77,635 research outputs found
Direct and dynamic detection of HIV-1 in living cells.
In basic and applied HIV research, reliable detection of viral components is crucial to monitor progression of infection. While it is routine to detect structural viral proteins in vitro for diagnostic purposes, it previously remained impossible to directly and dynamically visualize HIV in living cells without genetic modification of the virus. Here, we describe a novel fluorescent biosensor to dynamically trace HIV-1 morphogenesis in living cells. We generated a camelid single domain antibody that specifically binds the HIV-1 capsid protein (CA) at subnanomolar affinity and fused it to fluorescent proteins. The resulting fluorescent chromobody specifically recognizes the CA-harbouring HIV-1 Gag precursor protein in living cells and is applicable in various advanced light microscopy systems. Confocal live cell microscopy and super-resolution microscopy allowed detection and dynamic tracing of individual virion assemblies at the plasma membrane. The analysis of subcellular binding kinetics showed cytoplasmic antigen recognition and incorporation into virion assembly sites. Finally, we demonstrate the use of this new reporter in automated image analysis, providing a robust tool for cell-based HIV research
Open source bioimage informatics for cell biology
Significant technical advances in imaging, molecular biology and genomics have fueled a revolution in cell biology, in that the molecular and structural processes of the cell are now visualized and measured routinely. Driving much of this recent development has been the advent of computational tools for the acquisition, visualization, analysis and dissemination of these datasets. These tools collectively make up a new subfield of computational biology called bioimage informatics, which is facilitated by open source approaches. We discuss why open source tools for image informatics in cell biology are needed, some of the key general attributes of what make an open source imaging application successful, and point to opportunities for further operability that should greatly accelerate future cell biology discovery
Visualization and Correction of Automated Segmentation, Tracking and Lineaging from 5-D Stem Cell Image Sequences
Results: We present an application that enables the quantitative analysis of
multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence
microscopy images. The image sequences show stem cells together with blood
vessels, enabling quantification of the dynamic behaviors of stem cells in
relation to their vascular niche, with applications in developmental and cancer
biology. Our application automatically segments, tracks, and lineages the image
sequence data and then allows the user to view and edit the results of
automated algorithms in a stereoscopic 3-D window while simultaneously viewing
the stem cell lineage tree in a 2-D window. Using the GPU to store and render
the image sequence data enables a hybrid computational approach. An
inference-based approach utilizing user-provided edits to automatically correct
related mistakes executes interactively on the system CPU while the GPU handles
3-D visualization tasks. Conclusions: By exploiting commodity computer gaming
hardware, we have developed an application that can be run in the laboratory to
facilitate rapid iteration through biological experiments. There is a pressing
need for visualization and analysis tools for 5-D live cell image data. We
combine accurate unsupervised processes with an intuitive visualization of the
results. Our validation interface allows for each data set to be corrected to
100% accuracy, ensuring that downstream data analysis is accurate and
verifiable. Our tool is the first to combine all of these aspects, leveraging
the synergies obtained by utilizing validation information from stereo
visualization to improve the low level image processing tasks.Comment: BioVis 2014 conferenc
Self-assembly and potassium ion triggered disruption of peptide-based soft structures
This report describes formation of soft vesicular structures by a tetrapeptide and its disruption triggered by potassium ions
Exploring the relationship between the Engineering and Physical Sciences and the Health and Life Sciences by advanced bibliometric methods
We investigate the extent to which advances in the health and life sciences
(HLS) are dependent on research in the engineering and physical sciences (EPS),
particularly physics, chemistry, mathematics, and engineering. The analysis
combines two different bibliometric approaches. The first approach to analyze
the 'EPS-HLS interface' is based on term map visualizations of HLS research
fields. We consider 16 clinical fields and five life science fields. On the
basis of expert judgment, EPS research in these fields is studied by
identifying EPS-related terms in the term maps. In the second approach, a
large-scale citation-based network analysis is applied to publications from all
fields of science. We work with about 22,000 clusters of publications, each
representing a topic in the scientific literature. Citation relations are used
to identify topics at the EPS-HLS interface. The two approaches complement each
other. The advantages of working with textual data compensate for the
limitations of working with citation relations and the other way around. An
important advantage of working with textual data is in the in-depth qualitative
insights it provides. Working with citation relations, on the other hand,
yields many relevant quantitative statistics. We find that EPS research
contributes to HLS developments mainly in the following five ways: new
materials and their properties; chemical methods for analysis and molecular
synthesis; imaging of parts of the body as well as of biomaterial surfaces;
medical engineering mainly related to imaging, radiation therapy, signal
processing technology, and other medical instrumentation; mathematical and
statistical methods for data analysis. In our analysis, about 10% of all EPS
and HLS publications are classified as being at the EPS-HLS interface. This
percentage has remained more or less constant during the past decade
Potential of X-ray computed tomography for 3D anatomical analysis and microdensitometrical assessment in wood research with focus on wood modification
Studying structure and chemistry of wood and wood-based materials is the backbone of all wood research and many techniques are at hand to do so. A very valuable modality is X-ray computed tomography (CT), able to non-destructively probe the three-dimensional (3D) structure and composition. In this paper, we elaborate on the use of Nanowood, a flexible multi-resolution X-ray CT set-up developed at UGCT, the Ghent University Centre for X-ray Tomography. The technique has been used successfully in many different fields of wood science. It is illustrated how 3D structural and microdensitometrical data can be obtained using different scan set-ups and protocols. Its potential for the analysis of modified wood is exemplified, e.g. for the assessment of wood treated with hydrophobing agents, localisation of modification agents, pathway analysis related to functional tissues, dimensional changes due to thermal treatment, etc. Furthermore, monitoring of transient processes is a promising field of activity too
- …