Design Approaches to Expand the Toolkit for Building Cotranscriptionally Encoded RNA Strand Displacement Circuits.

Cotranscriptionally encoded RNA strand displacement (ctRSD) circuits are an emerging tool for programmable molecular computation, with potential applications spanning in vitro diagnostics to continuous computation inside living cells. In ctRSD circuits, RNA strand displacement components are continuously produced together via transcription. These RNA components can be rationally programmed through base pairing interactions to execute logic and signaling cascades. However, the small number of ctRSD components characterized to date limits circuit size and capabilities. Here, we characterize over 200 ctRSD gate sequences, exploring different input, output, and toehold sequences and changes to other design parameters, including domain lengths, ribozyme sequences, and the order in which gate strands are transcribed. This characterization provides a library of sequence domains for engineering ctRSD components, i.e., a toolkit, enabling circuits with up to 4-fold more inputs than previously possible. We also identify specific failure modes and systematically develop design approaches that reduce the likelihood of failure across different gate sequences. Lastly, we show the ctRSD gate design is robust to changes in transcriptional encoding, opening a broad design space for applications in more complex environments. Together, these results deliver an expanded toolkit and design approaches for building ctRSD circuits that will dramatically extend capabilities and potential applications.

Feedback regulation of crystal growth by buffering monomer concentration.

Crystallization is a ubiquitous means of self-assembly that can organize matter over length scales orders of magnitude larger than those of the monomer units. Yet crystallization is notoriously difficult to control because it is exquisitely sensitive to monomer concentration, which changes as monomers are depleted during growth. Living cells control crystallization using chemical reaction networks that offset depletion by synthesizing or activating monomers to regulate monomer concentration, stabilizing growth conditions even as depletion rates change, and thus reliably yielding desired products. Using DNA nanotubes as a model system, here we show that coupling a generic reversible bimolecular monomer buffering reaction to a crystallization process leads to reliable growth of large, uniformly sized crystals even when crystal growth rates change over time. Buffering could be applied broadly as a simple means to regulate and sustain batch crystallization and could facilitate the self-assembly of complex, hierarchical synthetic structures.

Identification and Individualization of Lophophora using DNA Analysis of the trnL/trnF Region and rbcL Gene.

Lophophora williamsii (peyote) is a small, spineless, greenish-blue cactus found in Mexico and the southwestern United States. Ingestion of the cactus can result in hallucinations due to its content of mescaline. In the United States, L. williamsii is classified as a Schedule I controlled substance. In this study, we use DNA analysis of the chloroplast trnL/trnF region and chloroplast rbcL gene to identify the individuals of Lophophora. Using the rbcL gene, Lophophora specimens could be distinguished from outgroups, but species within the genus could not be distinguished. The trnL/trnF region split the Lophophora genus into several groups based on the length and substructure of an AT-rich segment of the sequence. Our results indicate that the genetic variability at the trnL/trnF locus is greater than previously recognized. Although DNA structures at the trnL/trnF region and rbcL gene do not align with the classification of Lophophora species, they can be used to aid in forensic analysis.

DNA identification of Salvia divinorum samples.

Salvia divinorum (diviner's sage) is a plant in the mint family that produces an hallucinogenic compound, salvinorin A. The plant is used, often by chewing or smoking, as a "recreational" drug source and is regulated or banned in several states and countries. We describe a simple DNA technique, polymerase chain reaction of the ribulose bisphosphate carboxylase large subunit (rbcL) gene, that can distinguish S. divinorum leaf pieces from pieces of tobacco or cannabis. We have also found DNA sequences adjacent to the chloroplast leucine transfer RNA (trnL) gene that are specific to S. divinorum and distinguish it from other horticulturally popular Salvia species. We report some significant differences between the S. divinorum trnL sequences we determined and those now published in GenBank.

Antimutagenic specificities of two plant glycosylases, oxoguanine glycosylase and formamidopyrimidine glycosylase, assayed in vivo.

