scholarly journals A FIJI Macro for quantifying pattern in extracellular matrix

2019 ◽  
Author(s):  
Esther Wershof ◽  
Danielle Park ◽  
David J Barry ◽  
Robert P Jenkins ◽  
Antonio Rullan ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Quantitative Analysis ◽  
Comprehensive Description ◽  
Link Type ◽  
Wide Range ◽  
Automated Pipeline ◽  
Imagej Plugin

AbstractDiverse extracellular matrix patterns are observed in both normal and pathological tissue. However, most current tools for quantitative analysis focus on a single aspect of matrix patterning. Thus, an automated pipeline that simultaneously quantifies a broad range of metrics and enables a comprehensive description of varied matrix patterns is needed. To this end we have developed an ImageJ plugin called TWOMBLI, which stands for The Workflow Of Matrix BioLogy Informatics. TWOMBLI is designed to be quick, versatile and easy-to-use particularly for non-computational scientists. TWOMBLI can be downloaded from https://github.com/wershofe/TWOMBLI together with detailed documentation. Here we present an overview of the pipeline together with examples from a wide range of contexts where matrix patterns are generated.

scholarly journals A FIJI macro for quantifying pattern in extracellular matrix

2021 ◽  
Vol 4 (3) ◽  
pp. e202000880
Author(s):  
Esther Wershof ◽  
Danielle Park ◽  
David J Barry ◽  
Robert P Jenkins ◽  
Antonio Rullan ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Fractal Dimension ◽  
Quantitative Analysis ◽  
Comprehensive Description ◽  
End Points ◽  
Wide Range ◽  
Automated Pipeline ◽  
Cytoskeletal Networks ◽  
Alignment Length ◽  
Imagej Plugin

Diverse extracellular matrix patterns are observed in both normal and pathological tissue. However, most current tools for quantitative analysis focus on a single aspect of matrix patterning. Thus, an automated pipeline that simultaneously quantifies a broad range of metrics and enables a comprehensive description of varied matrix patterns is needed. To this end, we have developed an ImageJ plugin called TWOMBLI, which stands for The Workflow Of Matrix BioLogy Informatics. This pipeline includes metrics of matrix alignment, length, branching, end points, gaps, fractal dimension, curvature, and the distribution of fibre thickness. TWOMBLI is designed to be quick, versatile and easy-to-use particularly for non-computational scientists. TWOMBLI can be downloaded from https://github.com/wershofe/TWOMBLI together with detailed documentation and tutorial video. Although developed with the extracellular matrix in mind, TWOMBLI is versatile and can be applied to vascular and cytoskeletal networks. Here we present an overview of the pipeline together with examples from a wide range of contexts where matrix patterns are generated.

Precision and bias in quantitative EDS: ASTM results

1992 ◽  
Vol 50 (2) ◽  
pp. 1654-1655
Author(s):  
John J. Friel
Keyword(s):  
Stainless Steel ◽  
Quantitative Analysis ◽  
Mechanical Alloy ◽  
Dead Time ◽  
Test Program ◽  
Round Robin Test ◽  
Wide Range ◽  
American Society ◽  
Takeoff Angle ◽  
Standardless Analysis

Committee E-04 on Metallography of the American Society for Testing and Materials (ASTM) conducted an interlaboratory round robin test program on quantitative energy dispersive spectroscopy (EDS). The test program was designed to produce data on which to base a precision and bias statement for quantitative analysis by EDS. Nine laboratories were sent specimens of two well characterized materials, a type 308 stainless steel, and a complex mechanical alloy from Inco Alloys International, Inconel® MA 6000. The stainless steel was chosen as an example of a straightforward analysis with no special problems. The mechanical alloy was selected because elements were present in a wide range of concentrations; K, L, and M lines were involved; and Ta was severely overlapped with W. The test aimed to establish limits of precision that could be routinely achieved by capable laboratories operating under real world conditions. The participants were first allowed to use their own best procedures, but later were instructed to repeat the analysis using specified conditions: 20 kV accelerating voltage, 200s live time, ∼25% dead time and ∼40° takeoff angle. They were also asked to run a standardless analysis.

