Analysis of angiogenesis biomarkers for ramucirumab efficacy in patients with metastatic colorectal cancer from RAISE, a global, randomized, double-blind, phase III study

Background

The phase III RAISE trial (NCT01183780) demonstrated that the vascular endothelial growth factor (VEGF) receptor (VEGFR)-2 binding monoclonal antibody ramucirumab plus 5-fluororuracil, leucovorin, and irinotecan (FOLFIRI) significantly improved overall survival (OS) and progression-free survival (PFS) compared with placebo + FOLFIRI as second-line metastatic colorectal cancer (mCRC) treatment. To identify patients who benefit the most from VEGFR-2 blockade, the RAISE trial design included a prospective and comprehensive biomarker program that assessed the association of biomarkers with ramucirumab efficacy outcomes.

Patients and methods

Plasma and tumor tissue collection was mandatory. Overall, 1072 patients were randomized 1 : 1 to the addition of ramucirumab or placebo to FOLFIRI chemotherapy. Patients were then randomized 1 : 2, for the biomarker program, to marker exploratory (ME) and marker confirmatory (MC) groups. Analyses were carried out using exploratory assays to assess the correlations of baseline marker levels [VEGF-C, VEGF-D, sVEGFR-1, sVEGFR-2, sVEGFR-3 (plasma), and VEGFR-2 (tumor tissue)] with clinical outcomes. Cox regression analyses were carried out for each candidate biomarker with stratification factor adjustment.

Results

Biomarker results were available from >80% (n = 894) of patients. Analysis of the ME subset determined a VEGF-D level of 115 pg/ml was appropriate for high/low subgroup analyses. Evaluation of the combined ME + MC populations found that the median OS in the ramucirumab + FOLFIRI arm compared with placebo + FOLFIRI showed an improvement of 2.4 months in the high VEGF-D subgroup [13.9 months (95% CI 12.5-15.6) versus 11.5 months (95% CI 10.1-12.4), respectively], and a decrease of 0.5 month in the low VEGF-D subgroup [12.6 months (95% CI 10.7-14.0) versus 13.1 months (95% CI 11.8-17.0), respectively]. PFS results were consistent with OS. No trends were evident with the other antiangiogenic candidate biomarkers.

Conclusions

The RAISE biomarker program identified VEGF-D as a potential predictive biomarker for ramucirumab efficacy in second-line mCRC. Development of an assay appropriate for testing in clinical practice is currently ongoing.

Clinical trials registration

NCT01183780.

Xrd and Hrem Studies of Nanocrystalline Cu and Pd

Consolidated powders of nanocrystalline Cu and Pd have been studied by x-ray diffraction (XRD) and high resolution electron microscopy (HREM) as part of an investigation of the mechanical behavior of nanocrystalline pure metals. XRD line broadening measurements were made to estimate grain size, qualitative grain size distribution and average long range strains in a number of samples. Mean grain sizes range from 4-60 nm and have qualitatively narrow grain size distributions. Long range lattice strains are of the order of 0.2-3% in consolidated samples. These strains apparently persist and even increase in Cu samples after annealing at 0.35 Tm (498K) for 2h, accompanied by an apparent increase in grain size of e2x. Grain size, grain size distribution width and internal strains vary somewhat among samples produced under apparently identical processing conditions. HREM studies show that twins, stacking faults and low-index facets are abundant in as-consolidated nanocrystalline Cu samples. Methodology, results and analysis of XRD and HREM experiments are presented.

Tensile Strength and Creep Resistance in Nanocrystalline Cu, Pd and Ag

Measurements of tensile strength and creep resistance have been made on bulk samples of nanocrystalline Cu, Pd and Ag consolidated from powders by cold compaction. Samples of Cu-Cu2O have also been tested. Yield strength for samples with mean grain sizes of 5–80 nm and bulk densities on the order of 95% of theoretical density are increased 2–5 times over that measured in pure, annealed samples of the same composition with micrometer grain sizes. Ductility in the nanocrystalline Cu has exceeded 6% true strain, however, nanocrystalline Pd samples were much less ductile. Constant load creep tests performed at room temperature at stresses of >100 MPa indicate logarithmic creep. The mechanical properties results are interpreted to be due to grain size-related strengthening and processing flaw-related weakening.