The base-excision repair process protects genomes by removing and replacing altered bases in DNA. Two analogous glycosylases, oxoguanine glycosylase (OGG) and formamidopyrimidine glycosylase (FPG), can start the process by removing oxidized guanine, the most common modification that leads to misreading of DNA. Plants possess genes for both types of glycosylases. We have tested the hypothesis that the two enzymes in plants have diverged in their specificities by inserting the genes for each enzyme from Arabidopsis thaliana L. into Escherichia coli strains designed to indicate the frequencies of the six possible single-base changes. Both enzymes retain the ability to reduce the rate of GC-->TA transversion mutations. Both enzymes also reduce the frequency of two other base-change mutations, GC-->AT and AT-->TA. We do not find a divergence in the repair capabilities of the two enzymes, as measured in E. coli, although surprisingly FPG appears to increase the rate of mutations in one particular strain.

Requirement for abasic endonuclease gene homologues in Arabidopsis seed development.

Arabidopsis thaliana has three genes, Ape1L, Ape2, and Arp, that show homology to abasic (apurinic/apyrimidinic) endonuclease genes of bacterial, yeast, or animal cells. In bacteria, yeast, and animals, abasic endonucleases function in base excision repair of oxidized and other modified DNA bases. Here we report that plants with knock-out mutations in any one of Ape1L, Ape2, or Arp show no apparent differences from wild type in growth rate, growth habit, and fertility. However, coincident knock-out mutations in Ape1L and Ape2 are lethal and lead to abortion of developing embryos. Mutations of Arp are not deleterious, even in combination with one of the other two mutations. The results are consistent with the interpretation that the process of base excision repair, involving at least one intact copy of Ape1L or Ape2, is required in the process of embryogenesis.

DNA analysis of natural fiber rope.

When rope is found at a crime scene, the type of fiber is currently identified through its microscopic characteristics. However, these characteristics may not always unambiguously distinguish some types of rope from others. If rope samples contain cells from the plants of origin, then DNA analysis may prove to be a better way to identify the type of rope obtained from a crime scene. The objective of this project was to develop techniques of DNA analysis that can be used to differentiate between ropes made from Cannabis sativa L. (hemp), Agave sisalana Perrine (sisal), Musa textilis Née (abaca, "Manila hemp"), Linum usitatissimum L. (flax), and Corchorus olitorus L. (jute). The procedures included extracting the DNA from the rope, performing polymerase chain reaction (PCR) using the extracted DNA as a template, and analyzing the DNA products. A primer pair for PCR, chosen from within a chloroplast gene for the large subunit of ribulose bisphosphate carboxylase/oxygenase, was designed to be specific for plant DNA and complementary to the genes from all five plants. The resulting PCR fragments were approximately 771 base pairs long. The PCR fragments, distinguished through base sequence analysis or restriction enzyme analysis, could be used to identify the five different rope types. The procedure provides a useful addition to visual methods of comparing rope samples.

Stationary phase-induction of G-->T mutations in Escherichia coli.

A series of Escherichia coli mutants, constructed originally by Cupples and Miller [C.G. Cupples, J.H. Miller, A set of lacZ mutations in Escherichia coli that allow rapid detection of each of the six base substitutions, Proc. Natl. Acad. Sci. U.S.A. 86 (1989) 5345-5349], provides a unique system for quantifying base-change mutations, and the repair processes that limit their establishment, in bacteria under selective and non-selective conditions. We focussed on one strain in which a T-->G replacement inactivates the lacZ gene. Reversions of this strain can occur through oxidation of G, leading to G-->T transversions. We show that spontaneous reversions occurred both in lactose (selective) and glucose (non-selective) medium. The number of revertants per viable cell was much greater in medium containing lactose or both sugars than glucose alone. In glucose medium, the rate of reversion was highest below 0.6% glucose and strongly inhibited at and above that level. Evidence that reversions occurred through G-->T transversions in both lactose and glucose media came from two observations: by sequence analysis of a series of revertants and by comparing the reversion rates in strains possessing and lacking the mutM gene (encoding formamidopyrimidine DNA glycosylase, FPG). However, the rate of reversion was stimulated by reducing O2 to 1% and inhibited or delayed by increasing O2 to 90%. In mutM- cells grown on glucose medium, the proportion of revertants increased over a 5-day period. In contrast, in mutM+ cells, revertants appeared primarily during the first 2-3 days after plating; few new revertants appeared in the following days. These data imply that base excision repair initiated by FPG was less effective in the first 2 days and more effective later in stationary phase.

