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David J Patterson

Publications and source records attributed to David J Patterson.

10 recordsLinked to original sources
PubMed2006

Evaluating support for the current classification of eukaryotic diversity.

Perspectives on the classification of eukaryotic diversity have changed rapidly in recent years, as the four eukaryotic groups within the five-kingdom classification--plants, animals, fungi, and protists--have been transformed through numerous permutations into the current system of six "supergroups." The intent of the supergroup classification system is to unite microbial and macroscopic eukaryotes based on phylogenetic inference. This supergroup approach is increasing in popularity in the literature and is appearing in introductory biology textbooks. We evaluate the stability and support for the current six-supergroup classification of eukaryotes based on molecular genealogies. We assess three aspects of each supergroup: (1) the stability of its taxonomy, (2) the support for monophyly (single evolutionary origin) in molecular analyses targeting a supergroup, and (3) the support for monophyly when a supergroup is included as an out-group in phylogenetic studies targeting other taxa. Our analysis demonstrates that supergroup taxonomies are unstable and that support for groups varies tremendously, indicating that the current classification scheme of eukaryotes is likely premature. We highlight several trends contributing to the instability and discuss the requirements for establishing robust clades within the eukaryotic tree of life.

Animals↗
PubMed2006

Taxonomic indexing--extending the role of taxonomy.

Taxonomic indexing refers to a new array of taxonomically intelligent network services that use nomenclatural principles and elements of expert taxonomic knowledge to manage information about organisms. Taxonomic indexing was introduced to help manage the increasing amounts of digital information about biology. It has been designed to form a near basal layer in a layered cyberinfrastructure that deals with biological information. Taxonomic Indexing accommodates the special problems of using names of organisms to index biological material. It links alternative names for the same entity (reconciliation), and distinguishes between uses of the same name for different entities (disambiguation), and names are placed within an indefinite number of hierarchical schemes. In order to access all information on all organisms, Taxonomic indexing must be able to call on a registry of all names in all forms for all organisms. NameBank has been developed to meet that need. Taxonomic indexing is an area of informatics that overlaps with taxonomy, is dependent on the expert input of taxonomists, and reveals the relevance of the discipline to a wide audience.

Abstracting and Indexing↗
PubMed2006

Taxonomic informatics tools for the electronic Nomenclator Zoologicus.

Given the current trends, it seems inevitable that all biological documents will eventually exist in a digital format and be distributed across the internet. New network services and tools need to be developed to increase retrieval rates for documents and to refine data recovery. Biological data have traditionally been well managed using taxonomic principles. As part of a larger initiative to build an array of names-based network services that emulate taxonomic principles for managing biological information, we undertook the digitization of a major taxonomic reference text, Nomenclator Zoologicus. The process involved replicating the text to a high level of fidelity, parsing the content for inclusion within a database, developing tools to enable expert input into the product, and integrating the metadata and factual content within taxonomic network services. The result is a high-quality and freely available web application (http://uio.mbl.edu/NomenclatorZoologicus/) capable of being exploited in an array of biological informatics services.

Animals↗
PubMed2005

Improving the analysis of dinoflagellate phylogeny based on rDNA.

Phylogenetic studies of dinoflagellates are often conducted using rDNA sequences. In analyses to date, the monophyly of some of the major lineages of dinoflagellates remain to be demonstrated. There are several reasons for this uncertainty, one of which may be the use of models of evolution that may not closely fit the data. We constructed and examined alignments of SSU and partial LSU rRNA along with a concatenated alignment of the two molecules. The alignments showed several characteristics that may confound phylogeny reconstruction: paired helix (stem) regions that contain non-independently evolving sites, high levels of compositional heterogeneity among some of the sequences, high levels of incompatibility (homoplasy), and rate heterogeneity among sites. Taking into account these confounding factors, we analysed the data and found that the Gonyaulacales, a well-supported clade, may be the most recently diverged order. Other supported orders were, in the analysis based on SSU, the Suessiales and the Dinophysiales; however, the Gymnodiniales and Prorocentrales appeared to be polyphyletic. The Peridiniales without Heterocapsa species appeared as a monophyletic group in the analysis based on LSU; however, the support was low. The concatenated alignment did not provide a better phylogenetic resolution than the single gene alignments.

Animals↗
PubMed2005

Risk of proximal colorectal neoplasia among asymptomatic patients with distal hyperplastic polyps.

PURPOSE: Many guidelines on colorectal cancer screening do not consider distal hyperplastic polyps to be a marker for proximal neoplasia. However, 11 of 17 published studies have shown an increased risk of proximal neoplasia in patients with distal hyperplastic polyps. Our goal is to assess the risk of proximal neoplasia in asymptomatic patients with distal hyperplastic polyps, compared to those with distal tubular adenomas or no distal polyps. METHODS: We assessed proximal (cecum, ascending, transverse colon and splenic flexure) and distal polyps in patients undergoing screening colonoscopy, classifying them into 3 groups: distal hyperplastic polyps only; distal adenomas with or without hyperplastic polyps; no distal polyps. The prevalence of proximal neoplasia and advanced neoplasia (polyps > or =1 cm, villous adenomas, or cancer) was compared among these groups. RESULTS: Of 2357 patients, 427 (18%) had neoplasia, including 103 (4%) with advanced neoplasia. Proximal neoplasia occurred in 175 (9%) of 1896 patients with no distal polyps, compared with 28 (12%) of 237 with distal hyperplastic polyps (P = 0.20) and 64 (29%) of 224 with distal adenomas (P <0.0001). Proximal advanced neoplasia occurred in 39 (2%) patients with no distal polyps, compared with 4 (2%) with distal hyperplastic polyps (P = 0.70) and 9 (4%) with distal adenomas (P = 0.13). CONCLUSIONS: Patients with distal hyperplastic polyps, unlike those with distal adenomas, do not exhibit an increased risk for proximal neoplasia or proximal advanced neoplasia compared to those with no distal polyps. The discovery of hyperplastic polyps on screening sigmoidoscopy should not prompt colonoscopy.

