Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment

Protein folding is a fundamental process in biology, key to understanding many human diseases. Experimentally, proteins often appear to fold via simple two- or three-state mechanisms involving mainly native-state interactions, yet recent network models built from atomistic simulations of small proteins suggest the existence of many possible metastable states and folding pathways. We reconcile these two pictures in a combined experimental and simulation study of acyl-coenzyme A binding protein (ACBP), a two-state folder (folding time ~10 ms) exhibiting residual unfolded-state structure, and a putative early folding intermediate. Using single-molecule FRET in conjunction with side-chain mutagenesis, we first demonstrate that the denatured state of ACBP at near-zero denaturant is unusually compact and enriched in long-range structure that can be perturbed by discrete hydrophobic core mutations. We then employ ultrafast laminar-flow mixing experiments to study the folding kinetics of ACBP on the microsecond time scale. These studies, along with Trp-Cys quenching measurements of unfolded-state dynamics, suggest that unfolded-state structure forms on a surprisingly slow (~100 μs) time scale, and that sequence mutations strikingly perturb both time-resolved and equilibrium smFRET measurements in a similar way. A Markov state model (MSM) of the ACBP folding reaction, constructed from over 30 ms of molecular dynamics trajectory data, predicts a complex network of metastable stables, residual unfolded-state structure, and kinetics consistent with experiment but no well-defined intermediate preceding the main folding barrier. Taken together, these experimental and simulation results suggest that the previously characterized fast kinetic phase is not due to formation of a barrier-limited intermediate but rather to a more heterogeneous and slow acquisition of unfolded-state structure.

Microfluidic mixers for studying protein folding

The process by which a protein folds into its native conformation is highly relevant to biology and human health yet still poorly understood. One reason for this is that folding takes place over a wide range of timescales, from nanoseconds to seconds or longer, depending on the protein. Conventional stopped-flow mixers have allowed measurement of folding kinetics starting at about 1 ms. We have recently developed a microfluidic mixer that dilutes denaturant ~100-fold in ~8 μs. Unlike a stopped-flow mixer, this mixer operates in the laminar flow regime in which turbulence does not occur. The absence of turbulence allows precise numeric simulation of all flows within the mixer with excellent agreement to experiment. Laminar flow is achieved for Reynolds numbers Re ≤100. For aqueous solutions, this requires micron scale geometries. We use a hard substrate, such as silicon or fused silica, to make channels 5-10 μm wide and 10 μm deep (See Figure 1). The smallest dimensions, at the entrance to the mixing region, are on the order of 1 μm in size. The chip is sealed with a thin glass or fused silica coverslip for optical access. Typical total linear flow rates are ~1 m/s, yielding Re~10, but the protein consumption is only ~0.5 nL/s or 1.8 μL/hr. Protein concentration depends on the detection method: For tryptophan fluorescence the typical concentration is 100 μM (for 1 Trp/protein) and for FRET the typical concentration is ~100 nM. The folding process is initiated by rapid dilution of denaturant from 6 M to 0.06 M guanidine hydrochloride. The protein in high denaturant flows down a central channel and is met on either side at the mixing region by buffer without denaturant moving ~100 times faster (see Figure 2). This geometry causes rapid constriction of the protein flow into a narrow jet ~100 nm wide. Diffusion of the light denaturant molecules is very rapid, while diffusion of the heavy protein molecules is much slower, diffusing less than 1 μm in 1 ms. The difference in diffusion constant of the denaturant and the protein results in rapid dilution of the denaturant from the protein stream, reducing the effective concentration of the denaturant around the protein. The protein jet flows at a constant rate down the observation channel and fluorescence of the protein during folding can be observed using a scanning confocal microscope.

Factors affecting the spontaneous motion of condensate drops on superhydrophobic copper surfaces

The coalescence-induced condensate drop motion on some superhydrophobic surfaces (SHSs) has attracted increasing attention because of its potential applications in sustained dropwise condensation, water collection, anti-icing, and anticorrosion. However, an investigation of the mechanism of such self-propelled motion including the factors for designing such SHSs is still limited. In this article, we fabricated a series of superhydrophobic copper surfaces with nanoribbon structures using wet chemical oxidation followed by fluorization treatment. We then systematically studied the influence of surface roughness and the chemical properties of as-prepared surfaces on the spontaneous motion of condensate drops. We quantified the "frequency" of the condensate drop motion based on microscopic sequential images and showed that the trend of this frequency varied with the nanoribbon structure and extent of fluorination. More obvious spontaneous condensate drop motion was observed on surfaces with a higher extent of fluorization and nanostructures possessing sufficiently narrow spacing and higher perpendicularity. We attribute this enhanced drop mobility to the stable Cassie state of condensate drops in the dynamic dropwise condensation process that is determined by the nanoscale morphology and local surface energy.

Visualizing millisecond chaotic mixing dynamics in microdroplets: A direct comparison of experiment and simulation

In order to fully explore and utilize the advantages of droplet-based microfluidics, fast, sensitive, and quantitative measurements are indispensable for the diagnosis of biochemical reactions in microdroplets. Here, we report an optical detection technique using two-photon fluorescence lifetime imaging microscopy, with an aligning-summing and non-fitting division method, to depict two-dimensional (2D) maps of mixing dynamics by chaotic advection in microdroplets with high temporal and spatial resolution. The mixing patterns of two dye solutions inside droplets were quantitatively and accurately measured. The mixing efficiency in a serpentine droplet mixer was also quantified and compared with the simulation data. The mapped chaotic mixing dynamics agree well with the numerical simulation and theoretical prediction. This quantitative characterization is potentially applicable to the real-time kinetic study of biological and chemical reactions in droplet-based microfluidic systems.

