Current and emerging concepts in biological and analytical variation applied in clinical practice

A single laboratory result actually represents a range of possible values, and a given laboratory result is impacted not just by the presence or absence of disease, but also by biological variation of the measurand in question and analytical variation of the equipment used to make the measurement. Biological variation refers to variability in measurand concentration or activity around a homeostatic set point. Knowledge of biological and analytical variation can be used to facilitate interpretation of patient clinicopathologic data and is particularly useful for interpreting serial patient data and data at or near reference limits or clinical decision thresholds. Understanding how biological and analytical variation impact laboratory results is of increasing importance, because veterinarians evaluate serial data from individual patients, interpret data from multiple testing sites, and use expert consensus guidelines that include decision thresholds for clinicopathologic data interpretation. The purpose of our report is to review current and emerging concepts in biological and analytical variation and discuss how biological and analytical variation data can be used to facilitate clinicopathologic data interpretation. Inclusion of veterinary clinical pathologists having expertise in laboratory quality management and biological variation on research teams and veterinary practice guideline development teams is recommended, to ensure that various considerations for clinicopathologic data interpretation are addressed.     

Performance and genetic analysis of coast redwood cultivars for afforestation of converted grassland in California

New Forests - Afforestation of pasture sites results in a net reduction in atmospheric CO2. Coast redwood (Sequoia sempervirens) is well suited to carbon forestry due to its rapid growth and...     

Variability of flowering and 2n pollen production in diploid potatoes under high temperatures

Nine clones from a heat tolerant PHU-STN hybrid population were evaluated for flower production and percent normal, 2n and non-viable pollen under three temperature regimes at the Southeastern Plant Environmental Laboratories: 30/26, 26/22 and 22/18 C. No flowering was observed at 30/26 C. Flowering was irregular among seven of the clones at 26/22 C and 22/18 C. One clone produced numerous flowers at 26/22 C and 22/18 C. The plot of percent 2n pollen against time for this one clone under 22/18 C revealed a slope which was statistically different from zero but too small to be of practical value. The same plot of this clone under 26/22 C revealed a slope which was not statistically different from zero. Percent 2n pollen was statistically greater (at the 10% level of significance) in the 26/22 C chamber than the 22/18 C chamber.     

Using landscape metrics to characterize towns along an urban-rural gradient

Landscape Ecology - Urban-rural gradients are useful tools when examining the influence of human disturbances on ecological, social and coupled systems, yet the most commonly used gradient...     

Single-molecule DNA sequencing of a viral genome

The full promise of human genomics will be realized only when the genomes of thousands of individuals can be sequenced for comparative analysis. A reference sequence enables the use of short read length. We report an amplification-free method for determining the nucleotide sequence of more than 280,000 individual DNA molecules simultaneously. A DNA polymerase adds labeled nucleotides to surface-immobilized primer-template duplexes in stepwise fashion, and the asynchronous growth of individual DNA molecules was monitored by fluorescence imaging. Read lengths of >25 bases and equivalent phred software program quality scores approaching 30 were achieved. We used this method to sequence the M13 virus to an average depth of >150x and with 100% coverage; thus, we resequenced the M13 genome with high-sensitivity mutation detection. This demonstrates a strategy for high-throughput low-cost resequencing.     

Roles of NPM2 in chromatin and nucleolar organization in oocytes and embryos

Upon fertilization, remodeling of condensed maternal and paternal gamete DNA occurs to form the diploid genome. In Xenopus laevis, nucleoplasmin 2 (NPM2) decondenses sperm DNA in vitro. To study chromatin remodeling in vivo, we isolated mammalian NPM2 orthologs. Mouse NPM2 accumulates in oocyte nuclei and persists in preimplantation embryos. Npm2 knockout females have fertility defects owing to failed preimplantation embryo development. Although sperm DNA decondensation proceeds without NPM2, abnormalities are evident in oocyte and early embryonic nuclei. These defects include an absence of coalesced nucleolar structures and loss of heterochromatin and deacetylated histone H3 that normally circumscribe nucleoli in oocytes and early embryos, respectively. Thus, Npm2 is a maternal effect gene critical for nuclear and nucleolar organization and embryonic development.     

Ubistatins inhibit proteasome-dependent degradation by binding the ubiquitin chain

To identify previously unknown small molecules that inhibit cell cycle machinery, we performed a chemical genetic screen in Xenopus extracts. One class of inhibitors, termed ubistatins, blocked cell cycle progression by inhibiting cyclin B proteolysis and inhibited degradation of ubiquitinated Sic1 by purified proteasomes. Ubistatins blocked the binding of ubiquitinated substrates to the proteasome by targeting the ubiquitin-ubiquitin interface of Lys(48)-linked chains. The same interface is recognized by ubiquitin-chain receptors of the proteasome, indicating that ubistatins act by disrupting a critical protein-protein interaction in the ubiquitin-proteasome system.