Phytochemical evaluation of leaf extracts of Naringi crenulata (roxb.) Nicolson

2016 ◽  
Vol 5 (11) ◽  
pp. 5110
Author(s):  
Sartaj Ahmad Allayie ◽  
Mushtaq Ahmed Parray* ◽  
Bilal Ahmad Bhat ◽  
S. Hemalatha
Keyword(s):  
Quantitative Analysis ◽  
Solvent System ◽  
Great Promise ◽  
Phytochemical Analysis ◽  
Bioactive Constituents ◽  
Leaf Extracts ◽  
Traditional Medicines ◽  
The People ◽  
Wide Range ◽  
Rf Values

The use of traditional medicines holds a great promise as an easily available source as effective medicinal agents to cure a wide range of ailments among the people particularly in tropical developing countries like India. The present study investigates the qualitative and quantitative analysis of the major bioactive constituents of N. crenulata leaf extracts. The extractive values of aqueous, acetone and chloroform extracts were found to be 11.34, 4.24 and 6.06 respectively. Qualitative phytochemical analysis of these three solvent extracts confirm the presence of Alkaloids, Saponins, Flavonoids and Phenolic compounds in all the three extracts; however, these phytochemicals were more significant in aqueous extract. Quantitative analysis was carried out using TLC method by different solvent system. Amongst various solvent systems, Butanol: acetic acid: water (9: 0.9: 0.1 v/v/v) shows maximum resolution and number of spots produced at long UV (365 nm) and under iodine vapours. The TLC chromatograms constituted different coloured phytochemical compounds with different Rf values. It can be conveniently used to evaluate the quality of different area samples. This indicates that the leaves can be useful for treating different diseases because the therapeutic activity of a plant is due to the presence of particular class of compounds and thus can serve as potential sources of useful drugs in future.

scholarly journals RiboA: a web application to identify ribosome A-site locations in ribosome profiling data

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Danying Shao ◽  
Nabeel Ahmed ◽  
Nishant Soni ◽  
Edward P. O’Brien
Keyword(s):  
Integer Programming ◽  
Web Application ◽  
Stop Codon ◽  
Ribosome Profiling ◽  
Programming Method ◽  
Analysis Tool ◽  
Site Location ◽  
Link Type ◽  
Wide Range ◽  
A Site

Abstract Background Translation is a fundamental process in gene expression. Ribosome profiling is a method that enables the study of transcriptome-wide translation. A fundamental, technical challenge in analyzing Ribo-Seq data is identifying the A-site location on ribosome-protected mRNA fragments. Identification of the A-site is essential as it is at this location on the ribosome where a codon is translated into an amino acid. Incorrect assignment of a read to the A-site can lead to lower signal-to-noise ratio and loss of correlations necessary to understand the molecular factors influencing translation. Therefore, an easy-to-use and accurate analysis tool is needed to accurately identify the A-site locations. Results We present RiboA, a web application that identifies the most accurate A-site location on a ribosome-protected mRNA fragment and generates the A-site read density profiles. It uses an Integer Programming method that reflects the biological fact that the A-site of actively translating ribosomes is generally located between the second codon and stop codon of a transcript, and utilizes a wide range of mRNA fragment sizes in and around the coding sequence (CDS). The web application is containerized with Docker, and it can be easily ported across platforms. Conclusions The Integer Programming method that RiboA utilizes is the most accurate in identifying the A-site on Ribo-Seq mRNA fragments compared to other methods. RiboA makes it easier for the community to use this method via a user-friendly and portable web application. In addition, RiboA supports reproducible analyses by tracking all the input datasets and parameters, and it provides enhanced visualization to facilitate scientific exploration. RiboA is available as a web service at https://a-site.vmhost.psu.edu/. The code is publicly available at https://github.com/obrien-lab/aip_web_docker under the MIT license.

scholarly journals The proteome: structure, function and evolution

2006 ◽  
Vol 361 (1467) ◽  
pp. 441-451 ◽  
Author(s):  
Keiran Fleming ◽  
Lawrence A Kelley ◽  
Suhail A Islam ◽  
Robert M MacCallum ◽  
Arne Muller ◽  
...  
Keyword(s):  
Protein Function ◽  
Sequence Similarity ◽  
Structural Annotation ◽  
New Approach ◽  
Link Type ◽  
University College London ◽  
Automated Pipeline ◽  
3D Genomics ◽  
And Function ◽  
Structural Homologue

