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Synthesis of furo[3,4-c]furans using a rhodium(II)-catalyzed cyclization/Diels-Alder cycloaddition sequence.

A series of 2-alkynyl 2-diazo-3-oxobutanoates, when treated with a catalytic quantity of rhodium(II) acetate, afforded furo[3,4-c]furans in good yield. The reaction proceeds by addition of a rhodium-stabilized carbenoid onto the acetylenic pi-bond to give a vinyl carbenoid that subsequently cyclizes onto the neighboring carbonyl group to produce the furan ring. These furo[3,4-c]furans react with various dienophiles, furnishing anisole derivatives derived by loss of water from the initially formed Diels-Alder cycloadducts. The Rh(II)-catalyzed cyclization reaction was quite versatile with regard to the nature of the interacting carbonyl group. The methodology was applied to the synthesis of several oxa-polyheterocyclic systems by first generating a 2-alkoxy-substituted furan and then allowing it to undergo a subsequent intramolecular Diels-Alder cycloaddition. Ring opening of the resulting cycloadduct is followed by deprotonation to furnish a rearranged keto lactone. The potential use of this method for the synthesis of the alkaloid strychnine was probed using suitable model diazo compounds. To establish the viability of this approach, the Rh(II)-catalyzed cyclization/cycloaddition sequence of alpha-diazo amides 64 and 68 were studied. Both compounds underwent the sequential process in good overall yield, leading to novel pentacyclic products. The structural features of the resultant products present numerous opportunities for postcycloaddition manipulations that could be exploited to synthetic advantage.

Journal Article↗

The effect of replication on gene expression microarray experiments.

MOTIVATION: We examine the effect of replication on the detection of apparently differentially expressed genes in gene expression microarray experiments. Our analysis is based on a random sampling approach using real data sets from 16 published studies. We consider both the ability to find genes that meet particular statistical criteria as well as the stability of the results in the face of changing levels of replication. RESULTS: While dependent on the data source, our findings suggest that stable results are typically not obtained until at least five biological replicates have been used. Conversely, for most studies, 10-15 replicates yield results that are quite stable, and there is less improvement in stability as the number of replicates is further increased. Our methods will be of use in evaluating existing data sets and in helping to design new studies.

Animals↗

Aggressive pharmacologic donor management results in more transplanted organs.

BACKGROUND: Brain death results in adverse pathophysiologic effects in many cadaveric donors, resulting in cardiovascular instability and poor organ perfusion. Hormonal resuscitation (HR) has been reported to stabilize and improve cardiac function in brain-dead donors. The goal of this study was to examine the effect of HR on the brain-dead donor on the number of organs transplanted per donor. METHODS: A retrospective analysis of all brain-dead donors recovered in the United States from January 1, 2000, to September 30, 2001, was conducted. HR consisted of a methylprednisolone bolus and infusions of vasopressin and either triiodothyronine or L-thyroxine. Univariate analyses and multivariate logistic regression analyses were used to detect differences between the HR group and those donors who did not receive HR. RESULTS: Of 10,292 consecutive brain-dead donors analyzed, 701 received three-drug HR. Univariate analysis showed the mean number of organs from HR donors (3.8) was 22.5% greater than that from nonhormonal resuscitation donors (3.1) (P <0.001). Multivariate analyses showed that HR was associated with the following statistically significant increased probabilities of an organ being transplanted from a donor: kidney 7.3%, heart 4.7%, liver 4.9%, lung 2.8%, and pancreas 6.0%. Extrapolation of these probabilities to the 5,921 brain-dead donors recovered in 2001 was calculated to yield a total increase of 2,053 organs. CONCLUSION: HR stabilizes certain brain-dead donors and is associated with significant increases in organs transplanted per donor.

Adult↗

Eliminating transient artifacts in stabilized-image contrast thresholds.

In the measurements of contrast thresholds for stationary, stabilized images, the choice of the psychophysical procedure may profoundly affect the results by constraining the time course of the stimulus presentation. With some procedures, the subject is unable to ignore transients; as a result, he necessarily responds to onset and offset transients rather than to the intended stimulus. Here we report significant effects of (a) the rapidly of onset and (b) the duration of the stimulus on thresholds for stabilized sinusoidal-grating patterns; these effects occur with both forced-choice and standard yes/no procedures. No value of either parameter (a) or (b) can eliminate such presentation effects when these procedures are used. However, we have devised a new, continuous-presentation procedure that yields results that do not depend on these parameters. Contrast thresholds for stabilized and for unstabilized stimuli measured by this procedure differ by 1 log unit or more, in good agreement with the results obtained by careful use of the method of adjustment.

