Assessment of Optimal Selected Prognostic Factors

The identification and assessment of prognostic factors is one of the major tasks in clinical research. The assessment of one single prognostic factor can be done by recently established methods for using optimal cutpoints. Here, we suggest a method to consider an optimal selected prognostic factor from a set of prognostic factors of interest. This can be viewed as a variable selection method and is the underlying decision problem at each node of various tree building algorithms. We propose to use maximally selected statistics where the selection is defined over the set of prognostic factors and over all cutpoints in each prognostic factor. We demonstrate that it is feasible to compute the approximate null distribution. We illustrate the new variable selection test with data of the German Breast Cancer Study Group and of a small study on patients with diffuse large B‐cell lymphoma. Using the null distribution for a p‐value adjusted regression trees algorithm, we adjust for the number of variables analysed at each node as well. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Thermoregulation and roost selection by reproductive female big brown bats (Eptesicus fuscus) roosting in rock crevices

A free-ranging maternity colony of big brown bats Eptesicus fuscus roosting in rock crevices along the South Saskatchewan River in south-eastern Alberta, Canada, was studied to understand better the discrepancy that exists in the literature regarding torpor use by reproductive female bats. Using radio-telemetry, thermoregulatory patterns and roost microclimate were recorded for pregnant, lactating and post-lactating females. Relative torpor use is described in several ways: the proportion of days on which torpor was used, depth, minimum body temperature, time spent in torpor, and a comprehensive torpor unit (degree-min). Pregnant and lactating female E. fuscus used torpor to the same extent overall (degree-min), but pregnant bats used torpor less frequently and with more time in deep torpor. Torpor was used to the greatest extent after weaning (post-lactation). Evidence is presented that the cost:benefit ratio for deep and prolonged periods of torpor may be highest during lactation. Microclimates of rock-crevice roosts mirrored the use of torpor throughout reproduction by bats. Lactation roosts (deeper, larger opening size) were more thermally stable and remained warmer at night compared to the shallow roosts used by pregnant and post-lactating females. It is shown that conclusions about relative use of torpor can differ depending on the units of comparison, necessitating measurement of all aspects of torpor (depth, duration and frequency). Comprehensive measurements, individual-based normothermic temperatures, and a definition of torpor that accounts for all energy savings, allow a more accurate depiction of patterns and facilitates inter-study comparisons.     

Antagonism of microRNA-122 in mice by systemically administered LNA-antimiR leads to up-regulation of a large set of predicted target mRNAs in the liver

MicroRNA-122 (miR-122) is an abundant liver-specific miRNA, implicated in fatty acid and cholesterol metabolism as well as hepatitis C viral replication. Here, we report that a systemically administered 16-nt, unconjugated LNA (locked nucleic acid)-antimiR oligonucleotide complementary to the 5′ end of miR-122 leads to specific, dose-dependent silencing of miR-122 and shows no hepatotoxicity in mice. Antagonism of miR-122 is due to formation of stable heteroduplexes between the LNA-antimiR and miR-122 as detected by northern analysis. Fluorescence in situ hybridization demonstrated uptake of the LNA-antimiR in mouse liver cells, which was accompanied by markedly reduced hybridization signals for mature miR-122 in treated mice. Functional antagonism of miR-122 was inferred from a low cholesterol phenotype and de-repression within 24 h of 199 liver mRNAs showing significant enrichment for miR-122 seed matches in their 3′ UTRs. Expression profiling extended to 3 weeks after the last LNA-antimiR dose revealed that most of the changes in liver gene expression were normalized to saline control levels coinciding with normalized miR-122 and plasma cholesterol levels. Combined, these data suggest that miRNA antagonists comprised of LNA are valuable tools for identifying miRNA targets in vivo and for studying the biological role of miRNAs and miRNA-associated gene-regulatory networks in a physiological context.     

Shared patterns of species turnover between seaweeds and seed plants break down at increasing distances from the sea

We tested for correlations in the degree of spatial similarity between algal and terrestrial plants communities along 5500 km of temperate Australian coastline and whether the strength of correlation weakens with increasing distance from the coast. We identified strong correlations between macroalgal and terrestrial plant communities within the first 100 km from shore, where the strength of these marine–terrestrial correlations indeed weakens with increasing distance inland. As such, our results suggest that marine‐driven community homogenization processes decompose with increasing distance from the shore toward inland. We speculate that the proximity to the marine environment produces lower levels of community turnover on land, and this effect decreases progressively farther inland. Our analysis suggests underlying ecological and evolutionary processes that give rise to continental‐scale biogeographic influence from sea to land.     

Screening for antimicrobial resistance genes and virulence factors via genome sequencing

Second-generation genome sequencing and alignment of the resulting reads to in silico genomes containing antimicrobial resistance and virulence factor genes were used to screen for undesirable genes in 28 strains which could be used in human nutrition. No virulence factor genes were detected, while several isolates contained antimicrobial resistance genes.     

A high-throughput method for liquid chromatography–tandem mass spectrometry determination of plasma alkylresorcinols,biomarkers of whole grain wheat and rye intake

Plasma alkylresorcinols are increasingly analyzed in cohort studies to improve estimates of whole grain intake and their relationship with disease incidence. Current methods require large volumes of solvent (>10 ml/sample) and have relatively low daily sample throughput. We tested five different supported extraction methods for extracting alkylresorcinols from plasma and improved a normal-phase liquid chromatography coupled to a tandem mass spectrometer method to reduce sample analysis time. The method was validated and compared with gas chromatography–mass spectrometry analysis. Sample preparation with HybridSPE supported extraction was most effective for alkylresorcinol extraction, with recoveries of 77–82% from 100 μl of plasma. The use of 96-well plates allowed extraction of 160 samples per day. Using a 5-cm NH₂ column and heptane reduced run times to 3 min. The new method had a limit of detection and limit of quantification equivalent to 1.1–1.8 nmol/L and 3.5–6.1 nmol/L plasma, respectively, for the different alkylresorcinol homologues. Accuracy was 93–105%, and intra- and inter-batch precision values were 4–18% across different plasma concentrations. This method makes it possible to quantify plasma alkylresorcinols in 100 μl of plasma at a rate of at least 160 samples per day without the need for large volumes of organic solvents.     

Express Your LOV: An Engineered Flavoprotein as a Reporter for Protein Expression and Purification

In this work, we describe the utility of Light, Oxygen, or Voltage-sensing (LOV) flavoprotein domains from plant phototropins as a reporter for protein expression and function. Specifically, we used iLOV, an enhanced and more photostable variant of LOV. A pET-based plasmid for protein expression was constructed, encoding a C terminal iLOV-octahistidine (His8)-tag and a HRV 3C protease cleavage recognition site. Ten different proteins, with various sub-cellular locations, were cloned into the plasmid, creating iLOV-His8 tag fusions. To test protein expression and how iLOV could be used as a reporter, the proteins were expressed in three different cell lines, in four different culture media, at two different temperatures. To establish whether the presence of the iLOV tag could have an impact on the functionality, one of the proteins, EspG, was over-expressed and purified. EspG is an “effector” protein normally produced by enterohemorrhagic E. coli strains and “injected” into host cells via the T3SS. We tested functionality of EspG-iLOV fusion by performing functional studies of EspG in mammalian host cells. When EspG-iLOV was microinjected into the host cell, the Golgi apparatus was completely disrupted as had previously been observed for EspG.