This paper reports two studies to model the inter-relationships between protein sequence, structure and function. First, an automated pipeline to provide a structural annotation of proteomes in the major genomes is described. The results are stored in a database at Imperial College, London (3D-GENOMICS) that can be accessed at www.sbg.bio.ic.ac.uk . Analysis of the assignments to structural superfamilies provides evolutionary insights. 3D-GENOMICS is being integrated with related proteome annotation data at University College London and the European Bioinformatics Institute in a project known as e-protein ( http://www.e-protein.org/ ). The second topic is motivated by the developments in structural genomics projects in which the structure of a protein is determined prior to knowledge of its function. We have developed a new approach PHUNCTIONER that uses the gene ontology (GO) classification to supervise the extraction of the sequence signal responsible for protein function from a structure-based sequence alignment. Using GO we can obtain profiles for a range of specificities described in the ontology. In the region of low sequence similarity (around 15%), our method is more accurate than assignment from the closest structural homologue. The method is also able to identify the specific residues associated with the function of the protein family.

scholarly journals A method to construct the dynamic landscape of a bio-membrane with experiment and simulation

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Albert A. Smith ◽  
Alexander Vogel ◽  
Oskar Engberg ◽  
Peter W. Hildebrand ◽  
Daniel Huster
Keyword(s):  
Molecular Dynamics ◽  
Nmr Relaxation ◽  
Dynamics Simulation ◽  
Comprehensive Description ◽  
Correlation Times ◽  
Wide Range ◽  
Dynamic Landscape ◽  
C Nmr ◽  
Analysis Of Motion

AbstractBiomolecular function is based on a complex hierarchy of molecular motions. While biophysical methods can reveal details of specific motions, a concept for the comprehensive description of molecular dynamics over a wide range of correlation times has been unattainable. Here, we report an approach to construct the dynamic landscape of biomolecules, which describes the aggregate influence of multiple motions acting on various timescales and on multiple positions in the molecule. To this end, we use 13C NMR relaxation and molecular dynamics simulation data for the characterization of fully hydrated palmitoyl-oleoyl-phosphatidylcholine bilayers. We combine dynamics detector methodology with a new frame analysis of motion that yields site-specific amplitudes of motion, separated both by type and timescale of motion. In this study, we show that this separation allows the detailed description of the dynamic landscape, which yields vast differences in motional amplitudes and correlation times depending on molecular position.

scholarly journals Open Online Courses in Public Health: experience from Peoples-uni

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 170
Author(s):  
Richard F. Heller ◽  
Robert Zurynski ◽  
Alan Barrett ◽  
Omo Oaiya ◽  
Rajan Madhok
Keyword(s):  
Public Health ◽  
Online Courses ◽  
Open Educational Resources ◽  
Global Public Health ◽  
Academic Credit ◽  
Link Type ◽  
Wide Range ◽  
Separate Site ◽  
Online Learning Resources ◽  
Professional Audience

Open Online Courses (OOCs) are offered by Peoples-uni at http://ooc.peoples-uni.org to complement the courses run on a separate site for academic credit at http://courses.peoples-uni.org. They provide a wide range of online learning resources beyond those usually found in credit bearing Public Health courses. They are self-paced, and students can enrol themselves at any time and utilise Open Educational Resources free of copyright restrictions.  In the two years that courses have been running, 1174 students from 100 countries have registered and among the 1597 enrolments in 14 courses, 15% gained a certificate of completion. Easily accessible and appealing to a wide geographical and professional audience, OOCs have the potential to play a part in establishing global Public Health capacity building programmes.

scholarly journals Extragalactic Supergiants

2016 ◽  
Vol 12 (S329) ◽  
pp. 297-304
Author(s):  
Miguel A. Urbaneja ◽  
Rolf P. Kudritzki
Keyword(s):  
Quantitative Analysis ◽  
Chemical Composition ◽  
Optical Spectra ◽  
Host Galaxies ◽  
High Quality ◽  
Distant Galaxies ◽  
Wide Range

AbstractBlue supergiant stars of B and A spectral types are amongst the visually brightest non-transient astronomical objects. Their intrinsic brightness makes it possible to obtain high quality optical spectra of these objects in distant galaxies, enabling the study not only of these stars in different environments, but also to use them as tools to probe their host galaxies. Quantitative analysis of their optical spectra provide tight constraints on their evolution in a wide range of metallicities, as well as on the present-day chemical composition, extinction laws and distances to their host galaxies. We review in this contribution recent results in this field.

