scholarly journals Comparative genomics reveals new functional insights in uncultured MAST species

2021 ◽  
Author(s):  
Aurelie Labarre ◽  
David López-Escardó ◽  
Francisco Latorre ◽  
Guy Leonard ◽  
François Bucchini ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Genomic Data ◽  
Proton Pumps ◽  
Functional Annotations ◽  
The Core ◽  
Unicellular Eukaryotes ◽  
Microbial Eukaryotes ◽  
Core Energy ◽  
Marine Surface ◽  
Environmental Sequences

AbstractHeterotrophic lineages of stramenopiles exhibit enormous diversity in morphology, lifestyle, and habitat. Among them, the marine stramenopiles (MASTs) represent numerous independent lineages that are only known from environmental sequences retrieved from marine samples. The core energy metabolism characterizing these unicellular eukaryotes is poorly understood. Here, we used single-cell genomics to retrieve, annotate, and compare the genomes of 15 MAST species, obtained by coassembling sequences from 140 individual cells sampled from the marine surface plankton. Functional annotations from their gene repertoires are compatible with all of them being phagocytotic. The unique presence of rhodopsin genes in MAST species, together with their widespread expression in oceanic waters, supports the idea that MASTs may be capable of using sunlight to thrive in the photic ocean. Additional subsets of genes used in phagocytosis, such as proton pumps for vacuole acidification and peptidases for prey digestion, did not reveal particular trends in MAST genomes as compared with nonphagocytotic stramenopiles, except a larger presence and diversity of V-PPase genes. Our analysis reflects the complexity of phagocytosis machinery in microbial eukaryotes, which contrasts with the well-defined set of genes for photosynthesis. These new genomic data provide the essential framework to study ecophysiology of uncultured species and to gain better understanding of the function of rhodopsins and related carotenoids in stramenopiles.

scholarly journals CoreCruncher: Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets

2020 ◽  
Author(s):  
Connor D Harris ◽  
Ellis L Torrance ◽  
Kasie Raymann ◽  
Louis-Marie Bobay
Keyword(s):  
Core Genome ◽  
Genomic Data ◽  
Data Sets ◽  
The Core ◽  
Genomic Analyses ◽  
Massive Accumulation ◽  
Genome Comparisons

Abstract The core genome represents the set of genes shared by all, or nearly all, strains of a given population or species of prokaryotes. Inferring the core genome is integral to many genomic analyses, however, most methods rely on the comparison of all the pairs of genomes; a step that is becoming increasingly difficult given the massive accumulation of genomic data. Here, we present CoreCruncher; a program that robustly and rapidly constructs core genomes across hundreds or thousands of genomes. CoreCruncher does not compute all pairwise genome comparisons and uses a heuristic based on the distributions of identity scores to classify sequences as orthologs or paralogs/xenologs. Although it is much faster than current methods, our results indicate that our approach is more conservative than other tools and less sensitive to the presence of paralogs and xenologs. CoreCruncher is freely available from: https://github.com/lbobay/CoreCruncher. CoreCruncher is written in Python 3.7 and can also run on Python 2.7 without modification. It requires the python library Numpy and either Usearch or Blast. Certain options require the programs muscle or mafft.

scholarly journals Role of the core energy in the vortex Nernst effect

2014 ◽  
Vol 90 (18) ◽  
Author(s):  
Gideon Wachtel ◽  
Dror Orgad
Keyword(s):  
Nernst Effect ◽  
The Core ◽  
Core Energy

scholarly journals GenomeHubs: Simple containerised setup of a custom Ensembl database and web server for any species

2017 ◽  
Author(s):  
Richard J Challis ◽  
Sujai Kumar ◽  
Lewis Stevens ◽  
Mark Blaxter
Keyword(s):  
Web Server ◽  
Genomic Data ◽  
Web Interface ◽  
Ensembl Database ◽  
Functional Annotations ◽  
Genome Data ◽  
Genome Browsers ◽  
Genome Projects

As the generation and use of genomic datasets is becoming increasingly common in all areas of biology, the need for resources to collate, analyse and present data from one or more genome projects is becoming more pressing. The Ensembl platform is a powerful tool to make genome data and cross-species analyses easily accessible through a web interface and a comprehensive API. Here we introduce GenomeHubs, which provide a containerised environment to facilitate the setup and hosting of custom Ensembl genome browsers. This simplifies mirroring of existing content and import of new genomic data into the Ensembl database schema.GenomeHubs also provide a set of analysis containers to decorate imported genomes with results of standard analyses and functional annotations and support export to flat files, including EMBL format for submission of assemblies and annotations to INSDC.Database URL: http://GenomeHubs.org

scholarly journals A single-cell genome perspective on studying intracellular associations in unicellular eukaryotes

