Managing the Ethical Issues of Genomic Research using Pathology Specimens

Biobanks of human biospecimens involving tissue taken from surgery require close relationships with diagnostic pathology practices. As most of the tissue will be analysed using genetic or genomic technologies there is the possibility that new information is created that could be of relevance to the donors. Although attention has been recently focused on the responsibilities that may arise from researchers and biobanks in terms of giving back individual genetic research results (IGRRs) to research participants, little has been said in relation to the role of pathology services. In this Commentary, we summarise the issues with respect to pathology services and what guidelines and professional practice documents say about their responsibilities. We also provide points to consider in the development of an ethically defensible plan for giving back individual research results.     

Biomass and distribution of fine and coarse roots from blue oak (Quercus douglasii) trees in the northern Sierra Nevada foothills of California

This research adds to the limited data on coarse and fine root biomass for blue oak (Quercus douglasii Hook and Arn.), a California deciduous oak species found extensively throughout the interior foothills surrounding the Central Valley. Root systems of six blue oak trees were analyzed using three methods — backhoe excavation, quantitative pits, and soil cores. Coarse root biomass ranged from 7 to 177 kg per tree. Rooting depth for the main root system ranged from 0.5 to 1.5 m, with an average of 70% of excavated root biomass located above 0.5 m. Of the total biomass in excavated central root systems, primary roots (including burls) accounted for 56% and large lateral roots (> 20 mm diameter) accounted for 36%. Data from cores indicated that most biomass outside of the root crown was located in fine roots and that fine root biomass decreased with depth. At surface depths (0–20 cm), small-fine (< 0.5 mm diameter) roots accounted for 71%, large-fine (0.5–2.0 mm) for 25%, and coarse (> 2 mm) for 4% of total root biomass collected with cores. Mean fine root biomass density in the top 50 cm was 0.43 kg m⁻³. Fine root biomass did not change with increasing distance from the trees (up to approximately 5 m). Thus, fine roots were not concentrated under the tree canopies. Our results emphasize the importance of the smallest size class of roots (<0.5 mm), which had both higher N concentration and, in the area outside the central root system, greater biomass than large fine (0.5–2.0 mm) or coarse (> 2.0 mm) roots. This revised version was published online in June 2006 with corrections to the Cover Date.     

Molecular homology and DNA hybridization

Summary We reviewed the concept of homology, which can broadly be defined as a correspondence between characteristics that is caused by continuity of information (Van Valen 1982). The concept applies widely in molecular biology when correspondence is taken to mean a genetic relationship resulting from a unique heritable modification of a feature at some previous point in time. Such correspodence can be established for features within a single organism as well as between organisms, making paralogy a valid form of molecular homology under this definition. Molecular homology can be recognized at a variety of organizational levels, which are intedependent. For example, the recognition of homology at the site level involves a statement of homology at the sequence level, and vice versa. This hierarchy, the potential for nonhomologous identity at the site level, and such processes as sequence transposition combine to yield a molecular equivalent to complex structural homology at the anatomical level. As a result, statements of homology between heritable units can involve a valid sense of percent homology.We analyzed DNA hybridization with respect to the problems of recognizing homology and using it in phylogenetic inference. Under a model requiring continuous divergence among compared sequences, DNA hybridization distances embed evolutionary hierarchy, and groups inferred using pairwise methods of tree reconstruction are based on underlying patterns of apomorphic homology. Thus, symplesiomorphic homology will not confound DNA hybridization phylogenies. However, nonhomologous identities that act like apomorphic homologies can lead to inaccurate reconstructions. The main difference between methods of phylogenetic analysis of DNA sequences is that parsimony methods permit hypotheses of nonhomology, whereas distance methods do not.This article was presented at the C.S.E.O.L. Conference on DNA-DNA Hybridization and Evolution, Lake Arrowhead, California, May 11–14, 1989     

Arabidopsis actin depolymerizing factor4 modulates the stochastic dynamic behavior of actin filaments in the cortical array of epidermal cells

Actin filament arrays are constantly remodeled as the needs of cells change as well as during responses to biotic and abiotic stimuli. Previous studies demonstrate that many single actin filaments in the cortical array of living Arabidopsis thaliana epidermal cells undergo stochastic dynamics, a combination of rapid growth balanced by disassembly from prolific severing activity. Filament turnover and dynamics are well understood from in vitro biochemical analyses and simple reconstituted systems. However, the identification in living cells of the molecular players involved in controlling actin dynamics awaits the use of model systems, especially ones where the power of genetics can be combined with imaging of individual actin filaments at high spatial and temporal resolution. Here, we test the hypothesis that actin depolymerizing factor (ADF)/cofilin contributes to stochastic filament severing and facilitates actin turnover. A knockout mutant for Arabidopsis ADF4 has longer hypocotyls and epidermal cells when compared with wild-type seedlings. This correlates with a change in actin filament architecture; cytoskeletal arrays in adf4 cells are significantly more bundled and less dense than in wild-type cells. Several parameters of single actin filament turnover are also altered. Notably, adf4 mutant cells have a 2.5-fold reduced severing frequency as well as significantly increased actin filament lengths and lifetimes. Thus, we provide evidence that ADF4 contributes to the stochastic dynamic turnover of actin filaments in plant cells.     

Effects of Native Plant Species,Mycorrhizal Inoculum,and Mulch on Restoration of Reservoir Sediment Following Dam Removal,Elwha River,Olympic Peninsula,Washington

As dams across the country continue to age, successful restoration of dewatered reservoirs remains a critical factor in decisions regarding dam removal. Freshly exposed reservoir sediment may not support rapid reestablishment of native plant species due to poor fertility or absence of arbuscular mycorrhizal fungi propagules. This field study evaluated treatment effects involving combinations of native plants, mycorrhizal inoculum, and mulch on restoration of dewatered reservoir sediment over 20 months. Most plants, even those uninoculated, became mycorrhizal. In all treatments, sediment pH decreased, as did nitrogen and organic matter, compared to original reservoir sediment, while aggregate stability doubled from original anaerobic sediment. Revegetated plots with mulch had significantly greater vegetation cover and more native volunteer species compared to plots without mulch. The planted mulch treatment also decreased plot runoff tenfold, reducing erosion to the same degree. Indicators suggest that the primary benefit of mulch resulted in increased moisture retention making the planted mulch treatment most successful for restoration of reservoir sediment due to extensive native plant growth, improved soil characteristics, and reduced runoff and erosion compared to nonmulched plots. While results from this plot‐scale study suggest commercial mycorrhizal inoculum is unnecessary since natural inoculum sources sufficiently colonized plants, reservoir‐scale restoration may require creation of additional source areas to encourage rapid reestablishment of native plants and mycorrhizal fungi.     

Factors affecting sedimentational separation of bacteria from blood

Rapid diagnosis of blood infections requires fast and efficient separation of bacteria from blood. We have developed spinning hollow disks that separate bacteria from blood cells via the differences in sedimentation velocities of these particles. Factors affecting separation included the spinning speed and duration, and disk size. These factors were varied in dozens of experiments for which the volume of separated plasma, and the concentration of bacteria and red blood cells (RBCs) in separated plasma were measured. Data were correlated by a parameter of characteristic sedimentation length, which is the distance that an idealized RBC would travel during the entire spin. Results show that characteristic sedimentation length of 20 to 25 mm produces an optimal separation and collection of bacteria in plasma. This corresponds to spinning a 12-cm-diameter disk at 3,000 rpm for 13 s. Following the spin, a careful deceleration preserves the separation of cells from plasma and provides a bacterial recovery of about 61 ± 5%.