion and elastic properties correlates well with that expected from a biochemical point of view. The higher adhesion force measured could be either due to the different macromolecular nature of the patches, or to a mechanical adhesion effect due to the different plasticity of that zone. This work reveals the importance of taking into account the dynamic nature of the cell wall physico-chemical properties. Processes related to the normal cell-cycle, as division, can strongly alter the surface morphology and physico-chemical properties and cause important heterogeneities that might have a profound impact on the adhesion behavior of a single cell, which could not be detected by more macroscopic methods.     

Atomic force microscopy: a powerful tool to observe biomolecules at work

Atomic force microscopes (AFMs) move a sharp tip attached to a soft cantilever in a TV-raster-like pattern over a surface and record deflections of the tip that correspond to the surface topography. When operated in physiological solutions, an AFM allows biomolecules to be observed in their native environment. Progress in instrumentation, sample-preparation methods and recording conditions has provided images of biomolecules and their assemblies that reveal submolecular details. In addition, the AFM allows conformational changes to be observed directly. This article discusses these points and illustrates them with some pertinent examples.     

Chaperone binding at the ribosomal exit tunnel

The exit tunnel region of the ribosome is well established as a focal point for interaction between the components that guide the fate of nascent polypeptides. One of these, the chaperone trigger factor (TF), associates with the 50S ribosomal subunit through its N-terminal domain. Targeting of TF to ribosomes is crucial to achieve its remarkable efficiency in protein folding. A similar tight coupling to translation is found in signal recognition particle (SRP)-dependent protein translocation. Here, we report crystal structures of the E. coli TF ribosome binding domain. TF is structurally related to the Hsp33 chaperone but has a prominent ribosome anchor located as a tip of the molecule. This tip includes the previously established unique TF signature motif. Comparison reveals that this feature is not found in SRP structures. We identify a conserved helical kink as a hallmark of the TF structure that is most likely critical to ensure ribosome association.     

Optimal Information Transfer in the Cortex through Synchronization

In recent experimental work it has been shown that neuronal interactions are modulated by neuronal synchronization and that this modulation depends on phase shifts in neuronal oscillations. This result suggests that connections in a network can be shaped through synchronization. Here, we test and expand this hypothesis using a model network. We use transfer entropy, an information theoretical measure, to quantify the exchanged information. We show that transferred information depends on the phase relation of the signal, that the amount of exchanged information increases as a function of oscillations in the signal and that the speed of the information transfer increases as a function of synchronization. This implies that synchronization makes information transport more efficient. In summary, our results reinforce the hypothesis that synchronization modulates neuronal interactions and provide further evidence that gamma band synchronization has behavioral relevance.     

Sequence Determinants of a Microtubule Tip Localization Signal (MtLS)

Microtubule plus-end-tracking proteins (+TIPs) specifically localize to the growing plus-ends of microtubules to regulate microtubule dynamics and functions. A large group of +TIPs contain a short linear motif, SXIP, which is essential for them to bind to end-binding proteins (EBs) and target microtubule ends. The SXIP sequence site thus acts as a widespread microtubule tip localization signal (MtLS). Here we have analyzed the sequence-function relationship of a canonical MtLS. Using synthetic peptide arrays on membrane supports, we identified the residue preferences at each amino acid position of the SXIP motif and its surrounding sequence with respect to EB binding. We further developed an assay based on fluorescence polarization to assess the mechanism of the EB-SXIP interaction and to correlate EB binding and microtubule tip tracking of MtLS sequences from different +TIPs. Finally, we investigated the role of phosphorylation in regulating the EB-SXIP interaction. Together, our results define the sequence determinants of a canonical MtLS and provide the experimental data for bioinformatics approaches to carry out genome-wide predictions of novel +TIPs in multiple organisms.     

Structural insights into the membrane-anchoring mechanism of a cholesterol-dependent cytolysin

Perfringolysin O (PFO), a cytolytic toxin secreted by pathogenic Clostridium perfringens, forms large pores in cholesterol-containing membranes. Domain 4 (D4) of the protein interacts first with the membrane and is responsible for cholesterol recognition. By using several independent fluorescence techniques, we have determined the topography of D4 in the membrane-inserted oligomeric form of the toxin. Only the short hydrophobic loops at the tip of the D4 beta-sandwich are exposed to the bilayer interior, whereas the remainder of D4 projects from the membrane surface and is surrounded by water, making little or no contact with adjacent protein monomers in the oligomer. Thus, a limited interaction of D4 with the bilayer core seems to be sufficient to accomplish cholesterol recognition and initial binding of PFO to the membrane. Furthermore, D4 serves as the fulcrum around which extensive structural changes occur during the formation and insertion of the large transmembrane beta-barrel into the bilayer.