Harmonization: Developing Consistent Guidelines for Applying Mode of Action and Dosimetry Information to Cancer and Noncancer Risk Assessment

The 1983 book, Risk Assessment in the Federal Government: Managing the Process, recommended developing consistent inference guidelines for cancer risk assessment. Over the last 15 years, extensive guidance have been provided for hazard assessment for cancer and other endpoints. However, as noted in several recent reports, much less progress has occurred in developing consistent guidelines for quantitative dose response assessment methodologies. This paper proposes an approach for dose response assessment guided by consideration of mode of action (pharmacodynamics) and tissue dosimetry (pharmacokinetics). As articulated here, this systematic process involves eight steps in which available information is integrated, leading first to quantitative analyses of dose response behaviors in the test species followed by quantitative analyses of relevant human exposures. The process should be equally appropriate for both cancer and noncancer endpoints. The eight steps describe the necessary procedures for incorporating mechanistic data and provide multiple options based upon the mode of action by which the chemical causes the toxicity. Given the range of issues involved in developing such a procedure, we have simply sketched the process, focusing on major approaches for using toxicological data and on major options; many details remain to be filled in. However, consistent with the revised carcinogen risk assessment guidance (USEPA, 1996c), we propose a process that would ultimately utilize biologically based or chemical specific pharmacokinetic and pharmacodynamic models as the backbone of these analyses. In the nearer term, these approaches will be combined with analysis of data using more empirical models including options intended for use in the absence of detailed information. A major emphasis in developing any harmonized process is distinguishing policy decisions from those decisions that are affected by the quality and quantity of toxicological data. Identification of data limitations also identifies areas where further study should reduce uncertainty in the final risk evaluations. A flexible dose response assessment procedure is needed to insure that sound toxicological study results are appropriately used to influence risk management decision-making and to encourage the conduct of toxicological studies oriented toward application for dose response assessments.     

Sex pheromones and plasmid transfer in Enterococcus faecalis

Plasmid-free Enterococcus faecalis excrete peptides (sex pheromones) which specifically induce a mating response in strains harboring certain conjugative plasmids. The response is characterized by the synthesis of a "fuzzy" surface material, visible by electron microscopy, which is believed to facilitate the aggregation of donors and recipients. Transconjugants which receive a specific plasmid shut down the production of endogenous pheromone; however, they continue to produce pheromones specific for donors harboring different classes of plasmids. In this review, we summarize what is known about the biochemistry and genetics of this phenomenon. Some emphasis is given to the hemolysin plasmid pAD1 and the regulation of its conjugal transfer.     

Regulation of the pAD1 sex pheromone response in Enterococcus faecalis: effects of host strain and traA, traB, and C region mutants on expression of an E region pheromone-inducible lacZ fusion.

Pheromone-induced conjugal transfer of the hemolysin-bacteriocin plasmid pAD1 of Enterococcus faecalis is regulated by a cluster of determinants designated traA, traB, and regions C and E. The E region is believed to include a positive regulator that controls many structural genes related to conjugation. The pheromone-inducible Tn917-lac fusion NR5, located in the E region, is regulated by the products of traA, traB, and the C region. To more closely examine the effects of these genes on the induction of E region products, inserts in each of these genes were combined with the NR5 fusion in a novel approach involving triparental matings with a pAD1 miniplasmid and recombinational mutagenesis. Results indicate that (i) the traA gene product is a key repressor of the pheromone response; (ii) the traB gene product, in cooperation with a gene within or regulated by the E region, controls pheromone shutdown; (iii) a primary function of the C region gene product is in pheromone sensing, with secondary functions in pheromone shutdown and negative regulation; and (iv) the host in which the plasmid resides has a dramatic effect on the regulation of the NR5 fusion in traB and C region mutants. Numerous parallels were observed between the regulation of the NR5 fusion and the regulation of the aggregation and transfer response. These parallels aided in further defining the functions of particular regulatory determinants as well as further establishing the link between the regulation of the E region and the regulation of the aggregation and transfer response.     