2019 ◽  
Vol 374 (1786) ◽  
pp. 20190082 ◽  
Author(s):  
Tomáš Tyml ◽  
Shailesh V. Date ◽  
Tanja Woyke
Keyword(s):  
Single Cell ◽  
Evolutionary History ◽  
Unicellular Eukaryotes ◽  
Microbial Eukaryotes ◽  
Cell Genome ◽  
Cellular Dna ◽  
Diversity Of Life ◽  
Genome Information ◽  
The Relationship ◽  
Single Cell Genome

Single-cell genomics (SCG) methods provide a unique opportunity to analyse whole genome information at the resolution of an individual cell. While SCG has been extensively used to investigate bacterial and archaeal genomes, the technique has been rarely used to access the genetic makeup of uncultivated microbial eukaryotes. In this regard, the use of SCG can provide a wealth of information; not only do the methods allow exploration of the genome, they can also help elucidate the relationship between the cell and intracellular entities extant in nearly all eukaryotes. SCG enables the study of total eukaryotic cellular DNA, which in turn allows us to better understand the evolutionary history and diversity of life, and the physiological interactions that define complex organisms. This article is part of a discussion meeting issue ‘Single cell ecology’.

Electronic coupling between ligand and core energy states in dithiolate-monothiolate stabilized Au clusters

2015 ◽  
Vol 17 (29) ◽  
pp. 19342-19349 ◽  
Author(s):  
Tarushee Ahuja ◽  
Dengchao Wang ◽  
Zhenghua Tang ◽  
Donald A. Robinson ◽  
Jonathan W. Padelford ◽  
...  
Keyword(s):  
Electronic Coupling ◽  
The Core ◽  
Au Clusters ◽  
Core Energy ◽  
Electron Relaxation ◽  
Energy States

Multiple electron relaxation steps between the core and the ligands in Au130 dithiolate clusters were quantified.

Water Flux Partitioning for Eddy Covariance Data

2020 ◽  
Author(s):  
Jacob Nelson
Keyword(s):  
Eddy Covariance ◽  
Sap Flow ◽  
Meteorological Data ◽  
Water Flux ◽  
Carbon Fluxes ◽  
Seasonal Cycles ◽  
Flow Data ◽  
The Core ◽  
Core Energy ◽  
Flux Partitioning

<p>Here we present an overview of methods for partitioning evapotranspiration (ET) from eddy covariance data. We focus on methods that are designed to use the core energy and carbon fluxes, as well as meteorological data, and do not require supplemental measurements or campaigns. A comparison of three such methods for estimating transpiration (T) showed high correlations between them (R<sup>2</sup> of  daily T between 0.80 and 0.87) and higher correlations to daily stand T estimates from sap flow data (R<sup>2</sup> between 0.58 and 0.66) compared to the tower ET (R2 = 0.49). However, the three methods show significant differences in magnitude, with T/ET values ranging from 45% to 77%. Despite the differences in magnitude, the methods show plausible patterns with respect to LAI, seasonal cycles, WUE, and VPD; moreover, they represent an improvement compared to using ET as a proxy for T even when filtering for days after rain. Finally, we outline practical aspects of applying the methods, such as how to apply the methods and code availability.</p>

scholarly journals Impact of eigenvalues on the electron-phonon coupling strength of aluminium and its binary alloys

BIBECHANA ◽  
2014 ◽  
Vol 12 ◽  
pp. 35-39
Author(s):  
B. K. Kantha ◽  
S. K. Chakrabarti ◽  
I. S. Jha ◽  
B. P. Singh
Keyword(s):  
Superconducting State ◽  
Coupling Strength ◽  
Binary Alloys ◽  
State Parameter ◽  
Wave Parameter ◽  
Phonon Coupling ◽  
Energy Eigenvalues ◽  
The Core ◽  
Core Energy ◽  
Electron Phonon Coupling