A New Way To Detect Noncovalently Bonded Complexes of Biomolecules from Liquid Micro-Droplets by Laser Mass Spectrometry

2006 ◽  
Vol 59 (2) ◽  
pp. 109 ◽  
Author(s):  
Nina Morgner ◽  
Hans-Dieter Barth ◽  
Bernhard Brutschy
Keyword(s):  
Mass Spectrometry ◽  
Quantitative Analysis ◽  
Liquid Phase ◽  
Laser Pulses ◽  
Laser Mass Spectrometry ◽  
Native Solution ◽  
On Demand ◽  
Ir Laser ◽  
Intensity Threshold ◽  
Wide Range

A new version of laser mass-spectrometry is presented, which allows the quantitative analysis of specific biocomplexes in native solution. On-demand micro droplets, injected into vacuum, are irradiated by mid IR-laser pulses. Above a certain intensity threshold they explode due to the transmitted energy, setting free a fraction of the charged biomolecules which are then mass-analyzed. Amounts of analyte in the attomolar range may be detected with the ion intensity being linear over a wide range of molarity. Evidence is given that this method is soft, tolerant against various buffers, reflects properties of the liquid phase, and suitable for studying noncovalently bonded specific complexes. This is highlighted by results from antibiotics specifically binding into the minor groove of duplex DNA.

Usitatibacter rugosus gen. nov., sp. nov. and Usitatibacter palustris sp. nov., novel members of Usitatibacteraceae fam. nov. within the order Nitrosomonadales isolated from soil

2021 ◽  
Author(s):  
Selma Vieira ◽  
Katharina J. Huber ◽  
Meina Neumann-Schaal ◽  
Alicia Geppert ◽  
Manja Luckner ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Wide Range

Members of the metabolically diverse order Nitrosomonadales inhabit a wide range of environments. Two strains affiliated with this order were isolated from soils in Germany and characterized by a polyphasic approach. Cells of strains 0125_3T and Swamp67T are Gram-negative rods, non-motile, non-spore-forming, non-capsulated and divide by binary fission. They tested catalase-negative, but positive for cytochrome c-oxidase. Both strains form small white colonies on agar plates and grow aerobically and chemoorganotrophically on SSE/HD 1 : 10 medium, preferably utilizing organic acids and proteinaceous substrates. Strains 0125_3T and Swamp67T are mesophilic and grow optimally without NaCl addition at slightly alkaline conditions. Major fatty acids are C16 : 1  ω7c, C16 : 0 and C14 : 0. The major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyglycerol. The predominant respiratory quinone is Q-8. The G+C content for 0125_3T and Swamp67T was 67 and 66.1 %, respectively. The 16S rRNA gene analysis indicated that the closest relatives (<91 % sequence similarity) of strain 0125_3T were Nitrosospira multiformis ATCC 25196T, Methyloversatilis universalis FAM5T and Denitratisoma oestradiolicum AcBE2-1T, while Nitrosospira multiformis ATCC 25196T, Nitrosospira tenuis Nv1T and Nitrosospira lacus APG3T were closest to strain Swamp67T. The two novel strains shared 97.4 % 16S rRNA gene sequence similarity with one another and show low average nucleotide identity of their genomes (83.8 %). Based on the phenotypic, chemotaxonomic, genomic and phylogenetic analysis, we propose the two novel species Usitatibacter rugosus sp. nov (type strain 0125_3T=DSM 104443T=LMG 29998T=CECT 9241T) and Usitatibacter palustris sp. nov. (type strain Swamp67T=DSM 104440T=LMG 29997T=CECT 9242T) of the novel genus Usitatibacter gen. nov., within the novel family Usitatibacteraceae fam. nov.

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