HAMAP in 2015: updates to the protein family classification and annotation system

HAMAP (High-quality Automated and Manual Annotation of Proteins—available at http://hamap.expasy.org/) is a system for the automatic classification and annotation of protein sequences. HAMAP provides annotation of the same quality and detail as UniProtKB/Swiss-Prot, using manually curated profiles for protein sequence family classification and expert curated rules for functional annotation of family members. HAMAP data and tools are made available through our website and as part of the UniRule pipeline of UniProt, providing annotation for millions of unreviewed sequences of UniProtKB/TrEMBL. Here we report on the growth of HAMAP and updates to the HAMAP system since our last report in the NAR Database Issue of 2013. We continue to augment HAMAP with new family profiles and annotation rules as new protein families are characterized and annotated in UniProtKB/Swiss-Prot; the latest version of HAMAP (as of 3 September 2014) contains 1983 family classification profiles and 1998 annotation rules (up from 1780 and 1720). We demonstrate how the complex logic of HAMAP rules allows for precise annotation of individual functional variants within large homologous protein families. We also describe improvements to our web-based tool HAMAP-Scan which simplify the classification and annotation of sequences, and the incorporation of an improved sequence-profile search algorith

HAMAP in 2013, new developments in the protein family classification and annotation system

HAMAP (High-quality Automated and Manual Annotation of Proteins—available at http://hamap.expasy.org/) is a system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated annotation rules that specify annotations that apply to family members. HAMAP was originally developed to support the manual curation of UniProtKB/Swiss-Prot records describing microbial proteins. Here we describe new developments in HAMAP, including the extension of HAMAP to eukaryotic proteins, the use of HAMAP in the automated annotation of UniProtKB/TrEMBL, providing high-quality annotation for millions of protein sequences, and the future integration of HAMAP into a unified system for UniProtKB annotation, UniRule. HAMAP is continuously updated by expert curators with new family profiles and annotation rules as new protein families are characterized. The collection of HAMAP family classification profiles and annotation rules can be browsed and viewed on the HAMAP website, which also provides an interface to scan user sequences against HAMAP profile

Movies of cellular and sub-cellular motion by digital holographic microscopy

BACKGROUND: Many biological specimens, such as living cells and their intracellular components, often exhibit very little amplitude contrast, making it difficult for conventional bright field microscopes to distinguish them from their surroundings. To overcome this problem phase contrast techniques such as Zernike, Normarsky and dark-field microscopies have been developed to improve specimen visibility without chemically or physically altering them by the process of staining. These techniques have proven to be invaluable tools for studying living cells and furthering scientific understanding of fundamental cellular processes such as mitosis. However a drawback of these techniques is that direct quantitative phase imaging is not possible. Quantitative phase imaging is important because it enables determination of either the refractive index or optical thickness variations from the measured optical path length with sub-wavelength accuracy. Digital holography is an emergent phase contrast technique that offers an excellent approach in obtaining both qualitative and quantitative phase information from the hologram. A CCD camera is used to record a hologram onto a computer and numerical methods are subsequently applied to reconstruct the hologram to enable direct access to both phase and amplitude information. Another attractive feature of digital holography is the ability to focus on multiple focal planes from a single hologram, emulating the focusing control of a conventional microscope. METHODS: A modified Mach-Zender off-axis setup in transmission is used to record and reconstruct a number of holographic amplitude and phase images of cellular and sub-cellular features. RESULTS: Both cellular and sub-cellular features are imaged with sub-micron, diffraction-limited resolution. Movies of holographic amplitude and phase images of living microbes and cells are created from a series of holograms and reconstructed with numerically adjustable focus, so that the moving object can be accurately tracked with a reconstruction rate of 300ms for each hologram. The holographic movies show paramecium swimming among other microbes as well as displaying some of their intracellular processes. A time lapse movie is also shown for fibroblast cells in the process of migration. CONCLUSION: Digital holography and movies of digital holography are seen to be useful new tools for visualization of dynamic processes in biological microscopy. Phase imaging digital holography is a promising technique in terms of the lack of coherent noise and the precision with which the optical thickness of a sample can be profiled, which can lead to images with an axial resolution of a few nanometres