Using an evolutionary algorithm and parallel computing for haplotyping in a general complex pedigree with multiple marker loci

Background  

Haplotype reconstruction is important in linkage mapping and association mapping of quantitative trait loci (QTL). One widely used statistical approach for haplotype reconstruction is simulated annealing (SA), implemented in SimWalk2. However, the algorithm needs a very large number of sequential iterations, and it does not clearly show if convergence of the likelihood is obtained.     

Improving the Development and Use of Biologically Based Dose Response Models (BBDR) in Risk Assessment

Biologically based dose-response (BBDR) models predict health outcomes (response) resulting from the presence of a toxicant at a biological target (dose). The benefits of BBDR models are many, and research programs are increasingly focusing on mechanistic research to support model development; however, progress has been slow. Impediments to progress include the complexity of dose response modeling, the need for a multidisciplinary team and consistent funding support, and difficulty in identifying and extracting the needed data. Of immediate concern is the lack of transparency of published models to the supporting data and literature, difficulty in accessing model code and simulation conditions sufficient to allow independent replication of results, and absence of well-defined quality criteria. Suggestions are presented to improve the development and use of BBDR models in risk assessment and to address the above limitations. Examples from BBDR models for methylmercury neurotoxicity and 5-fluorouracil embryotoxicity are presented to illustrate the suggestions including what kinds of databases are needed to support model development and transparency, quality assurance for modeling, and how the internet can advance database development and collaboration within the biological modeling community.     

Failure to Use Cubicles and Concentrate Dispenser by Heifers after Transfer from Rearing Accommodation to Milking Herd

Thirty-three dairy farms in the Norwegian counties of ?stfold and Akershus in which cubicle sheds had been in use for at least one year and with a herd size of less than 60 cows, were contacted and asked to participate in a study. The study focused on heifers' use of cubicles and concentrate dispenser just after being transferred from rearing accommodation to the milking herd. For each heifer, the farmer recorded cubicle use once nightly between 9 and 11 pm. The daily amount of concentrate released in the dispenser and the allotted daily ration were also recorded. The recording period was 15 consecutive days for cubicle use and 7 days for concentrate dispenser use. Cubicle refusal behaviour, i.e. lying outside the cubicles, was analysed by logistic regression using rearing accommodation of heifers, herd size, heifer age, and housing layout as independent variables, and herd as a clustering variable. On Day 2 after transfer, 34% of the heifers were showing cubicle refusal behaviour (N = 340). By Day 15 this percentage had dropped to 23. Cubicle refusal was lower throughout the whole period among heifers which used the cubicles on the 3 first days after transfer compared to those which did not. This tendency could also be detected several months later. The analysis showed cubicle refusal to be significantly associated with rearing accommodation (OR = 6.1, c.i._95%OR = 1.5–24.3, P = 0.01) and cubicle layout in the shed (OR = 0.2, c.i._95%OR = 0.0–0.7, P = 0.01). None of the tested variables were found to be significant for failure to use the concentrate dispenser, a behaviour which was less frequent than cubicle refusal. However, 8 percent of the heifers did not visit the dispenser at all throughout the 7 days of observation.     

Changes in Triphasic Mechanical Properties of Proteoglycan-Depleted Articular Cartilage Extracted from Osmotic Swelling Behavior Monitored Using High-Frequency Ultrasound

This study aims to obtain osmosis-induced swelling strains of normal and proteoglycan (PG) depleted articular cartilage using an ultrasound system and to investigate the changes in its mechanical properties due to the PG depletion using a layered triphasic model. The swelling strains of 20 cylindrical cartilage-bone samples collected from different bovine patellae were induced by decreasing the concentration of bath saline and monitored by the ultrasound system. The samples were subsequently digested by a trypsin solution for approximately 20 min to deplete proteoglycans, and the swelling behaviors of the digested samples were measured again. The bi-layered triphasic model proposed in our previous study (Wang et al., J Biomech Eng-Trans ASME 2007; 129: 413-422) was used to predict the layered aggregate modulus Hafrom the data of depth-dependent swelling strain, fixed charge density and water content. It was found that the region near the bone, for the normal specimens, had a significantly higher aggregate modulus (Ha₁= 20.6±18.2 MPa) in comparison with the middle zone and the surface layer (Ha₂= 7.8±14.5 MPa and Ha₃= 3.6±3.2 MPa, respectively) (p < 0.001). The normalized thickness of the deep layer h₁ was 0.68±0.20. After the trypsin digestion, the parametric values decreased to Ha₁ = 13.6±9.6 MPa, Ha₂ = 6.7±11.5 MPa, Ha₃ = 2.7±3.2 MPa, and h₁ = 0.57±0.28. Other models were also used to analyze data and the results were compared. This study showed that high-frequency ultrasound measurement combined with the triphasic modeling was capable of nondestructively quantifying the alterations in the layered mechanical properties of the proteoglycan-depleted articular cartilage.     

