Anthocyanins in berries exhibited anti-atherogenicity and antiplatelet activities in a metabolic syndrome population

Metabolic syndrome (MetS) is a global challenge for atherosclerosis. It was hypothesized that a four-week consumption of anthocyanin supplements by MetS patients who had three or more risk factors linked with metabolic syndrome would have a greater improvement in cardiometabolic biomarkers and would also reduce the risk of thrombosis. A total of 55 participants in two groups of Normal healthy and MetS (age 25-75y) were given 320 mg anthocyanin supplements twice daily for 4 weeks. Platelet coagulant activities, lipid profiles, fasting blood glucose, and inflammatory and oxidative stress biomarkers were measured before and after supplementation to evaluate the atheroprotective effects of anthocyanins in the study subjects. Four weeks of anthocyanin supplementation significantly decreased cardiometabolic risk factors including the average serum fasting blood glucose (FBG) (by 13.3%, P < .05) and lipid profiles by significant reduction in triglyceride (by 24.9%, P < .05) and LDL-C (by 33.1%, P < .05) in the MetS group. Anthocyanin supplementation also decreased high sensitivity C-reactive protein (hs-CRP) level (by 28%, P < .05) in females. However, no significant differences in serum UA (uric acid) and HDL-C were observed between anthocyanin pre- and post-treatment in both groups. Moreover, Anthocyanin supplements decreased ADP-induced platelet activation configuration expressed as P-selectin by 40% (P < .05). There was a positive correlation between decreased hs-CRP values and the levels of LDL-C and FBG in the MetS group (P < .05). These results support the hypothesis that anthocyanin supplementation exerts anti-atherogenicity effects by improving cardiometabolic risk factors and reducing thrombogenicity in the MetS population.

A surrogate-based metaheuristic global search method for beam angle selection in radiation treatment planning

An important element of radiation treatment planning for cancer therapy is the selection of beam angles (out of all possible coplanar and non-coplanar angles in relation to the patient) in order to maximize the delivery of radiation to the tumor site and minimize radiation damage to nearby organs-at-risk. This category of combinatorial optimization problem is particularly difficult because direct evaluation of the quality of treatment corresponding to any proposed selection of beams requires the solution of a large-scale dose optimization problem involving many thousands of variables that represent doses delivered to volume elements (voxels) in the patient. However, if the quality of angle sets can be accurately estimated without expensive computation, a large number of angle sets can be considered, increasing the likelihood of identifying a very high quality set. Using a computationally efficient surrogate beam set evaluation procedure based on single-beam data extracted from plans employing equallyspaced beams (eplans), we have developed a global search metaheuristic process based on the nested partitions framework for this combinatorial optimization problem. The surrogate scoring mechanism allows us to assess thousands of beam set samples within a clinically acceptable time frame. Tests on difficult clinical cases demonstrate that the beam sets obtained via our method are of superior quality.

HREM of the {111} surfaces of iron oxide nanoparticles

Mixed phase Fe3O4-gamma-Fe2O3 (magnetite-maghemite) iron oxide nanoparticles have been fabricated by colloidal routes. HRTEM/HRSTEM images of the nanoparticles show the presence of [111] facets that terminate with enhanced contrast, which is shown to be caused by the presence of additional cations at the edges of the nanoparticles. HRTEM images were taken on a FEI CM200 FEGTEM, a JEOL 3100 with a LaB6 source, and a double aberration corrected JEOL-JEM 2200FS FEGTEM. The enhanced contrast effect was observed on the [111] surface atomic layers resolved using each machine. HRSTEM images, taken on an aberration corrected STEM, resolved enhanced contrast at specific surface sites. Exit wave reconstruction was also carried out on focal series taken on a double aberration corrected JEOL-JEM 2200FS and showed similar highly resolved enhanced contrast at specific surface cation sites. It is apparent that additional cations are occupying the [111] terminating layers of these nanoparticle surfaces. The use of different microscopes and techniques in this paper provides strong evidence that the enhanced contrast is a real effect and not an effect caused by microscope aberrations.

Calculations of HREM image intensity using Monte Carlo integration

We have developed a numerical approach for the accurate and efficient calculation of HREM image intensity formed using a partially coherent source. The approach is based on Monte Carlo integration, and is suitable for use in general image restoration methods using a series of images. The accuracy of this approach is compared with calculations based on the transmission cross coefficient (TCC) for strong scattering objects, as a function of the number of sampling points, defocus, atomic number and specimen thickness. Its efficiency is compared with that of exact TCC calculations based on equally-spaced sampling of the beam divergence and focal spread distributions. The results indicate that the Monte Carlo approach is particularly advantageous for nonlinear image restoration algorithms.

Spinal anesthesia in an extremely low birth weight infant

A case of spinal anesthesia in an extremely low birth weight male infant (body weight of 930 g at time of surgery) is presented. He was born prematurely at a gestational age of 27 weeks because of a placenta tumor and had to undergo inguinal herniotomy at 34 weeks postconceptional age. He had bronchopulmonary dysplasia and oxygen supply was still required because of frequent deterioration of oxygen saturation. Spinal anesthesia was performed successfully without any complications. Relevant aspects concerning the technique and management of spinal anesthesia in preterm infants are discussed.

A new method for the determination of the wave aberration function for high-resolution TEM

A new method is presented for the determination of the antisymmetric coefficients of the wave aberration function from a tableau of tilted illumination images. The approach is based on measurements of the apparent defocus and two-fold astigmatism using a phase correlation function and phase contrast index calculated from a short focus series acquired at each tilt. This method is shown to be suitable for a wide range of specimens and is sufficiently accurate for exit plane wave restoration at 0.1 nm resolution. Experimental examples of this approach are provided and the method is compared to results obtained from measurements of conventional power spectra.

A composite method for the determination of the chirality of single walled carbon nanotubes

An approach to the unambiguous determination of the conformation of individual single walled nanotubes utilizing high-resolution transmission electron microscopy and digital image processing is described. The exit plane wave of single walled nanotubes restored from a focal series of images is used in a stepwise characterization procedure utilizing both the phase of the real space restoration and its Fourier transform. A combination of these complementary characterization steps yields an accurate measurement of the chiral vector for an individual nanotube.

