1,721,191 research outputs found
Two way street - complementary methods
No full textThe 2014 CCP4 Study Weekend, held at the University of Nottingham, covered the subject of complementary methods. While CCP4 meetings generally cycle through the main crystallography software topics of data processing, phasing, molecular replacement and refinement, memorable meetings in the past were also held on topics such as macromolecular complexes (2006) and low-resolution structure determination (2008). The topic of the 2014 meeting reflected the fact that various methods can complement the traditional crystallographic approaches in order to shed light on the dynamics, interactions and higher order structures of the macromolecules on which we work. In addition, these complementary techniques can also assist us in the process of protein structure determination.The biological systems we study are invariably multi-component and are involved in complex dynamic processes; indeed more than half of the macromolecules deposited in the PDB are oligomeric. In recent years, the extraordinary developments that have taken place in the techniques available in molecular biophysics provide macromolecular crystallographers with a strong driving force to integrate their results into a more complete understanding of the systems under study. Whilst NMR (nuclear magnetic resonance) and EM (electron microscopy) are two of the classic complementary methods, today spectroscopic, scattering, calorimetric and numerous other techniques are commonly used in our laboratories. Likewise, synchrotron beamlines today have advanced from being simple producers of bright X-rays to experimental set-ups with multiple on-line detectors, and synchrotron facilities have become major cross-disciplinary science hubs with a multitude of methods and equipment available. CCP4 is therefore rightly engaging with developers of these important techniques, which augment our work, to fully exploit their potential as tools for the structural biologist.The first session of the meeting was on biophysics, and was chaired and introduced by Mike Hough (Essex). A fascinating description by Huaying Zhao (NIH, Bethesda) covered new computational methods for combining various biophysical measurements in the analysis of multi-component protein complexes. This was followed by a presentation on the application of several such methods by Ehmke Pohl (Durham) and a review and presentation of software for in crystallo spectroscopic techniques by Florian Dworkowski (SLS). Antoine Royant (ESRF) then gave an insightful presentation on the capabilities of the ESRF Cryobench facility for various spectroscopic investigations of protein crystals.The next session, which was chaired by Edward Snell (Hauptman–Woodward Institute), was concerned with optimal strategies for the collection of solution scattering data – measurements that allow description of protein and other macromolecular assemblies. A presentation from Javier Pérez (Soleil) described the application of these methods to membrane proteins embedded in lipid/detergent. In the subsequent two presentations, Frank Gabel (IBS Grenoble) discussed the uniqueness of model predictions obtained by SAXS techniques and Adam Round (ESRF) described a software tool for automated SAXS data collection and online feedback.It is evident that the availability and recent developments in these methods challenge the crystal-centred way in which we work, as it is essential to understand what’s in that crystal. It was therefore logical to address the question of how we presently bring our samples into the X-ray beam. In the session on crystal manipulation, chaired by Frank von Delft (Diamond/Oxford), Alex Soares (BNL) outlined fascinating methods for mounting crystals and simultaneous ligand-screening, involving use of acoustic droplets. Alternative approaches for fully automated crystal mounting were then described by Florent Cipriani (EMBL, Grenoble). Next, Joseph Lyons (Aarhus) described methods for automatically locating microcrystals at the synchrotron beamline and Dianfan Li (Dublin) told us about an application of serial femtosecond crystallography using the free-electron laser to study membrane proteins crystallized in the lipid cubic phase (LCP). Finally, Robin Owen (Diamond) gave a presentation on room temperature in situ data collection. While the session focused on presently available techniques at synchrotron radiation sources, it is clear that free-electron laser applications will change the way in which we look at crystal mounting, as they provide the opportunity to add time-resolution to the crystallographic experiment.The classic NMR and EM methods were presented on day two of the meeting, and progress on the respective CCPs is covered in this issue. The session on EM was chaired and introduced by Helen Saibil (Birkbeck, London) who also reported on a new facility at the Diamond Light Source, providing 24/7 access to EM modelled on the crystallography BAG system (Block Allocation Group). A fascinating account of the theory and practice of EM studies of heterogeneous macromolecular complexes was presented by Elena Orlova (also Birkbeck). Following this, Werner Kühlbrandt (MPI, Frankfurt) gave an intriguing and wide-ranging lecture on the applications of single-particle imaging, molecular tomography and high-resolution cryo-EM. In his words (‘watch out!’), these herald a new phase of EM where we can expect to see a revolution in resolution because of new detector technology, similar to what has happened over the last