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Find video protocols related to scientific articles indexed in Pubmed.
Unidirectional P-body transport during the yeast cell cycle.
PLoS ONE
PUBLISHED: 01-01-2014
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P-bodies belong to a large family of RNA granules that are associated with post-transcriptional gene regulation, conserved from yeast to mammals, and influence biological processes ranging from germ cell development to neuronal plasticity. RNA granules can also transport RNAs to specific locations. Germ granules transport maternal RNAs to the embryo, and neuronal granules transport RNAs long distances to the synaptic dendrites. Here we combine microfluidic-based fluorescent microscopy of single cells and automated image analysis to follow p-body dynamics during cell division in yeast. Our results demonstrate that these highly dynamic granules undergo a unidirectional transport from the mother to the daughter cell during mitosis as well as a constrained "hovering" near the bud site half an hour before the bud is observable. Both behaviors are dependent on the Myo4p/She2p RNA transport machinery. Furthermore, single cell analysis of cell size suggests that PBs play an important role in daughter cell growth under nutrient limiting conditions.
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Quantitative analysis of dynamic association in live biological fluorescent samples.
PLoS ONE
PUBLISHED: 01-01-2014
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Determining vesicle localization and association in live microscopy may be challenging due to non-simultaneous imaging of rapidly moving objects with two excitation channels. Besides errors due to movement of objects, imaging may also introduce shifting between the image channels, and traditional colocalization methods cannot handle such situations. Our approach to quantifying the association between tagged proteins is to use an object-based method where the exact match of object locations is not assumed. Point-pattern matching provides a measure of correspondence between two point-sets under various changes between the sets. Thus, it can be used for robust quantitative analysis of vesicle association between image channels. Results for a large set of synthetic images shows that the novel association method based on point-pattern matching demonstrates robust capability to detect association of closely located vesicles in live cell-microscopy where traditional colocalization methods fail to produce results. In addition, the method outperforms compared Iterated Closest Points registration method. Results for fixed and live experimental data shows the association method to perform comparably to traditional methods in colocalization studies for fixed cells and to perform favorably in association studies for live cells.
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Quantitative analysis of colony morphology in yeast.
BioTechniques
PUBLISHED: 01-01-2014
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Microorganisms often form multicellular structures such as biofilms and structured colonies that can influence the organism's virulence, drug resistance, and adherence to medical devices. Phenotypic classification of these structures has traditionally relied on qualitative scoring systems that limit detailed phenotypic comparisons between strains. Automated imaging and quantitative analysis have the potential to improve the speed and accuracy of experiments designed to study the genetic and molecular networks underlying different morphological traits. For this reason, we have developed a platform that uses automated image analysis and pattern recognition to quantify phenotypic signatures of yeast colonies. Our strategy enables quantitative analysis of individual colonies, measured at a single time point or over a series of time-lapse images, as well as the classification of distinct colony shapes based on image-derived features. Phenotypic changes in colony morphology can be expressed as changes in feature space trajectories over time, thereby enabling the visualization and quantitative analysis of morphological development. To facilitate data exploration, results are plotted dynamically through an interactive Yeast Image Analysis web application (YIMAA; http://yimaa.cs.tut.fi) that integrates the raw and processed images across all time points, allowing exploration of the image-based features and principal components associated with morphological development.
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Multi-scale Gaussian representation and outline-learning based cell image segmentation.
BMC Bioinformatics
PUBLISHED: 08-12-2013
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High-throughput genome-wide screening to study gene-specific functions, e.g. for drug discovery, demands fast automated image analysis methods to assist in unraveling the full potential of such studies. Image segmentation is typically at the forefront of such analysis as the performance of the subsequent steps, for example, cell classification, cell tracking etc., often relies on the results of segmentation.
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Leukemia prediction using sparse logistic regression.
PLoS ONE
PUBLISHED: 01-01-2013
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We describe a supervised prediction method for diagnosis of acute myeloid leukemia (AML) from patient samples based on flow cytometry measurements. We use a data driven approach with machine learning methods to train a computational model that takes in flow cytometry measurements from a single patient and gives a confidence score of the patient being AML-positive. Our solution is based on an [Formula: see text] regularized logistic regression model that aggregates AML test statistics calculated from individual test tubes with different cell populations and fluorescent markers. The model construction is entirely data driven and no prior biological knowledge is used. The described solution scored a 100% classification accuracy in the DREAM6/FlowCAP2 Molecular Classification of Acute Myeloid Leukaemia Challenge against a golden standard consisting of 20 AML-positive and 160 healthy patients. Here we perform a more extensive validation of the prediction model performance and further improve and simplify our original method showing that statistically equal results can be obtained by using simple average marker intensities as features in the logistic regression model. In addition to the logistic regression based model, we also present other classification models and compare their performance quantitatively. The key benefit in our prediction method compared to other solutions with similar performance is that our model only uses a small fraction of the flow cytometry measurements making our solution highly economical.
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Probabilistic analysis of gene expression measurements from heterogeneous tissues.