Scattering invariant modes of light in complex media

Random scattering of light in disordered media is an intriguing phenomenon of fundamental relevance to various applications. While techniques such as wavefront shaping and transmission matrix measurements have enabled remarkable progress for advanced imaging concepts, the most successful strategy to obtain clear images through a disordered medium remains the filtering of ballistic light. Ballistic photons with a scattering-free propagation are, however, exponentially rare and no method so far can increase their proportion. To address these limitations, we introduce and experimentally implement here a new set of optical states that we term Scattering Invariant Modes (SIMs), whose transmitted field pattern is the same, irrespective of whether they scatter through a disordered sample or propagate ballistically through a homogeneous medium. We observe SIMs that are only weakly attenuated in dense scattering media, and show in simulations that their correlations with the ballistic light can be used to improve imaging inside scattering materials

Improving economic evaluations in stroke : A report from the ESO Health Economics Working Group

Introduction Approaches to economic evaluations of stroke therapies are varied and inconsistently described. An objective of the European Stroke Organisation (ESO) Health Economics Working Group is to standardise and improve the economic evaluations of interventions for stroke. Methods The ESO Health Economics Working Group and additional experts were contacted to develop a protocol and a guidance document for data collection for economic evaluations of stroke therapies. A modified Delphi approach, including a survey and consensus processes, was used to agree on content. We also asked the participants about resources that could be shared to improve economic evaluations of interventions for stroke. Results Of 28 experts invited, 16 (57%) completed the initial survey, with representation from universities, government, and industry. More than half of the survey respondents endorsed 13 specific items to include in a standard resource use questionnaire. Preferred functional/quality of life outcome measures to use for economic evaluations were the modified Rankin Scale (14 respondents, 88%) and the EQ-5D instrument (11 respondents, 69%). Of the 12 respondents who had access to data used in economic evaluations, 10 (83%) indicated a willingness to share data. A protocol template and a guidance document for data collection were developed and are presented in this article. Conclusion The protocol template and guidance document for data collection will support a more standardised and transparent approach for economic evaluations of stroke care.Peer reviewe

Organizações sociais e agroecologia: construção de identidades e transformações sociais.

No presente trabalho, procuramos discutir as transformações ocorridas no espaço da agricultura familiar pós-Revolução Verde, especialmente a partir do movimento contestatório engendrado por organizações sociais que defendem o ideário agroecológico. Inicialmente, procurou-se compreender como a identidade a e realidade social são construídas e reconstruídas socialmente. Utilizou-se uma abordagem fenomenológica para investigar como se dá a ruptura com a realidade convencional e a transição para a agroecologia. Com base nas evidências empíricas, é possível dizer que a agroecologia participa da ressignificação positiva da identidade social dos agricultores. Entretanto, o reconhecimento da nova identidade passa pelo questionamento da realidade dominante a partir de crises vividas pelos agricultores. Sua manutenção requer partilhá-la intersubjetivamente com um grupo ou organização

The 'indigenous native peasant' trinity: imagining a plurinational community in Evo Morales's Bolivia

Over the last two decades Latin America has been a laboratory for the implementation of new models of state and citizenship. In Bolivia the (neo)liberal multicultural paradigm dominant in the 1990s has recently been replaced by a plurinational paradigm, which implies a deepening of the decentralization process and the strengthening of rights for traditionally marginalized social sectors. This paper describes the process of construction of a plurinational ‘imagined community’ and, in particular, of one of its core narratives: The ‘indigenous native peasant’. I argue that the negotiation of this collective identity and its inclusion as one of the core ideas in the new constitution is the result of a contingent strategy in response to a highly conflictive scenario, which has not been, however, able to trigger a change in the way people identify themselves. Yet in recent years, social movements’ identities have been shaped by centrifugal forces. These forces should be understood as the result of a process of collective actors’ adaptation to institutional and regulatory reforms and contribute to explaining the increase of new intrasocietal conflicts linked to the redefinition of citizenship and territorial boundaries