Mathematical design of prokaryotic clone-based microarrays

Background  

Clone-based microarrays, on which each spot represents a random genomic fragment, are a good alternative to open reading frame-based microarrays, especially for microorganisms for which the complete genome sequence is not available. Since the generation of a genomic DNA library is a random process, it is beforehand uncertain which genes are represented. Nevertheless, the genome coverage of such an array, which depends on different variables like the insert size and the number of clones in the library, can be predicted by mathematical approaches. When applying the classical formulas that determine the probability that a certain sequence is represented in a DNA library at the nucleotide level, massive amounts of clones would be necessary to obtain a proper coverage of the genome.     

Similar structural basis for membrane localization and protein priming by an RNA-dependent RNA polymerase

Protein primers are used to initiate genomic synthesis of several RNA and DNA viruses, although the structural details of the primer-polymerase interactions are not yet known. Poliovirus polymerase binds with high affinity to the membrane-bound viral protein 3AB but uridylylates only the smaller peptide 3B in vitro. Mutational analysis of the polymerase identified four surface residues on the three-dimensional structure of poliovirus polymerase whose wild-type identity is required for 3AB binding. These mutants also decreased 3B uridylylation, arguing that the binding sites for the membrane tether and the protein primer overlap. Mutation of flanking residues between the 3AB binding site and the polymerase active site specifically decreased 3B uridylylation, likely affecting steps subsequent to binding. The physical overlap of sites for protein priming and membrane association should facilitate replication initiation in the membrane-associated complex.     

Anti-α-fodrin antibodies do not add much to the diagnosis of Sjögren's syndrome

The presence of anti-α-fodrin autoantibodies has been reported to be a highly specific and sensitive test for the diagnosis of Sjögren's syndrome (SjS). We looked (in Nijmegen) for anti-α-fodrin, anti-Ro60, and anti-La autoantibodies in a cohort of 51 patients with rheumatic diseases (primary SjS [21], secondary SjS [6], rheumatoid arthritis [RA] [12], systemic lupus erythematosus [SLE] [6], and scleroderma [6]) and in 28 healthy subjects, using ELISA, immunoblotting, and immunoprecipitation. The same samples were analyzed with an alternative anti-α-fodrin ELISA in Hanover. The Nijmegen ELISA of the sera from primary SjS showed sensitivities of 43% and 48% for IgA- and IgG-type anti-α-fodrin antibodies, respectively. The Hanover ELISA showed sensitivities of 38% and 10% for IgA- and IgG-type anti-α-fodrin antibodies, respectively. The ELISAs for α-fodrin showed six (Nijmegen) and four (Hanover) anti-α-fodrin-positive RA sera. IgA and IgG anti-fodrin antibodies were also present in four patients with secondary SjS. The sensitivities of Ro60 and La-antibodies in the Nijmegen ELISA were 67% and 62%, respectively. Unlike anti-α-fodrin antibodies, all anti-Ro60 and anti-La positive sera could be confirmed by immunoblotting or RNA immunoprecipitation. Thus, anti-Ro and anti-La autoantibodies were more sensitive than anti-α-fodrin autoantibodies in ELISA and were more frequently confirmed by other techniques. Anti-La antibodies appear to be more disease-specific than anti-α-fodrin antibodies, which are also found in RA sera. Therefore, the measurement of anti-α-fodrin autoantibodies does not add much to the diagnosis of Sjögren's syndrome.