scholarly journals ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

2019 ◽  
Author(s):  
Silas Kieser ◽  
Joseph Brown ◽  
Evgeny M. Zdobnov ◽  
Mirko Trajkovski ◽  
Lee Ann McCue
Keyword(s):  
Data Processing ◽  
Sequence Data ◽  
Microbial Populations ◽  
Valuable Insight ◽  
Genome Databases ◽  
Abundance Estimates ◽  
And Function ◽  
User Friendly ◽  
Insight Into ◽  
Metagenome Sequence

AbstractBackgroundMetagenomics and metatranscriptomics studies provide valuable insight into the composition and function of microbial populations from diverse environments, however the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers.ResultsHere we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome and metatranscriptome data. Genome-centric resolution and abundance estimates are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license.ConclusionATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome and metatranscriptome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.

Binding of Tetrahymena dynein to axonemes of Marsilea vestita lacking the outer dynein arm

1985 ◽  
Vol 73 (1) ◽  
pp. 299-310
Author(s):  
J.S. Hyams
Keyword(s):  
Electron Microscopy ◽  
Polyacrylamide Gel Electrophoresis ◽  
Valuable Insight ◽  
Marsilea Vestita ◽  
Thin Section Electron Microscopy ◽  
Section Electron ◽  
And Function ◽  
Relationship Of ◽  
The Relationship ◽  
Insight Into

Axonemes from the heterosporous water fern Marsilea vestita were fixed in the presence of tannic acid and examined by thin-section electron microscopy. Transverse sections revealed the normal 9+2 configuration except for the absence of the outer of the two dynein arms. Both arms were normally preserved in parallel preparations of Chlamydomonas axonemes. Isolated dynein from the ciliated protozoon Tetrahymena bound to Marsilea axonemes at the site normally occupied by the outer arm. Dynein binding was partially reversed by ATP as judged by both electron microscopy and polyacrylamide gel electrophoresis. This system should provide a valuable insight into the biochemistry and function of the inner dynein arm and the relationship of the two arms to motility in more conventionally equipped axonemes.

scholarly journals Chromosomics: Bridging the Gap between Genomes and Chromosomes

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 627 ◽  
Author(s):  
Janine E. Deakin ◽  
Sally Potter ◽  
Rachel O’Neill ◽  
Aurora Ruiz-Herrera ◽  
Marcelo B. Cioffi ◽  
...  
Keyword(s):  
Cell Biology ◽  
Sequence Data ◽  
Full Potential ◽  
Genome Plasticity ◽  
Sequencing Technology ◽  
Research Areas ◽  
And Function ◽  
New Generation ◽  
Insight Into

The recent advances in DNA sequencing technology are enabling a rapid increase in the number of genomes being sequenced. However, many fundamental questions in genome biology remain unanswered, because sequence data alone is unable to provide insight into how the genome is organised into chromosomes, the position and interaction of those chromosomes in the cell, and how chromosomes and their interactions with each other change in response to environmental stimuli or over time. The intimate relationship between DNA sequence and chromosome structure and function highlights the need to integrate genomic and cytogenetic data to more comprehensively understand the role genome architecture plays in genome plasticity. We propose adoption of the term ‘chromosomics’ as an approach encompassing genome sequencing, cytogenetics and cell biology, and present examples of where chromosomics has already led to novel discoveries, such as the sex-determining gene in eutherian mammals. More importantly, we look to the future and the questions that could be answered as we enter into the chromosomics revolution, such as the role of chromosome rearrangements in speciation and the role more rapidly evolving regions of the genome, like centromeres, play in genome plasticity. However, for chromosomics to reach its full potential, we need to address several challenges, particularly the training of a new generation of cytogeneticists, and the commitment to a closer union among the research areas of genomics, cytogenetics, cell biology and bioinformatics. Overcoming these challenges will lead to ground-breaking discoveries in understanding genome evolution and function.

scholarly journals Identification of the Protein Glycation Sites in Human Myoglobin as Rapidly Induced by d-Ribose

Molecules ◽  
2021 ◽  
Vol 26 (19) ◽  
pp. 5829
Author(s):  
Jing-Jing Liu ◽  
Yong You ◽  
Shu-Qin Gao ◽  
Shuai Tang ◽  
Lei Chen ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Performance ◽  
Protein Glycation ◽  
Valuable Insight ◽  
Liquid Chromatography Mass Spectrometry ◽  
Post Translational Modification ◽  
Lysine Residues ◽  
Human Myoglobin ◽  
And Function ◽  
Insight Into