Adenoma↗
PubMed2002

Clinical outcomes in patients who undergo extracorporeal shock wave lithotripsy for chronic calcific pancreatitis.

BACKGROUND: There is controversy as to whether extracorporeal shock wave lithotripsy fragmentation and ERCP retrieval of pancreatic stones are associated with relief of chronic pain or relapsing attacks of pancreatitis. Our most recent experience with this technology is reviewed. METHODS: Forty patients with chronic calcific pancreatitis who required extracorporeal shock wave lithotripsy between 1995 and 2000 to facilitate pancreatic duct stone removal were retrospectively reviewed. Data collected included patient presentation, number of lithotripsy and ERCP sessions required, complications, and outcomes measures to include pre- and post-ESWL pain scale, monthly oxycodone (5 mg)-equivalent pills ingested, yearly hospitalizations, and need for subsequent surgery. RESULTS: A single extracorporeal shock wave lithotripsy session was required for 35 patients who underwent a total of 86 ERCPs to achieve complete stone extraction from the main pancreatic duct. Minor complications occurred in 20%. There was one episode of pancreatic sepsis that was treated with antibiotics and removal of an occluded pancreatic prosthesis. At a mean [SD] follow-up of 2.4 (0.6) years, 80% of patients had avoided surgery and there was a statistically significant decrease in pain scores (6.9 [1.3] vs. 2.9 [1.1]; p = 0.001), yearly hospitalizations for pancreatitis (3.9 [1.9] vs. 0.9 [0.9]; p = 0.001), and oxycodone-equivalent narcotic medication ingested monthly (125 [83] vs. 81 [80]; p = 0.03). CONCLUSIONS: Extracorporeal shock wave lithotripsy fragmentation of pancreatic duct calculi in conjunction with endoscopic clearance of the main pancreatic duct is associated with significant improvement in clinical outcomes in most patients with chronic pancreatitis.

Adult↗
PubMed2002

Evolutionary history of "early-diverging" eukaryotes: the excavate taxon Carpediemonas is a close relative of Giardia.

Diplomonads, such as Giardia, and their close relatives retortamonads have been proposed as early-branching eukaryotes that diverged before the acquisition-retention of mitochondria, and they have become key organisms in attempts to understand the evolution of eukaryotic cells. In this phylogenetic study we focus on a series of eukaryotes suggested to be relatives of diplomonads on morphological grounds, the "excavate taxa". Phylogenies of small subunit ribosomal RNA (SSU rRNA) genes, alpha-tubulin, beta-tubulin, and combined alpha- + beta-tubulin all scatter the various excavate taxa across the diversity of eukaryotes. But all phylogenies place the excavate taxon Carpediemonas as the closest relative of diplomonads (and, where data are available, retortamonads). This novel relationship is recovered across phylogenetic methods and across various taxon-deletion experiments. Statistical support is strongest under maximum-likelihood (ML) (when among-site rate variation is modeled) and when the most divergent diplomonad sequences are excluded, suggesting a true relationship rather than an artifact of long-branch attraction. When all diplomonads are excluded, our ML SSU rRNA tree actually places retortamonads and Carpediemonas away from the base of the eukaryotes. The branches separating excavate taxa are mostly not well supported (especially in analyses of SSU rRNA data). Statistical tests of the SSU rRNA data, including an "expected likelihood weights" approach, do not reject trees where excavate taxa are constrained to be a clade (with or without parabasalids and Euglenozoa). Although diplomonads and retortamonads lack any mitochondria-like organelle, Carpediemonas contains double membrane-bounded structures physically resembling hydrogenosomes. The phylogenetic position of Carpediemonas suggests that it will be valuable in interpreting the evolutionary significance of many molecular and cellular peculiarities of diplomonads.

Animals↗
PubMed1999

The Diversity of Eukaryotes.

The discipline of evolutionary protistology has emerged in the past 30 yr. There is as yet no agreed view of how protists are interrelated or how they should be classified. The foundations of a stable taxonomic superstructure for the protists and other eukaryotes lie in cataloging the diversity of the major monophyletic lineages of these organisms. The use of common patterns of cell organization (ultrastructural identity) seems to provide us with the most robust hypotheses of such lineages. These lineages are placed in 71 groups without identifiable sister taxa. These groups are here referred to as "major building blocks." For the first time, the compositions, ultrastructural identities, synapomorphies (where available), and subgroups of the major building blocks are summarized. More than 200 further lineages without clear identities are listed. This catalog includes all known major elements of the comprehensive evolutionary tree of protists and eukaryotes. Different approaches among protistologists to issues of nomenclature, ranking, and definitions of these groups are discussed, with particular reference to two groups-the stramenopiles and the Archezoa. The concept of "extended in-group" is introduced to refer to in-groups and the most proximate sister group and to assist in identifying the hierarchical location of taxa.

eukaryotes↗