Study of Nanophase TiO2 Grain Boundaries by Raman Spectroscopy

Raman spectra have been recorded for as-consolidated nanophase TiO2 samples with differing grain sizes and on samples annealed in air at a variety of temperatures up to 1273 K. The nanophase samples with the smallest grain size, about 12 nm average diameter, could have 15-30% of their atoms in grain boundaries; nevertheless, the strong Raman-active lines representative of the rutile structure were found to dominate all of the observed spectra, independent of grain size and annealing treatment. These lines were quite broad in the as-consolidated nanophase samples, equally in 12 nm and 100 nm grain-size compacts, but sharpened considerably upon annealing at elevated temperatures. The Raman data give no indication of grain-boundary structures in nanophase TiO2 that are significantly different from those in conventional polycrystals. However, defect structures within the grains, which anneal out at elevated temperatures, are evidenced by changes in the Raman spectra.

High Resolution Electron Microscopy of Grain Boundaries in Nanophase Palladium

Using high resolution electron microscopy, consolidated nanophase palladium samples were examined following electrolytic thinning after a hydriding - dehydriding cycle at 310 K. Due to the small size and random orientations of the individual grains, a large number of grain boundaries were available for examination. Some of these yielded adequate imaging conditions to allow observation of the lattice structure in the grain boundary regions. Image simulations were performed to determine the sensitivity of the technique to lattice disorder. The results of these studies suggest that grain boundary structures in nanophase palladium are similar to those in conventional coarse-grained polycrystals.

Small Angle Neutron Scattering from Nanophase Titanium As A Function of Oxidation

Nanophase titanium, prepared by the gas-condensation method both as aggregated powder and in lightly compacted discs, has been studied by conventional small angle neutron scattering, and by use of contrast variation methods. The contrast has been changed (a), isotopically, by means of deuterated/protonated solvents distilled into the specimen and (b) by progressive incremental oxidation of the Ti particles using fixed doses of low-pressure oxygen. It was shown that some evolution of the small angle pattern for lightly compacted nanophase Ti occurred over a period of several months at 300 K. Contrast matching by external solvent works well and has allowed the scattering lengths of oxidized and unoxidized specimens to be followed. The results imply that the scattering from metal and oxide can be separated under suitable conditions. The partial oxidation experiments indicate that there is both a fast and slow oxidation at 300 K. Also, during slow oxidation, high scattering length density scattering centers were formed whose number increased, but whose size remained the same at about 2 nm; these centers are tentatively assumed to be TiO2.

Processing and Properties of Nanophase Oxides

Nanophase oxides (Al2O3, MgO, ZnO and TiO2), with typical grain sizes in the range 2–20 nm, have been synthesized by the condensation of ultrafine particles in a convective inert gas followed by their collection and in-situ consolidation in vacuum at ambient temperature. These new materials, owing to the reduced scale of their grains along with the enhanced cleanliness of their grain boundaries, are found to have significantly improved properties relative to those of their coarser-grained, conventionally-prepared counterparts. Nanophase rutile (TiO2) with an initial mean grain diameter of 12 nm, for example, has been found to sinter at 400 to 600°C lower temperatures than conventional rutile powders, without the need for compacting or sintering aids, while retaining a small grain size. Additionally, the importance of the extremely clean surfaces obtained with the gas condensation method has been demonstrated by comparing the sintering behavior of powders with and without air exposure prior to consolidation. The research completed on the processing and properties of nanophase ceramics is reviewed, and the potential for engineering advanced ceramics using the nanophase processing method is discussed.

Sintering of Nanophase TiO2 At 550°C

Samples of nanophase TiO2 were prepared by the condensation of Ti vapors into clusters, their in situ oxidation to TiO2, and their consolidation into thin disks. Small angle neutron scattering was measured in the as-consolidated condition and after selected isothermal sintering anneals of up to 23 h at 550°C. The maximum entropy analysis method was used to obtain the size distributions of the scattering centers from the scattering curves. The results are interpreted in terms of a microstructural model consisting of nanometer sized grains of TiO2 separated by about 0.5 nm wide boundary regions, which contain voids and TiO2 of ≤60–70% of bulk density.