Protein glycation is an important protein post-translational modification and is one of the main pathogenesis of diabetic angiopathy. Other than glycated hemoglobin, the protein glycation of other globins such as myoglobin (Mb) is less studied. The protein glycation of human Mb with ribose has not been reported, and the glycation sites in the Mb remain unknown. This article reports that d-ribose undergoes rapid protein glycation of human myoglobin (HMb) at lysine residues (K34, K87, K56, and K147) on the protein surface, as identified by ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) and electrospray ionization tandem mass spectrometry (ESI-MS/MS). Moreover, glycation by d-ribose at these sites slightly decreased the rate of the met heme (FeIII) in reaction with H2O2 to form a ferryl heme (FeIV=O). This study provides valuable insight into the protein glycation by d-ribose and provides a foundation for studying the structure and function of glycated heme proteins.

scholarly journals Cellular sensing of micron-scale curvature: a frontier in understanding the microenvironment

Open Biology ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 190155 ◽  
Author(s):  
Richard K. Assoian ◽  
Nathan D. Bade ◽  
Caroline V. Cameron ◽  
Kathleen J. Stebe
Keyword(s):  
Molecular Mechanisms ◽  
Radius Of Curvature ◽  
Valuable Insight ◽  
Glass Plastic ◽  
Cell Behaviour ◽  
Flat Surfaces ◽  
Biological Studies ◽  
And Function ◽  
Insight Into

The vast majority of cell biological studies examine function and molecular mechanisms using cells on flat surfaces: glass, plastic and more recently elastomeric polymers. While these studies have provided a wealth of valuable insight, they fail to consider that most biologically occurring surfaces are curved, with a radius of curvature roughly corresponding to the length scale of cells themselves. Here, we review recent studies showing that cells detect and respond to these curvature cues by adjusting and re-orienting their cell bodies, actin fibres and nuclei as well as by changing their transcriptional programme. Modelling substratum curvature has the potential to provide fundamental new insight into cell behaviour and function in vivo .

scholarly journals VOLPES: an interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences

2019 ◽  
Vol 47 (W1) ◽  
pp. W632-W635 ◽  
Author(s):  
Lukas Bartonek ◽  
Bojan Zagrovic
Keyword(s):  
Nucleic Acids ◽  
Physicochemical Properties ◽  
Sequence Data ◽  
Structural Disorder ◽  
Biological Sequence ◽  
Web Based ◽  
Starting Point ◽  
User Friendly ◽  
Insight Into ◽  
Sequence Position

Abstract The structure, dynamics and, ultimately, biological function of proteins and nucleic acids are determined by the physicochemical properties of their primary sequences. Such properties are frequently captured via one-dimensional profile plots depicting a given physicochemical variable as a function of sequence position. Hydrophobicity, charge or structural disorder in proteins or nucleobase-density in nucleic acids are routinely visualized in this manner to analyze sequences at a glance. Such visualizations, however, are typically created case-by-case in a purely static manner, employ fixed visualization parameters only and do not enable a quantitative comparison between different sequences. Here, we present VOLPES (volpes.univie.ac.at), a user-friendly web server and the corresponding JavaScript library that enable a fully interactive, multifunctional visualization, analysis and comparison of the physicochemical properties of protein and nucleic-acid sequences, allowing unprecedented insight into biological sequence data and creating a starting point for further in-depth exploration.

Structure and function of neural networks in the retina

1988 ◽  
Vol 46 ◽  
pp. 26-27
Author(s):  
Peter Sterling
Keyword(s):  
Ganglion Cells ◽  
Three Dimensional ◽  
Structure And Function ◽  
Synaptic Connections ◽  
Visual Axis ◽  
One Dimensional ◽  
Cat Retina ◽  
Ultrathin Sections ◽  
And Function ◽  
Insight Into

The synaptic connections in cat retina that link photoreceptors to ganglion cells have been analyzed quantitatively. Our approach has been to prepare serial, ultrathin sections and photograph en montage at low magnification (˜2000X) in the electron microscope. Six series, 100-300 sections long, have been prepared over the last decade. They derive from different cats but always from the same region of retina, about one degree from the center of the visual axis. The material has been analyzed by reconstructing adjacent neurons in each array and then identifying systematically the synaptic connections between arrays. Most reconstructions were done manually by tracing the outlines of processes in successive sections onto acetate sheets aligned on a cartoonist's jig. The tracings were then digitized, stacked by computer, and printed with the hidden lines removed. The results have provided rather than the usual one-dimensional account of pathways, a three-dimensional account of circuits. From this has emerged insight into the functional architecture.

