scholarly journals PGFinder, a novel analysis pipeline for the consistent, reproducible, and high-resolution structural analysis of bacterial peptidoglycans

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Ankur V Patel ◽  
Robert D Turner ◽  
Aline Rifflet ◽  
Adelina E Acosta-Martin ◽  
Andrew Nichols ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Structural Features ◽  
Significant Advance ◽  
Analysis Pipeline ◽  
Unusual Amino Acids ◽  
Manual Analysis ◽  
Analysis Workflow ◽  
Reproducible Analysis ◽  
Automated Tools ◽  
Cell Envelopes

Many software solutions are available for proteomics and glycomics studies, but none are ideal for the structural analysis of peptidoglycan (PG), the essential and major component of bacterial cell envelopes. It icomprises glycan chains and peptide stems, both containing unusual amino acids and sugars. This has forced the field to rely on manual analysis approaches, which are time-consuming, labour-intensive, and prone to error. The lack of automated tools has hampered the ability to perform high-throughput analyses and prevented the adoption of a standard methodology. Here, we describe a novel tool called PGFinder for the analysis of PG structure and demonstrate that it represents a powerful tool to quantify PG fragments and discover novel structural features. Our analysis workflow, which relies on open-access tools, is a breakthrough towards a consistent and reproducible analysis of bacterial PGs. It represents a significant advance towards peptidoglycomics as a full-fledged discipline.

scholarly journals PGfinder, a novel analysis pipeline for the consistent, reproducible and high- resolution structural analysis of bacterial peptidoglycans

2021 ◽  
Author(s):  
Ankur V Patel ◽  
Robert D Turner ◽  
Aline Rifflet ◽  
Adelina E Acosta-Martin ◽  
Andrew Nichols ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Structural Features ◽  
Significant Advance ◽  
Analysis Pipeline ◽  
Manual Analysis ◽  
Peptidoglycan Structure ◽  
Analysis Workflow ◽  
Reproducible Analysis ◽  
Automated Tools ◽  
Cell Envelopes

Many software solutions are available for proteomics and glycomics studies, but none are ideal for the structural analysis of peptidoglycan, the essential and major component of bacterial cell envelopes. It is comprised of glycan chains and peptide stems, both containing unusual amino acids and sugars. This has forced the field to rely on manual analysis approaches, which are time-consuming, labour-intensive, and prone to error. The lack of automated tools has hampered the ability to perform high-throughput analyses and prevented the adoption of a standard methodology. Here, we describe a novel tool called PGfinder for the analysis of peptidoglycan structure and demonstrate that it represents a powerful tool to quantify PG fragments and discover novel structural features. Our analysis workflow, which relies on open-access tools, is a breakthrough towards a consistent and reproducible analysis of bacterial peptidoglycans. It represents a significant advance towards peptidoglycomics as a full-fledged discipline.

Geology, Structural Analysis, and Paragenesis of the Arrow Uranium Deposit, Western Athabasca Basin, Saskatchewan, Canada: Implications for the Development of the Patterson Lake Corridor

2020 ◽  
Author(s):  
Sean Hillacre ◽  
Kevin Ansdell ◽  
Brian McEwan
Keyword(s):  
Structural Analysis ◽  
Uranium Deposit ◽  
Regional Scale ◽  
Structural Features ◽  
White Mica ◽  
Uranium Mineralization ◽  
Fault System ◽  
Thin Sections ◽  
Athabasca Basin ◽  
Quartz Veins

Abstract Recent significant discoveries of uranium mineralization in the southwestern Athabasca basin, northern Saskatchewan, Canada, have been associated with a series of geophysical conductors along a NE- to SW-trending structural zone, termed the Patterson Lake corridor. The Arrow deposit (indicated mineral resource: 256.6 Mlb U3O8; grade 4.03% U3O8) is along this trend, hosted exclusively in basement orthogneisses of the Taltson domain, and is the largest undeveloped uranium deposit in the basin. This study is the first detailed analysis of a deposit along this corridor and examines the relationships between the ductile framework and brittle reactivation of structures, mineral paragenesis, and uranium mineralization. Paragenetic information from hundreds of drill core samples and thin sections was integrated with structural analysis utilizing over 18,000 measurements of various structural features. The structural system at Arrow is interpreted as a partitioned, strike-slip–dominated, brittle-ductile fault system of complex Riedel-style geometry. The system developed along subvertical, NE- to SW-trending dextral high-strain zones formed syn- to post-D3 deformation, which were the focus of extensive premineralization metasomatism (quartz flooding, sericitization, chloritization), within the limb domain of a regional-scale fold structure. These zones evolved through post-Athabasca dextral and sinistral reactivation events, creating brittle fault linkages and dilation zones, allowing for hydrothermal fluid migration and resulting uraninite precipitation and associated alteration (white mica, chlorite, kaolinite, hematite, quartz veins). This study of the structural context of Arrow is important as it emphasizes that protracted reactivation of deep-seated structures and their subsidiaries was a fundamental control on uranium mineralization in the southwestern Athabasca basin.