[Management of pediatric airway--anatomy, physiology and new developments in clinical practice]

Due to the special features of paediatric anatomy and physiology, the expected and unexpected difficult paediatric airway is one of the major challenges to every anaesthesiologist, paediatrician and emergency physician. During the last years, some new devices have been made available to improve airway management in children and infants, and several studies have advanced our understanding of the risks and benefits of our clinical practice. Certain risk factors for airway related problems during anaesthesia in children having a "cold" have been identified, and there are new aspects of the controversy concerning the use of cuffed endotracheal tube (ETT) in children. New video assisted systems have been introduced for the management of the difficult airway in paediatric patients, and new applications for well-known devices have been suggested, e.g. the laryngeal mask airway (LMA) serving as guidance for fibreoptic intubation. Recent studies have also demonstrated specific problems with the LMA in infants, as well as possible advantages of a new prototype LMA for children, similar to the ProSeal. Furthermore, the following review presents data about the use of the Cuffed Oropharyngeal Airway (COPA) and the Laryngeal Tube (LT) in paediatric patients.

A new method for the determination of the wave aberration function for high resolution TEM 1. Measurement of the symmetric aberrations

A new method for the accurate determination of the symmetric coefficients of the wave aberration function has been developed. The relative defoci and displacements of images in a focus series are determined from an analysis of the phase correlation function between pairs of images, allowing the restoration of an image wave even when focus and specimen drift are present. Subsequently, the absolute coefficients of both defocus and 2-fold astigmatism are determined with a phase contrast index function. Overall this method allows a very accurate automated aberration determination even for largely crystalline samples with little amorphous contamination. Using experimental images of the complex oxide Nb16W18O94 we have demonstrated the new method and critically compared it with existing diffractogram based aberration determinations. A series of protocols for practical implementation is also given together with a detailed analysis of the accuracy achieved. Finally a focal series restoration of Nb16W18O94 with symmetric aberrations determined automatically using this method is presented.

Dose homogeneity as a function of source activity in optimized I-125 prostate implant treatment plans

PURPOSE

In conventional treatment planning for permanent I-125 prostate implants, it has been suggested that lower seed activities result in more homogeneous dose distributions and also less overdose of the critical structures. We sought to determine if this hypothesis holds by analyzing treatment plans constructed using an automated optimized approach.

METHODS AND MATERIALS

We studied treatment plans for 10 patients using mixed-integer programming and the branch-and-bound method. Two mixed-integer models (that yielded somewhat different treatment plans) were developed: a "basic" model and a "dose homogeneity" model. For each resulting treatment plan, we examined dose homogeneity (by evaluating the dose non-uniformity ratio [DNR] and the full-width half-maximum [FWHM] of the differential dose-volume histogram [DVH]) as a function of three different source activities (0.35 mCi, 0.44 mCi, and 0.66 mCi). In addition, target coverage and critical structure dose distributions were evaluated. Plans using multiple source activities were also evaluated for resulting dose inhomogeneities.

RESULTS

The homogeneity model results in a more homogeneous dose distribution than the basic model. DNR is lowered by an average of 42% (standard deviation [SD] = 19%), 39% (SD = 21%), and 33% (SD = 21%) for the 0.35 mCi, 0.44 mCi, and 0.66 mCi seeds, respectively, when the homogeneity model is employed over the basic model. Corresponding average decreases in the FWHM of the DVH for 0.35 mCi, 0.44 mCi, and 0.66 mCi, respectively, are 29 Gy (SD = 28 Gy), 24 Gy (SD = 22 Gy), and 27 Gy (SD = 13 Gy). Seeds of 0.35 mCi and 0.44 mCi result in the lowest DNR and narrower FWHM of the DVH relative to 0.66 mCi seeds. In general, the 0.44 mCi seeds produce greater target coverage and require fewer seeds and needles than the 0.35 mCi seeds. Although 0.66 mCi seeds result in the greatest target coverage, they yield highest critical structure doses. They also yield solutions requiring the least number of seeds and needles. However, the dose distributions from 0.66 mCi seeds are highly inhomogeneous. Multiple source activities in the same treatment plan produce dose distributions that are comparable in homogeneity to 0.44 mCi seed implants.

CONCLUSIONS

Even when an optimization model that seeks to minimize dose inhomogeneity is employed, all factors involved in seed implants make 0.44 mCi the best activity choice in comparison with 0.35 mCi and 0.66 mCi.

An iterative sequential mixed-integer approach to automated prostate brachytherapy treatment plan optimization

Conventional treatment planning for interstitial prostate brachytherapy is generally a 'trial and error' process in which improved treatment plans are generated by iteratively changing, via expert judgement, the configuration of sources within the target volume in order to achieve a satisfactory dose distribution. We have utilized linear mixed-integer programming (MIP) and the branch-and-bound method, a deterministic search algorithm, to generate treatment plans. The rapidity of dose falloff from an interstitial radioactive source requires fine sampling of the space in which dose is calculated. This leads to a large and complex model that is difficult to solve as a single 3D problem. We have therefore implemented an iterative sequential approach that optimizes pseudo-independent 2D slices to achieve a fine-grid 3D solution. Using our approach, treatment plans can be generated in 20-45 min on a 200 MHz processor. A comparison of our approach with the manual 'trial and error' approach shows that the optimized plans are generally superior. The dose to the urethra and rectum is usually maintained below harmful levels without sacrificing target coverage. In the event that the dose to the urethra is undesirably high, we present a refined optimization approach that lowers urethra dose without significant loss in target coverage. An analysis of the sensitivity of the optimized plans to seed misplacement during the implantation process is also presented that indicates remarkable stability of the dose distribution in comparison with manual treatment plans.

Discrete atom imaging of one-dimensional crystals formed within single-walled carbon nanotubes

The complete crystallography of a one-dimensional crystal of potassium iodide encapsulated within a 1.6-nanometer-diameter single-walled carbon nanotube has been determined with high-resolution transmission electron microscopy. Individual atoms of potassium and iodine within the crystal were identified from a phase image that was reconstructed with a modified focal series restoration approach. The lattice spacings within the crystal are substantially different from those in bulk potassium iodide. This is attributed to the reduced coordination of the surface atoms of the crystal and the close proximity of the van der Waals surface of the confining nanotube.

