BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

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Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Within uncharacterized groups, DNA barcodes, short DNA sequences that are present in a wide range of species, can be used to assign organisms into species. We propose an automatic procedure that sorts the sequences into hypothetical species based on the barcode gap, which can be observed whenever the divergence among organisms belonging to the same species is smaller than divergence among organisms from different species. We use a range of prior intraspecific divergence to infer from the data a model-based one-sided confidence limit for intraspecific divergence. The method, called Automatic Barcode Gap Discovery (ABGD), then detects the barcode gap as the first significant gap beyond this limit and uses it to partition the data. Inference of the limit and gap detection are then recursively applied to previously obtained groups to get finer partitions until there is no further partitioning. Using six published data sets of metazoans, we show that ABGD is computationally efficient and performs well for standard prior maximum intraspecific divergences (a few per cent of divergence for the five data sets), except for one data set where less than three sequences per species were sampled. We further explore the theoretical limitations of ABGD through simulation of explicit speciation and population genetics scenarios. Our results emphasize in particular the sensitivity of the method to the presence of recent speciation events, via (unrealistically) high rates of speciation or large numbers of species. In conclusion, ABGD is fast, simple method to split a sequence alignment data set into candidate species that should be complemented with other evidence in an integrative taxonomic approach.

ABGD, Automatic Barcode Gap Discovery for primary species delimitation

DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF–atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK–psbI spacer, and trnH–psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.

/pdf/a-dna-barcode-for-land-plants-3fs5bo85qv.pdf

A DNA barcode for land plants.

Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity

Prescottia glazioviana is a rare and poorly known species, for which this paper clarifies the circumscription, indicating for the first time diagnostic morphological features that were missing in the original description. An amended description, distribution data and a detailed illustration are presented. Previously known from only two collections from Rio de Janeiro State, P. glazioviana is reported for the first time in Minas Gerais State, Brazil.

Clarification on the circumscription of Prescottia glazioviana (Cranichidinae, Orchidaceae)

In the process of reviewing the relevant literature revision and analysing available botanical specimens for the compilation of a checklist of Orchidaceae for the State of Bahia (Brazil), we identified some taxonomic issues that are dealt with in this paper.

Orchidaceae of Bahia, Brazil: notes on taxonomy and nomenclature

http://209.141.50.37/Neodiversity/default/download_pdf/artigo.pdf.8f9c7ed705efdb8d.6e656f642e3131312e312e706466.pdf

Nomenclatural notes on Laeliinae-VII. New combinations in Cattleya for species and nothospecies originally described in Hoffmannseggella (Orchidaceae)

A taxonomic revision of Capanemia (Orchidaceae) was completed after morphological, nomenclatural and phylogenetic studies. Our analyses do not support the infrageneric classification (Capanemia sect. Capanemia and Capanemia sect. Planifolia) proposed by Pabst in the seventies and recovered Sanderella as the sister group of Capanemia, albeit with low statistical support. We herein recognized six species of Capanemia, proposed five new synonyms, designated one lectotype and excluded one name.

Capanemia (Oncidiinae): an orchid genus revised and simplified

Corrigendum to "Phylogenetic relationships of Echinolaena and Ichnanthus within Panicoideae (Poaceae) reveal two new genera of tropical grasses" [Mol. Phylogenet. Evol. 93 (2015) 212-233].

Cássio van den Berg

Papers

Clarification on the circumscription of Prescottia glazioviana (Cranichidinae, Orchidaceae)

Orchidaceae of Bahia, Brazil: notes on taxonomy and nomenclature

Nomenclatural notes on Laeliinae-VII. New combinations in Cattleya for species and nothospecies originally described in Hoffmannseggella (Orchidaceae)

Capanemia (Oncidiinae): an orchid genus revised and simplified

Corrigendum to "Phylogenetic relationships of Echinolaena and Ichnanthus within Panicoideae (Poaceae) reveal two new genera of tropical grasses" [Mol. Phylogenet. Evol. 93 (2015) 212-233].