Studies of the aggregation of an amyloidogenic α-synuclein peptide fragment

2005 ◽  
Vol 33 (5) ◽  
pp. 1113-1115 ◽  
Author(s):  
J. Madine ◽  
A.J. Doig ◽  
A. Kitmitto ◽  
D.A. Middleton
Keyword(s):  
Structural Analysis ◽  
Characteristic Feature ◽  
Neurodegenerative Disorders ◽  
Lewy Bodies ◽  
Structural Features ◽  
Full Length ◽  
Peptide Fragment ◽  
Structural Investigations ◽  
Detailed Structural Analysis ◽  
Β Sheet

The deposition of α-syn (α-synuclein) fibrils in Lewy bodies is a characteristic feature of individuals with neurodegenerative disorders. A peptide comprising the central residues 71–82 of α-syn [α-syn(71–82)] is capable of forming β-sheet-rich, amyloid-like fibrils with similar morphologies to fibrils of the full-length protein, providing a useful model of pathogenic α-syn fibrils that is suitable for detailed structural analysis. We have studied the morphology and gross structural features of α-syn(71–82) fibrils formed under different conditions in order to obtain reliable conditions for producing fibrils for further structural investigations. The results indicate that the rate of aggregation and the morphology of the fibrils formed are sensitive to pH and temperature.

scholarly journals Understanding Structural Features of Microbial Lipases–-An Overview

2008 ◽  
Vol 3 ◽  
pp. ACI.S551 ◽  
Author(s):  
John Geraldine Sandana Mala ◽  
Satoru Takeuchi
Keyword(s):  
Structural Analysis ◽  
Candida Rugosa ◽  
Structural Data ◽  
Data Bank ◽  
Candida Rugosa Lipase ◽  
Structural Features ◽  
X Ray Crystallography ◽  
Versatile Tool ◽  
Microbial Lipases

The structural elucidations of microbial lipases have been of prime interest since the 1980s. Knowledge of structural features plays an important role in designing and engineering lipases for specific purposes. Significant structural data have been presented for few microbial lipases, while, there is still a structure-deficit, that is, most lipase structures are yet to be resolved. A search for ‘lipase structure’ in the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) returns only 93 hits (as of September 2007) and, the NCBI database ( http://www.ncbi.nlm.nih.gov ) reports 89 lipase structures as compared to 14719 core nucleotide records. It is therefore worthwhile to consider investigations on the structural analysis of microbial lipases. This review is intended to provide a collection of resources on the instrumental, chemical and bioinformatics approaches for structure analyses. X-ray crystallography is a versatile tool for the structural biochemists and is been exploited till today. The chemical methods of recent interests include molecular modeling and combinatorial designs. Bioinformatics has surged striking interests in protein structural analysis with the advent of innumerable tools. Furthermore, a literature platform of the structural elucidations so far investigated has been presented with detailed descriptions as applicable to microbial lipases. A case study of Candida rugosa lipase (CRL) has also been discussed which highlights important structural features also common to most lipases. A general profile of lipase has been vividly described with an overview of lipase research reviewed in the past.

scholarly journals Reproducible Analysis Pipeline for Data Streams: Open-Source Software to Process Data Collected With Mobile Devices

2021 ◽  
Vol 3 ◽  
Author(s):  
Julio Vega ◽  
Meng Li ◽  
Kwesi Aguillera ◽  
Nikunj Goel ◽  
Echhit Joshi ◽  
...  
Keyword(s):  
Open Source ◽  
Data Streams ◽  
Data Science ◽  
Wearable Devices ◽  
Mobile Sensors ◽  
Sensor Data ◽  
Process Data ◽  
Analysis Pipeline ◽  
Ground Truth Data ◽  
Reproducible Analysis

Smartphone and wearable devices are widely used in behavioral and clinical research to collect longitudinal data that, along with ground truth data, are used to create models of human behavior. Mobile sensing researchers often program data processing and analysis code from scratch even though many research teams collect data from similar mobile sensors, platforms, and devices. This leads to significant inefficiency in not being able to replicate and build on others' work, inconsistency in quality of code and results, and lack of transparency when code is not shared alongside publications. We provide an overview of Reproducible Analysis Pipeline for Data Streams (RAPIDS), a reproducible pipeline to standardize the preprocessing, feature extraction, analysis, visualization, and reporting of data streams coming from mobile sensors. RAPIDS is formed by a group of R and Python scripts that are executed on top of reproducible virtual environments, orchestrated by a workflow management system, and organized following a consistent file structure for data science projects. We share open source, documented, extensible and tested code to preprocess, extract, and visualize behavioral features from data collected with any Android or iOS smartphone sensing app as well as Fitbit and Empatica wearable devices. RAPIDS allows researchers to process mobile sensor data in a rigorous and reproducible way. This saves time and effort during the data analysis phase of a project and facilitates sharing analysis workflows alongside publications.

