134 research outputs found
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
Genetic Diversity of Dahongjun, the Commercially Important “Big Red Mushroom” from Southern China
BACKGROUND: In southern China, a wild ectomycorrhizal mushroom commonly called "Dahongjun" or "Big Red Mushroom" by the local residents, has been harvested, consumed, and/or exported as an exotic food for many years. Although ecologically and economically important, very little is known about this mushroom, including its diversity and population structure. METHODOLOGY AND PRINCIPAL FINDINGS: In this study, we analyzed 122 samples from five local populations representing the known distribution ranges of this mushroom in southern China. We investigated the genetic diversity and geographic structure of this mushroom using sequences from four DNA fragments. Our analyses identified that this mushroom contained at least three divergent lineages: one corresponds to a recently described species Russula griseocarnosa from southern China and the remaining two likely represent two novel species. While these lineages were prominently structured geographically based on ITS sequences, evidence for ancient and/or recent gene flow was also identified within individual lineages. In addition, a local population from Ailaoshan in central Yunnan Province where 85 of our 122 specimens came from showed clear evidence of recombination. CONCLUSION AND SIGNIFICANCE: The ectomycorrhizal mushroom "Dahongjun" from southern China is a species complex with at least three divergent lineages. These lineages are largely geographically structured and there is evidence for recombination in nature. Our results indicate mature Dahongjun mushrooms with abundant basidiospores are important for the reproduction of this mushroom in nature and that individual populations of this species should be managed separately
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. Reannotated
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.B.R. and C.L.S. acknowledge support from the Intramural Research
Program of the National Institutes of Health, National Library of
MedicinePeer Reviewe
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. Reannotated
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.The Intramural Research Programs
of the National Center for Biotechnology Information, National
Library of Medicine and the National Human Genome Research
Institute, both at the National Institutes of Health.http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353am201
Corneal confocal microscopy detects a reduction in corneal endothelial cells and nerve fibres in patients with acute ischemic stroke
YesEndothelial dysfunction and damage underlie cerebrovascular disease and ischemic stroke. We
undertook corneal confocal microscopy (CCM) to quantify corneal endothelial cell and nerve
morphology in 146 patients with an acute ischemic stroke and 18 age-matched healthy control
participants. Corneal endothelial cell density was lower (P<0.001) and endothelial cell area (P<0.001)
and perimeter (P<0.001) were higher, whilst corneal nerve fbre density (P<0.001), corneal nerve
branch density (P<0.001) and corneal nerve fbre length (P=0.001) were lower in patients with acute
ischemic stroke compared to controls. Corneal endothelial cell density, cell area and cell perimeter
correlated with corneal nerve fber density (P=0.033, P=0.014, P=0.011) and length (P=0.017,
P=0.013, P=0.008), respectively. Multiple linear regression analysis showed a signifcant independent
association between corneal endothelial cell density, area and perimeter with acute ischemic stroke
and triglycerides. CCM is a rapid non-invasive ophthalmic imaging technique, which could be used to
identify patients at risk of acute ischemic stroke.Qatar National Research Fund Grant BMRP2003865
A Matter of Time: The Influence of Recording Context on EEG Spectral Power in Adolescents and Young Adults with ADHD
Multigene Sequencing Provides a Suitable Epitype, Barcode Sequences and a Precise Systematic Position for the Enigmatic, African Cantharellus miniatescens.
Activation of olefins via asymmetric Brønsted acid catalysis
The activation of olefins for asymmetric chemical synthesis traditionally relies on transition metal catalysts. In contrast, biological enzymes with Brønsted acidic sites of appropriate strength can protonate olefins and thereby generate carbocations that ultimately react to form natural products. Although chemists have recently designed chiral Brønsted acid catalysts to activate imines and carbonyl compounds, mimicking these enzymes to protonate simple olefins that then engage in asymmetric catalytic reactions has remained a substantial synthetic challenge. Here, we show that a class of confined and strong chiral Brønsted acids enables the catalytic asymmetric intramolecular hydroalkoxylation of unbiased olefins. The methodology gives rapid access to biologically active 1,1-disubstituted tetrahydrofurans, including (–)-Boivinianin A
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