Cumulative risk assessment lessons learned: a review of case studies and issue papers.

Cumulative risk assessments (CRAs) examine potential risks posed by exposure to multiple and sometimes disparate environmental stressors. CRAs are more resource intensive than single chemical assessments, and pose additional challenges and sources of uncertainty. CRAs may examine the impact of several factors on risk, including exposure magnitude and timing, chemical mixture composition, as well as physical, biological, or psychosocial stressors. CRAs are meant to increase the relevance of risk assessments, providing decision makers with information based on real world exposure scenarios that improve the characterization of actual risks and hazards. The U.S. Environmental Protection Agency has evaluated a number of CRAs, performed by or commissioned for the Agency, to seek insight into CRA concepts, methods, and lessons learned. In this article, ten case studies and five issue papers on key CRA topics are examined and a set of lessons learned are identified for CRA implementation. The lessons address the iterative nature of CRAs, importance of considering vulnerability, need for stakeholder engagement, value of a tiered approach, new methods to assess multiroute exposures to chemical mixtures, and the impact of geographical scale on approach and purpose.

Second-generation covalent TMP-tag for live cell imaging.

Chemical tags are now viable alternatives to fluorescent proteins for labeling proteins in living cells with organic fluorophores that have improved brightness and other specialized properties. Recently, we successfully rendered our TMP-tag covalent with a proximity-induced reaction between the protein tag and the ligand-fluorophore label. This initial design, however, suffered from slow in vitro labeling kinetics and limited live cell protein labeling. Thus, here we report a second-generation covalent TMP-tag that has a fast labeling half-life and can readily label a variety of intracellular proteins in living cells. Specifically, we designed an acrylamide-trimethoprim-fluorophore (A-TMP-fluorophore v2.0) electrophile with an optimized linker for fast reaction with a cysteine (Cys) nucleophile engineered just outside the TMP-binding pocket of Escherichia coli dihydrofolate reductase (eDHFR) and developed an efficient chemical synthesis for routine production of a variety of A-TMP-probe v2.0 labels. We then screened a panel of eDHFR:Cys variants and identified eDHFR:L28C as having an 8-min half-life for reaction with A-TMP-biotin v2.0 in vitro. Finally, we demonstrated live cell imaging of various cellular protein targets with A-TMP-fluorescein, A-TMP-Dapoxyl, and A-TMP-Atto655. With its robustness, this second-generation covalent TMP-tag adds to the limited number of chemical tags that can be used to covalently label intracellular proteins efficiently in living cells. Moreover, the success of this second-generation design further validates proximity-induced reactivity and organic chemistry as tools not only for chemical tag engineering but also more broadly for synthetic biology.

Ordered and dynamic assembly of single spliceosomes.

The spliceosome is the complex macromolecular machine responsible for removing introns from precursors to messenger RNAs (pre-mRNAs). We combined yeast genetic engineering, chemical biology, and multiwavelength fluorescence microscopy to follow assembly of single spliceosomes in real time in whole-cell extracts. We find that individual spliceosomal subcomplexes associate with pre-mRNA sequentially via an ordered pathway to yield functional spliceosomes and that association of every subcomplex is reversible. Further, early subcomplex binding events do not fully commit a pre-mRNA to splicing; rather, commitment increases as assembly proceeds. These findings have important implications for the regulation of alternative splicing. This experimental strategy should prove widely useful for mechanistic analysis of other macromolecular machines in environments approaching the complexity of living cells.

An in vivo covalent TMP-tag based on proximity-induced reactivity.

