Thessen Anne E.

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Anne E.

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Now showing 1 - 5 of 5
  • Article
    Data issues in the life sciences
    (Pensoft Publishers, 2011-11-28) Thessen, Anne E. ; Patterson, David J.
    We review technical and sociological issues facing the Life Sciences as they transform into more data-centric disciplines - the “Big New Biology”. Three major challenges are: 1) lack of comprehensive standards; 2) lack of incentives for individual scientists to share data; 3) lack of appropriate infrastructure and support. Technological advances with standards, bandwidth, distributed computing, exemplar successes, and a strong presence in the emerging world of Linked Open Data are sufficient to conclude that technical issues will be overcome in the foreseeable future. While motivated to have a shared open infrastructure and data pool, and pressured by funding agencies in move in this direction, the sociological issues determine progress. Major sociological issues include our lack of understanding of the heterogeneous data cultures within Life Sciences, and the impediments to progress include a lack of incentives to build appropriate infrastructures into projects and institutions or to encourage scientists to make data openly available.
  • Preprint
    Intra- and interspecies differences in growth and toxicity of Pseudo-nitzschia while using different nitrogen sources
    ( 2009-01) Thessen, Anne E. ; Bowers, Holly A. ; Stoecker, Diane K.
    Clonal cultures of plankton are widely used in laboratory experiments and have contributed greatly to knowledge of microbial systems. However, many physiological characteristics vary drastically between strains of the same species, calling into question our ability to make ecologically relevant inferences about populations based on studying one or a few strains. This study included nineteen non-axenic strains of three species of the diatom Pseudo-nitzschia isolated primarily from the mid-Atlantic coastal region of the United States. Toxin (domoic acid) production and growth rates were measured in cultures using different nitrogen sources (NH4+, NO3- and urea) and growth irradiances. The strains exhibited broad differences in growth rate and toxin content even between strains isolated from the same water sample. The influence of bacteria on toxin production was not investigated. Both P. multiseries clones produced toxin, yet preferentially used different nitrogen sources. Only two out of nine P. calliantha and two out of five P. fraudulenta isolates were toxic and domoic acid content varied by orders of magnitude. All three species had variable intraspecies growth rates on each nitrogen source, but P. fraudulenta strains had the broadest range. Light-limited growth rate and maximum growth rate in P. fraudulenta and P. multiseries varied with species. These findings show the importance of defining intra- and interspecies variability in ecophysiology and toxicity. Ecologically relevant functional diversity in the form of ecotypes or cryptic species appears to be present in the genus Pseudo-nitzschia.
  • Article
    The taxonomic significance of species that have only been observed once : the genus Gymnodinium (Dinoflagellata) as an example
    (Public Library of Science, 2012-08-30) Thessen, Anne E. ; Patterson, David J. ; Murray, Shauna A.
    Taxonomists have been tasked with cataloguing and quantifying the Earth’s biodiversity. Their progress is measured in code-compliant species descriptions that include text, images, type material and molecular sequences. It is from this material that other researchers are to identify individuals of the same species in future observations. It has been estimated that 13% to 22% (depending on taxonomic group) of described species have only ever been observed once. Species that have only been observed at the time and place of their original description are referred to as oncers. Oncers are important to our current understanding of biodiversity. They may be validly described species that are members of a rare biosphere, or they may indicate endemism, or that these species are limited to very constrained niches. Alternatively, they may reflect that taxonomic practices are too poor to allow the organism to be re-identified or that the descriptions are unknown to other researchers. If the latter are true, our current tally of species will not be an accurate indication of what we know. In order to investigate this phenomenon and its potential causes, we examined the microbial eukaryote genus Gymnodinium. This genus contains 268 extant species, 103 (38%) of which have not been observed since their original description. We report traits of the original descriptions and interpret them in respect to the status of the species. We conclude that the majority of oncers were poorly described and their identity is ambiguous. As a result, we argue that the genus Gymnodinium contains only 234 identifiable species. Species that have been observed multiple times tend to have longer descriptions, written in English. The styles of individual authors have a major effect, with a few authors describing a disproportionate number of oncers. The information about the taxonomy of Gymnodinium that is available via the internet is incomplete, and reliance on it will not give access to all necessary knowledge. Six new names are presented – Gymnodinium campbelli for the homonymous name Gymnodinium translucens Campbell 1973, Gymnodinium antarcticum for the homonymous name Gymnodinium frigidum Balech 1965, Gymnodinium manchuriensis for the homonymous name Gymnodinium autumnale Skvortzov 1968, Gymnodinium christenum for the homonymous name Gymnodinium irregulare Christen 1959, Gymnodinium conkufferi for the homonymous name Gymnodinium irregulare Conrad & Kufferath 1954 and Gymnodinium chinensis for the homonymous name Gymnodinium frigidum Skvortzov 1968.
  • Article
    Pseudo-nitzschia physiological ecology, phylogeny, toxicity, monitoring and impacts on ecosystem health
    (Elsevier B.V., 2011-11-03) Trainer, Vera L. ; Bates, Stephen S. ; Lundholm, Nina ; Thessen, Anne E. ; Cochlan, William P. ; Adams, Nicolaus G. ; Trick, Charles G.
    Over the last decade, our understanding of the environmental controls on Pseudo-nitzschia blooms and domoic acid (DA) production has matured. Pseudo-nitzschia have been found along most of the world's coastlines, while the impacts of its toxin, DA, are most persistent and detrimental in upwelling systems. However, Pseudo-nitzschia and DA have recently been detected in the open ocean's high-nitrate, low-chlorophyll regions, in addition to fjords, gulfs and bays, showing their presence in diverse environments. The toxin has been measured in zooplankton, shellfish, crustaceans, echinoderms, worms, marine mammals and birds, as well as in sediments, demonstrating its stable transfer through the marine food web and abiotically to the benthos. The linkage of DA production to nitrogenous nutrient physiology, trace metal acquisition, and even salinity, suggests that the control of toxin production is complex and likely influenced by a suite of environmental factors that may be unique to a particular region. Advances in our knowledge of Pseudo-nitzschia sexual reproduction, also in field populations, illustrate its importance in bloom dynamics and toxicity. The combination of careful taxonomy and powerful new molecular methods now allow for the complete characterization of Pseudo-nitzschia populations and how they respond to environmental changes. Here we summarize research that represents our increased knowledge over the last decade of Pseudo-nitzschia and its production of DA, including changes in worldwide range, phylogeny, physiology, ecology, monitoring and public health impacts.
  • Article
    Applications of natural language processing in biodiversity science
    (Hindawi Publishing, 2012) Thessen, Anne E. ; Cui, Hong ; Mozzherin, Dmitry
    Centuries of biological knowledge are contained in the massive body of scientific literature, written for human-readability but too big for any one person to consume. Large-scale mining of information from the literature is necessary if biology is to transform into a data-driven science. A computer can handle the volume but cannot make sense of the language. This paper reviews and discusses the use of natural language processing (NLP) and machine-learning algorithms to extract information from systematic literature. NLP algorithms have been used for decades, but require special development for application in the biological realm due to the special nature of the language. Many tools exist for biological information extraction (cellular processes, taxonomic names, and morphological characters), but none have been applied life wide and most still require testing and development. Progress has been made in developing algorithms for automated annotation of taxonomic text, identification of taxonomic names in text, and extraction of morphological character information from taxonomic descriptions. This manuscript will briefly discuss the key steps in applying information extraction tools to enhance biodiversity science.