Aluminium is a third group element according to the periodic table. Chemically it is a reactive metal often forming complexes within its binary alloys. In the present work we have dealt with the impact of eigenvalues on the superconducting state parameter viz. the electron-phonon coupling strength of this metal. We have also dealt with the same for two binary alloys of it viz. aluminium-magnesium and aluminium-zinc. For this purpose we have computed the non-local screened form factor for each of them. Initially the orthogonalised plane wave parameter has been taken as unity. Thereafter Vashishta-Singwi form of exchange and correlation is employed. The core energy eigenvalues of Herman-Skillman have been used. Our results are quite satisfactory for the metal as well as its present alloys. Our computation reveals that the superconducting state parameter can be reasonably reproduced by Harrison’s first principle pseudopotential technique along with McMillan’s formalism provided a proper choice of the core energy eigenvalues is made.DOI: http://dx.doi.org/10.3126/bibechana.v12i0.11699BIBECHANA 12 (2015) 35-39

scholarly journals EukRef: phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution

2018 ◽  
Author(s):  
Javier del Campo ◽  
Martin Kolisko ◽  
Vittorio Boscaro ◽  
Luciana F. Santoferrara ◽  
Ramon Massana ◽  
...  
Keyword(s):  
Sequence Data ◽  
Sequencing Data ◽  
Environmental Sequencing ◽  
Eukaryotic Diversity ◽  
Microbial Eukaryotes ◽  
Reference Databases ◽  
Environmental Sequences ◽  
Lineage Diversity

AbstractEnvironmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain errors, and struggle to keep pace with rapidly changing eukaryotic taxonomy, the influx of novel diversity, and computational challenges related to assembling the high-quality alignments and trees needed for accurate characterization of lineage diversity. EukRef (eukref.org) is a community driven initiative that addresses these challenges by bringing together taxonomists with expertise spanning the complete eukaryotic tree of life and microbial ecologists that actively use environmental sequencing data for the purpose of developing reliable reference databases across the diversity of microbial eukaryotes. EukRef organizes and facilitates rigorous sequence data mining and annotation by providing protocols, guidelines and tools to do so.

scholarly journals Lipids are the preferred substrate of the protist Naegleria gruberi, relative of a human brain pathogen

2018 ◽  
Author(s):  
Michiel L. Bexkens ◽  
Verena Zimorski ◽  
Maarten J. Sarink ◽  
Hans Wienk ◽  
Jos F. Brouwers ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Genomic Analysis ◽  
Strictly Aerobic ◽  
Genome Data ◽  
Core Energy ◽  
Branched Respiratory Chain ◽  
Growth Substrates ◽  
Final Electron ◽  
Naegleria Gruberi

SUMMARYNaegleria gruberi is a free-living non-pathogenic amoeboflagellate and relative of Naegleria fowleri, a deadly pathogen causing primary amoebic meningoencephalitis (PAM). A genomic analysis of N. gruberi exists, but physiological evidence for its core energy metabolism or in vivo growth substrates is lacking. Here we show that N. gruberi trophozoites need oxygen for normal functioning and growth and that they furthermore shun both glucose and amino acids as growth substrates. Trophozoite growth depends mainly upon lipid oxidation via a mitochondrial branched respiratory chain, both ends of which require oxygen as final electron acceptor. Growing N. gruberi trophozoites thus have a strictly aerobic energy metabolism with a marked substrate preference for the oxidation of fatty acids. Analyses of N. fowleri genome data and comparison with those of N. gruberi indicate that N. fowleri has the same type of metabolism. Specialization to oxygen-dependent lipid breakdown represents a hitherto unprecedented metabolic strategy in protists.

Modeling of {311} Defects

1999 ◽  
Vol 568 ◽  
Author(s):  
G. Hobler ◽  
C.S. Rafferty
Keyword(s):  
Experimental Data ◽  
Rate Constant ◽  
Strain Energy ◽  
Reaction Rate ◽  
Reaction Rate Constant ◽  
Rate Equations ◽  
The Core ◽  
Core Energy ◽  
Wide Range ◽  
Improved Model

ABSTRACTAn improved model of {311} defect evolution is developed based on the rate equations approach. A new expression for the reaction rate constant is presented that is based on the assumption that interstitials may react with the {311} defects along their whole surface. The energetics of {311} defects is treated by calculating the strain energy within the framework of the theory of dislocations in isotropic continua. Using the core energy of the atoms in the defects as the only fit parameter, we explain a wide range of experimental data. Furthermore, we apply the model to investigate closure assumptions used in moments models and propose a new two-moments model that uses the rate equations solver as a pre-processor.

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