Chemical tags for live cell imaging are emerging as viable alternatives to the fluorescent proteins for labeling proteins with small molecule probes. Among reported chemical tags, trimethoprim (TMP)-tag stands out for having sufficient cell permeability and selectivity to allow imaging of intracellular proteins. TMP-tag provides a noncovalent label in which the protein of interest is fused to E. coli dihydrofolate reductase (DHFR) and then labeled with a cell-permeable TMP-probe heterodimer. To complement the utility of the noncovalent TMP-tag, we sought to render the TMP-tag covalent for applications such as single-molecule tracking and pulse-chase labeling that would benefit from a more permanent modification. On the basis of the long-standing use of proximity-induced reactivity for irreversible inhibitor design and its more recent application to in vitro chemical biology tools, we designed an eDHFR variant with a unique cysteine residue positioned to react with an acrylamide electrophile installed on the TMP-probe label. In vitro experiments show that the eDHFR:L28C nucleophile reacts rapidly and quantitatively with the TMP-acrylamide-probe. Most significantly, the balance in reactivity provided by the acrylamide electrophile allows intracellular proteins tagged with eDHFR:L28C to be labeled with a TMP-acrylamide-fluorescein heterotrimer in live cells with minimal background. Thus, the TMP electrophile described here can be used immediately as a covalent chemical tag in live cells. Moreover, proximity-induced reactivity is shown to be sufficiently selective for use in a living cell, suggesting a general approach for the development of orthogonal covalent chemical tags from existing noncovalent ligand-protein pairs.

Thermal chemistry of bicyclo[4.2.0]oct-2-enes.

At 300 degrees C, bicyclo[4.2.0]oct-2-ene (1) isomerizes to bicyclo[2.2.2]oct-2-ene (2) via a formal [1,3] sigmatropic carbon migration. Deuterium labels at C7 and C8 were employed to probe for two-centered stereomutation resulting from C1-C6 cleavage and for one-centered stereomutation resulting from C1-C8 cleavage, respectively. In addition, deuterium labeling allowed for the elucidation of the stereochemical preference of the [1,3] migration of 1 to 2. The two possible [1,3] carbon shift outcomes reflect a slight preference for migration with inversion rather than retention of stereochemistry; the si/sr product ratio is approximately 1.4. One-centered stereomutation is the dominant process in the thermal manifold of 1, with lesser amounts of fragmentation and [1,3] carbon migration processes being observed. All of these observations are consistent with a long-lived, conformationally promiscuous diradical intermediate.

Deuterium kinetic isotope effects and mechanism of the thermal isomerization of bicyclo[4.2.0]oct-7-ene to 1,3-cyclooctadiene.

The thermal conversion of cis-bicyclo[4.2.0]oct-7-ene to cis,cis-1,3-cyclooctadiene might involve a direct disrotatory ring opening, or it might possibly take place by way of cis,trans-1,3-cyclooctadiene. This cis,trans-diene might possibly form the more stable cis,cis isomer through a [1,5] hydrogen shift or a trans-to-cis isomerization about the trans double bond. Deuterium kinetic isotope effect determinations for the isomerizations of 2,2,5,5-d(4)-bicyclo[4.2.0]oct-7-ene and 7,8-d(2)-bicyclo[4.2.0]oct-7-ene rule out these two alternatives because the observed effects are much smaller than would be anticipated for these mechanisms: k(H)/k(D)(d(4)) at 250 degrees C is 1.17 (1.04 per D), and k(H)/k(D)(d(2)) at 238 degrees C is 1.20 (1.10 per D). The direct disrotatory ring opening route remains the preferred mechanism.

Thermal disrotatory electrocyclic isomerization of cis-bicyclo[4.2.0]oct-7-ene to cis,cis-1,3-cyclooctadiene.

[reaction: see text] The ratio of observed rate constants, k/k', for thermal isomerizations of cis-bicyclo[4.2.0]oct-7-ene and its 2,2,5,5-d(4) analogue to cis,cis-1,3-cyclooctadienes at 250 degrees C is 1.17, indicative of a secondary, not a primary, deuterium kinetic isotope effect. The reaction does not occur through a [1,5] hydrogen shift from the transient cis,trans-1,3-cyclooctadiene intermediate to form the observed cis,cis-diene product.