Differential Threshold↗

Reactions of H(3)Al.NMe(3) with E(SiMe(3))(3) (E = P, As). Structural Characterization of the Trimer [H(2)AlP(SiMe(3))(2)](3) and Base-Stabilized Adduct [H(2)AlAs(SiMe(3))(2)].NMe(3) and Their Thermal Decomposition toward Nanocrystalline AlP and AlAs, Respectively.

Dehydrosilylation reactions in diethyl ether between H(3)Al.NMe(3) and E(SiMe(3))(3) afforded for E = P a high yield of the trimer [H(2)AlP(SiMe(3))(2)](3) (1), while for E = As a monomeric base-stabilized adduct [H(2)AlAs(SiMe(3))(2)].NMe(3) (2) as well as its degradation solid product were obtained. No reaction occurred for E = N. The single-crystal X-ray structure determination for 1 yielded a planar six-membered ring of alternating four-coordinated Al and P centers. The structural solution for 2 revealed the monomeric unit [H(2)AlAs(SiMe(3))(2)] stabilized by coordination of NMe(3) at the Al site. Pyrolysis of 1 at 450 degrees C promoted further dehydrosilylation and yielded a product which by XRD spectroscopy showed the onset of AlP crystallinity while at 950 degrees C afforded nanocrystalline AlP with 5 nm average particle size. Pyrolysis of 2 at 450 degrees C resulted in the formation of nanocrystalline AlAs with 2 nm average particle size. Under applied pyrolysis conditions for 1 and 2, the target elimination-condensation pathway via dehydrosilylation was accompanied by other decomposition side reactions and retention of some contaminant residues.

Journal Article↗

Comparison of proteins involved in pilus synthesis and mating pair stabilization from the related plasmids F and R100-1: insights into the mechanism of conjugation.

F and R100-1 are closely related, derepressed, conjugative plasmids from the IncFI and IncFII incompatibility groups, respectively. Heteroduplex mapping and genetic analyses have revealed that the transfer regions are extremely similar between the two plasmids. Plasmid specificity can occur at the level of relaxosome formation, regulation, and surface exclusion between the two transfer systems. There are also differences in pilus serology, pilus-specific phage sensitivity, and requirements for OmpA and lipopolysaccharide components in the recipient cell. These phenotypic differences were exploited in this study to yield new information about the mechanism of pilus synthesis, mating pair stabilization, and surface and/or entry exclusion, which are collectively involved in mating pair formation (Mpf). The sequence of the remainder of the transfer region of R100-1 (trbA to traS) has been completed, and the complete sequence is compared to that of F. The differences between the two transfer regions include insertions and deletions, gene duplications, and mosaicism within genes, although the genes essential for Mpf are conserved in both plasmids. F+ cells carrying defined mutations in each of the Mpf genes were complemented with the homologous genes from R100-1. Our results indicate that the specificity in recipient cell recognition and entry exclusion are mediated by TraN and TraG, respectively, and not by the pilus.

Bacterial Proteins↗

Effect of pH and temperature on the stability of UV-induced repairable pyrimidine hydrates in DNA.

UV irradiation of cytosine yields 6-hydroxy-5,6-dihydrocytosine (cytosine hydrate) whether the cytosine is in solution as base, nucleoside, or nucleotide or on the DNA backbone. Cytosine hydrate decomposes by elimination of water, yielding cytosine, or by irreversible deamination, yielding uracil hydrate, which, in turn, decomposes by dehydration yielding uracil. To determine how pH and temperature affect these decomposition reactions, alternating poly(dG-[3H]dC) copolymer was irradiated at 254 nm and incubated under different conditions of pH and temperature. The cytosine hydrate and uracil hydrate content of the DNA was determined by the use of Escherichia coli endonuclease III, which releases pyrimidine hydrates from DNA by virtue of its DNA glycosylase activity. Uracil content was determined by using uracil-DNA glycosylase. The rate of decomposition of cytosine hydrate to cytosine was determined at 4 temperatures at pH 3.1, 5.4, and 7.4. The Ea was determined from the rates by using the Arrhenius equation and proved to be the same at pH 5.4 and 7.4, although the decomposition rate at pH 5.4 was faster at all temperatures. At pH 3.1, the Ea was reduced. These results suggest that the dehydration reaction is affected by two discrete protonations, most probably of the N-3 and the OH group of C-6 of cytosine hydrate. The deamination of cytosine hydrate to uracil hydrate was maximal at pH 3.1 at all temperatures. The doubly protonated cytosine hydrate probably is the common intermediate for both competing decomposition reactions, explaining why cytosine hydrate is prone to deamination at acid pH.(ABSTRACT TRUNCATED AT 250 WORDS)

Cytosine↗

Using evolutionary information and ancestral sequences to understand the sequence-function relationship in GLP-1 agonists.