Characterisation of the signal and noise transfer of CCD cameras for electron detection

Methods to characterise the performance of CCD cameras for electron detection are investigated with particular emphasis on the difference between the transfer of signal and noise. Similar to the Modulation Transfer Function MTF, which describes the spatial frequency dependent attenuation of contrast in the image, we introduce a Noise Transfer Function NTF that describes the transfer of the Poisson noise that is inevitably present in any electron image. A general model for signal and noise transfer by an image converter is provided. This allows the calculation of MTF and NTF from Monte-Carlo simulations of the trajectories of electrons and photons in the scintillator and the optical coupling of the camera. Furthermore, accurate methods to measure the modulation and noise transfer functions experimentally are presented. The spatial-frequency dependent Detection Quantum Efficiency DQE, an important figure of merit of the camera which has so far not been measured experimentally, can be obtained from the measured MTF and NTF. The experimental results are in good agreement with the simulations and show that the NTF at high spatial frequencies is in some cases by a factor of four higher than the MTF. This implies that the noise method, which is frequently used to measure the MTF, but in fact measures the NTF, gives over-optimistic results. Furthermore, the spatial frequency dependent DQE is lower than previously assumed.

Mammalian DNA polymerases alpha, beta, gamma, delta, and epsilon incorporate fialuridine (FIAU) monophosphate into DNA and are inhibited competitively by FIAU Triphosphate

Fialuridine [FIAU, 1-(2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl)-5- iodouridine] was used in clinical trials for chronic hepatitis B virus infection and was extremely toxic. Evidence suggested targets of FIAU toxicity included mitochondria, but toxic mechanisms were unclear. Since FIAU is a thymidine analog, we reasoned that triphosphorylated FIAU (FIAUTP) could be incorporated into mitochondrial DNA by DNA pol-gamma and into genomic DNA by DNA polymerases alpha, beta, delta, and epsilon. All five purified mammalian DNA polymerases incorporated FIAUMP into the nascent DNA chain during in vitro DNA synthesis. When FIAUTP was substituted for dTTP, oligonucleotide products were generated efficiently by DNA pol-gamma and were similar to those generated in the presence of the four normal dNTPs. In contrast, oligonucleotide products generated by the four nuclear DNA polymerases in the presence of FIAUTP were significantly reduced in length relative to those generated in the presence of dTTP. In parallel kinetic assays, FIAUTP competitively inhibited the accumulation of radiolabeled dTTP into DNA by DNA pol-gamma. The Ki with DNA pol-gamma was 0.04 microM, the lowest Ki among the mammalian DNA polymerases. Competition between FIAUTP and dTTP and the relative ease of accumulation of FIAUMP in mitochondrial DNA by DNA pol-gamma in vitro together may relate to clinical FIAU toxicity.

Cardiac mitochondrial DNA polymerase-gamma is inhibited competitively and noncompetitively by phosphorylated zidovudine

Zidovudine (azidothymidine [AZT]) inhibits human immunodeficiency virus replication and reduces the severity of acquired immunodeficiency syndrome. A limiting side effect of AZT is a mitochondrial cardiac and skeletal myopathy in which the pharmacologically active derivative of AZT (AZT triphosphate) plays a critical role. The present study determined biochemical mechanisms of AZT-induced mitochondrial toxicity and identified AZT triphosphate as an inhibitor of DNA polymerase-gamma in vitro. Inhibition kinetics were defined using purified bovine cardiac mitochondrial DNA polymerase-gamma and AZT triphosphate in vitro. The Km for deoxythymidine triphosphate was 0.8 +/- 0.3 mumol/L. AZT triphosphate incubation with DNA polymerase-gamma in vitro resulted in mixed kinetics with a competitive Ki of 1.8 +/- 0.2 mumol/L and a noncompetitive Ki' of 6.8 +/- 1.7 mumol/L. These Ki and Ki' values were strikingly higher than values for retroviral reverse transcriptase but lower than values for other cellular DNA polymerases. These data support previous molecular and morphological findings in clinical AZT mitochondrial myopathy and in models of AZT myopathy in vivo. Biochemical findings suggest that inhibition of mitochondrial DNA polymerase-gamma may be integral to the pathogenesis of AZT-induced myopathy.

Structure-function analysis of DNA polymerase-beta using monoclonal antibodies: identification of a putative nucleotide binding domain

DNA polymerase-beta was purified from Novikoff hepatoma and used as an antigen in an in vitro immunization system to produce monoclonal antibodies. These reagents surprisingly showed cross-reactivity to a number of proteins, including several DNA polymerases. Nearly all of these proteins possess nucleotide binding sites, which suggested the potential value of using the monoclonals to elucidate structure-function relationships within polymerase-beta. Furthermore, these antibodies were able to partially neutralize (40-50%) polymerase-beta activity, and this effect could be blocked by dNTP1 but not by dNMP or rNTP. The limited neutralization phenomenon is at least partially explained by the weak binding affinity of these antibodies. Scatchard analysis of immunoprecipitation data predicted a Kd of 1.8 x 10(-8) M. Epitope mapping studies showed that the region of polymerase-beta recognized by one of the monoclonal antibodies is within residues 235-335, and sequence homology studies indicated that the epitope is probably located in the region of amino acids 283-320. At least a portion of this area, namely residues 301-308 and 311-315, appears to be part of a nucleotide binding domain which has sequence homology with a portion of the highly conserved ATP binding site in adenylate kinase.

Interaction of the heat shock protein GroEL of Escherichia coli with single-stranded DNA-binding protein: suppression of ssb-113 by groEL46

Previous studies from our laboratory have shown that an allele of the heat shock protein GroEL (groEL411) is able to specifically suppress some of the physiological defects of the single-stranded DNA-binding protein mutation ssb-1. A search for additional alleles of the groE genes which may act as suppressors for ssb mutations has led to the identification of groEL46 as a specific suppressor of ssb-113. It has very little or no effect on ssb-1 or ssb-3. All of the physiological defects of ssb-113, including temperature-sensitive growth, temperature-sensitive DNA synthesis, sensitivity to UV irradiation, methyl methanesulfonate, and bleomycin, and reduced recombinational capacity, are restored to wild-type levels. The ssb-113 allele, however, is unable to restore sensitivity of groEL46 cells to phage lambda. The mechanism of suppression of ssb-113 by groEL46 appears to differ from that of ssb-1 by groEL411. The data suggest that GroEL may interact with single-stranded DNA-binding protein in more than one domain.