A comparison of two DNA base excision repair glycosylases from Arabidopsis thaliana.

Plants contain the genes for both formamidopyrimidine-DNA glycosylase (FPG) and oxoguanine glycosylase (OGG). These enzymes play analogous roles in the base excision repair pathways of bacteria (FPG) and archaea, yeast, and mammals (OGG). Why have plants retained both genes? We tested one hypothesis by comparing the specificities of Arabidopsis FPG and OGG purified from Escherichia coli expression clones. Using depurinated DNA as substrate, the specific activity of Arabidopsis FPG was higher than that of Arabidopsis OGG. Using DNA oxidized by treatment with light in the presence of methylene blue, the specific activities of Arabidopsis FPG and OGG were equal. Using an oligonucleotide containing one oxoguanine (paired with C) and labeled with fluorescein, the specific activity of Arabidopsis OGG was greater than that of either FPG. The results support the hypothesis that genes for the two enzymes have been retained during evolution of plants for their specialized enzyme activities.

Novel expression pattern of cytosolic Gln synthetase in nitrogen-fixing root nodules of the actinorhizal host, Datisca glomerata.

Gln synthetase (GS) is the key enzyme of primary ammonia assimilation in nitrogen-fixing root nodules of legumes and actinorhizal (Frankia-nodulated) plants. In root nodules of Datisca glomerata (Datiscaceae), transcripts hybridizing to a conserved coding region of the abundant nodule isoform, DgGS1-1, are abundant in uninfected nodule cortical tissue, but expression was not detectable in the infected zone or in the nodule meristem. Similarly, the GS holoprotein is immunolocalized exclusively to the uninfected nodule tissue. Phylogenetic analysis of the full-length cDNA of DgGS1-1 indicates affinities with cytosolic GS genes from legumes, the actinorhizal species Alnus glutinosa, and nonnodulating species, Vitis vinifera and Hevea brasilensis. The D. glomerata nodule GS expression pattern is a new variant among reported root nodule symbioses and may reflect an unusual nitrogen transfer pathway from the Frankia nodule microsymbiont to the plant infected tissue, coupled to a distinctive nitrogen cycle in the uninfected cortical tissue. Arg, Gln, and Glu are the major amino acids present in D. glomerata nodules, but Arg was not detected at high levels in leaves or roots. Arg as a major nodule nitrogen storage form is not found in other root nodule types except in the phylogenetically related Coriaria. Catabolism of Arg through the urea cycle could generate free ammonium in the uninfected tissue where GS is expressed.

Polyphenol glucosylating activity in cell suspensions of grape (Vitis vinifera).

Stilbenes are phenolic molecules that have antifungal effects in the plant and antioxidant and anti-cancer effects when consumed in the human diet. Glycosylation of stilbenes increases their solubility and may make them more easily absorbed by the intestine. We have found an activity in extracts of cultured cells of Vitis vinifera (cv. Gamay Freaux) that glucosylates the stilbene resveratrol to form piceid. The Km for UDP-Glucose was 1.2 mM, and the Km for resveratrol was 0.06 mM, values similar to those of other phenolic glucosyltransferases. We investigated the resveratrol glucosylating activity of the enzyme extracted from cells grown under different light treatments (dark, visible light, light + ultraviolet (UVC) radiation) and found the activity to be unaffected or slightly reduced. In contrast, UVC light strongly stimulated extractable quercetin glucosyltransferase activity. These results, combined with analysis of phenolic compounds extracted from the differently treated cells, suggest that the resveratrol glucosyltransferase is distinct from the glucosyltransferase(s) active on other phenolics.

Hydrogen peroxide-induced chilling tolerance in mung beans mediated through ABA-independent glutathione accumulation.

