Synote: development of a Web-based tool for synchronized annotations

This paper discusses the development of a Web-based media annotation application named Synote, which addresses the important issue that while the whole of a multimedia resource on the Web can be easily bookmarked, searched, linked to and tagged, it is still difficult to search or associate notes or other resources with a certain part of a resource. Synote supports the creation of synchronized notes, bookmarks, tags, links, images and text captions. It is a freely available application that enables any user to make annotations in and search annotations to any fragment of a continuous multimedia resource in the most used browsers and operating systems. In the implementation, Synote categorized different media resources and synchronized them via time line. The presentation of synchronized resources makes full use of Web 2.0 AJAX technology to enrich interoperability for the user experience. Positive evaluation results about the performance, efficiency and effectiveness of Synote were returned when using it with students and teachers for a number of undergraduate courses

Synote: Enhancing Multimedia E-Learning with Synchronised Annotation

This paper discusses the development of a collaborative hypertext application named Synote. Multimedia has become technically easier to create, but while the WHOLE of a media resource can be easily bookmarked, searched, linked to and tagged, it is still difficult to find or associate notes or other resources with a certain PART of a resource. Synote addresses the important and pervasive user need of making multimedia Web resources easier to access, search, manage and exploit for learners teachers and other users through developing an application that supports the creation of synchronised notes, bookmarks, tags, links, images and text captions. Synote has been developed based on requirements for such a Web based e-learning environment, identified by various studies. The performance, efficiency and effectiveness of Synote was evaluated by using it with students and teachers for a number of undergraduate courses and this has shown that they like using Synote and want more recordings and lectures in this format to be made available to them

Holliday junction branch migration driven by AAA+ ATPase motors

Holliday junctions are key intermediate DNA structures during genetic recombination. One of the first Holliday junction-processing protein complexes to be discovered was the well conserved RuvAB branch migration complex present in bacteria that mediates an ATP-dependent movement of the Holliday junction (branch migration). Although the RuvAB complex served as a paradigm for the processing of the Holliday junction, due to technical limitations the detailed structure and underlying mechanism of the RuvAB branch migration complex has until now remained unclear. Recently, structures of a reconstituted RuvAB complex actively-processing a Holliday junction were resolved using time-resolved cryo-electron microscopy. These structures showed distinct conformational states at different stages of the migration process. These structures made it possible to propose an integrated model for RuvAB Holliday junction branch migration. Furthermore, they revealed unexpected insights into the highly coordinated and regulated mechanisms of the nucleotide cycle powering substrate translocation in the hexameric AAA+ RuvB ATPase. Here, we review these latest advances and describe areas for future research

Enhancing learning using synchronised multimedia annotation

Audio and Video has become easier to record and store but while users can easily bookmark, search, link to, or tag the WHOLE of a recording available on the web (e.g. YouTube) they cannot easily find, or associate their notes or resources with, PART of that recording. This project therefore addresses the important user need of making multimedia web resources easier to access, search, manage, and exploit for learners, teachers and other users through developing Synote, a unique web based application that supports the collaborative creation of synchronised bookmarks called Synmarks, containing notes, tags and links. Synote has been developed using JAVA and the Google Web Toolkit and is able to play audio or video recordings stored by users on their chosen web accessible space. Since the Synote server only stores the text annotations, millions of hours of recordings can be catered for. The performance, efficiency and effectiveness of Synote was evaluated by using it with students and teachers for a number of undergraduate courses and this has shown that they like using Synote and want more recordings and lectures to be available in this way. Synote enables learners to: search text transcripts for specific topics and then replay recordings from that point; read captions to support learning style preference, deafness, or a second language; learn more easily from the colloquial style of transcribed text; insert a bookmark to be able to continue later from where they left off; link to sections of recordings from other resources or share these sections with others; tag and highlight sections of recordings/transcripts to revisit later for clarification; annotate recordings with notes and URLs of related resources to support revision; annotate recordings of group meetings to provide evidence for assessment. Synote enables teachers to: index their recordings using syllabus topic tags; provide synchronized slides and text captions to accompany podcasts; identify which topics need further clarification from learners’ notes and tags; provide feedback on learner-created recordings of presentations; tag recordings with URLs of related resources; link to and re-use sections of existing multimedia without having to edit the recording. A typical example scenario that demonstrates the use of Synote is: "Mike records a narrated PowerPoint of his lecture and as the students are leaving his class he uploads this into Synote which automatically creates a clickable index from the slide titles and a transcript synchronised with the recording of his voice and the slides. He quickly adds some questions students should think about for next week as well as the URLs of some other resources (including a section of a recording he made the previous year) and synchronises these with the relevant parts of lecture. By the time Sally, one of Mike’s students, sits down at a computer all Mike’s material is available on the web allowing her to search the slides and text transcript and notes for specific topics and then replay the recording from that point, automatically highlighting currently spoken words. She annotates the recording at specific points with notes made from the text book to aid exam revision and also tags and highlights a section of the transcript she doesn't understand fully for Mike to clarify. Before going to lunch and logging off she prints out some information she wants to discuss with her group and inserts a synchronised bookmark into the recording to be able to continue later from where she left off.