Bioinformatics
PUBLISHED: 07-14-2010
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Tissue heterogeneity, arising from multiple cell types, is a major confounding factor in experiments that focus on studying cell types, e.g. their expression profiles, in isolation. Although sample heterogeneity can be addressed by manual microdissection, prior to conducting experiments, computational treatment on heterogeneous measurements have become a reliable alternative to perform this microdissection in silico. Favoring computation over manual purification has its advantages, such as time consumption, measuring responses of multiple cell types simultaneously, keeping samples intact of external perturbations and unaltered yield of molecular content.
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Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images.
BMC Bioinformatics
PUBLISHED: 05-13-2010
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Several algorithms have been proposed for detecting fluorescently labeled subcellular objects in microscope images. Many of these algorithms have been designed for specific tasks and validated with limited image data. But despite the potential of using extensive comparisons between algorithms to provide useful information to guide method selection and thus more accurate results, relatively few studies have been performed.
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Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network.
PLoS ONE
PUBLISHED: 04-15-2010
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Molecular interaction networks establish all cell biological processes. The networks are under intensive research that is facilitated by new high-throughput measurement techniques for the detection, quantification, and characterization of molecules and their physical interactions. For the common model organism yeast Saccharomyces cerevisiae, public databases store a significant part of the accumulated information and, on the way to better understanding of the cellular processes, there is a need to integrate this information into a consistent reconstruction of the molecular interaction network. This work presents and validates RefRec, the most comprehensive molecular interaction network reconstruction currently available for yeast. The reconstruction integrates protein synthesis pathways, a metabolic network, and a protein-protein interaction network from major biological databases. The core of the reconstruction is based on a reference object approach in which genes, transcripts, and proteins are identified using their primary sequences. This enables their unambiguous identification and non-redundant integration. The obtained total number of different molecular species and their connecting interactions is approximately 67,000. In order to demonstrate the capacity of RefRec for functional predictions, it was used for simulating the gene knockout damage propagation in the molecular interaction network in approximately 590,000 experimentally validated mutant strains. Based on the simulation results, a statistical classifier was subsequently able to correctly predict the viability of most of the strains. The results also showed that the usage of different types of molecular species in the reconstruction is important for accurate phenotype prediction. In general, the findings demonstrate the benefits of global reconstructions of molecular interaction networks. With all the molecular species and their physical interactions explicitly modeled, our reconstruction is able to serve as a valuable resource in additional analyses involving objects from multiple molecular -omes. For that purpose, RefRec is freely available in the Systems Biology Markup Language format.
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Bright field microscopy as an alternative to whole cell fluorescence in automated analysis of macrophage images.
PLoS ONE
PUBLISHED: 08-28-2009
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Fluorescence microscopy is the standard tool for detection and analysis of cellular phenomena. This technique, however, has a number of drawbacks such as the limited number of available fluorescent channels in microscopes, overlapping excitation and emission spectra of the stains, and phototoxicity.
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Bioactive acellular implant induces angiogenesis and adipogenesis and sustained soft tissue restoration in vivo.
Tissue Eng Part A
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Soft tissue defects resulting from trauma, tumor resection, or congenital causes provide a challenging problem to reconstructive surgery and tissue engineering. Current therapeutic procedures lack the ability to induce rapid formation of neovascularization. Therefore, to date, no adequate application for the reconstruction of soft tissue defects is available. We have previously shown that bioactive factors extracted from adipose tissue (adipose tissue extract [ATE]) induce both adipogenesis and angiogenesis in vitro. These bioactive factors were incorporated into hyaluronan (HA) hydrogel, and the ATE-HA implant-induced angiogenesis and adipogenesis were studied. The developed implant was shown to gradually release the bioactive factors, and the presence of the implant in human adipose stem cell culture was able to induce adipogenic differentiation as evaluated by Oil-red-O staining. In animal experiments, the implants were placed under dorsal subcutis of rodents. Either rat- (rATE, allograft) or human- (hATE, xenograft) derived ATE was incorporated into implants. Local inflammation reactions, angiogenesis, and adipogenesis were followed from 1 week to 40 weeks. Angiogenesis was assessed by microvessel density analysis; adipogenesis was assessed by automated image analysis, and immunological effects by immunostaining and counting inflammatory cells. The key requirements for soft tissue replacement--host compatibility, bioactivity, and sustainability--were all achieved with the novel ATE-HA implant. This acellular implant induced microvessel induction early after implantation and adipose tissue deposition from 12 weeks onward as well as subcutaneous tissue volume increase. The ATE-HA implant was replaced by mature adipose tissue with capillaries, nerve bundles, and healthy connective tissue without local inflammation or capsule formation. The large fat pads remained in tissue until the end of the follow-up time, for 9 months. No adverse effects were detected at the site of implantation, and according to irritating ranking, the ATE-implant was considered to have excellent biocompatibility. The results demonstrate that an acellular HA hydrogel implant induces significant increase in adipogenesis and angiogenesis in vivo compared to the plain HA implant, and ATE has excellent potential for use in tissue engineering for sustained reconstruction of soft tissue defects.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.