A Small Angle Neuitron Scattering Investigation of Compacted Nanophase TiO2 and Pd

Nanocrystalline compacts of TiO2 and Pd were prepared by first condensing the Ti or Pd vapors in an inert gas atmosphere. The Ti was oxidized in situ to TiO2. Samples were prepared by scraping off and compacting the nanophase materials into thin disks. The small angle neutron scattering was measured in the as-prepared condition and after isothermal anneals of up to 23 hrs at 550°C for the TiO2 and up to 3.3 hrs at 300°C for the Pd. Scattering data were obtained in absolute cross sections. Integrated small angle scattering and maximum entropy methods were used in estimating the structural parameters. The results are interpreted in terms of a model which consists of nanometer sized grains of the materials separated by boundary regions which are, on average, much less dense than the respective bulk materials; 21% for the TiO2 and about 56% for Pd. However, the boundary regions contain voids or pores, which contribute to these density decrements. Possible sources of error are discussed.

Synthesis, Characterization, and Properties of Nanophase Ceramics

Ultrafine-grained ceramics have been synthesized by the production of ultrafine (2–20 nm) particles, using the gas-condensation method, followed by their in-situ, ultra-high vacuum consolidation at room temperature. These new nanophase ceramics have properties that are significantly improved relative to those of their coarser-grained, conventionally-prepared counterparts. For example, nanophase rutile (TiO2) with an initial mean grain diameter of 12 nm sinters at 400 to 600°C lower temperatures than conventional powders, without the need for compacting or sintering aids. The sintered nanophase rutile exhibits both improved microhardness and fracture characteristics. These property improvements result from the reduced scale of the grains and the increased cleanliness of the particle surfaces and the subsequently-formed grain boundaries. Research completed on the synthesis, characterization, and properties of nanophase ceramics is reviewed and the potential for using the nanophase synthesis method for engineering new and/or improved ceramics and composites is considered.

Is Superplasticity in the Future of Nanophase Materials?

The ultrafine grain sizes and high diffusivities in nanophase materials assembled from atomic clusters suggest that these materials may have a strong tendency toward superplastic mechanical behavior. Both small grain size and enhanced diffusivity can be expected to lead to increased diffusional creep rates as well as to a significantly greater propensity for grain boundary sliding. Recent mechanical properties measurements at room temperature on nanophase Cu, Pd, and TiO2, however, give no indications of superplasticity. Nonetheless, significant ductility has been clearly demonstrated in these studies of both nanophase ceramics and metals. The synthesis of cluster-assembled nanophase materials is described and the salient features of what is known of their structure and mechanical properties is reviewed. Finally, the answer to the question posed in the title is addressed.

Conditioned responses in courtship behavior of normal and mutant Drosophila

Male courtship behaviour in Drosophila melanogaster is modified by prior sexual experience. Whereas naive males nearly always court virgin females persistently, males previously paired with unreceptive fertilized females subsequently court virgin females in an abbreviated manner, if at all. The probability of diminished male courtship is directly related to the duration of the prior "conditioning" period with a fertilized female. Naive males court fertilized females less vigorously than they court virgins; this depression of male behavior occurs even if the male is blind or if the fertilized female cannot actively reject his courtship. These results suggest that fertilized females are a source of both courtship-provoking and courtship-inhibiting olfactory cues and that the central association of these cues in males is sufficient to bring about the retention of modified courtship behavior. Mutant "amnesiac" males, selected as memory-deficient in a learning test unrelated to courtship [Quinn, W. G., Sziber, P. P. & Booker, R. (1979) Nature (London) 277, 212-214], are trainable by exposure to fertilized females, but the experience-dependent behavior-diminished courtship performance-wanes abnormally rapidly-i.e., less than 1 hour, compared to 2-3 hr for wild-type flies.

Human mesenchymal stem cell adhesion and proliferation in response to ceramic chemistry and nanoscale topography

Modification of the chemistry and surface topography of nanophase ceramics was used to provide biomaterial formulations designed to direct the adhesion and proliferation of human mesenchymal stem cells (HMSCs). HMSC adhesion was dependent upon both the substrate chemistry and grain size, but not on surface roughness or crystal phase. Specifically, cell adhesion on alumina and hydroxyapatite was significantly reduced on the 50 and 24 nm surfaces, as compared with the 1500 and 200 nm surfaces, but adhesion on titania substrates was independent of grain size. HMSC proliferation was minimal on the 50 and 24 nm substrates of any chemistry tested, and thus significantly lower than the densities observed on either the 1500 or 200 nm surfaces after 3 or more consecutive days of culture. Furthermore, HMSC proliferation was enhanced on the 200 nm substrates, compared with results obtained on the 1500 nm substrates after 7 or more days of culture. HMSC proliferation was independent of both substrate surface roughness and crystal phase. Rat osteoblast and fibroblast adhesion and proliferation exhibited similar trends to that of HMSCs on all substrates tested. These results demonstrated the potential of nanophase ceramic surfaces to modulate functions of HMSCs, which are pertinent to biomedical applications such as implant materials and devices.

