1,721,046 research outputs found
Probing intra- and intermolecular forces on single molecules with the AFM: towards the measurement of forces holding nucleic acids nanostructures together
No full textMany reports have witnessed the potential of the atomic force microscope as a force sensor for probing the forces that hold molecules together. Accurate molecular design allowed us, amongst others, to study the unbinding forces between ligands and receptors (Valle et al. 2008) or to study protein unfolding (Samorì et al. 2005; Sandal et al. 2008) and to characterize on the single-molecule level the different protein conformations present in a populations.
While there are many examples of force studies on proteins, the availability of data for pulling nucleic acids is more limited and it includes primarily optical tweezers studies. For example, processes such as the (over )stretching of DNA or the unfolding of RNA hairpins were characterized. We are interested in extending the possibilities for the characterization of the behaviour of nucleic-acids nanostructures under force and to employ the atomic force microscope (as it can study higher forces and apply them faster). Towards this goal, we are currently trying to upgrade our force-sensing instrumentation and to design and realize an appropriate molecular design that could be helpful in the collection of force data and in its interpretation.
As previously shown by Professor Julio Fernandez, an AFM force spectroscopy apparatus can be used in a force-clamp mode, where the tensile force stretching a molecule is held constant at a pre-set value and the molecule extension is measured over time. This operational mode can yield interesting molecular information that are complementary or supplementary to those obtained with the more traditional AFM pulling mode (pulling at a constant velocity and measuring the force). In order to operate an AFM in this fashion, though, it is necessary to implement a fast force control process and to use a very fast piezoelectric actuator. In the context of a collaborative project, we built a custom-made force-clamp AFM machine based on the fastest available piezoelectric scanner. The instrument control and data acquisition is obtained through a real-time Linux application that was developed locally. The performance of this instrument has been already tested by performing protein pulling experiments on well-characterized specimens.
Force-spectroscopy experiments can be significantly simplified if the molecular bridge under tension has certain known features. First, there must be a molecular spacer, so that the interesting bond or structure is put under tension when the AFM probe is far from the substrate surface, thus avoiding non-specific forces. Secondly, it is useful to design specimens to be oligomeric in their structure, as the repetition of the same force-induced event many times in a single pulling run has distinctive advantages, as shown in the pulling of multi-modular proteins or in similarly designed systems (Valle et al. 2008). According to this strategy, we are preparing a nucleic acid architecture designed for putting under tension a series of nanostructures and thus to study their breakdown under the application of forces (in the standard pulling mode and in the more novel force-clamp mode
Surface Implementation of the Hybridization Chain Reaction Towards the Enhancement of DNA Biosensors Signal
No full textOur goal is to test simple strategies to attain high signals from DNA hybridization events. These strategies can be used towards the realization of simple, economic, portable point-of-care detection devices, to be used for diagnostics or environmental monitoring.
Hybridization Chain Reaction is an isothermal polymerization process. In this, the formation of high-molecular weight double-stranded nucleic-acid structures is triggered by the presence of a single-stranded oligonucleotide initiator (Dirks and Pierce 2004). Such polymerization needs only a limited number of oligonucleotides and no enzymes or other reactants, so it seems directly amenable of use in analytical assays.
In the preliminary experiments that we present in this poster, we tested a possible implementation of the hybridization chain reaction as a surface-bound reaction. The chain reaction is triggered by a surface DNA hybridization event, such as those involved in the recognition between a surface-bound probe oligonucleotide and a soluble analyte nucleic acid.
As our current interest goes towards label-free detection strategies, we verified the success of the chain reaction both by standard techniques such as gel electrophoresis and spectrofluorimetry and also by using chemo-electronic measurements. Charged-based capacitance measurement of DNA hybridization is amenable of miniaturization for microfluidic microfabricated biosensor implementation (Guiducci, Stagni et al. 2004). Our still unoptimized results demonstrate a clear advantage in the biosensor read-out when the hybridization chain reaction is used as a pre-reading signal-enhancement step
DNA Parallelograms as Addressable Vessels for Functional Chemical Moieties
No full textComplex function arises in biology from the proximity and relations amongst different functional units. Often, separate containers are employed in order to segregate specialized function within a cell, or in order to control reactions by facilitated substrates and products diffusion. Self-assembled nucleic-acids nanostructures can serve as templates for the designed assembly of different functional units that can be stably attached at locations defined with nanometer accuracy.
In this poster, a few examples are presented where the self-assembled DNA parallelogram, originally designed by Ned Seeman (Sha, Liu et al. 2000), can be used as a relatively rigid template for the assembly of different functional elements, such as oligonucleotides, fluorophores, proteins.
Depending on its structure, the functional units can be included in the assembly of the parallelogram, or added later after the assembly is completed. This yields the possibility of building nanostructures with a number of different hierarchical levels of complexity, for instance allowing recycling of the functional units without need of breaking down the more complex parallelogram structure. DNA parallelograms can also be polymerized, yielding the possibility of preparing 1D or 2D multi-functionalized templates with controlled distance between multiple functional units (Brucale, Zuccheri et al. 2006).
As in the case of fluorophores, it can be shown that the rigidity and addressability of the parallelogram tile enables a high degree of control of the relation among the functional units: the measured FRET between two organic dyes is greater than in other less flexible structures where the dyes could in principle be located at the same distance one from the other.
As these templates can bind multiple different elements, controlling their location and interaction, it is in principle possible to design functional nano-objects such as smart toxins (by assembling lytic enzymes with homing peptides or antibodies), small enzyme nanofactories (keeping multiple enzymes close in space) or smart-binders (multifunctional rigid binders that can bind and select particular conformational states of macromoleculas)
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
- …
