138 research outputs found
Calculation of electron density of periodic systems using non-orthogonal localised orbitals
Methods for calculating an electron density of a periodic crystal constructed
using non-orthogonal localised orbitals are discussed. We demonstrate that an
existing method based on the matrix expansion of the inverse of the overlap
matrix into a power series can only be used when the orbitals are highly
localised (e.g. ionic systems). In other cases including covalent crystals or
those with an intermediate type of chemical bonding this method may be either
numerically inefficient or fail altogether. Instead, we suggest an exact and
numerically efficient method which can be used for orbitals of practically
arbitrary localisation. Theory is illustrated by numerical calculations on a
model system.Comment: 12 pages, 4 figure
Ionic structure and photoabsorption in medium sized sodium clusters
We present ground-state configurations and photoabsorption spectra of Na-7+,
Na-27+ and Na-41+. Both the ionic structure and the photoabsorption spectra of
medium-size sodium clusters beyond Na-20 have been calculated self-consistently
with a nonspherical treatment of the valence electrons in density functional
theory. We use a local pseudopotential that has been adjusted to experimental
bulk properties and the atomic 3s level of sodium. Our studies have shown that
both the ionic structure of the ground state and the positions of the plasmon
resonances depend sensitively on the pseudopotential used in the calculation,
which stresses the importance of its consistent use in both steps.Comment: 4 pages, 3 figures. Accepted for publication in PRB, tentatively July
15th, 1998 some typos corrected, brought to nicer forma
Ionic and electronic structure of sodium clusters up to N=59
We determined the ionic and electronic structure of sodium clusters with even
electron numbers and 2 to 59 atoms in axially averaged and three-dimensional
density functional calculations. A local, phenomenological pseudopotential that
reproduces important bulk and atomic properties and facilitates structure
calculations has been developed. Photoabsorption spectra have been calculated
for , , and to
. The consistent inclusion of ionic structure considerably
improves agreement with experiment. An icosahedral growth pattern is observed
for to . This finding is supported by
photoabsorption data.Comment: To appear in Phys. Rev. B 62. Version with figures in better quality
can be requested from the author
Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi
Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi
Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi
Taxonomic Reliability of DNA Sequences in Public Sequence Databases: A Fungal Perspective
BACKGROUND: DNA sequences are increasingly seen as one of the primary information sources for species identification in many organism groups. Such approaches, popularly known as barcoding, are underpinned by the assumption that the reference databases used for comparison are sufficiently complete and feature correctly and informatively annotated entries. METHODOLOGY/PRINCIPAL FINDINGS: The present study uses a large set of fungal DNA sequences from the inclusive International Nucleotide Sequence Database to show that the taxon sampling of fungi is far from complete, that about 20% of the entries may be incorrectly identified to species level, and that the majority of entries lack descriptive and up-to-date annotations. CONCLUSIONS: The problems with taxonomic reliability and insufficient annotations in public DNA repositories form a tangible obstacle to sequence-based species identification, and it is manifest that the greatest challenges to biological barcoding will be of taxonomical, rather than technical, nature
Taxonomic annotation of public fungal ITS sequences from the built environment - A report from an April 10-11, 2017 workshop (Aberdeen, UK)
The UNITE database community gratefully acknowledges support from the Alfred P. Sloan Foundation. HN and CW gratefully acknowledges financial support from Stiftelsen Olle Engkvist Byggmästare, Stiftelsen Lars Hiertas Minne, Kapten Carl Stenholms Donationsfond, and Birgit och Birger Wålhströms Minnesfond. CW gratefully acknowledges a Marie Skłodowska-Curie post doctoral grant from the ERC. Leho Tedersoo is gratefully acknowledged for providing helpful feedback on an earlier draft of this manuscript.Peer reviewedPublisher PD
Tree diversity and species identity effects on soil fungi, protists and animals are context dependent
Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se
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