Analysis of nanoindentation response of diatom frustules

Diatom frustules have been suggested for numerous nanotechnological applications. Experimental studies using nanoindenter have shown that the hardness and the stiffness of the frustules vary with location of indentation. To gain further insight, a computational framework has been developed where the Berkovich nanoindentation experiments were simulated by a rigid-deformable contact process. Three different approaches that provide progressively increasing level of understanding of the deformation behavior of frustules were adopted. The differences in the mechanical responses of the frustule due to variation of indentation location, size of pores, and distribution of pores were analyzed. It has been found that the effective stiffness of the frustule is linearly related to the porosity level and does not depend on the frustule size or its pore architecture. It has been shown that a 3D porous shell computational model is more appropriate to simulate the experimentally obtained mechanical response of diatom frustules.

The transcriptome of the rat hypothalamic-neurohypophyseal system is highly strain-dependent

We have used microarrays to comprehensively describe the transcriptomes of the supraoptic nucleus (SON), the paraventricular nucleus (PVN) and the neurointermediate lobe of adult male Sprague-Dawley (SD) and Wistar-Kyoto (WKY) rats, as well as the PVN of Wistar rats. Comparison of these gene lists has enabled us to identify surprisingly large differences in hypothalamic-neurohypophyseal system gene expression patterns in these three strains. We have also shown that different transcript populations are enriched in the PVN and the SON of SD and WKY rats. The transcriptome differences catalogued here may be molecular substrates for the neuro-humoral phenotypic differences exhibited by different strains of rats.

Different response of articular chondrocyte subpopulations to surface motion

OBJECTIVE

To investigate the effect of surface motion on the gene expression of proteoglycan 4 (PRG4), hyaluronan synthases (HAS1, HAS2) and on the hyaluronan (HA) and proteoglycan 4 (PRG4) release of chondrocytes from different zones of bovine articular cartilage.

DESIGN

Superficial zone, deep zone, full thickness, and superficial/deep 1:1 mixed chondrocytes were seeded into 3D polyurethane scaffolds and stimulated using our bioreactor that approximates kinematics and surface motion characteristics of natural joints. One hour of surface motion superimposed on cyclic compression was applied twice a day over 3 consecutive days. Scaffolds were cut into top and bottom sections and analyzed for gene expression of PRG4, HAS1, and HAS2.

RESULTS

Depending on the cell population, the gene expression levels increased within 8 days of culture in unloaded scaffolds, with a stronger increase in the top compared to the bottom sections. Mechanical loading further enhanced the messenger RNA (mRNA) levels in all cell types, with most pronounced up-regulations observed for the PRG4 expression in deep zone and the HAS2 expression in superficial zone cells. The effect of the biochemical and biomechanical environment appeared to be additive, resulting in highest mRNA levels in the top sections of loaded constructs. Bioreactor stimulation also enhanced the HA release in all cell populations. Full thickness chondrocytes experienced the greatest effect on HAS1 mRNA expression and HA release, indicating that the interaction between cell populations may promote HA synthesis compared to subpopulations alone.

CONCLUSIONS

Reciprocating sliding can be an efficient tool for generating tissue-engineered constructs from various chondrocyte populations by providing a functional cartilage-synovial interface.

In vivo regulation of p21 by the Kruppel-like factor 6 tumor-suppressor gene in mouse liver and human hepatocellular carcinoma

Kruppel-like factor (KLF) 6 is a tumor-suppressor gene functionally inactivated by loss of heterozygosity, somatic mutation and/or alternative splicing that generates a dominant-negative splice form, KLF6-SV1. Wild-type KLF6 (wtKLF6) expression is decreased in many human malignancies, which correlates with reduced patient survival. Additionally, loss of the KLF6 locus in the absence of somatic mutation in the remaining allele occurs in a number of human cancers, raising the possibility that haploinsufficiency of the KLF6 gene alone contributes to cellular growth dysregulation and tumorigenesis. Our earlier studies identified the cyclin-dependent kinase inhibitor p21 as a transcriptional target of the KLF6 gene in cultured cells, but not in vivo. To address this issue, we have generated two genetic mouse models to define the in vivo role of KLF6 in regulating cell proliferation and p21 expression. Transgenic overexpression of KLF6 in the liver resulted in a runted phenotype with decreased body and liver size, with evidence of decreased hepatocyte proliferation, increased p21 and reduced proliferating cell nuclear antigen expression. In contrast, mice with targeted deletion of one KLF6 allele (KLF6+/-) display increased liver mass with reduced p21 expression, compared to wild type littermates. Moreover, in primary hepatocellular carcinoma samples, there is a significant correlation between wtKLF6 and p21 mRNA expression. Combined, these data suggest that haploinsufficiency of the KLF6 gene may regulate cellular proliferation in vivo through decreased transcriptional activation of the cyclin-dependent kinase inhibitor p21.

