Archaeal nucleic acids in picoplankton from great lakes on three continents

Phylogenetic analysis of PCR-amplified 16S rRNA genes revealed the presence of archaea in picoplankton collected from the Laurentian Great Lakes in North America, Africas Lake Victoria, and Lakes Ladoga and Onega in northeastern Eurasia. From 1 to 10% of the rRNA extracted from size-fractionated picoplankton (>0.2 µm but <1.2 µm) collected in the epilimnion and hypolimnion of these lakes was specific to the Archaea, whereas the majority of rRNA was derived from Bacteria. Analysis of the 16S rRNA genes cloned from these samples indicated they were closely related to crenarchaeal sequences that have been widely characterized from marine environments. The presence of nearly identical 16S rDNA clones in several of these geographically disparate lakes suggests a cosmopolitan distribution of specific subgroups of these Archaea in freshwater environments. Despite their abundance in the water column of freshwater lakes, we have no representatives of these crenarchaea in pure culture, and so their physiological characteristics and ecological role remain unknown. Present address (B.P. Keough): Department of Microbiology and Molecular Genetics, Bio-Physical Sciences Building, Michigan State University, East Lansing, MI 48823, Phone: (517) 355-6463; Fax: (517) 353-8957     

The Escherichia coli twin-arginine translocase: conserved residues of TatA and TatB family components involved in protein transport

The Escherichia coli Tat system serves to export folded proteins harbouring an N-terminal twin-arginine signal peptide across the cytoplasmic membrane. In this report we have studied the functions of conserved residues within the structurally related TatA and TatB proteins. Our results demonstrate that there are two regions within each protein of high sequence conservation that are critical for efficient Tat translocase function. The first region is the interdomain hinge between the transmembrane and the amphipathic alpha-helices of TatA and TatB proteins. The second region is within the amphipathic helices of TatA and TatB. In particular an invariant phenylalanine residue within TatA proteins is essential for activity, whereas a string of glutamic acid residues on the same face of the amphipathic helix of TatB is important for function.     

An overview of terrorism and its impact on biomedical research facilities

Since the '9/11' and anthrax-contaminated-letter events of 2001, American society has given the term "bioterrorism" much attention. The author clarifies the definitions associated with bioterrorism and terrorism, provides an historical perspective regarding bioweapons, defines and characterizes the types of agents used as bioweapons, reviews pertinent bioterrorism legislation, and concludes by assessing the impact of these elements on biomedical research facilities.     

Synthesis and characterization of palladium complexes of 3-nitroformazans

3-Nitroformazans react with bis(1,1,1,5,5,5-hexafluroacetylacetonato)palladium to afford monometallic complexes. The complexes were characterized via X-ray crystallography, cyclic voltammetry, and electronic spectroscopy. The nature of the aryl substituents on the formazan ligands had a profound effect on the structure and spectroscopy of the complexes, with o-substituted aromatic rings twisted with respect to the ligand, while the p-tolyl substituted derivative adopted a planar structure. The complexes undergo irreversible reductions near ?1 V versus Fc/Fc⁺.     

Comparing benthic biogeochemistry at a sandy and a muddy site in the Celtic Sea using a model and observations

Results from a 1D setup of the European Regional Seas Ecosystem Model (ERSEM) biogeochemical model were compared with new observations collected under the UK Shelf Seas Biogeochemistry (SSB) programme to assess model performance and clarify elements of shelf-sea benthic biogeochemistry and carbon cycling. Observations from two contrasting sites (muddy and sandy) in the Celtic Sea in otherwise comparable hydrographic conditions were considered, with the focus on the benthic system. A standard model parameterisation with site-specific light and nutrient adjustments was used, along with modifications to the within-seabed diffusivity to accommodate the modelling of permeable (sandy) sediments. Differences between modelled and observed quantities of organic carbon in the bed were interpreted to suggest that a large part (>90%) of the observed benthic organic carbon is biologically relatively inactive. Evidence on the rate at which this inactive fraction is produced will constitute important information to quantify offshore carbon sequestration. Total oxygen uptake and oxic layer depths were within the range of the measured values. Modelled depth average pore water concentrations of ammonium, phosphate and silicate were typically 5–20% of observed values at the muddy site due to an underestimate of concentrations associated with the deeper sediment layers. Model agreement for these nutrients was better at the sandy site, which had lower pore water concentrations, especially deeper in the sediment. Comparison of pore water nitrate with observations had added uncertainty, as the results from process studies at the sites indicated the dominance of the anammox pathway for nitrogen removal; a pathway that is not included in the model. Macrofaunal biomasses were overestimated, although a model run with increased macrofaunal background mortality rates decreased macrofaunal biomass and improved agreement with observations. The decrease in macrofaunal biomass was compensated by an increase in meiofaunal biomass such that total oxygen demand remained within the observed range. The permeable sediment modification reproduced some of the observed behaviour of oxygen penetration depth at the sandy site. It is suggested that future development in ERSEM benthic modelling should focus on: (1) mixing and degradation rates of benthic organic matter, (2) validation of benthic faunal biomass against large scale spatial datasets, (3) incorporation of anammox in the benthic nitrogen cycle, and (4) further developments to represent permeable sediment processes.     