An EPR study to determine the relative nucleic acid binding affinity of single-stranded DNA-binding protein from Escherichia coli

A direct quantitative determination by EPR of the nucleic acid binding affinity relationship of the single-stranded DNA-binding protein (SSB) from Escherichia coli at close to physiological NaCl concentration is reported. Titrations of (DUAP, dT)n, an enzymatically spin-labeled (dT)n, with SSB in 20 mM Tris-HCl (pH 8.1), 1 mM sodium EDTA, 0.1 mM dithiothreitol, 10% (w/v) glycerol, 0.05% Triton with either low (5 mM), intermediate (125 mM) or high 200 mM) NaCl content, reveal the formation of a high nucleic acid density complex with a binding stoichiometry (s) of 60 to 75 nucleotides per SSB tetramer. Reverse titrations, achieved by adding (DUAP, dT)n to SSB-containing solutions, form a low nucleic acid density complex with an s = 25 to 35 in the buffer with low NaCl content (5 mM NaCl). The complex with an s = 25 to 35 is converted to the high nucleic acid density complex by increasing the NaCl content to 200 mM. It is, therefore, metastable and forms only under reverse titration conditions in low NaCl. The relative apparent affinity constant Kapp of SSB for various unlabeled single-stranded nucleic acids was determined by EPR competition experiments with spin-labeled nucleic acids as macromolecular probes in the presence of the high nucleic acid density complex. The Kapp of SSB exhibits the greatest affinity for (dT)n as was previously found for T4 gene 32 protein (Bobst, A.M., Langemeier, P.W., Warwick-Koochaki, P.E., Bobst, E.V. and Ireland, J.C. (1982) J. Biol. Chem. 257, 6184) and gene 5 protein (Bobst, A.M., Ireland, J.C. and Bobst, E.V. (1984) J. Biol. Chem. 259, 2130) by EPR competition assays. In contrast, however, SSB does not display several orders of magnitude greater affinity for (dT)n than for other single stranded DNAs as is the case with both gene 5 and T4 gene 32 protein. The relative Kapp values for SSB in the above buffer with 125 mM NaCl are: Kapp(dT)n = 4KappfdDNA = 40Kapp(dA)n = 200Kapp(A)n.

The single-stranded DNA-binding protein of Escherichia coli

The single-stranded DNA-binding protein (SSB) of Escherichia coli is involved in all aspects of DNA metabolism: replication, repair, and recombination. In solution, the protein exists as a homotetramer of 18,843-kilodalton subunits. As it binds tightly and cooperatively to single-stranded DNA, it has become a prototypic model protein for studying protein-nucleic acid interactions. The sequences of the gene and protein are known, and the functional domains of subunit interaction, DNA binding, and protein-protein interactions have been probed by structure-function analyses of various mutations. The ssb gene has three promoters, one of which is inducible because it lies only two nucleotides from the LexA-binding site of the adjacent uvrA gene. Induction of the SOS response, however, does not lead to significant increases in SSB levels. The binding protein has several functions in DNA replication, including enhancement of helix destabilization by DNA helicases, prevention of reannealing of the single strands and protection from nuclease digestion, organization and stabilization of replication origins, primosome assembly, priming specificity, enhancement of replication fidelity, enhancement of polymerase processivity, and promotion of polymerase binding to the template. E. coli SSB is required for methyl-directed mismatch repair, induction of the SOS response, and recombinational repair. During recombination, SSB interacts with the RecBCD enzyme to find Chi sites, promotes binding of RecA protein, and promotes strand uptake.

Interaction of a folded chromosome-associated protein with single-stranded DNA-binding protein of Escherichia coli, identified by affinity chromatography

A single-stranded DNA-binding protein (SSB) affinity column was prepared by optimizing the coupling of Escherichia coli single-stranded DNA-binding protein to Affi-Gel 10. The bound SSB retained its ability to specifically bind single-stranded DNA. When nuclease-treated cell extracts were incubated with the SSB beads overnight at 4 degrees C, a major protein of Mr = 25,000 was bound. At shorter incubation times, two additional proteins of Mr = 32,000 and 36,000 were also detected. In the absence of nuclease treatment, eight additional proteins ranging from Mr = 14,000 to 160,000 also bound to the affinity column. The major Mr = 25,000 protein has been shown to be a folded chromosome-associated protein. Its binding to SSB is strongly enhanced by the addition of DNA polymerase III or DNA polymerase III holoenzyme.

Purification and enzymological characterization of DNA-dependent ATPase IV from the Novikoff hepatoma

DNA-dependent ATPase IV has been purified to near homogeneity from the Novikoff rat hepatoma. The enzyme is devoid of DNA polymerase, RNA polymerase, exonuclease, endonuclease, phosphomonoesterase, 3'- or 5'-phosphodiesterase, polynucleotide kinase, protein kinase, topoisomerase, helicase or DNA reannealing activities at a detection level of 10(-5) to 10(-7) relative to the ATPase activity. The enzyme is a monomer of Mr 110,000, has a sedimentation coefficient of 5.9 S, a Stokes radius of 40 A and a frictional coefficient of 1.32. In the presence of Mg2+ ion and a polynucleotide effector, ATPase IV hydrolyzes either ATP or dATP to the nucleoside diphosphate plus Pi. Other ribo- or deoxyribonucleoside triphosphates are not substrates. ATPase IV utilizes double-stranded DNA and single-stranded DNA as effector; however, it does not utilize poly(dT). The Km for dsDNA or ssDNA is 2.2 microM (nucleotide). A variety of ATP analogues were found to be competitive inhibitors of ATPase IV.