Identification of B cell epitopes at the C-terminus of latency-associated nuclear protein of the kaposi's sarcoma-associated herpesvirus

The latency-associated nuclear antigen (LANA) of Kaposi's sarcoma-associated herpesvirus (KSHV) plays a key role in the induction of cell transformation, maintenance of viral episome, and modulation of immune response in human. To identify the presence of B cell epitopes within C-terminus of LANA and to characterize the monoclonal antibodies (MAbs) against this protein, we expressed the C-terminal region at aa 794-1000 of LANA (pLANA-C) in Escherichia coli as a fusion protein. KSHV-positive human sera were able to recognize the recombinant LANA-C in the Western blot analysis and ELISA. Mapping of antigenic epitopes of pLANA-C by KSHV-positive human sera revealed two B cell antigenic epitopes located at aa 846-854 and aa 794-822. The MAb 3F11 recognized a region between at aa 840 to 846 of LANA and exhibited a strong and specific binding to both pLANA-C and native viral LANA. These findings showed that pLANA-C and MAb 3F11 could be used for the detection of KSHV antibodies in human sera and for the advanced study of biological functions of LANA.

Catalytic oxidation of benzene using DBD corona discharges

Plasma oxidation of benzene (C(6)H(6)) in oxygen and nitrogen was investigated using a dielectric barrier discharge (DBD) reactor with or without MnO2 or TiO2 at atmospheric pressure and without external heating except plasma heating. An alternative current power supply was used to generate corona discharges for the plasma oxidation. The energy density was controlled under 200 J/L to keep an increase in gas temperature less than 167 K. C(6)H(6) was oxidized to carbon monoxide (CO) and dioxide (CO(2)). Typically, the energy efficiency at an energy density of 92J/L was about 0.052, 0.039, and 0.024 mol/kWh with MnO2, TiO2, and without MnO2 and TiO2, respectively. Benzene oxidation mechanism was mentioned. A comparison on energy efficiency as a function of initial concentration of hydrocarbons, inorganic sulphur compounds, and chloro (fluoro and bromo) carbons was given.

Pre-treatment PSA doubling time (PSADT) predicts biochemical response to chemotherapy in patients with androgen sensitive PSA progression after local therapy

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Background: As phase III studies are developed in patients with androgen sensitive (AS) PSA progression after local therapy, efforts to stratify patients based on likelihood of benefit is critical. In an effort to define a pretreatment PSADT cutoff that predicts chemotherapy response in AS patients for use in hypothesis testing in phase III studies, we assessed patients with pretreatment PSA data in two of our prior published phase II studies of docetaxel (D) or mitoxantrone (M) chemotherapy in patients with AS PSA progression without metastasis. Methods: A retrospective analysis of PSADT was performed on 36 pts with AS PSA progression following local therapy without metastasis with available pretreatment PSA values (23 pts with D and 13 pts with M). PSADT was calculated as [LN(2)]/b, where b is the slope of the regression of LN(PSA) vs time. A t-test was used to compare the PSADT of responders vs non-responders; ANOVA was used for the combined data. A logistic regression analysis with ROC curves was used to evaluate the value of PSADT in discriminating response. Results: Mean PSADT of patients with ≥50% decrease in PSA with therapy was 204 vs. 99 days (P = 0.02). For D only, mean PSADT of pts with any PSA decrease (mean 52%) vs. increase was 211 vs. 115 days (P = 0.04). The mean PSADT of pts with ≥50% PSA decrease only on D was 203 vs. 174 days (P = 0.31). Overall, logistic regression analysis showed that PSADT is a good test to discriminate which pts will have some decrease in PSA while on treatment (P = 0.03). ROC curves (AUC = 0.807) for pts with a decline in PSA on treatment showed that the best balance of sensitivity and specificity was for a PSA DT cutoff of 70 days (sens = 70.0%, spec = 71.4%). Sensitivity was highest at a DT of 50 days (85%), and specificity at 180 days (93%). Conclusions: This study suggests that pretreatment PSADT may be a useful predictor of response to therapy in patients with AS PSA progression after local therapy, but will require larger confirmatory studies. A PSADT cutoff of 70 days can be considered to stratify patients in future trials in this patient population.