Déjà vu--a study of duplicate citations in Medline

MOTIVATION: Duplicate publication impacts the quality of the scientific corpus, has been difficult to detect, and studies this far have been limited in scope and size. Using text similarity searches, we were able to identify signatures of duplicate citations among a body of abstracts. RESULTS: A sample of 62,213 Medline citations was examined and a database of manually verified duplicate citations was created to study author publication behavior. We found that 0.04% of the citations with no shared authors were highly similar and are thus potential cases of plagiarism. 1.35% with shared authors were sufficiently similar to be considered a duplicate. Extrapolating, this would correspond to 3500 and 117,500 duplicate citations in total, respectively. Availability: eTBLAST, an automated citation matching tool, and Déjà vu, the duplicate citation database, are freely available at http://invention.swmed.edu/ and http://spore.swmed.edu/dejavu     

Complete amino acid sequence of human cartilage link protein (CRTL1) deduced from cDNA clones and chromosomal assignment of the gene

Little is known about the primary amino acid structure of human cartilage link protein (CRTL1). We screened a human genomic library with a cDNA encoding the 3' untranslated region and the adjoining B1 domain of chicken link protein. One clone was isolated and characterized. A 3.5-kb EcoRI-KpnI fragment from this genomic clone that contains the human B1 exon was used to map the gene to chromosome 5q13----q14.1. The same fragment was used to screen a cDNA library prepared from mRNA of Caco-2, a human colon tumor cell line. Two overlapping clones were isolated and shown to encode all of CRTL1. The deduced amino acid sequence is 354 residues long. The amino acid sequence shows a striking degree of identity to the porcine (96%), rat (96%), and chicken (85%) link protein sequences. Furthermore, there is greater than 86% homology between the 3' untranslated region of the genes encoding human and porcine link proteins. These results indicate that there has been strong evolutionary pressure against changes in the coding and 3' untranslated regions of the gene encoding cartilage link protein.     

Protocol of a prospective study on the diagnostic value of transcranial duplex scanning of the substantia nigra in patients with parkinsonian symptoms

Background  

Parkinson's disease (PD) is the second most common neurodegenerative disorder. As there is no definitive diagnostic test, its diagnosis is based on clinical criteria. Recently transcranial duplex scanning (TCD) of the substantia nigra in the brainstem has been proposed as an instrument to diagnose PD. We and others have found that TCD scanning of substantia nigra duplex is a relatively accurate diagnostic instrument in patients with parkinsonian symptoms. However, all studies on TCD so far have involved well-defined, later-stage PD patients, which will obviously lead to an overestimate of the diagnostic accuracy of TCD.     

Copy number variation across European populations

Genome analysis provides a powerful approach to test for evidence of genetic variation within and between geographical regions and local populations. Copy number variants which comprise insertions, deletions and duplications of genomic sequence provide one such convenient and informative source. Here, we investigate copy number variants from genome wide scans of single nucleotide polymorphisms in three European population isolates, the island of Vis in Croatia, the islands of Orkney in Scotland and the South Tyrol in Italy. We show that whereas the overall copy number variant frequencies are similar between populations, their distribution is highly specific to the population of origin, a finding which is supported by evidence for increased kinship correlation for specific copy number variants within populations.     

Respiratory responses to long-term temperature exposure in the box turtle,Terrapene ornata

Summary In late February, seven box turtles were collected with body temperatures between 7 and 9°C. Ventilation, gas exchange and end-tidal and were recorded at 5, 10, 15 and 25°C, the animals being at each temperature for 2 to 3 weeks. There was a pronounced diurnal rhythm of breathing frequency at all temperatures. At 5°C the mean 24-h frequency was only 3.7 breaths h^–1. At 15°C the frequency was 16 times higher with a 17-fold increase of ventilation. Oxygen uptake only changed from 3.4 to 12.7 ml·kg^–1·h^–1. Consequently, the ratio (ventilation, ml BTPS/O₂ uptake, ml STPD) increased from 12.5 at 5°C to 48 at 15°C, but decreased to 24 at 25°C. The decrease of this ratio during cold exposure contrasts with an increase of the ratio during cooling earlier reported for fresh water turtles,Pseudemys. Cutaneous CO₂ elimination was important at low temperature. This caused a decrease of the pulmonary gas exchange ratio so that end-tidal remained low at 5°C in spite of an end-tidal of only 54 Torr.