Suppression of the Escherichia coli ssb-1 mutation by an allele of groEL

A series of spontaneous suppressors to the temperature-sensitive phenotype of the single-stranded DNA-binding protein mutation ssb-1 were isolated. A genomic library of EcoRI fragments from one of these suppressor strains was prepared by using pBR325 as the cloning vector. A 10.0-kilobase class of inserts was identified as carrying the ssb-1 gene itself. A second class of 8.3-kilobase inserts was shown to contain the groE region by (i) restriction analysis, (ii) Southern hybridization of the 8.3-kilobase insert to groE+ DNA, and (iii) identification of the gene products by similar migration on polyacrylamide gels. Subcloning demonstrated that an intact mutant groEL gene was necessary for suppression and that plasmids carrying the 8.3-kilobase insert could suppress mutants carrying groES- but not groEL- genes for phage lambda growth. The suppressor, designated as groEL411, was specific for the ssb-1 allele. In ssb-1 groEL411 cells, DNA synthesis stopped after a shift to 42.5 degrees C but rapidly recovered within minutes. The data suggest a direct interaction between the single-stranded DNA-binding protein and GroEL proteins in DNA replication.

The relative rate of synthesis and levels of single-stranded DNA binding protein during induction of SOS repair in Escherichia coli

Induction of the SOS response in Escherichia coli results in an increase in the relative rate of synthesis of single-stranded DNA binding protein (SSB). In contrast to RecA protein, this increase is slow and does not lead to higher SSB levels. The significance of ssb induction to SOS repair is discussed.

Purification and characterization of an inorganic pyrophosphatase from the extreme thermophile Thermus aquaticus

An inorganic pyrophosphatase was purified over 600-fold to homogeneity as judged by polyacrylamide gel electrophoresis. The enzyme is a tetramer of Mr = 84,000, has a sedimentation coefficient of 5.8S, a Stokes radius of 3.5 nm, and an isoelectric point of 5.7. Like the enzyme of Escherichia coli, the pyrophosphatase appears to be made constitutively. The pH and temperature optima are 8.3 and 80 degrees C, respectively. The Km for PPi is 0.6 mM. A divalent cation is essential, with Mg2+ preferred. The enzyme uses only PPi as a substrate.

Variability in the nucleic acid binding site size and the amount of single-stranded DNA-binding protein in Escherichia coli

The Escherichia coli single-stranded DNA binding protein (SSB), essential for DNA replication, recombination and repair, can undergo a thermally induced irreversible conformational change which does not eliminate its biological activity, but changes the number of nucleotides it covers (binding site size) when binding to a single-stranded nucleic acid lattice. The binding site size of native and conformationally changed SSB was also found to be a function of the molecular mass of the polynucleotide, an observation which is unusual for single-stranded DNA binding proteins and will greatly affect the affinity relationship of this protein for nucleic acids. A radioimmunoassay used to quantitate in SSB level in cells revealed the number of SSB tetramers to be larger than initial estimates by a factor of as much as six. All these data suggest that the biological role of SSB and its mechanism of action is by far more complex than originally assumed.

A new DNA-dependent ATPase from Escherichia coli. Purification and characterization of ATPase IV

A new DNA-dependent ATPase named ATPase IV has been purified to apparent homogeneity from Escherichia coli as a by-product of DNA polymerase III purification. The enzyme has a specific activity of 360 mumol of ATP hydrolyzed per min/mg of protein. The purified enzyme exists as monomer with a molecular weight of 81,000. It sediments in a glycerol gradient as a single species of 4.5 S. The enzyme has considerable activity at 0 degree C and has a Q10 of 3.8. In the presence of a DNA effector and magnesium ion, the enzyme will hydrolyze ATP, dATP, GTP, or dGTP to a nucleoside diphosphate plus orthophosphate with a Km of 0.20, 0.50, 0.60, and 1.30 mM, respectively. The guanine nucleotides, however, are only 25-35% as effective as substrates compared with the adenine nucleotides. ATPase IV shows strong substrate inhibition by ATP, but not dATP, above 0.2 mM. The polynucleotide effector requirement can be satisfied by either single-stranded or double-stranded DNA. The enzyme binds the effector very tightly with a Km of 3 X 10(-8) M (nucleotide) for G4 DNA. The enzyme is inhibited by E. coli single-stranded DNA-binding protein, a variety of ATP analogues and N-ethylmaleimide. The relationship of ATPase IV to DNA polymerase III holoenzyme is discussed.

A novel single-stranded DNA-binding protein from the Novikoff hepatoma which stimulates DNA polymerase beta. Purification and general characterization

We have isolated and purified to homogeneity a novel single-stranded DNA-binding protein from the Novikoff hepatoma. This protein is distinguished from other eukaryotic DNA-binding proteins by binding weakly, but cooperatively, to single-stranded DNA, by its ability to partially destabilize a double helix at 37 degrees C, and by its ability to stimulate DNA polymerase beta. The protein exists as a globular monomer of Mr = 48,000 and is capable of binding 45-49 nucleotides. It does not form a complex with the polymerase, but binds the DNA template, allowing an increased rate and extent of DNA synthesis. The enhancement of synthesis is greatest with larger gap-sized templates and with low polymerase concentrations. The mechanism of stimulation is thought to be due largely to placing the template strand into a conformation that facilitates rapid polymerization rather than strand displacement in advance of the polymerase. This protein has been named SSB-48.

Deoxyribonucleic acid dependent adenosinetriphosphatases from the Novikoff hepatoma. Characterization of a homogeneous adenosinetriphosphatase that stimulates DNA polymerase beta

Five chromatographically distinct DNA-dependent ATPase activities have been identified in high salt-detergent extracts of the Novikoff hepatoma. One of these, ATPase III, has been purified to apparent homogeneity as judged by polyacrylamide gel electrophoresis and has a specific activity of 12 mumol of ATP hydrolyzed min-1 (mg of protein)-1. The enzyme, a dimer of Mr 65000 subunits, has a sedimentation coefficient of 7.0 S in both high salt and low salt, a Stokes radius of 43 A, and a frictional coefficient of 1.31. In the presence of Mg2+ ion and a polynucleotide effector, the enzyme catalyzes hydrolysis of ATP or dATP to a diphosphate with a Km of 206 microM and 110 microM, respectively, for the two substrates. Although single-stranded effectors are preferred, the enzyme has significant activity with double-stranded effectors. The Km for effector is 0.4 microM (nucleotide). The analogues adenosine 5'-O-(3-thiotriphosphate) (ATP gamma S), dideoxyadenosine triphosphate (ddATP), and adenosine 5'-(alpha, beta-methylenetriphosphate) (alpha, beta-Me-ATP) are competitive inhibitors of the enzyme while adenosine tetraphosphate (ATP-P), 8-bromoadenosine 5'-triphosphate (8-Br-ATP), 5'-adenylyl imidodiphosphate (AMP-PNP), and adenosine 5'-(beta, gamma-methylenetriphosphate) (beta, gamma-Me-ATP) do not inhibit. The enzyme is insensitive to nalidixic acid, novobiocin, and berenil but is sensitive to N-ethylmaleimide. ATPase III is capable of stimulating DNA polymerase beta on duplex DNA, but this effect is abolished in the presence of ATP gamma S. Polymerase stimulation is further enhanced in the presence of a single-stranded DNA-binding protein. These data suggest that ATPase III may play a role in DNA repair.