scholarly journals Structural analysis of disordered dimer packings

Soft Matter ◽  
2021 ◽  
Vol 17 (39) ◽  
pp. 8877-8890
Author(s):  
Esma Kurban ◽  
Adrian Baule
Keyword(s):  
Structural Analysis ◽  
Structural Features ◽  
Density Peak

We identify structural features that accompany the formation of the density peak in jammed disordered packings of dimer shaped particles.

scholarly journals Structural Analysis in Transit System Using Network Theory Case of Guadalajara, Mexico

Urban Science ◽  
2021 ◽  
Vol 5 (4) ◽  
pp. 87
Author(s):  
Orlando Barraza ◽  
Miquel Estrada
Keyword(s):  
Structural Analysis ◽  
Network Theory ◽  
Planning Process ◽  
Structural Features ◽  
Transport Network ◽  
Structural Elements ◽  
Transit System ◽  
Transit Network ◽  
Network Properties ◽  
In Transit

Structural analysis in a transit network is a key aspect used to evaluate in a planning process. In this sense, the use of network science was applied in this work to generate a framework of the main structural features of a transport network. In this case, an alternative transport network in Guadalajara, Mexico was taken as an example. The network properties selected were grade of accessibility, spatial friction, and vulnerability. In the case of the grade of accessibility, this propriety makes reference to the efficiency of the travel time that the network gives due to its structural features. The spatial friction measures how direct in terms of distance the trips that the network provides are, and the vulnerability relates to the ease with which the network can comprise its performance by affectations to their nodes or links. In this sense, this work presents a detailed methodology and a set of open-source tools that can be used to measure these key structural elements for decision making.

scholarly journals ELEMENTAL, PHASE, AND STRUCTURAL ANALYSIS OF GALLSTONES WITH HIATAL HERNIAS IN PATIENTS OF KHARKIV REGION

2020 ◽  
pp. 52-59
Author(s):  
N.P. Dikiy ◽  
E.P. Bereznyak ◽  
V.V. Boyko ◽  
E.P. Medvedeva ◽  
K.Yu. Parhomenko ◽  
...  
Keyword(s):  
Calcium Carbonate ◽  
Structural Analysis ◽  
Hiatal Hernia ◽  
Phase Analysis ◽  
Mixed Type ◽  
Calcium Phosphates ◽  
Structural Features ◽  
Inorganic Compound ◽  
Gamma Activation ◽  
Ir Spectrometry

Gamma activation method on linac NSC KIPT, IR-spectrometry and crystal-optical investigations have been used to determinate the content of elements, the phase analysis and structural features of a different organic and inorganic compound in gallstones of patients with hiatal hernia in Kharkiv region. It is shown that it is possible to establish the presence in gallstones of such compounds as bilirubin and its salts, calcium phosphates, calcium carbonate, and different microelements. In the main, the patients of the Kharkiv region have gallstones of mixed type with a combination of cholesterol, calcium carbonate bilirubinate.

scholarly journals pywindow: Automated Structural Analysis of Molecular Pores

2018 ◽  
Author(s):  
Marcin Miklitz ◽  
Kim Jelfs
Keyword(s):  
Molecular Dynamics ◽  
Structural Analysis ◽  
Automated Analysis ◽  
Structural Features ◽  
Molecular Materials ◽  
Framework Materials ◽  
Molecular Cages ◽  
Metal Organic ◽  
Python Package

<p>Structural analysis of molecular pores can yield important information on their behaviour in solution and in the bulk. We developed pywindow, a python package that allows for the automated analysis of structural features of porous molecular materials, such as molecular cages. Our analysis includes the cavity diameter, number of windows, window diameters and average molecular diameter. Molecular dynamics trajectories of can also be analysed to explore the influence of flexibility. We present the methodology, validation and application of pywindow for the analysis of molecular pores, metal-organic polyhedra and some instances of framework materials. pywindow is freely available from github.com/JelfsMaterialsGroup/pywindow.</p>

Structural Analysis of the Laser Welding Co-Cr-Mo-(Ti) Alloys for Removable Partial Dentures

2015 ◽  
Vol 638 ◽  
pp. 91-97
Author(s):  
Alexandru Ghiban ◽  
Brandusa Ghiban ◽  
Cristina Maria Bortun ◽  
Mihai Buzatu
Keyword(s):  
Structural Analysis ◽  
Laser Welding ◽  
Structural Features ◽  
Butt Joint ◽  
Welding Parameter ◽  
Optimal Parameters ◽  
Ti Alloys ◽  
Comparison Results ◽  
Parameter Values ◽  
Cocrmo Alloys

Optimization of fractured or destroyed removable partial dentures realized from CoCrMo alloys are possible due to modern welding equipments. The aim of study was to offer the processing and welding optimal parameters for some long lasting prosthetic pieces made of a new alloy from the system CoCrMoTi. Laser welding equipments was a Mini Laser XXS (Orotig Italia) and the tested samples were welded in butt joint, without filler material. There are presented in comparison results concerning macro and micro structural analysis made on stereomicroscope and microscope type OLYMPUS. Finally a correlation between different welding parameter values and structural features was made for the new dental cobalt alloy.

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