Specimens at the Center: An Informatics Workflow and Toolkit for Specimen-level analysis of Public DNA database data

Major public DNA databases — NCBI GenBank, the DNA DataBank of Japan (DDBJ), and the European Molecular Biology Laboratory (EMBL) — are invaluable biodiversity libraries. Systematists and other biodiversity scientists commonly mine these databases for sequence data to use in phylogenetic studies, but such studies generally use only the taxonomic identity of the sequenced tissue, not the specimen identity. Thus studies that use DNA supermatrices to construct phylogenetic trees with species at the tips typically do not take advantage of the fact that for many individuals in the public DNA databases, several DNA regions have been sampled; and for many species, two or more individuals have been sampled. Thus these studies typically do not make full use of the multigene datasets in public DNA databases to test species coherence and select optimal sequences to represent a species. In this study, we introduce a set of tools developed in the R programming language to construct individual-based trees from NCBI GenBank data and present a set of trees for the genus Carex (Cyperaceae) constructed using these methods. For the more than 770 species for which we found sequence data, our approach recovered an average of 1.85 gene regions per specimen, up to seven for some specimens, and more than 450 species represented by two or more specimens. Depending on the subset of genes analyzed, we found up to 42% of species monophyletic. We introduce a simple tree statistic—the Taxonomic Disparity Index (TDI)—to assist in curating specimen-level datasets and provide code for selecting maximally informative (or, conversely, minimally misleading) sequences as species exemplars. While tailored to the Carex dataset, the approach and code presented in this paper can readily be generalized to constructing individual-level trees from large amounts of data for any species group

Remarks on the type locality and current status of the foraminiferal species Rzehakina epigona (Rzehak, 1895)

A likely topotype locality is proposed for Rzehakina epigona. As the type specimen of Silicina epigona Rzehak, 1895 is assumed to be lost, we undertook a search for new material in the type area, Zdounky village in Moravia. A single locality provided a total of 138 Rzehakina specimens. The greenish grey marly clays sampled here contain a rich fauna of both planktonic and benthic foraminifers belonging to the Abathomphalus mayaroensis Zone. In addition to R. epigona, rare specimens attributable to R. inclusa, R. lata, R. minima and even a typical form of R. fissistomata are present at the Zdounky locality. Biometrical analysis was carried out on 52 complete specimens using the involution value "Z" and the length/breadth ratio. Most of the Rzehakina epigona topotypes form a tight cluster with "Z" values between 4 and 15%, although forms that appear transitional to R. lata have Z values of around 20%. The length/breadth ratio is more variable, with values ranging between 1.2 and 2.0. However, the Z value measured from Rzehak's type figure is significantly higher and outside the range of variability of this cluster of specimens. We conclude that Rzehak's drawing may be imprecise. Unfortunately, we were not able to study the inner structure of these specimens owing to the lack of internal filling in these specimens. The unfavourable preservation and low abundance of specimens from the type locality do not enable a proper revision of the species Rzehakina epigona at this time

An annotated catalogue of the Odonata collection of Guido Lanfranco at the National Museum of Natural History in Malta

An annotated list of the Odonata collection of Guido Lanfranco, is provided. The specimens were captured between 1952 and 1971, and may be the oldest surviving specimens caught and still available in local collections from Malta. Almost all locally occurring species are represented, with some specimens collected in sites and habitats that have since been destroyed by urban development. A portion of the specimens bear no data labels and do not contribute to the knowledge of the distribution of the species. During the cataloguing process, specimens in poor condition were restored.peer-reviewe

DNA extraction from museum specimens of parasitic Hymenoptera.