Influence of single-stranded DNA-binding protein on recA induction in Escherichia coli

Two ssb mutants of Escherichia coli, which carry a lesion in the single-strand DNA-binding protein (SSB), are sensitive to UV-irradiation. We have investigated the influence of SSB on the "SOS" repair pathway by examining the levels of recA protein synthesis. These strains fail to induce normal levels of recA protein after treatment with nalidixic acid or ultraviolet light. The level of recA protein synthesis in wild-type cells is about three times greater than ssb cells. This deficiency in ssb mutants occurs in all strains and at all temperatures tested (30-41.5 degrees). In contrast, the ssb-1 mutation has no effect on temperature-induced recA induction in a recA441 (tif-1) strain. Cells carrying ssb+ plasmids and overproducing normal DNA-binding protein surprisingly are moderately UV-sensitive and have reduced levels of recA protein synthesis. Together these results establish that single-strand DNA-binding protein is involved in the induction of recA, and accounts, at least in part, for the UV sensitivity of ssb mutants. Three possible mechanisms to explain the role of SSB are discussed.

The product of the lexC gene of Escherichia coli is single-stranded DNA-binding protein

Extracts from lexC113 cells could not support phage G4 DNA-dependent replication unless supplemented with single-stranded DNA-binding protein. Purified lexC113 binding protein supported synthesis in a reconstituted replication assay, using purified proteins at 30 but not at 42 degrees C, indicating that the product of the lexC113 gene is an altered single-stranded DNA-binding protein.

Interaction of mammalian deoxyribonuclease V, a double strand 3' to 5' and 5' to 3' exonuclease, with deoxyribonucleic acid polymerase-beta from the Novikoff hepatoma

Novikoff hepatoma stimulatory factor IV has been resolved from the DNA polymerase-beta on a single-stranded DNA-cellulose column and then purified to > 95% homogeneity on hydroxylapatite. A single band of Mr = 12,000 is found on sodium dodecyl sulfate-polyacrylamide gels. Addition of factor IV to a DNA synthesis reaction causes (i) an increase in initial velocity, (ii) a prolongation of linear synthesis, and (iii) an increase in extent of incorporation. In the absence of factor IV, the reaction reaches a plateau in approximately 1 h. Factor IV, added at this point, causes resumption of synthesis with kinetics similar to when factor IV was present from the start. When factor IV is present, synthesis is followed by DNA degradation, indicating nuclease activity. Factor IV is shown to be an exonuclease which hydrolyzes double-stranded substrates in both the 3' to 5' and 5' to 3' directions at similar rates. Factor IV interacts with the 3.3 S beta-polymerase forming an aggregate sedimenting at 4.1 S and containing both polymerase and exonuclease activities. Analysis of fractions containing a beta-polymerase . exonuclease complex on polyacrylamide gels suggests a stoichiometry of 1:1. The exonuclease shows a strong preference for double-stranded substrates and is most active on poly(dA-dT). It can hydrolyze chains containing either a 3'- or 5'-phosphoryl or a 5'- or 3'-hydroxyl terminus. The product of digestion is predominantly 5'-nucleoside monophosphates. The enzyme cannot hydrolyze di- or trinucleotides, lacks RNase-H activity, and will not liberate thymine dimers from UV-irradiated DNA. The exonuclease has an alkaline pH optimum and requires a divalent cation. Since the properties of this exonuclease are unlike those of previously described mammalian DNases, we have named this enzyme mammalian DNase V.

Complement activation induced by rabbit rheumatoid factor

Rabbit rheumatoid factor produced in animals by hyperimmunized with group C streptococcal vaccine activated guinea pig complement. Anti-streptococcal serum was fractionated by Sephacryl S-200 chromatography into excluded (19S) and included (7S) material and examined for hemolytic activity in a sensitive homologous hemolytic assay system. In the presence of complement, both 19S and 7S antistreptococcal serum fractions induced lysis of bovine (ox) erythrocytes coated with mildly reduced and carboxymethylated rabbit anti-erythrocyte immunoglobulin G. That rabbit rheumatoid factor was responsible for the observed hemolytic activity was substantiated by hemolytic inhibition assays. Significant inhibition of hemolysis was effected when antistreptococcal serum fractions were incubated in the presence of human immunoglobulin G, rabbit immunoglobulin G, and Fc, whereas, no inhibition was detected when the same fractions were tested in the presence of rabbit Fab or F(ab')2 fragments. Deaggregation of inhibitor preparations revealed a preferential reactivity of rheumatoid factor for rabbit immunoglobulin G. In addition to the rheumatoid factor-dependent hemolytic activity observed in humoral preparations, immunoglobulin G-specific antibody-forming cells in spleen and peripheral blood lymphocyte isolates were enumerated by plaque-forming cell assay.

A temperature-sensitive single-stranded DNA-binding protein from Escherichia coli

A temperature-sensitive single-stranded DNA-binding protein (SSB) has been purified from mutant Escherichia coli (ssb-1) cells by use of affinity chromatography on blue dextran-Sepharose. An altered amino acid sequence in the mutant protein is apparent in tryptic digests, confirming that the ssb mutation is in the structural gene. The mutant protein is less effective than the wild type in protecting single-stranded DNA from nuclease S1 digestion and in inhibiting DNA-dependent ATPases. The purified protein supports replication of phage G4 DNA in vitro at 30 degrees C, although higher levels of mutant protein, 4-fold higher than wild type, are needed to do so. The mutant protein becomes less active in supporting replication above 30 degrees C and becomes inactive at 42 degrees C within 1 min. Activity is restored upon return to 20 degrees C. Despite its temperature sensitivity in vivo and in vitro, the mutant binding protein can renature fully after exposure to 100 degrees C. Thus, the mutant protein is both heat-stable and functionally temperature-sensitive.