No significant financial relationships to disclose.

Utility of the SEER-Medicare data to identify medical androgen deprivation therapy

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Background: Researchers are increasingly using SEER-Medicare data to measure the use of various cancer therapies. However, the validity and completeness of Medicare data as a source of information for identifying medical androgen deprivation has not been established. In this study, we compared the classification of ADT use based on SEER-Medicare linked data and medical record review. Methods: Among patients who were included in the Prostate Cancer Outcomes Study (PCOS) aged 65 or older and have Medicare part A and B coverage as their primary health insurance, their use of medical androgen deprivation therapy (ADT) identified from the SEER-Medicare data was compared with the results of medical record review. The linkage of the datasets was accomplished by using encrypted IDs. Two algorithms were evaluated. Algorithm A defines ADT use liberally, if at least one of the following HCPCS codes is present: J1950, J9202, J9217, J9218, or J9219. Algorithm B, developed by the authors to identify consistent androgen deprivation, defines ADT only if there is evidence of treatment lasting for 3 months or longer, indicated by either the 12-month treatment J9219 or at least 3 months of treatment with J9202 or J9217. Results: For the 673 patients eligible for this validation study, algorithm A has a sensitivity of 92.5% and a specificity of 85.2% in identifying medical ADT compared to medical record review (see table ), while algorithm B has a sensitivity of 81.8% and a specificity of 88.9% ( Table 1 ). When the study was further restricted to patients with Medicare insurance only (N=142), both algorithms improved: 96.2% sensitivity and 85.6% specificity for algorithm A, and 88.5% sensitivity and 91.1% specificity for algorithm B. Conclusions: Both algorithms have reasonable sensitivity and specificity. Medicare claims can be used to track ADT use for the treatment of prostate cancer in the Medicare population.

[Table: see text]

No significant financial relationships to disclose.

Variation in local treatment of prostate cancer by hospital within New Jersey

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Background: Although prostate cancer diagnosis and treatment vary through the US, few studies have assessed variations in local therapy between multiple hospitals located within a very narrow geographic region. Methods: To determine the variation of diagnosis and treatment of prostate cancer between hospitals in a local region, data was derived and analyzed from 1,301 patients from fifteen Cancer Institute of New Jersey Oncology Group network hospitals. Tumor registry data from patients with a histological confirmed diagnosis of prostate cancer accessioned over a one-year period between January 1, 2003 and December 31, 2003 was analyzed by a multivariate logistic regression model. Results: Median age of the cohort was 66 and mean number of cases diagnosed at these hospitals for this period was 87 (26–161). When the cohort was assessed overall, 192 cases assessed were African American, 1049 Caucasian, 51 Hispanic, and 32 Asian. Median Gleason score was 6. A total of 463 patients underwent Prostatectomy, and 538 had radiation therapy. Multivariate analysis demonstrated that age and hospital were associated with use of surgery versus no surgery. Race and Gleason score were not associated with use of surgery in this group of hospitals. Multivariate analysis also demonstrated that age and hospital were associated with utilizing radiation therapy versus not utilizing radiation therapy. Again, race and Gleason score were not associated with utilization of radiation therapy in these NJ hospitals. Conclusions: Overall, the most important factors predicting for surgery, and radiation therapy, were age and hospital, which were independent of race and Gleason score. These data support our ongoing assessment of hospital and geographic characteristics that may be responsible for these associations.

No significant financial relationships to disclose.