Modifications of multi-wall carbon nanotubes with B-containing vapor and their effects on the properties of boron carbide matrix nanocomposites

Multi-wall carbon nanotubes were modified by heating them together with elemental boron powder. B4C crystals grew on the surfaces of the nanotubes, and electron diffraction patterns showed an orientation dependence of the surface B4C and the underlying carbon in the nanotubes. There was no reaction of the nanotubes with solid B2O3 alone. Composites of the modified nanotubes in a B4C matrix showed a small increase of density over sintered B4C.

Molecular Evolution of Antibody Affinity for Sensitive Detection of Botulinum Neurotoxin Type A

Botulism is caused by botulinum neurotoxin (BoNT), the most poisonous substance known. Potential use of BoNT as a biothreat agent has made development of sensitive assays for toxin detection and potent antitoxin for treatment of intoxication a high priority. To improve detection and treatment of botulism, molecular evolution and yeast display were used to increase the affinity of two neutralizing single chain Fv (scFv) antibodies binding BoNT serotype A (BoNT/A). Selection of yeast displayed scFv libraries was performed using methods to select for both increased association rate constant (k(on)) and decreased dissociation rate constants (k(off)). A single cycle of error prone mutagenesis increased the affinity of the 3D12 scFv 45-fold from a K(D) of 9.43x10(-10)M to a K(D) of 2.1x10(-11)M. Affinity of the HuC25 scFv was increased 37-fold from 8.44x10(-10)M to 2.26x10(-11)M using libraries constructed by both random and site directed mutagenesis. scFv variable region genes were used to construct IgG for use in detection assays and in vivo neutralization studies. While IgG had the same relative increases in affinity as scFv, (35-fold and 81-fold, respectively, for 3D12 and HuC25) higher solution equilibrium binding constants were observed for the IgG, with the 3D12 K(D) increasing from 6.07x10(-11)M to 1.71x10(-12)M and the HuC25 K(D) increasing from 4.51x10(-11)M to 5.54x10(-13)M. Affinity increased due to both an increase in k(on), as well as slowing of k(off). Higher affinity antibodies had increased sensitivity, allowing detection of BoNT/A at concentrations as low as 1x10(-13)M. The antibodies will also allow testing of the role of affinity in in vivo toxin neutralization and could lead to the generation of more potent antitoxin.

Using an in vivo phagemid system to identify non-compatible loxP sequences

The site-specific recombination system of bacteriophage P1 is composed of the Cre recombinase that recognizes a 34-bp loxP site. The Cre/loxP system has been extensively used to manipulate eukaryotic genomes for functional genomic investigations. The creation of additional heterologous loxP sequences potentially expands the utility of this system, but only if these loxP sequences do not recombine with one another. We have developed a stringent in vivo assay to examine the degree of recombination between all combinations of each previously published heterologous loxP sequence. As expected, homologous loxP sequences efficiently underwent Cre-mediated recombination. However, many of the heterologous loxP pairs were able to support recombination with rates varying from 5 to 100%. Some of these loxP sequences have previously been reported to be non-compatible with one another. Our study also confirmed other heterologous loxP pairs that had previously been shown to be non-compatible, as well as defined additional combinations that could be used in designing new recombination vectors.

Using an in vivo phagemid system to identify non-compatible loxP sequences

The site-specific recombination system of bacteriophage P1 is composed of the Cre recombinase that recognizes a 34-bp loxP site. The Cre/loxP system has been extensively used to manipulate eukaryotic genomes for functional genomic investigations. The creation of additional heterologous loxP sequences potentially expands the utility of this system, but only if these loxP sequences do not recombine with one another. We have developed a stringent in vivo assay to examine the degree of recombination between all combinations of each previously published heterologous loxP sequence. As expected, homologous loxP sequences efficiently underwent Cre-mediated recombination. However, many of the heterologous loxP pairs were able to support recombination with rates varying from 5 to 100%. Some of these loxP sequences have previously been reported to be non-compatible with one another. Our study also confirmed other heterologous loxP pairs that had previously been shown to be non-compatible, as well as defined additional combinations that could be used in designing new recombination vectors.