Single-strand binding protein enhances fidelity of DNA synthesis in vitro

The effect of Escherichia coli single-strand binding protein on the accuracy of in vitro DNA synthesis has been determined by using two independent methods. By using the synthetic polynucleotide poly[d(A-T)] and measuring dGTP misincorporation or by using phi X174 DNA and measuring nucleotide substitutions, we found that binding protein increases the fidelity of DNA synthesis by as much as 10-fold. This increase is observed with DNA polymerases of divergent sources and is progressive with increasing concentration of binding protein. The increased accuracy observed with DNA polymerases lacking a 3' leads to 5' exonuclease points to a mechanism other than augmented proofreading. In accord with the properties of single-strand binding proteins, it is suggested that increased fidelity is a result of enhanced base selection by the DNA polymerase, resulting from increased rigidity of the template due to its interaction with binding protein.

Mutant single-strand binding protein of Escherichia coli: genetic and physiological characterization

A mutation in the Escherichia coli gene for single-strand binding protein results in temperature-sensitive deoxyribonucleic acid replication (R. R. Meyer, J. Glassberg, and A. Kornberg, Proc. Natl. Acad. Sci. U.S.A. 76:1702-1705, 1979). The mutant (ssb-1) is also more sensitive to ultraviolet irradiation and about one-fifth as active in recombination. Single-strand binding protein is thus implicated in repair and recombination as well as in replication. The mutation in ssb is located between uvrA and melA at 90.8 min on the genetic map. The ssb gene appears to be allelic with lexC, a gene with a proposed role in regulating inducible deoxyribonucleic acid repair.

An Escherichia coli mutant defective in single-strand binding protein is defective in DNA replication

An Escherichia coli mutant, temperature-sensitive for DNA synthesis in vivo and in vitro, is defective in single-strand binding protein (SSB; DNA-binding protein). Conversion of phage G4 single strands to the duplex form is defective in crude enzyme fractions of the mutant and is complemented by pure wild-type SSB. Radioimmunoassays of mutant extracts show normal levels of material crossreacting with anti-SSB antibody. SSB purified to homogeneity from the mutant is active, with lower specific activity, in the reconstituted G4 replication assay at 30 degrees C, but virtually inactive at 42 degrees C. Surprisingly, the mutant protein, like the wild-type protein, survives heating at 100 degrees C. Thus, mutant SSB is structurally heat-resistant but is functionally thermosensitive in vitro and in vivo. Both the in vivo and in vitro defects are tightly linked in transductions by phage P1. The mutation in the binding protein, designated ssb-1, is located between 90 and 91 min on the E. coli genetic map.

Purification and properties of DNA polymerase-beta from guinea pig liver

Deoxyribonucleic acid polymerase-beta (EC 2.7.7.7) has been purified over 100 000-fold from a whole cell extract of guinea pig liver. The enzyme yields a single stainable band when subjected to non-denaturing polyacrylamide gel electrophoresis, and this band corresponds to the DNA polymerase activity when a sister gel is sliced and assayed. The final fraction has a specific activity of 21 000 units/mg; this value can be increased significantly by addition of various components, including glycols, polyamines or any of several protein factors which can be purified from the crude extract. The DNA polymerase-beta lacks detectable exonuclease or endonuclease activity, has an alkaline pH optimum and has a requirement for all four deoxyribonucleoside triphosphates, a divalent cation and a primer-template for maximal activity. While activated DNA is the preferred primer-template, the enzyme is capable of utilizing native and denatured DNA as well as several synthetic polynucleotides as primer-templates. The latter are especially effective when manganese is the divalent cation. Magnesium, at 10 mM, is the preferred divalent cation when activated DNA is used. Manganese, and to a lesser extent cobalt, can substitute for magnesium while zinc and calcium cannot. The beta-polymerase has a half-life of 10 min at 40 degrees C and this is increased in the presence of either DNA or NaCl. The enzyme is stimulated by glycols, polyamines and NaCal or KCl, and is inhibited by several known inhibitors of DNA polymerase activity including o-phenanthroline, heparin, organic solvents and sulfhydryl blocking agents. Guinea pig liver DNA polymerase-beta is remarkably similar to the rat Novikoff hepatoma beta-polymerase with respect to its isoelectric point of 8.4 and its molecular weight of 32 000 as determined by sucrose gradient centrifugation under high or low salt conditions or sodium dodecyl sulfate-polyacrylamide gel electrophoresis. This similarity is further extended to the removal, at the final step in purification, of a protein capable of stimulating the homogeneous enzyme. Removal of this protein could explain the lower molecular weight of the guinea pig and other rodent-derived beta-polymerases, when compared to the beta-polymerases from other systems.

The subliminal perception of movement and the course of autokinesis

The course of autokinesis is shown to be sensitive to the real movement of a surrounding stimulus. With the supraliminal presentation of this stimulus, apparent movement in a direction opposite to that of the real movement is induced. With the subliminal presentation of the same stimulus the real movement serves to inhibit autokinesis by inducing brief periods of stationarity between the phases of upward and downward apparent movement. The results confirm previous findings that the movement of a stimulus may be discriminated without there being any perceptual (phenomenal) adjunct.

Novikoff hepatoma deoxyribonucleic acid polymerase. Identification of a stimulatory protein bound to the beta-polymerase

The Novikoff hepatoma DNA polymerase-beta sediments as a 7.3S form in crude extracts but during purification sediments as a 4.1S form (after diethylaminoethyl-Sephadex chromatography) or as a 3.3S form (after DNA-cellulose chromatography). If 0.25 M ammonium sulfate or 0.5 M NaCl is included in the sucrose gradients, the 7.3S form sediments at 3.3 S; after removal of the salt, it sediments again at 7.3 S, indicating the reversibility of the aggregation phenomenon. By careful adjustment of ionic strength in the gradient, four distinct and reproducible forms of the enzyme sedimenting at 7.3, 5.8, 4.1, and 3.3 S can be generated. The isoelectric point of the DNA polymerase also changes during purification; the 7.3S form has a pI of 7.5, while the 4.1S form isoelectrically focuses at a pH of 8.5. During DNA-cellulose chromatography, the Novikoff beta-polymerase is separated from a stimulatory factor designated as Novikoff factor IV. Factor IV is a protein as shown by its sensitivity to protease and resistance to nucleases. It is responsible for converting the 3.3S enzyme to the 4.1S form since the 3.3S homogeneous DNA polymerase-beta sediments at 4.1 S in the presence of factor IV. Factor IV confers stability to the polymerase in low ionic strength buffers as well as stability to heat denaturation. Factor IV has the ability to increase the activity of the 3.3S homogeneous polymerase by about fourfold.

