Identifiability in biobanks: models,measures, and mitigation strategies

The collection and sharing of person-specific biospecimens has raised significant questions regarding privacy. In particular, the question of identifiability, or the degree to which materials stored in biobanks can be linked to the name of the individuals from which they were derived, is under scrutiny. The goal of this paper is to review the extent to which biospecimens and affiliated data can be designated as identifiable. To achieve this goal, we summarize recent research in identifiability assessment for DNA sequence data, as well as associated demographic and clinical data, shared via biobanks. We demonstrate the variability of the degree of risk, the factors that contribute to this variation, and potential ways to mitigate and manage such risk. Finally, we discuss the policy implications of these findings, particularly as they pertain to biobank security and access policies. We situate our review in the context of real data sharing scenarios and biorepositories.     

Analysis of flavonoids in flower petals of soybean near-isogenic lines for flower and pubescence color genes

W1, W3, W4, and Wm genes control flower color, whereas T and Td genes control pubescence color in soybean. W1, W3, Wm, and T are presumed to encode flavonoid 3'5'-hydroxylase (EC 1.14.13.88), dihydroflavonol 4-reductase (EC 1.1.1.219), flavonol synthase (EC 1.14.11.23), and flavonoid 3'-hydroxylase (EC 1.14.13.21), respectively. The objective of this study was to determine the structure of the primary anthocyanin, flavonol, and dihydroflavonol in flower petals. Primary component of anthocyanin in purple flower cultivars Clark (W1W1 w3w3 W4W4 WmWm TT TdTd) and Harosoy (W1W1 w3w3 W4W4 WmWm tt TdTd) was malvidin 3,5-di-O-glucoside with delphinidin 3,5-di-O-glucoside as a minor compound. Primary flavonol and dihydroflavonol were kaempferol 3-O-gentiobioside and aromadendrin 3-O-glucoside, respectively. Quantitative analysis of near-isogenic lines (NILs) for flower or pubescence color genes, Clark-w1 (white flower), Clark-w4 (near-white flower), Clark-W3w4 (dilute purple flower), Clark-t (gray pubescence), Clark-td (near-gray pubescence), Harosoy-wm (magenta flower), and Harosoy-T (tawny pubescence) was carried out. No anthocyanins were detected in Clark-w1 and Clark-w4, whereas a trace amount was detected in Clark-W3w4. Amount of flavonols and dihydroflavonol in NILs with w1 or w4 were largely similar to the NILs with purple flower suggesting that W1 and W4 affect only anthocyanin biosynthesis. Amount of flavonol glycosides was substantially reduced and dihydroflavonol was increased in Harosoy-wm suggesting that Wm is responsible for the production of flavonol from dihydroflavonol. The recessive wm allele reduces flavonol amount and inhibits co-pigmentation between anthocyanins and flavonols resulting in less bluer (magenta) flower color. Pubescence color genes, T or Td, had no apparent effect on flavonoid biosynthesis in flower petals.     

Recurrence of Down syndrome associated with microchromosome

Summary We report a family with five members presenting an extra bisatellited microchromosome. Two of them also present trisomy 21. We discuss the relationship between trisomy and the extra chromosome.     

Microbial eco-physiological profiles to estimate the biological restoration of a trichloroethylene-contaminated soil

In the present study, the effectiveness of two plants, Medicago sativa L. and Dittrichia viscosa L., and a biostimulation method based on the use of an olive waste vermicompost, to restore the original quality of a trichloroethylene-contaminated soil was evaluated using eco-physiological profiles. These were designed in form of sun-ray plots by combining soil enzyme activities (dehydrogenase, alkaline phosphatase, β-glucosidase, urease and o-diphenol oxidase), bacterial population size via real-time PCR, Shannon diversity index values for PCR-denaturing gradient gel electrophoresis profiles, and genetic diversity θ_(π) of the sequenced Proteobacteria of the different treatments. The eco-physiological profiles coupling biochemical and molecular parameters could be used as a valuable index for monitoring the success of a restoration scheme, estimating the quality of both contaminated and restored soils. Particularly remarkable was the interaction between vermicompost and D. viscosa, the only treatment that improved biochemical and microbiological restoration in such a way that an eco-physiological profile greater than that of the uncontaminated soil was noticed. The results showed the need to combine chemical analysis and microbiological measurements for evaluating the efficacy of soil remediation techniques.