Enhanced osteoclast-like cell functions on nanophase ceramics

Synthesis of tartrate-resistant acid phosphatase (TRAP) and formation of resorption pits by osteoclast-like cells, the bone-resorbing cells, on nanophase (that is, material formulations with grain sizes less than 100nm) alumina and hydroxyapatite (HA) were investigated in the present in vitro study. Compared to conventional (that is, grain sizes larger than 100 nm) ceramics, synthesis of TRAP was significantly greater in osteoclast-like cells cultured on nanophase alumina and on nanophase HA after 10 and 13 days, respectively. In addition, compared to conventional ceramics, formation of resorption pits was significantly greater by osteoclast-like cells cultured on nanophase alumina and on nanophase HA after 7, 10, and 13 days, respectively. The present study, therefore, demonstrated, for the first time, enhanced osteoclast-like cell function on ceramic surfaces with nanometer-size surface topography.

Mechanisms of enhanced osteoblast adhesion on nanophase alumina involve vitronectin

The role, including concentration, conformation, and bioactivity, of adsorbed vitronectin in enhancing osteoblast adhesion on nanophase alumina was investigated in the present study. Vitronectin adsorbed in a competitive environment in the highest concentration on nanophase alumina compared to conventional alumina. Enhanced adsorption of vitronectin on nanophase alumina was possibly due to decreased adsorption of apolipoprotein A-I and/or increased adsorption of calcium on nanophase alumina. In a novel manner, the present study utilized surface-enhanced Raman scattering (SERS) to determine the conformation of vitronectin adsorbed on nanophase alumina. These results provided the first evidence of increased unfolding of vitronectin adsorbed on nanophase alumina. Increased adsorption of calcium on nanophase alumina may affect the conformation of adsorbed vitronectin specifically to promote unfolding of the macromolecule to expose cell-adhesive epitopes recognized by specific cell-membrane receptors. Results of the present study also provided evidence of dose-dependent inhibition of osteoblast adhesion on nanophase alumina pretreated with vitronectin following preincubation (and thus blocking respective cell-membrane receptors) with either Arginine-Glycine-Aspartic Acid-Serine (RGDS) or Lysine-Arginine-Serine-Arginine (KRSR). These events, namely, enhanced vitronectin adsorption, comformation, and bioactivity, may explain the increased osteoblast adhesion on nanophase alumina.

Mass spectral analysis of a protein complex using single-chain antibodies selected on a peptide target: applications to functional genomics

Genome projects are identifying an ever-increasing number of genes, accelerating the need for reagents to study the expression of these genes and elucidate the function and cellular location of the gene products. Our goal was to develop a strategy to allow human single-chain variable fragment (scFv) antibodies to be used for these endeavors. A library containing 7x10(9) individual variants was displayed by bacteriophage and selected against a biotinylated peptide corresponding to the C-terminal 15 amino acid residues of Ku86, one component of a heterodimer involved in double-stranded DNA break repair. Four unique scFv antibodies were recovered that not only recognized the selected peptide, but also the intact protein. Three of the scFv antibodies were expressed in soluble form and recognized Ku86 by Western analysis. The affinity of one of the scFv antibodies for Ku86 was 16 nM as measured by BIAcore analysis. scFv immunoprecipitation of Ku86 also isolated the other component of the heterodimer, Ku70, as determined by Western analysis and mass spectrometry. These results demonstrate the utility of scFv antibodies as invaluable reagents for functional genomics.

Specific proteins mediate enhanced osteoblast adhesion on nanophase ceramics

Osteoblast, fibroblast, and endothelial cell adhesion on nanophase (that is, materials with grain sizes less than 100 nm) alumina, titania, and hydroxyapatite (HA) was investigated using in vitro cellular models. Osteoblast adhesion was significantly (p < 0.01) greater after 4 h on nanophase alumina, titania, and HA than it was on conventional formulations of the same ceramics. In contrast, compared to conventional alumina, titania, and HA, after 4 h fibroblast adhesion was significantly (p < 0.01) less on nanophase ceramics. Examination of the underlying mechanism(s) of cell adhesion on nanophase ceramics revealed that these ceramics adsorbed significantly (p < 0.01) greater quantities of vitronectin, which, subsequently, may have contributed to the observed select enhanced adhesion of osteoblasts. Select enhanced osteoblast adhesion was independent of surface chemistry and material phase but was dependent on the surface topography (specifically on grain and pore size) of nanophase ceramics. The capability of synthesizing and processing nanomaterials with tailored (through, for example, specific grain and pore size) structures and topographies to control select subsequent cell functions provides the possibility of designing the novel proactive biomaterials (that is, materials that elicit specific, timely, and desirable responses from surrounding cells and tissues) necessary for improved implant efficacy.