Novikoff hepatoma deoxyribonucleic acid polymerase. Sensitivity of the beta-polymerase to sulfhydryl blocking agents

Unlike other beta-class eukaryotic DNA polymerases, the enzyme purified from the Novikoff hepatoma is inhibited by both sulfhydryl blocking agents N-ethylmaleimide (NEM) and p-hydroxymercuribenzoate (pHMB). The degree of sensitivity varies depending on the enzyme purity, pH of the reaction, and the presence of sulfhydryl reducing agents. Novikoff beta-polymerase activity is unaffected by the presence of 2-mercaptoethanol (2-Me) or dithiothreitol (DTT); however, the combination of 2-mercaptoethanol and NEM or pHMB acts to reverse the inhibition of the sulfhydryl blocking agent. The reversal of inhibition involves more than just a titration of NEM with 2-mercaptoethanol since a) the combination of these two reagents actually stimulates the DNA polymerase, and b) dithiothreitol did not reverse the inhibition. Binding of the polymerase to DNA did not affect the enzyme sensitivity to NEM.

Novikoff hepatoma deoxyribonucleic acid polymerase. Purification and properties of a homogeneous beta polymerase

Deoxyribonucleic acid polymerase-beta (EC 2.7.7.7) FROM THE Novikoff hepatoma has been purified over 200 000-fold (based on the increase in specific activity), by ammonium sulfate fractionation and chromatography on DEAE-Sephadex, phosphocellulose, hydroxylapatite, and DNA-cellulose. The enzyme is remarkably stable through all stages of purification until DNA-cellulose chromatography when it must be kept in buffers containing 0.5 M NaCl and 1 mg/ml bovine serum albumin for stability. The enzyme appears to be homogeneous as evidenced by a single stainable band when subjected to electrophoresis in polyacrylamide gels of different porosity. The stainable band corresponds to the DNA polymerase as determined by slicing sister gels and assaying for enzyme activity. The specific activity of the homogeneous preparation is about 60 000 units/mg. The enzyme lacks detectable exonuclease or endonuclease activity. It has a molecular weight of 32 000 as determined by sodium dodecylsulfate-polyacrylamide gel electrophoresis. In sucrose gradients, the molecular weight is estimated at 31 000. The isoelectric point of the hydroxylapatite fraction enzyme is 8.5. The Novikoff beta-polymerase requires all four deoxyribonucleoside triphosphates, primer-template, and a divalent cation for maximal activity. The apparent Km for total deoxyribonucleoside triphosphate is 7-8 muM and for DNA 125 mug/ml. Activated DNA, rendered 7% acid soluble by DNase I, is the preferred primer-template, although a number of synthetic polynucleotides can by efficiently utilized, particularly in the presence of Mm2+ optimum is 7 mM; the Mn2+ optimum is 1 mM. The pH optimum is 8.4 in Tris-HCl or 9.2 in glycine buffer. The beta-polymerase is sstimulated about twofold by NaCl or KCl at an optimum of 50-100 MM, and the enzyme maintains considerable activity at high ionic strengths. The DNA polymerase is inhibited by ethanol, acetone, and a variety of known polymerase inhibitors. Glycols stimulate the enzyme as does spermine or spermidine. Unlike most beta-polymerases, the Novikoff enzyme is moderately sensitive to N-ethylmaleimide.

Isolation and purification of mediators of cell proliferation

An attempt was made to isolate and purify the important biological mediators that cause an increase in proliferative activity of fibroblasts following tissue injury. DNA synthesis and cellular growth, using cultured WI-38 fibroblasts, and DNA synthesis in an in vitro assay, using purified DNA polymerase, were stimulated by factors extracted from the lysosomal-mitochondrial fraction of normal guinea pig liver. These factors precipitated in 45 percent to 60 percent ethanol. They were insensitive to treatment with RNase, DNase and heating to 56 C for 30 minutes, but were inactivated at 100 C. isoelectric focusing of the active ethanol-precipitate resolved activity into five discrete fractions, one of which has been purified, using ion-exchange chromatography. The presence of these factors in normal tissue may explain the increase in proliferative activity of fibroblasts and other cells in the early stages of wound healing, via release caused by injury.

Stimulation of DNA polymerase by factors isolated from Novikoff hepatoma

Extracts of Novikoff hepatoma cells contain factors capable of stimulating in vitro DNA synthesis several fold. The activity can be resolved into three separate protein peaks on DEAE-Sephadex. Two of these, factors II and III, have been purified and partially characterized. Both factors increase the initial rate of DNA synthesis and allow synthesis to proceed much longer. If either factor is added after synthesis by the DNA polymerase has reached a plateau, resumption of synthesis occurs. The factors appear to have different modes of action or sites of action since they show an additive effect even when a single one is used at saturating conditions. These factors are present in normal rat liver but at a concentration less than 5% of that found in the tumor cells. When tested with several highly purified DNA polymerases (DNA nucleotidyltransferase, EC 2.7.7.7), the factors show a much greater stimulation of homologous, non-mitochondrial enzymes (rat liver nuclear-, rat liver cytoplasmic-, or Novikoff-DNA polymerases) when compared with rat liver or calf liver mitochondrial-, Escherichia coli I-, or sea urchin nuclear-DNA polymerases. The mechanism of action of these factors is not known at present. No enzymatic activity has been associated with factor III. Highly purified, but not homogeneous, preparations of factor II contain low levels of endonuclease; it has not been established whether endonuclease is a contaminant or is responsible for the stimulating activity.