Transient oxidative shock induced by pretreatment of leaves with H2O2 effectively increased chilling tolerance in mung bean and Phalaenopsis. Seedlings of the chilling-tolerant (V3327) cultivar of mung bean (Vignaradiata L.) were employed to study the mechanism of H2O2-induced chilling tolerance. Pretreatment with 200 mM H2O2 increased survival rates of seedlings chilled at 4°C for 36 h from 30% to 70%. The same treatment also lowered the electrolyte leakage from 86% to 21%. Time-course analysis immediately after the treatment demonstrated that exogenous application of H2O2 did not alter the endogenous H2O2 level of the plants. This observation suggests that the primary receptor for the exogenous H2O2 is localized on the leaf surface or in some other way isolated from the endogenous H2O2 pool. Oxidative shock inhibited the induction of the antioxidant enzymes, ascorbate peroxidase and catalase; however, it substantially increased glutathione content both under chilling and control conditions. Combined pretreatment of mung bean plants with abscisic acid and H2O2 showed no synergistic effect on glutathione content and decreased survival rate relative to treatment with either compound alone. These results suggest that the H2O2-induced chilling tolerance in these plants might be mediated by an elevation of glutathione content and is independent of the ABA mechanism of chilling protection.

H2O2 treatment induces glutathione accumulation and chilling tolerance in mung bean.

Mung bean (Vigna radiata L. cv. TN5, a chilling-sensitive cultivar) was employed to evaluate the importance of glutathione in hydrogen peroxide (H2O2)-induced chilling tolerance. Seeds germinated at 25°C for 7d were subjected to different periods of chilling treatment, prior to analysis of the glutathione contents of their leaves. In a comparison of acclimation temperatures from 2-12°C, it was found that an 8°C acclimation for 36 h induced a 5.7-fold increase, the highest glutathione level among the temperatures tested. Seedlings acclimated at 8°C for 36 h showed 97% survival after a 36-h, 4°C chilling stress, compared with 33% survival of non-acclimated plants. Pretreatment with 200 mM H2O2 for 12 h before a 36-h, 4°C chilling treatment increased glutathione levels by 30% and reduced electrolyte leakage to 43%, relative to the untreated control. Treated seedlings also showed a survival rate of 71% after the same chilling treatment. Application of 1 mM buthionine sulfoximine, a specific inhibitor of glutathione synthesis, reversed the protection against chilling stress provided to seedlings either by acclimation at 8°C for 36 h or H2O2 pretreatment. The role of glutathione in chilling acclimation or H2O2-pretreatment-induced chilling tolerance is thus confirmed.

Pharmacokinetics of fentanyl in lumbar and cervical CSF following lumbar epidural and intravenous administration.

Fentanyl (1 microgram/kg body weight) was administered intravenously and via a lumbar epidural catheter (in random order) on 2 separate occasions to 6 patients with chronic pain associated with non-terminal disease states. Frequent blood samples were collected from an indwelling intravenous catheter and CSF samples were collected via spinal needles inserted in the cervical (C7-T1 interspace) and lumbar (L3.4 interspace) regions at 0, 5, 10, 20, 30 and 45 min after fentanyl administration. The concentration of fentanyl in blood and CSF samples were quantified by a sensitive and selective gas-liquid chromatography assay. Visual analogue pain scores (VAPS) were recorded every 5 min for the first hour. Coded syringes (one containing the appropriate fentanyl dose while the other contained an equivalent volume of saline) allowed the investigator administering the fentanyl and assessing VAPS to remain blinded as to which route of administration actually contained the fentanyl. There was minimal vascular uptake of fentanyl following epidural administration. Similarly, the permeation of fentanyl into cervical and lumbar CSF following intravenous administration was minimal and erratic such that only 4 of the 60 CSF samples had detectable fentanyl concentrations. In contrast, there was a rapid penetration of fentanyl across the dura mater following lumbar epidural administration. There was significantly fentanyl in lumbar CSF samples by 10 min in 5 patients, and by 20 min in all 6 patients. The mean maximum lumbar CSF concentration was 19.1 ng/ml, while the time associated with these maximum concentrations was 22.5 min. The mean maximum cervical CSF fentanyl concentrations were 10% of the lumbar CSF concentrations.(ABSTRACT TRUNCATED AT 250 WORDS)