At the same time that molecular researchers are improving techniques to extract DNA from museum specimens, this increased demand for access to museum specimens has created tension between the need to preserve specimens for maintaining collections and morphological research and the desire to conduct molecular analyses. To address these concerns, we examined the suitability of non-invasive DNA extraction techniques on three species of parasitic Hymenoptera (Braconidae), and test the effects of body size (parasitoid species), age (time since collection), and DNA concentration from each extract on the probability of amplifying meaningful fragments of two commonly used genetic loci. We found that age was a significant factor for determining the probability of success for sequencing both 28S and COI fragments. While the size of the braconid parasitoids significantly affected the total amount of extracted DNA, neither size nor DNA concentration were significant factors for the amplification of either gene region. We also tested several primer combinations of various lengths, but were unable to amplify fragments longer than ~150 base pairs. These short fragments of 28S and COI were however sufficient for species identification, and for the discovery of within species genetic variation

Machine for use in monitoring fatigue life for a plurality of elastomeric specimens

An improved machine is described for use in determining the fatigue life for elastomeric specimens. The machine is characterized by a plurality of juxtaposed test stations, specimen support means located at each of the test stations for supporting a plurality of specimens of elastomeric material, and means for subjecting the specimens at each of said stations to sinusoidal strain at a strain rate unique with respect to the strain rate at which the specimens at each of the other stations is subjected to sinusoidal strain

Ultrasonic metal etching for metallographic analysis

Ultrasonic etching delineates microstructural features not discernible in specimens prepared for metallographic analysis by standard chemical etching procedures. Cavitation bubbles in ultrasonically excited water produce preferential damage /etching/ of metallurgical phases or grain boundaries, depending on hardness of metal specimens

Field Studies of Cantharidin Orientation by \u3ci\u3eNeopyrochroa Flabellata\u3c/i\u3e (Coleoptera: Pyrochroidae)

During field studies conducted in south-central Michigan in 1977 and 1980. 109 specimens of Neopyrochroa flabellata were observed and collected at filter papers baited with cantharidin. Only the two highest concentrations used (39.2 mg. 392 j.Lg) elicited responses. and the beetles did not prefer one over the other. In the 24-h studies, most specimens were observed at the cantharidin baits between dusk and 0100 hrs (61 %; n = 14). and 0430-0630 hrs (26%; n = 6). Only two of the 109 specimens were female

Surface microstructural changes of spark plasma sintered zirconia after grinding and annealing

Spark plasma sintered zirconia (3Y-TZP) specimens have been produced of 140 nm 372 nm and 753 nm grain sizes by sintering at 1250 °C, 1450 °C and 1600 °C, respectively. The sintered zirconia specimens were grinded using a diamond grinding disc with an average diamond particle size of about 60 µm, under a pressure of 0.9 MPa. The influence of grinding and annealing on the grain size has been analysed. It was shown that thermal etching after a ruff grinding of specimens at 1100 °C for one hour induced an irregular surface layer of about a few hundred nanometres in thickness of recrystallized nano-grains, independently of the initial grain size. However, if the ground specimens were exposed to higher temperature, e.g. annealing at 1575 °C for one hour, the nano-grain layer was not observed. The resulted grain size was similar to that achieved by the same heat treatments on carefully polished specimens. Therefore, by appropriate grinding and thermal etching treatments, nanograined surface layer can be obtained which increases the resistance to low temperature degradation.Peer ReviewedPostprint (author's final draft

Dependence of TIMP-1 plasma levels on preanalytical specimen handling

Background: Tissue inhibitor of metalloproteinases-1 (TIMP-1) in blood might be a helpful biomarker in various diseases. However, various authors report that TIMP-1 is dependent on preanalytical procedures. Our study was performed to determine how storage conditions and time to centrifugation influence TIMP-1. Materials and Methods: Twenty-six blood specimens were collected from each of 20 volunteers. Two specimens from each person were centrifuged/measured within 1 h after venipuncture and frozen at -80 degrees C. They were thawed once or twice within 72 h. Eight specimens were stored at 20 degrees C in daylight, 8 at 20 degrees C covered and 8 at 4 C in daylight. Four of each of these 8 specimens were mixed once a day until centrifugation. A mixed and an unmixed specimen of each group was centrifuged/measured after 3, 6, 24 and 72 h. Results: TIMP-1 increased after freeze/ thaw (p < 0.001). Mixing blood specimens more than once caused increased TIMP-1 (p < 0.001). TIMP-1 increased within 3 h of storage (p < 0.001). The increase was lower in specimens covered and refrigerated (p < 0.001). Conclusion: TIMP-1 is unstable and has to be evaluated carefully. Blood should be centrifuged directly after venipuncture. For routine application, specimen handling must be standardized and carefully followed. Research should be done on specimens handled identically. Copyright (C) 2008 S. Karger AG, Basel