Spectrum of single- and multiexon NF1 copy number changes in a cohort of 1,100 unselected NF1 patients

Neurofibromatosis type 1 (NF1), the most common tumor-predisposing disorder in humans, is caused by defects in the NF1 tumor-suppressor gene. Comprehensive mutation analysis applying RNA-based techniques complemented with FISH analysis achieves mutation detection rates of approximately 95% in NF1 patients. The majority of mutations are minor lesions, and approximately 5% are total gene deletions. We found 13 single- and/or multiexon deletions/duplications out of 1,050 detected mutations using our RNA-based approach in a cohort of 1,100 NF1 patients and confirmed these changes using multiplex ligation-dependent probe amplification (MLPA). With MLPA, we found another 12 novel multiexon deletion/duplications in 55 NF1 patients for whom analysis with multiple assays had not revealed a NF1 mutation, including 50 previously analyzed comprehensively. The extent of the 22 deletions and 3 duplications varied greatly, and there was no clustering of breakpoints. We also evaluated the sensitivity of MLPA in identifying deletions in a mosaic state. Furthermore, we tested whether the MLPA P122 NF1 area assay could distinguish between type I deletions, with breakpoints in low-copy repeats (NF1-LCRs), and type II deletions, caused by aberrant recombination between the JJAZ gene and its pseudogene. Our study showed that intragenic deletions and/or duplications represent only approximately 2% of all NF1 mutations. Although MLPA did not substantially increase the mutation detection rate in NF1 patients, it was a useful first step in a comprehensive mutation analysis scheme to quickly pinpoint patients with single- or multiexon deletions/duplications as well as patients with a total gene deletion who will not need full sequencing of the complete coding region.

CSF-1 regulation of osteoclastogenesis for tooth eruption

The dental follicle regulates the alveolar bone resorption needed for tooth eruption. In the rat first mandibular molar, a decrease in the expression of osteoprotegerin (OPG) in the dental follicle at day 3 enables the osteoclastogenesis needed for eruption to occur. Because colony-stimulating factor-1 (CSF-1) is maximally expressed in the dental follicle at day 3, it was hypothesized that CSF-1 down-regulates OPG gene expression in the dental follicle in vivo. To test this, we compared the expression of OPG in osteopetrotic toothless (tl/tl) rats deficient in CSF-1 with expression in their normal littermates for given ages. OPG gene expression was found to be higher in the dental follicle of the tl/tl mutants than in normals. Transfecting short interfering RNA specific for CSF-1 mRNA into dental follicle cells resulted in an up-regulation of OPG expression. Thus, these studies support our hypothesis that the down-regulation of OPG needed for tooth eruption is mediated by CSF-1.

Ribosomal RNA supplementation highly reinforced cell-free translation activity of wheat germ

We have constructed an inexpensive, highly efficient eukaryotic cell-free translation system. Wheat germ rRNA (WG rRNA) was prepared by phenol/chloroform (P/C) extraction, a simple and quick method, from wheat germ, an inexpensive and commercially available by-product of flour production. Addition of a small amount of WG rRNA into a wheat germ cell-free translation system increased the protein productivity of the system 6- to 8-fold. Isolated 18S or 28S rRNA alone enhanced the protein production only 2-fold or 3.9-fold, respectively, at maximum. On the other hand, their equimolar mixture enhanced the production as much as the whole WG rRNA, indicating 18S and 28S rRNA synergistically functioned to enhance protein synthesis. Addition of WG rRNA slightly improved the stability of mRNA in the cell-free translation system, which explained only partly the enhancement of protein production. Addition of WGE or ribosome containing approximately the same amount of rRNA in the form of protein-rRNA complex as WG rRNA added to the system did not increase the protein production in the translation system. When ribosome in the cell-free translation system was replaced with WG rRNA, the system did not exhibit any detectable translation activity, indicating that the translation activity of WG rRNA is negligible in comparison with that of ribosome. These results indicated that WG rRNA affected some mechanisms regulating the translation rate in wheat germ cell-free system, resulting in increased protein production.

Chronology and regulation of gene expression of RANKL in the rat dental follicle

Tooth eruption in the rat requires bone resorption resulting from a major burst of osteoclastogenesis on postnatal day 3 and a minor burst of osteoclastogenesis on postnatal day 10 in the alveolar bone of the first mandibular molar. The dental follicle regulates the major burst on postnatal day 3 by down-regulating its osteoprotegerin (OPG) gene expression to enable osteoclastogenesis to occur. To determine the role of receptor activator of nuclear factor-kappa B ligand (RANKL) in tooth eruption, its gene expression was measured on postnatal days 1-11 in the dental follicle. The results show that RANKL expression was significantly elevated on postnatal days 9-11 in comparison to low expression levels at earlier time-points. As OPG expression is high at this latter time-point, this increase in RANKL expression would be needed for stimulating the minor burst of osteoclastogenesis. Tumor necrosis factor-alpha enhances RANKL gene expression in vitro and it may be responsible for up-regulating RANKL in vivo. Transforming growth factor-beta1 and interleukin-1alpha also enhance RANKL gene expression in vitro but probably have no effect in vivo because they are maximally expressed early. Bone morphogenetic protein-2 acts to down-regulate RANKL expression in vitro and, in vivo, may promote alveolar bone growth in the basal region of the tooth.