Specific proteins mediate enhanced osteoblast adhesion on nanophase ceramics

Osteoblast, fibroblast, and endothelial cell adhesion on nanophase (that is, materials with grain sizes less than 100 nm) alumina, titania, and hydroxyapatite (HA) was investigated using in vitro cellular models. Osteoblast adhesion was significantly (p < 0.01) greater after 4 h on nanophase alumina, titania, and HA than it was on conventional formulations of the same ceramics. In contrast, compared to conventional alumina, titania, and HA, after 4 h fibroblast adhesion was significantly (p < 0.01) less on nanophase ceramics. Examination of the underlying mechanism(s) of cell adhesion on nanophase ceramics revealed that these ceramics adsorbed significantly (p < 0.01) greater quantities of vitronectin, which, subsequently, may have contributed to the observed select enhanced adhesion of osteoblasts. Select enhanced osteoblast adhesion was independent of surface chemistry and material phase but was dependent on the surface topography (specifically on grain and pore size) of nanophase ceramics. The capability of synthesizing and processing nanomaterials with tailored (through, for example, specific grain and pore size) structures and topographies to control select subsequent cell functions provides the possibility of designing the novel proactive biomaterials (that is, materials that elicit specific, timely, and desirable responses from surrounding cells and tissues) necessary for improved implant efficacy.

Enhanced functions of osteoblasts on nanophase ceramics

Select functions of osteoblasts (bone-forming cells) on nanophase (materials with grain sizes less than 100 nm) alumina, titania, and hydroxyapatite (HA) were investigated using in vitro cellular models. Compared to conventional ceramics, surface occupancy of osteoblast colonies was significantly less on all nanophase ceramics tested in the present study after 4 and 6 days of culture. Osteoblast proliferation was significantly greater on nanophase alumina, titania, and HA than on conventional formulations of the same ceramic after 3 and 5 days. More importantly, compared to conventional ceramics, synthesis of alkaline phosphatase and deposition of calcium-containing mineral was significantly greater by osteoblasts cultured on nanophase than on conventional ceramics after 21 and 28 days. The results of the present study provided the first evidence of enhanced long-term (on the order of days to weeks) functions of osteoblasts cultured on nanophase ceramics; in this manner, nanophase ceramics clearly represent a unique and promising class of orthopaedic/dental implant formulations with improved osseointegrative properties.

Use of DNA, RNA, and chimeric templates by a viral RNA-dependent RNA polymerase: evolutionary implications for the transition from the RNA to the DNA world

All polynucleotide polymerases have a similar structure and mechanism of catalysis, consistent with their evolution from one progenitor polymerase. Viral RNA-dependent RNA polymerases (RdRp) are expected to have properties comparable to those from this progenitor and therefore may offer insight into the commonalities of all classes of polymerases. We examined RNA synthesis by the brome mosaic virus RdRp on DNA, RNA, and hybrid templates and found that precise initiation of RNA synthesis can take place from all of these templates. Furthermore, initiation can take place from either internal or penultimate initiation sites. Using a template competition assay, we found that the BMV RdRp interacts with DNA only three- to fourfold less well than it interacts with RNA. Moreover, a DNA molecule with a ribonucleotide at position -11 relative to the initiation nucleotide was able to interact with RdRp at levels comparable to that observed with RNA. These results suggest that relatively few conditions were needed for an ancestral RdRp to replicate DNA genomes.

