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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

C. L. Schoch, B. Robbertse, V. Robert, D. Vu, G. Cardinali, L. Irinyi, W. Meyer, R. H. Nilsson, K. Hughes, A. N. Miller, P. M. Kirk, K. Abarenkov (+89 others)
2014 Database: The Journal of Biological Databases and Curation  
Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.  ...  Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater.  ...  Non-type/reference sequences with low LQI until better sequences are obtained.The UNITE database for molecular identification of fungi represents another approach to improve sequence accuracy and fungal  ... 
doi:10.1093/database/bau061 pmid:24980130 pmcid:PMC4075928 fatcat:oqjotp6vvzbrtdddii6nc67zy4

Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches

Rebecca Yahr, Conrad L. Schoch, Bryn T. M. Dentinger
2016 Philosophical Transactions of the Royal Society of London. Biological Sciences  
Paul Kirk, Nathalie van de Wiele and Barbara Robbertse are thanked for assistance with data for figures 1 and 2.  ...  Katy Hayden, Pete Hollingsworth and two reviewers improved earlier drafts of this manuscript.  ...  Schoch CL et al. 2014 Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi. Database-J. Biol. Databases Curation 2014, bau061.  ... 
doi:10.1098/rstb.2015.0336 pmid:27481788 pmcid:PMC4971188 fatcat:edv4cciribarpesgoz6v4tljze

Xylariales: First results of mycological exploration in the Sangay and Llanganates National Park, Ecuador

María-Fernanda Guevara, Paula Salazar, Bence Mátyás, María-Eugenia Ordoñez
2018 F1000Research  
Schoch CL, Robbertse B, Robert V, et al.: Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi. Database (Oxford). 2014; 2014; pii: bau061.  ...  This data contributes with base information on the biodiversity of the Parks, necessary to design and implement measures for the conservation of fungi in Ecuador.  ...  Barnes and Cristina E. Toapanta for their contribution to the development of the present research.  ... 
doi:10.12688/f1000research.13623.1 pmid:30057751 pmcid:PMC6051188 fatcat:j7uz33girfbqpj4qhhzgnms4ue

Identifying and Naming Plant-Pathogenic Fungi: Past, Present, and Future

Pedro W. Crous, David L. Hawksworth, Michael J. Wingfield
2015 Annual Review of Phytopathology  
Scientific names are crucial in communicating knowledge about fungi. In plant pathology, they link information regarding the biology, host range, distribution, and potential risk.  ...  Implementing the one fungus-one name system and linking names to validated type specimens, cultures, and reference sequences will provide the foundation on which the future of plant pathology and the communication  ...  Groenewald for reading an earlier draft of this paper and for his valuable contributions.  ... 
doi:10.1146/annurev-phyto-080614-120245 pmid:26047568 fatcat:svv5rzlnhvdmlo3tqc4fb2wzea

The new microbiology: Cultivating the future of microbiome-directed medicine

Connie W.Y. Ha, Suzanne Devkota
2020 American Journal of Physiology - Gastrointestinal and Liver Physiology  
The discovery of human-associated microscopic life forms has captivated the scientific community since their first documentation in the 17th century.  ...  for biotechnology.  ...  Recovering a single organism within the mixed community is akin to finding a needle in a haystack.  ... 
doi:10.1152/ajpgi.00093.2020 pmid:32996782 pmcid:PMC7792672 fatcat:pr7xtq46ljfh5mt5wvqufjmvva

Volume 36 Number 2

2015 Microbiology Australia  
References Acknowledgements The work on Candida-macrophage interactions in the Traven and Acknowledgements The authors thank Sharon Chen for information on the additional Australian human Microsphaeropsis  ...  Schoch, C.L. et al. (2014) Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.  ...  Scientific Name Common Name Geographical origin and/or place held Reference Aparasphenodon sp.  ... 
doi:10.1071/mav36n2 fatcat:fen4h2owr5fntdtq6otiuzup3m

3. What is Biodiversity? [chapter]

John Wilson, Richard Primack
2019 Conservation Biology in Sub-Saharan Africa  
Taxonomists (and the people assisting them) explore nature, collect specimens of plants, animals, and other organisms, describe/name those specimens, and store the specimens in permanent collections, such  ...  When a species is formally described, it is given a unique two-part name, known as a binomial name. For example, the binomial name for the lion is Panthera leo.  ...  The individuals within Trying to find threatened species in aquatic systems can be like trying to find a needle in a haystack.  ... 
doi:10.11647/obp.0177.03 fatcat:lruiku5byfcnvecauxzqcf4y54

Precambrian Paleobiology: Precedents, Progress, and Prospects

J. William Schopf
2021 Frontiers in Ecology and Evolution  
Walcott, glimmerings of the previously "unknown and unknowable" early fossil record came to light – but Walcott's Precambrian finds were also discounted.  ...  It was not until the breakthrough advances of the 1950's and the identification of modern stromatolites (1956), Precambrian phytoplankton in shales (1950's), stromatolitic microbes in cherts (1953), and  ...  into a proverbial "needle in a haystack hunt."  ... 
doi:10.3389/fevo.2021.707072 doaj:989cfd3add7d40898dce810ebef6067e fatcat:tfz6pvv57be43ptw7qae3wivpa