The role of c-Jun in the AP-1 activation induced by naturally occurring isothiocyanates

Despite strong evidence that isothiocyanates (ITCs) inhibit cancer development, there are also reports that some of them induce or promote carcinogenesis. The molecular basis of the latter is largely unknown. We report here that all three ITCs that caused urinary bladder cancer in rats, including allyl ITC, benzyl ITC, and phenethyl ITC, increased the transactivation of activator protein 1 (AP-1) and AP-1 DNA binding in human bladder cancer UM-UC-3 cells. Amongst all Fos and Jun family members examined, only were the levels of c-Jun and Fra-2 consistently elevated by the ITCs. However, whereas c-Jun was identified as the predominant component in the AP-1 DNA binding complex, Fra-2 was not detected, suggesting that c-Jun may be mainly responsible for ITC-induced AP-1 activation. c-Jun was also induced by the ITCs in other bladder cancer cell lines (both human and rat) and by their N-acetylcysteine derivatives--their main urinary metabolites. c-Jun induction by the ITCs appears to involve both transcriptional activation and protein phosphorylation; the latter resulted from activation of c-Jun N-terminal kinase by the ITCs. Because c-Jun has been implicated in cancer development, including human bladder cancer, our data suggest that c-Jun activation may play an important role in ITC-induced bladder carcinogenesis.

Investigation of mechanical properties of diatom frustules using nanoindentation

Diatom frustules have been identified as potential candidate materials for nanotechnology applications. However, for successful engineering applications, their mechanical properties must be fully determined. Toward this end, indentation hardness and elastic properties frustules of the centric diatom Coscinodiscus concinnus were evaluated using nanoindentation. A series of nanoindentation tests were performed on the outer surfaces of frustules at various locations. Analysis of the indentations revealed that the Young's modulus and hardness values appear to be strongly dependent on the location of the indentation. The modulus varied from 0.591 to 2.768 GPa in the center and 0.347 to 2.446 GPa at locations away from the center. Similarly, frustule hardness varied between 0.033 and 0.116 GPa in the center and between 0.076 and 0.12 GPa away from the center. Another series of nanoindentation tests were performed on the frustules (positioned in both concave and convex orientations) at various locations to analyze the failure mode. It was found that the failure modes in each of the orientations were also drastically different. In convex orientation, cracks initiated along the sharp edges of the indentation were followed by circular ring cracks, whereas in concave orientation only cracks along the sharp edges (corresponding to the three edges of the indenter) were revealed. The porosity and the nonplanar nature of the frustules make it difficult to extract the mechanical properties accurately at each location.

Regulation of secretion of osteoprotegerin in rat dental follicle cells

Tooth eruption requires alveolar bone resorption and formation, both of which appear to be regulated by the dental follicle. Osteoclastogenesis needed for this bone resorption appears to occur as a result of a reduction in the expression of the osteoprotegerin (OPG) gene in the dental follicle at a specific time. This reduction in expression is mediated in vitro in the follicle cells by colony-stimulating factor-1 (CSF-1) and parathyroid hormone-related protein (PTHrP). Using enzyme-linked immunosorbent assays and immunoblotting, this study shows that the reduction in expression of OPG after incubation of the dental follicle cells in either CSF-1 or PTHrP also results in a reduction in its secretion. We also show, by laser capture microdissection, that PTHrP is expressed in vivo in the stellate reticulum such that it could inhibit OPG expression via a paracrine effect on the follicle. Bone formation is enhanced by OPG secretion, and incubation of the follicle cells with bone morphogenetic protein-2 (BMP-2) enhances OPG secretion. Thus, a reduction in secretion of the OPG protein at defined times may promote the osteoclastogenesis and alveolar bone resorption needed for eruption, and enhancement of OPG secretion at other times may promote alveolar bone formation.