Osteoblast adhesion on nanophase ceramics

Osteoblast adhesion on nanophase alumina (Al2O3) and titania (TiO2) was investigated in vitro. Osteoblast adhesion to nanophase alumina and titania in the absence of serum from Dulbecco's modified Eagle medium (DMEM) was significantly (P < 0.01) less than osteoblast adhesion to alumina and titania in the presence of serum. In the presence of 10% fetal bovine serum in DMEM osteoblast adhesion on nanophase alumina (23 nm grain size) and titania (32 nm grain size) was significantly (P < 0.05) greater than on conventional alumina (177 nm grain size) and titania (2.12 microm grain size), respectively, after 1, 2, and 4 h. Further investigation of the dependence of osteoblast adhesion on alumina and titania grain size indicated the presence of a critical grain size for osteoblast adhesion between 49 and 67 nm for alumina and 32 and 56 nm for titania. The present study provides evidence of the ability of nanophase alumina and titania to simulate material characteristics (such as surface grain size) of physiological bone that enhance protein interactions (such as adsorption, configuration, bioactivity, etc.) and subsequent osteoblast adhesion.

Moieties in an RNA promoter specifically recognized by a viral RNA-dependent RNA polymerase

RNAs 33 nucleotides in length can direct accurate initiation of subgenomic RNA synthesis by the brome mosaic virus RNA-dependent RNA polymerase (RdRp), provided that the native sequences are maintained at five positions: -17, -14, -13, -11, and the +1 initiation site. The functional groups in the bases of these essential nucleotides required to interact with RdRp were examined by using chemically synthesized RNAs containing base analogs at each of the five positions. Analysis using a template competition assay revealed that the mode of recognition for the initiation nucleotide (+1) is distinct from that of the other essential nucleotides in the promoter. Competition experiments also determined that three template nucleotides are sufficient for stable interaction with RdRp. These results identify base moieties in the brome mosaic virus subgenomic promoter required for efficient RNA synthesis and support the hypothesis that the recognition of a RNA promoter by a viral RdRp is analogous to the recognition of DNA promoters by DNA-dependent RNA polymerases.

Mechanistic analysis of RNA synthesis by RNA-dependent RNA polymerase from two promoters reveals similarities to DNA-dependent RNA polymerase

The brome mosaic virus (BMV) RNA-dependent RNA polymerase (RdRp) directs template-specific synthesis of (-)-strand genomic and (+)-strand subgenomic RNAs in vitro. Although the requirements for (-)-strand RNA synthesis have been characterized previously, the mechanism of subgenomic RNA synthesis has not. Mutational analysis of the subgenomic promoter revealed that the +1 cytidylate and the +2 adenylate are important for RNA synthesis. Unlike (-)-strand RNA synthesis, which required only a high GTP concentration, subgenomic RNA synthesis required high concentrations of both GTP and UTP. Phylogenetic analysis of the sequences surrounding the initiation sites for subgenomic and genomic (+)-strand RNA synthesis in representative members of the alphavirus-like superfamily revealed that the +1 and +2 positions are highly conserved as a pyrimidine-adenylate. GDP and dinucleotide primers were able to more efficiently stimulate (-)-strand synthesis than subgenomic synthesis under conditions of limiting GTP. Oligonucleotide products of 6-, 7-, and 9-nt were synthesized and released by RdRp in 3-20-fold molar excess to full-length subgenomic RNA. Termination of RNA synthesis by RdRp was not induced by template sequence alone. Our characterization of the stepwise mechanism of subgenomic and (-)-strand RNA synthesis by RdRp permits comparisons to the mechanism of DNA-dependent RNA synthesis.

Sequence-specific recognition of a subgenomic RNA promoter by a viral RNA polymerase

RNA templates of 33 nucleotides containing the brome mosaic virus (BMV) core subgenomic promoter were used to determine the promoter elements recognized by the BMV RNA-dependent RNA polymerase (RdRp) to initiate RNA synthesis. Nucleotides at positions -17, -14, -13, and -11 relative to the subgenomic initiation site must be maintained for interaction with the RdRp. Changes to every other nucleotide at these four positions allow predictions for the base-specific functional groups required for RdRp recognition. RdRp contact of the nucleotide at position -17 was suggested with a template competition assay. Comparison of the BMV subgenomic promoter to those from other plant and animal alphaviruses shows a remarkable degree of conservation of the nucleotides required for BMV subgenomic RNA synthesis. We show that the RdRp of the plant-infecting BMV is capable of accurately, albeit inefficiently, initiating RNA synthesis from the subgenomic promoter of the animal-infecting Semliki Forest virus. The sequence-specific recognition of RNA by the BMV RdRp is analogous to the recognition of DNA promoters by DNA-dependent RNA polymerases.