Glucagon-like peptide-1 (GLP-1) is an incretin hormone with therapeutic potential for type 2 diabetes. A variety of GLP-1 sequences are known from amphibian species, and some of these have been tested here and found to be able to bind and activate the human GLP-1 receptor. While little difference was observed for the in vitro potency for the human GLP-1 receptor, larger differences were found in the enzymatic stability of these peptides. Two peptides showed increased enzymatic stability, and they group together phylogenetically, though they originate from Amphibia and Reptilia. We have used ancestral sequence reconstruction to analyze the evolution of these GLP-1 molecules, including the synthesis of new peptides. We find that the increased stability could not be observed in the resurrected peptides from the common ancestor of frogs, even though they maintain the ability to activate the human GLP-1 receptor. Another method, using residue mapping on evolutionary branches yielded peptides that had maintained potency towards the receptor and also showed increased stability. This represents a new approach using evolutionary data in protein engineering.

Amino Acid Sequence↗

Improved isolation of cardiomyocytes by trypsination in addition to collagenase treatment.

The present study was undertaken to develop an improved and stabilized method for isolating cardiomyocytes from perfused rat heart. Different lots of the commercial collagenases used for isolating cardiomyocytes give variable results both with respect to the total cell yield and the percentage of elongated cells obtained. When trypsin was present both before and during collagenase treatment of the tissue, the performance of the collagenases was improved and stabilized, and a high and stable cell yield (7.5 x 10(6) cells per heart), and a high percentage of elongated cells (about 70%) was regularly obtained. The cells possessed alpha 1-adrenergic binding sites with binding properties (Bmax = 43.5 fmol/mg protein and Kd = 125.5 pmol/l) in agreement with values previously reported. The cells were able to respond functionally, as the cellular uptake of 86Rb+ increased by 18% after alpha 1-adrenoceptor stimulation with phenylephrine. These criteria indicate that the cells were well preserved during the isolation procedure.

Animals↗

Repeatability of Model Genetic Coefficients Derived from Soybean Performance Trials across Different States.

Crop model testing in diverse environments is essential if modelers wish to make applications or extrapolations to those environments. A recent study demonstrated the effectiveness of optimization techniques for deriving cultivar coefficients for the CROPGRO-Soybean model from typical information provided by soybean performance tests. The objectives of this study were (i) to explore the extent to which cultivar coefficients developed by these approaches from crop performance tests are stable across different regions, (ii) to test the CROPGRO-Soybean model's ability to predict phenology and seed yield using cultivar coefficients that were developed in different regions, and (iii) to investigate whether 3 yr of crop performance data are adequate for developing stable genetic coefficients. A stepwise procedure was applied to derive cultivar coefficients for 10 common cultivars grown in different environments in Georgia and North Carolina. Regarding the transportability of cultivar coefficients across states, we found that the critical daylength coefficients were the most reliable cultivar traits. We found less stability of the cultivar traits that control genetic differences in seed yield potential. The estimated cultivar coefficients developed in Georgia enabled CROPGRO to predict yield and harvest maturity in North Carolina within 3.8% and 3.5 d, respectively, from the observed averages. Using the cultivar coefficients developed from North Carolina environments allowed us to simulate the actual mean yield and harvest maturity in Georgia to within 2.5% and 2.0 d. Furthermore, the model's ability to predict seed yield and maturity with cultivar coefficients developed from 3 yr of data was nearly as good as that derived from much larger data sets.

Journal Article↗

Radiation and thermal stabilities of adenine nucleotides.

We have investigated in detail radiation and thermal stabilities and transformations of adenosine mono- and triphosphates in liquid and frozen solid aqueous solutions within a wide range of absorbed radiation dose (up to 75 kGy) and temperature (up to 160 degrees C). Dephosphorylation is the main pathway of high temperature hydrolysis of adenine nucleotides. Basic thermodynamic and kinetic parameters of this process have been determined. Radiolysis of investigated compounds at room temperature results in scission of N-glycosidic bond with a radiation yield about of 1 mol/100 eV. Solution freezing significantly enhances radiation stability of nucleotides as well as other biomolecules. This circumstance is essential in the discussion of panspermia concepts.