ten years in the X-ray field with the advent of solid-state detectors and millisecond exposures. Alan Brown (MRC, Cambridge) reported on methods in ribosome structure determination for the interpretation of high-resolution EM data, as the borders between EM and X-ray structures now dissolve and X-ray crystallographic software can be used in EM refinement.The subsequent session on protein dynamics was chaired by Arwen Pearson (Leeds/Hamburg) and included a presentation by John Christodoulou (UCL) on the unique insights provided by NMR spectroscopy on the dynamics, disorder and meta-stability of proteins. Next up, Fraser MacMillan (UEA) presented a number of applications of electron paramagnetic resonance in studying metalloproteins and spin-labelled macromolecular assemblies. Finally, the methods available to study the molecular dynamics of biomacromolecules were presented by Sarah Harris (Leeds), who demonstrated that these approaches, in the same way as experimental biophysical methods, powerfully complement structure determination.The final session dealt with a different aspect of providing complementary structural information. Since nearly three quarters of entries in the PDB contain a ligand and indeed the atomic description for many structures could well be incomplete as these most likely contain unknown ligands, we initially thought we might address this, but instead decided to focus on the subject of drug design, which was introduced and chaired by Dave Brown (Kent). Following on from the previous topics on biophysical methods and NMR, the presentation by Glyn Williams (Astex) included the applications of NMR in drug screening. This was followed by a description of approaches for the identification of binding pockets in proteins and ligand screening by Judit Debreczeni (Astra Zeneca). The session concluded with a demonstration of some of the related features of the new CCP4 GUI by Martin Noble (Newcastle).As organizers, we were aware of the time constraints in a two-day meeting and we can perhaps partially redress the necessary limited selection of topics by touching briefly on a number of other complementary techniques in the structural biologist’s armory. One feature of X-ray diffraction is that hydrogen atoms are nearly always poorly defined in the final structure due to the low scattering factor of this element. In contrast, neutrons have a much higher cross section and thus are far more sensitive to hydrogen than X-rays, and the isotope of hydrogen, deuterium, scatters neutrons as strongly as does carbon. Deuterium can be introduced into protein crystals by vapour diffusion or soaking and non-exchangeable hydrogen atoms can be replaced by expressing the protein in deuterated growth media, using techniques which are largely routine in the NMR field. Along with improvements in detectors and pulsed sources, these techniques have allowed neutron diffraction data to be collected from much smaller crystals than ever before, thus shedding important mechanistic light on a number of enzymes. Another technique, which has allowed studies of catalytic mechanisms is the X-ray Laue method, due to the speed with which the data can be collected following initiation of the reaction. Recent advances in this field include the study of laser-triggered reactions where the light pulses can be synchronized with the synchrotron beam by use of single-bunch mode and/or high-speed X-ray beam choppers. Finally, an open question not addressed in the meeting is how we deposit all these complementary data with our structure.We would like to wholeheartedly compliment the speakers and chairs for their excellent contributions to all sessions of the 2014 Study Weekend. We especially thank those who contributed papers to the current journal issue, which, we hope, constitutes an informative record of a very memorable meeting. We also thank the CCP4 administrative staff (Karen McIntyre, Carol Malpass and Shirley Miller) for their pivotal support in the organization of the meeting
X-Ray Diffraction Images For Human Recombinant 5-Aminolevulinic Acid Dehydratase (Alad).
No full textX-ray diffraction images for recominant human 5-aminolevulinic acid dehydratase (ALAD) collected at ESRF (Grenoble) beam line ID14-2 using an ADSC Quantum 4 detector to a resolution of 2.8 Å. A series of 1 ̊ oscillation images were recorded with an exposure time of 10 seconds per image. More details are given with the scanned notes and the log file. </span
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Full text link“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
Full text linkWe 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
Full text linkWe 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
A microfluidic based system for analysis of single cells based on Ca2+ flux
No full textA microfluidic format-based system has been developed for in situ monitoring of the calcium flux response to agonists using Chinese hamster ovary (CHO) cells. The assay is based on measuring the fluorescent intensity of the calcium-sensitive indicator, Fluo-4 AM, and was performed in a modified glass chip channel, whose surface was functionalised using a silanisation method with 3-aminopropyltriethoxysilane (APTS) (enabling the cells to be immobilised on the channel surface). CHO cells calcium flux response was measured for different agonists over a range of concentrations. Cells and reagents were introduced into the chip in a continuous flow as a series of plugs in a given sequence
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