Study of the resistor material of an automotive spark plug by use of the charge-up effect along with elemental mapping in an electron microprobe

1991 ◽  
Vol 49 ◽  
pp. 742-743
Author(s):  
D. R. Liu ◽  
S. S. Shinozaki ◽  
J. S. Park ◽  
B. N. Juterbock
Keyword(s):  
Electron Microprobe ◽  
Present Report ◽  
Coated Sample ◽  
Valuable Insight ◽  
Elemental Mapping ◽  
Spark Plug ◽  
Carbon Coated ◽  
Electron Image ◽  
Electron Imaging ◽  
Insight Into

The electric and thermal properties of the resistor material in an automotive spark plug should be stable during its service lifetime. Containing many elements and many phases, this material has a very complex microstructure. Elemental mapping with an electron microprobe can reveal the distribution of all relevant elements throughout the sample. In this work, it is demonstrated that the charge-up effect, which would distort an electron image and, therefore, is normally to be avoided in an electron imaging work, could be used to advantage to reveal conductive and resistive zones in a sample. Its combination with elemental mapping can provide valuable insight into the underlying conductivity mechanism of the resistor.This work was performed in a CAMECA SX-50 microprobe. The spark plug used in the present report was a commercial product taken from the shelf. It was sectioned to expose the cross section of the resistor. The resistor was known not to contain the precious metal Au as checked on the carbon coated sample. The sample was then stripped of carbon coating and re-coated with Au.

Update: Behavioral Management of Unilateral Vocal Fold Paralysis and Paresis

2019 ◽  
Vol 4 (3) ◽  
pp. 474-482
Author(s):  
Sarah L. Schneider
Keyword(s):  
Vocal Fold ◽  
Treatment Plan ◽  
Traumatic Injury ◽  
Voice Therapy ◽  
Valuable Insight ◽  
Behavioral Management ◽  
Use Patterns ◽  
Vocal Quality ◽  
And Function ◽  
Voice Use

PurposeVocal fold motion impairment (VFMI) can be the result of iatrogenic or traumatic injury or may be idiopathic in nature. It can result in glottic incompetence leading to changes in vocal quality and ease. Associated voice complaints may include breathiness, roughness, diplophonia, reduced vocal intensity, feeling out of breath with talking, and vocal fatigue with voice use. A comprehensive interprofessional voice evaluation includes auditory-perceptual voice evaluation, laryngeal examination including videostroboscopy, acoustic and aerodynamic voice measures. These components provide valuable insight into laryngeal structure and function and individual voice use patterns and, in conjunction with stimulability testing, help identify candidacy for voice therapy and choice of therapeutic techniques.ConclusionA comprehensive, interprofessional evaluation of patients with VFMI is necessary to assess the role of voice therapy and develop a treatment plan. Although there is no efficacy data to support specific voice therapy techniques for treating VFMI, considerations for various techniques are provided.

Quantum Mechanical Interpretation of the Ultra-Low Energy Methyl-Rotation Dynamics in Porous Metal-Organic Frameworks Probed by Low-Frequency Vibrational Spectroscopy and ab initio Simulations

2018 ◽  
Author(s):  
Qi Li ◽  
Adam J. Zaczek ◽  
Timothy M. Korter ◽  
J. Axel Zeitler ◽  
Michael T. Ruggiero
Keyword(s):  
Ab Initio ◽  
Metal Organic Frameworks ◽  
Low Frequency ◽  
Rotor Dynamics ◽  
Quantum Mechanical ◽  
Valuable Insight ◽  
Void Space ◽  
Ab Initio Simulations ◽  
Metal Organic ◽  
Insight Into

<div>Understanding the nature of the interatomic interactions present within the pores of metal-organic frameworks</div><div>is critical in order to design and utilize advanced materials</div><div>with desirable applications. In ZIF-8 and its cobalt analogue</div><div>ZIF-67, the imidazolate methyl-groups, which point directly</div><div>into the void space, have been shown to freely rotate - even</div><div>down to cryogenic temperatures. Using a combination of ex-</div><div>perimental terahertz time-domain spectroscopy, low-frequency</div><div>Raman spectroscopy, and state-of-the-art ab initio simulations,</div><div>the methyl-rotor dynamics in ZIF-8 and ZIF-67 are fully charac-</div><div>terized within the context of a quantum-mechanical hindered-</div><div>rotor model. The results lend insight into the fundamental</div><div>origins of the experimentally observed methyl-rotor dynamics,</div><div>and provide valuable insight into the nature of the weak inter-</div><div>actions present within this important class of materials.</div>

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