2018
Pulse sensors have become popular due to their use in health-monitors like the Fitbit. The sensors used are cheap, simple and pretty reliable at getting a reasonable indication of heart rate in daily use. They work by sensing the change in light absorption or reflection by blood as it pulses …
Pulse sensors are a common feature of fitness monitors, used to track your activity and cardiac fitness over time. These external monitors use the reflection and absorption of bright green/infra-red light to detect the pulse wave travelling down the artery — a technique called photoplethysmography (PPG). This same techique is …
2016
Because of the low stoichiometry of protein phosphorylation, targeted enrichment prior to LC–MS/MS analysis is still essential. The trend in phosphoproteome analysis is shifting toward an increasing number of biological replicates per experiment, ideally starting from very low sample amounts, placing new demands on enrichment protocols to make …
Epstein-Barr virus, a B-lymphotropic herpesvirus, is the cause of infectious mononucleosis, has strong aetiologic links with several malignancies and has been implicated in certain autoimmune diseases. Efforts to develop a prophylactic vaccine to prevent or reduce EBV-associated disease have, to date, focused on the induction of neutralising antibody responses. However …
Current biomarkers of renal disease in systemic vasculitis lack predictive value and are insensitive to early damage. To identify novel biomarkers of renal vasculitis flare, we analysed the longitudinal urinary metabolomic profile of a rat model of anti-neutrophil cytoplasmic antibody (ANCA) vasculitis. Wistar-Kyoto (WKY) rats were immunised with human myeloperoxidase …
Common bean (Phaseolus vulgaris L.) is one of the most consumed staple foods worldwide. Little is known about the molecular mechanisms controlling seed development. This study aims to comprehensively describe proteome dynamics during seed development of common bean. A high-throughput gel-free proteomics approach (LC–MS/MS) was conducted on seeds …
2015
1D 1H NMR is a commonly applied to metabolomic studies, being well suited to untargeted analysis of complex biofluids. It has been successfully applied to the classification and diagnosis of a number of diseases including [ref].
There are a number of important steps that must be applied prior 1D …
Metabolomics studies have been reported for virtually all of the main rheumatologic diseases, although notably none yet for SSc. Our own group has demonstrated the use of urinary metabolic fingerprint analysis to predict responses to anti-TNF, and we have suggested that metabolites resulting from TNF-driven cachexia are among the useful …
2014
Background Metabolomics is a systems approach to the analysis of cellular processes through small-molecule metabolite profiling. Standardisation of sample handling and acquisition approaches has contributed to reproducibility. However, the development of robust methods for the analysis of metabolomic data is a work-in-progress. The tools that do exist are often not …
This notebook demonstrates automatic phase correction algorithms implemented for nmrglue. Two standard algorithms are implemented:
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ACME algorithm by Chen Li et al. Journal of Magnetic Resonance 158 (2002) 164-168
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Naive peak minima minimisation
The outputs for the two algorithms are shown below. Automatic phase correction can be used through the …
This notebook uses a subset of the available processing features in NMRLab (+Metabolab) to process 1D NMR spectra. The output is saved as a CSV file that can be imported into pandas, PLS_Toolbox or any other package for subsequent analysis.
To use this workbook you will need an installation of …
MetaboHunter is a web service for automated assignment of 1D raw, bucketed or peak picked NMR spectra. Identification is performed in comparison to two publicly available databases (HMDB, MMCD) of NMR standard measurements. More information about the algorithm is available in the published paper:
Tulpan, D., Leger, S., Belliveau, L …
This notebook is a quick demo of a BioCyc Web API I've released for Python. While incomplete the API offers access to most basic attributes for metabolites, proteins, reactions, pathways and organisms in the database. The Python interface comes with an disk-based caching mechanism under ~/.biocyc that greatly reduces the …
Analyzing a dot blot in ImageJ by background subtraction and measuring the integrated density of each dot. This dot blot image is available in the File/Open Samples menu in ImageJ 1.33s or later.
Method
- This method usually requires background correction of the image, which can be done using …
Determining the level of cellular fluorescence from fluorescence microscopy images in ImageJ
- Open ImageJ. Note: ImageJ may be freely downloaded from here
- Select the cell of interest using any of the drawing/selection tools (i.e. rectangle, circle, polygon or freeform)
- From the Analyze menu select “set measurements”. Make sure …
This short demo shows analysis of a publically available GEO dataset using Pathomx, with a workflow build using the new visual editor (available in the next release).
You can download the example dataset from here.
Pathomx is an open-source workflow-based scientific analysis application. Source code is available here with packaged …
2013
Short demo of an experimental analysis of metabolomic (NMR) data using Pathomx. Metabolomic test dataset produced from THP-1 cells grown under normal and hypoxic conditions. Spectra (2D 1H JRES) have been pre-processed and quantified using the BML-NMR service.
The video shows an example analysis from processed data through to metabolic …
Cytoscape 3.0.2 was released on 1st August, a bugfix release for the 3.x series. However, there is a compatibility issue with the latest Java update from Apple resulting in Cytoscape hanging on startup. I'd followed advice found elsewhere to update to the latest Java version with no …
Background: Macrophages are abundant in the synovium of RA and are the major source of many inflammatory cytokines, including TNFα. Disease severity correlates strongly with both synovial macrophage abundance and activation status but inversely with oxygen levels. Given the importance of oxygen to cell metabolism, differentiation and function, we hypothesized …
OBJECTIVE: Anti-tumor necrosis factor (anti-TNF) therapies are highly effective in rheumatoid arthritis (RA) and psoriatic arthritis (PsA), but a significant number of patients exhibit only a partial or no therapeutic response. Inflammation alters local and systemic metabolism, and TNF plays a role in this. We undertook this study to determine …
Inflammation is an important component of normal responses to infection and injury. However, chronic activation of the immune system, due to aberrant responses to normal stimuli, can lead to the establishment of a persistent inflammatory state. Such inflammatory conditions are often debilitating, and are associated with a number of important …
2012
Metabolomics in the Analysis of Inflammatory Diseases is chapter 11 in the open-access book Metabolomics edited by Ute Roessner.
Metabolomics is a rapidly emerging field in life sciences, which aims to identify and quantify metabolites in a biological system. Analytical chemistry is combined with sophisticated informatics and statistics tools to …
2011
Background: Macrophages have a wide range of immunological and non-immunological functions, ranging from clearance of apoptotic cells, tissue remodelling, and release of pro and anti-inflammatory mediators at sites of tissue damage or infection. Subsets of phenoty- pically distinct macrophages may be uniquely adapted to perform these roles. Phenotypically and functionally …
Macrophages have a wide range of immunological and non-immunological functions in the host, ranging from clearance of apoptotic cells, tissue remodelling, and release of pro and anti-inflammatory mediators at site of tissue damage or infection. Within these wide-ranging functions however, subsets of macrophages show unique phenotypic adaptations to their role …
Epstein-Barr virus is a γ-herpesvirus endemic (>90%) in the human population and implicated in a variety of lymphomas and solid tumours including Hodgkin’s lymphoma, Burkitt’s lymphoma and post-transplant lymphoproliferative disorder. Despite the prevalence of EBV, little is known about the mechanisms of early infection, including the role of …
Established 1980