Structural snapshots of human PepT1 and PepT2 reveal mechanistic insights into substrate and drug transport across epithelial membranes

The uptake of peptides in mammals plays a crucial role in nutrition and inflammatory diseases. This process is mediated by promiscuous transporters of the solute carrier family 15, which form part of the major facilitator superfamily. Besides the uptake of short peptides, peptide transporter 1 (PepT1) is a highly abundant drug transporter in the intestine and represents a major route for oral drug delivery. PepT2 also allows renal drug reabsorption from ultrafiltration and brain-to-blood efflux of neurotoxic compounds. Here, we present cryogenic electron microscopy (cryo-EM) structures of human PepT1 and PepT2 captured in four different states throughout the transport cycle. The structures reveal the architecture of human peptide transporters and provide mechanistic insights into substrate recognition and conformational transitions during transport. This may support future drug design efforts to increase the bioavailability of different drugs in the human body

Helical reconstruction of and needle filaments attached to type 3 basal bodies.

Gram-negative pathogens evolved a syringe-like nanomachine, termed type 3 secretion system, to deliver protein effectors into the cytoplasm of host cells. An essential component of this system is a long helical needle filament that protrudes from the bacterial surface and connects the cytoplasms of the bacterium and the eukaryotic cell. Previous structural research was predominantly focused on reconstituted type 3 needle filaments, which lacked the biological context. In this work we introduce a facile procedure to obtain high-resolution cryo-EM structure of needle filaments attached to the basal body of type 3 secretion systems. We validate our approach by solving the structure of Salmonella PrgI filament and demonstrate its utility by obtaining the first high-resolution cryo-EM reconstruction of Shigella MxiH filament. Our work paves the way to systematic structural characterization of attached type 3 needle filaments in the context of mutagenesis studies, protein structural evolution and drug development

StarMap: a user-friendly workflow for Rosetta-driven molecular structure refinement

Cryogenic electron microscopy (cryo-EM) data represent density maps of macromolecular systems at atomic or near-atomic resolution. However, building and refining 3D atomic models by using data from cryo-EM maps is not straightforward and requires significant hands-on experience and manual intervention. We recently developed StarMap, an easy-to-use interface between the popular structural display program ChimeraX and Rosetta, a powerful molecular modeling engine. StarMap offers a general approach for refining structural models of biological macromolecules into cryo-EM density maps by combining Monte Carlo sampling with local density-guided optimization, Rosetta-based all-atom refinement and real-space B-factor calculations in a straightforward workflow. StarMap includes options for structural symmetry, local refinements and independent model validation. The overall quality of the refinement and the structure resolution is then assessed via analytical outputs, such as magnification calibration (pixel size calibration) and Fourier shell correlations. Z-scores reported by StarMap provide an easily interpretable indicator of the goodness of fit for each residue and can be plotted to evaluate structural models and improve local residue refinements, as well as to identify flexible regions and potentially functional sites in large macromolecular complexes. The protocol requires general computer skills, without the need for coding expertise, because most parts of the workflow can be operated by clicking tabs within the ChimeraX graphical user interface. Time requirements for the model refinement depend on the size and quality of the input data; however, this step can typically be completed within 1 d. The analytical parts of the workflow are completed within minutes

Multimedia Annotation and Community Folksonomy Building

Multimedia has become technically easier to create (e.g. recording lectures) but while users can easily bookmark, search, link to, or tag (i.e. classify) the WHOLE of a podcast or video recording available on the web they cannot easily find, or associate their notes or resources with, PART of that recording. This paper discusses how to meet the important and pervasive user need of making multimedia web resources (e.g. podcasts) easier to access, search, manage, and exploit for learners, teachers and other users through developing technologies that support the creation of synchronised notes, bookmarks, tags, links, images and text caption

Structure and dynamics of a mycobacterial type VII secretion system

Mycobacterium tuberculosis is the cause of one of the most important infectious diseases in humans, which leads to 1.4 million deaths every year1. Specialized protein transport systems—known as type VII secretion systems (T7SSs)—are central to the virulence of this pathogen, and are also crucial for nutrient and metabolite transport across the mycobacterial cell envelope2,3. Here we present the structure of an intact T7SS inner-membrane complex of M. tuberculosis. We show how the 2.32-MDa ESX-5 assembly, which contains 165 transmembrane helices, is restructured and stabilized as a trimer of dimers by the MycP$_5$ protease. A trimer of MycP$_5$ caps a central periplasmic dome-like chamber that is formed by three EccB$_5$ dimers, with the proteolytic sites of MycP$_5$ facing towards the cavity. This chamber suggests a central secretion and processing conduit. Complexes without MycP$_5$ show disruption of the EccB5 periplasmic assembly and increased flexibility, which highlights the importance of MycP$_5$ for complex integrity. Beneath the EccB$_5$–MycP$_5$ chamber, dimers of the EccC5 ATPase assemble into three bundles of four transmembrane helices each, which together seal the potential central secretion channel. Individual cytoplasmic EccC5 domains adopt two distinctive conformations that probably reflect different secretion states. Our work suggests a previously undescribed mechanism of protein transport and provides a structural scaffold to aid in the development of drugs against this major human pathogen