Entomopathogenicity and Biological Attributes of Himalayan Treasured Fungus Ophiocordyceps sinensis (Yarsagumba)

Bikash Baral
2017 Journal of Fungi  
interaction keeps them lagging behind in parallel studies of fungi associated with agro-ecology, forest pathology and medical biology.  ...  fungal parasites, and the molecular mechanisms involved therein, are clearly documented.  ...  Most harvesters reveal its difficulty as equivalent to browsing for a needle in a haystack.  ... 
doi:10.3390/jof3010004 pmid:29371523 pmcid:PMC5715966 fatcat:ow5xj27vf5hgfji7ag7cybm4ra

Current Trends in Diagnostics of Viral Infections of Unknown Etiology

Daniel Kiselev, Alina Matsvay, Ivan Abramov, Vladimir Dedkov, German Shipulin, Kamil Khafizov
2020 Viruses  
Could high throughput sequencing (HTS) become the future gold standard in molecular diagnostics of viral infections?  ...  Data harvested with HTS could not only augment diagnostics and help to choose the correct therapy, but also facilitate research in epidemiology, genetics and virology.  ...  Researchers are forced to search for target sequences amongst a handful of "junk" reads, employing time and computer power to solve this "needle in a haystack" sort of challenge.  ... 
doi:10.3390/v12020211 pmid:32074965 pmcid:PMC7077230 fatcat:mty6borcxffppirung4xfbt6hu

131(3) Full Issue PDF

Dwayne Lepitzki
2018 Canadian field-naturalist  
For most species, juveniles largely outnumbered adults. Juveniles were relatively less abundant in 2012 than in 2011.  ...  Considering the entire shorebird community, abundance of individuals peaked in early September. Peak abundance occurred earlier for adults than for juveniles.  ...  George for providing advice and references relating to these occurrences over many years and in the preparation of this paper and J. Richardson for helpful comments on an earlier version.  ... 
doi:10.22621/cfn.v131i3.2072 fatcat:n6ugefecird7zhmhcgml5zdxsm

Beetles (Coleoptera) of Peru: A Survey of the Families. Lampyridae

M. A. Branham
2015 Journal of the Kansas Entomological Society  
Put it in 70 percent isopropyl alcohol (rubbing alcohol) and send it to me. ... Dear Caren, Thanks for sending the specimen.  ...  that there is definitely a reason for the presence of bioluminescence in some fungi, in some places in the world.  ...  "He tells me that's his job, to light up in the dark. And that's why you can find him in almost every park." So, once again I listened and listened with all my might.  ... 
doi:10.2317/kent-88-02-248-250.1 fatcat:34kswteyovb3to5xhtfgvscxue

Mitosis – The story

James Wakefield, Conly Rieder, Herbert Macgregor
2011 Chromosome Research  
I'm sure I'm the only one that has ever serially sectioned one, let alone many, whole sea-urchin zygotes looking for centrioles-basically two needles in a haystack.  ...  It's worth noting that the molecular mechanism for correcting errors in kinetochore attachment, which I think is the most recent spectacular finding on mitosis, was discovered through a combination of  ... 
doi:10.1007/s10577-010-9174-3 pmid:21213038 fatcat:hw2yoitcwvgtzhu64gw4fblt7q

A Robust Framework for Microbial Archaeology

Christina Warinner, Alexander Herbig, Allison Mann, James A. Fellows Yates, Clemens L. Weiß, Hernán A. Burbano, Ludovic Orlando, Johannes Krause
2017 Annual review of genomics and human genetics (Print)  
Finally, we outline standards and precautions to guide future research in the field.  ...  We give special attention to the process of identifying, validating, and authenticating ancient microbes using high-throughput DNA sequencing data.  ...  For ancient pathogenomic studies, it is the basis for identifying the proverbial pathogen needle in a haystack of background DNA, and for ancient microbiome studies, it is essential for identifying community  ... 
doi:10.1146/annurev-genom-091416-035526 pmid:28460196 pmcid:PMC5581243 fatcat:l3id6vomknbc7fivsttppucwhe

Prokaryotic, Fungal, and Unicellular Eukaryotic Core Communities Across Three Sympatric Marine Sponges From the Southwestern Atlantic Coast Are Dominated Largely by Deterministic Assemblage Processes

Cristiane C. P. Hardoim, Gisele Lôbo-Hajdu, Márcio R. Custódio, Pablo R. Hardoim
2021 Frontiers in Microbiology  
Thus, this survey addressed the holobiome of the sponge species in the São Paulo region (Brazil) for the first time and investigated the contribution of neutral and niche processes of prokaryotic, fungal  ...  Deterministic processes were primarily responsible for the assembly of microbial communities in all sponge species, while neutral processes of prokaryotic and fungal community assembly were also detected  ...  Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.  ... 
doi:10.3389/fmicb.2021.674004 pmid:34168631 pmcid:PMC8217869 fatcat:6ysawisrnfbkjcljzq7i5lqcja
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