Adenine Nucleotides↗

Sandostatin labeled with 99mTc: in vitro stability, in vivo validity and comparison with 111In-DTPA-octreotide.

Sandostatin, a synthetic octapeptide analog of a native hormone somatostatin, was labeled with a commonly available, inexpensive radionuclide, 99mTc, and evaluated for its suitability for in vivo imaging. Labeling was accomplished by reduction of the cystine bridge, which provided two sulfhydryl groups for chelation with 99mTc. The complex was examined for thermodynamic stability in vitro and in experimental animals. Receptor specificity of the complex was determined using rat brain cortex membrane rich in somatostatin receptors, and its tissue distribution was studied in nude mice bearing human prostate cancer. In these studies, 99mTc-labeled oxytocin, a nonspecific peptide with similar molecular weight, served as a control and 111In-DTPA-octreotide served as a standard. The labeling method was simple, did not require protecting and deprotecting functional groups and yields were high (ca. 70%). The in vitro and in vivo stability was excellent, and Kd values were in the nanomolar range, similar to those of 111In-DTPA-octreotide. At 24 hours post-injection, the tumor uptake for 99mTc-Sandostatin, expressed as percent of injected dose per gram (% ID/g), was higher, but the tumor/blood and tumor/muscle ratios were lower than those for 111In-DTPA-octreotide. This agent, with its improved target-to-nontarget ratios, should prove to be of value for imaging somatostatin receptor-positive tumors.

Animals↗

Carbohydrate structures of three novel phosphoinositol-containing sphingolipids from the yeast Histoplasma capsulatum.

From the yeast phase of the human pathogen Histoplasma capsulatum, three novel glycolipids were isolated, shown to react with sera from histoplasmosis patients, and partially characterized: compound V, ceramide-P-inositol-[mannose2]; compound VI, ceramide-P-inositol-[mannose2, galactose]; compound VIII, an isomer of compound VI [Barr, K., & Lester, R.L. (1984) Biochemistry (preceding paper in this issue)]. Ammonolysis of these lipids has yielded all the carbohydrate (oligosaccharides V, VI, and VIII) as novel, intact oligosaccharides suitable for characterization. Anomeric configurations were determined by specific glycosidase digestion and by the stability of peracetylated saccharides to CrO3 oxidation. Linkages were established by methylation analysis. These experiments yielded the following structural assignments: (formula; see text) The occurrence of galactofuranose is novel for glycosphingolipids, and it is noteworthy that compound VI is immunoreactive.

Carbohydrate Conformation↗

Improving the refolding yield of interleukin-4 through the optimization of local interactions.

Interleukin-4 (IL-4) is a multifunctional cytokine that plays an important role in the regulation of various immune responses. However, the development of IL-4 or IL-4 variants into potential therapeutic drugs is hindered by the low efficiency of the in vitro refolding process of this protein. In this work, we have investigated the improvement of the refolding yield of IL-4 using two different rational design approaches. The first one is based on the so-called inverse hydrophobic effect and involved the replacement of a solvent exposed, non-conserved, hydrophobic residue (W91) by serine. This led to an increase in stability of 1.4 kcal mol(-1) and shifted the midpoint transition temperature (Tm) from 62 to 70 degrees C. The second approach is based on the stabilization of alpha-helices through the introduction of favorable local interactions. This strategy resulted in the following helix sequence for helix C of IL-4, 68ASAAEANRHKQLIRFLKRLDRNLWGLAG95. The mutant protein was stabilized by 0.5 kcal mol(-1), the Tm shifted to 68 degrees C, and a two-fold increase in the refolding yield was consistently observed. Our results make the large-scale production of IL-4 derivatives economically more viable, suggest that a similar approach can be applied to other related proteins, and may represent a general strategy to improve in vitro refolding yields through the selective optimization of the stability of alpha-helices.

Amino Acid Sequence↗

Ligand-linked stability of mutants of the C-domain of calmodulin.

There is a necessary energetic linkage between ligand binding and stability in biological molecules. The critical glutamate in Site 4 was mutated to create two mutants of the C-domain of calmodulin yielding E140D and E140Q. These proteins were stably folded in the absence of calcium, but had dramatically impaired binding of calcium. We determined the stability of the mutant proteins in the absence and presence of calcium using urea-induced unfolding monitored by circular dichroism (CD) spectroscopy. These calcium-dependent unfolding curves were fit to models that allowed for linkage of stability to binding of a single calcium ion to the native and unfolded states. Simultaneous analysis of the unfolding profiles for each mutant yielded estimates for calcium-binding constants that were consistent with results from direct titrations monitored by fluorescence. Binding to the unfolded state was not an important energetic contributor to the ligand-linked stability of these mutants.

Amino Acid Sequence↗

Selection, design, and characterization of a new potentially therapeutic ribozyme.

An in vitro selection was designed to identify RNA-cleaving ribozymes predisposed for function as a drug. The selection scheme required the catalyst to be trans-acting with phosphodiesterase activity targeting a fragment of the Kras mRNA under simulated physiological conditions. To increase stabilization against nucleases and to offer the potential for improved functionality, modified sequence space was sampled by transcribing with the following NTPs: 2'-F-ATP, 2'-F-UTP, or 2'-F-5-[(N-imidazole-4-acetyl) propylamine]-UTP, 2'-NH2-CTP, and GTP. Active motifs were identified and assessed for their modified NMP and divalent metal dependence. The minimization of the ribozyme's size and the ability to substitute 2'-OMe for 2'-F and 2'-NH2 moieties yielded the motif from these selections most suited for both nuclease stability and therapeutic development. This motif requires only two 2'-NH2-Cs and functions as a 36-mer. Its substrate sequence requirements were determined to be 5'-Y-G-H-3'. Its half-life in human serum is >100 h. In physiologically relevant magnesium concentrations [approximately 1 mM] its kcat = 0.07 min(-1), Km = 70 nM. This report presents a novel nuclease stable ribozyme, designated Zinzyme, possessing optimal activity in simulated physiological conditions and ready for testing in a therapeutic setting.

Base Sequence↗

2-(Perfluoroalkyl)ethanols by Thermal Alkylation of Ambidentate Lactams with 2-(Perfluoroalkyl)-1-iodoalkanes, in the Presence of Added Water. A Change in Mechanism and Stoichiometry of the Reaction. Isolation of a Water Adduct of the Lactim Ether Intermediate.

Thermal alkylation of amides by an alkyl halide gives alcohols and esters, and the intriguing behavior of ambidentate lactams in this reaction with 2-(perfluoroalkyl)-1-iodoethanes and lactam 2 is summarized in Scheme 1. 2-(Perfluoroalkyl)ethanols (3) are the principal alkylation product, and there is obtained a range of coproducts in varying amounts. A lactim ether salt (6.HI) is the first reaction intermediate in a sequence of reactions. For delta-valerolactam (8) or epsilon-caprolactam (11), conversion to 3 falls precipitously and R(F)CH=CH(2) (4) becomes a major product. However, when water is introduced, alkylation rate of 2 by iodoalkane 1 increases, the conversion to 3 and 4 decreases, and a new lactim ether salt, 7.HI (the water adduct of 6.HI), is formed. Conversion to 3 is suppressed because coproduct 2 is weakly basic and the equilibrium lies on the side of the basic amine salt (7.HI). The mass spectrum of 2-hydroxy-2-[[(2-(perfluorohexyl)ethyl]oxy]pyrrolidine (7) includes the parent ion and a fragment (m/z = 131) of the intact pyrrolidine ring with an attached hydroxy group. Basic hydrolysis of product mixtures containing 7.HI in a protic solvent gives a high yield of 3 and 2. The higher lactams, 8 or 11, with 1 and water give the lactam salts efficiently; yield of 4 is low and yield of 3, by subsequent reaction with base, is high. With water present, the reaction rates of 8 and 1 are greater than for 2 and 1; water increases both the alkylation step and the water displacement step. Improved homogeneity of reaction mixtures and a specific solvent effect in which water stabilizes the bipolar transition state may be responsible for improved rates and yields.

Journal Article↗

Rapid colorimetric micromethod for free fatty acids.

Free fatty acids (FFA), the uranyl ion, and the basic dye Rhodamine B form colored complexes, which are extractable into toluene or benzene. Fatty acids of different chain lengths above C(10) and different degrees of unsaturation gave constant molar yield. Complexes in toluene alone are unstable, especially in the light, but a small amount of aqueous uranyl acetate stabilizes them sufficiently for determination. At constant uranyl and Rhodamine B concentrations, a plot of optical density vs. FFA concentration yields two straight lines of different slope, i.e., a biphasic standard curve. Phospholipids interfere, and must be removed with zeolite during FFA extraction. Recovery of FFA added to rat plasma was very similar to that with titration. Assay of rat and dog plasma samples under fasting and fed conditions gave good agreement with the titration method. Values of human plasma samples tended to be higher by the colorimetric procedure; a few samples gave significant disagreement. The method compares well with previous methods in sensitivity and accuracy, and offers advantages in speed, simplicity, and possibly specificity.

Animals↗