P1-09-06: Single Nucleotide Polymorphisms in the BRMS1 and SIPA1 Metastasis Suppressor Genes as Prognostic Markers in Breast Cancer Patients

Introduction: Single nucleotide polymorphisms (SNPs) in the metastasis suppressors BRMS1 and SIPA1 may affect metastatic efficiency. BRMS1 affects apoptosis, colonization, cell adhesion, and invasive potential. Loss of BRMS1 expression has been correlated with younger age at diagnosis and reduced survival time in patients with progesterone-receptor (PR) negative, HER2−positive tumors. SIPA1 affects extracellular matrix gene expression and cell adhesion, and while SNPs have been associated with node positive, estrogen-receptor (ER)/PR negative tumors, evidence for a relationship with survival has been conflicting. Identifying SNPs that affect risk of recurrence and survival may improve the ascertainment of patients who require aggressive adjuvant therapy following a diagnosis of breast cancer. We evaluated associations between seven BRMS1 and SIPA1 SNPs and recurrence and survival in patients with primary breast cancer.

Methods: We identified 1,015 incident breast cancer patients who received surgery at Roswell Park Cancer Institute (RPCI) and participated in the DataBank and BioRepository (DBBR) resource. Participants completed an epidemiologic questionnaire and provided a blood sample prior to surgery or other treatment. Clinical and pathologic data were linked to de-identified participant data in the DBBR database. SNPs in BRMS1 (rs11537993, rs3116068, and rs1052566) and SIPA1 (rs75894763, rs746429, rs3741378, and rs2306364) were genotyped by RPCI's Genomics facility using Sequenom® iPLEX Gold and Taqman® real-time PCR assays. Cox proportional hazards regression was used to estimate hazard ratios and 95% confidence intervals.

Results: The median follow-up time was 33 months, and 49 deaths and 42 recurrences occurred. Tumors were more likely to be larger, node positive, ER/PR negative, and high grade among patients who experienced a recurrence or death. Recurrence was less likely in older patients and those with higher body mass index, although the latter association was nonsignificant (p=0.06). Patients with at least one variant allele of the BRMS1 rs3116068 genotype experienced shorter overall survival compared to patients with the homozygous common genotype (HR=2.05, 95% CI 1.15−3.63, rs3116068 AG+AA compared to GG). The remaining SNPs were not associated with overall survival, and none of the SNPs were associated with recurrence.

Conclusions: In our data, the variant allele of rs3116068 was more common among women whose breast cancer was node negative and HER2−positive, compared to those with the common rs3116068 allele. The rs3116068 variant allele is also associated with poorer survival. While our findings do not support a role for common SNPs in the SIPA1 gene in breast cancer prognosis, BRMS1 rs3116068 may be a useful prognostic biomarker. Future goals are to examine additional SNPs in BRMS1 and other metastasis-related genes in a larger, racially diverse population.

Funding: This research was supported by a gift from the Jayne and Phil Hubbell Family. The DBBR and Genomics Facility are RPCI Cancer Center Support Grant shared resources, supported by P30 CA016056-32. Ms. Roberts is a DOD Predoctoral Award recipient (BC10068) and Dr. Ambrosone is funded by the Breast Cancer Research Foundation.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-09-06.

Proliferation of dental follicle-derived cell populations in heat-stress conditions

OBJECTIVES

Isolation and purification of adult stem cells (ASC) are a great challenge. Our objectives were to determine whether ASC are more heat-tolerant than non-stem cells, and to explore if ASC could be enriched by heat-stress treatments.

MATERIALS AND METHODS

Rat dental follicle cells were cultured in a variety of media to obtain either a heterogeneous cell population (H-DFC) consisting of stem cells and non-stem cells, or a homogenous cell population (DFC) containing non-stem cells only. Real-time RT-PCR was conducted to compare expression of heat-shock proteins (HSPs) between the two populations. To study heat tolerance, H-DFC and DFC were incubated under heat-stress conditions and cell proliferation was evaluated by alamar blue reduction assay. Furthermore, cells resulting from heat-stress treatments were evaluated for differentiation capability and expression of stem cell markers.

RESULTS

H-DFC expressed higher levels of HSP110, HSP70s and HSP27s than did DFC. H-DFC increased levels of proliferation at 40 °C compared to controls grown at 37 °C; no significant reduction in proliferation occurred at temperatures below 40.5 °C. In contrast, DFC showed significant reduction in proliferation under all heat-stress treatments. Heat-stressed H-DFC had increased differentiation capability and increased expression of stem cell markers.

CONCLUSION

Stem cells appear to be more tolerant to heat stress than non-stem cells. Incubation of a heterogeneous cell population in heat-stress conditions resulted in increased stem cell numbers.

Analysis and design of a modular underactuated mechanism for robotic fingers

This paper presents an analysis of the design problems and requirements for underactuated mechanisms for robotic fingers. The case of performing a grasping task is considered and a solution is proposed that consists of a series of linked underactuated mechanisms. Optimality criteria are analysed with the aim of formulating a general design algorithm based on a suitable optimization problem. An example of a four-phalanx modular finger is used to highlight the practical feasibility of the proposed modular design concepts and procedures.

First Report of Xylella fastidiosa in Peach in New Mexico

Xylella fastidiosa is a gram-negative bacterium that causes disease in a wide variety of plants such as grapes, citrus trees, oleanders, and elm and coffee trees. This bacterium is xylem limited and causes disease symptoms such as leaf scorch, stunting of plant growth, branch dieback, and fruit loss. The presence of X. fastidiosa was previously reported in New Mexico where it was found to be infecting chitalpa plants and grapevines (3). In the summer of 2010, peach (Prunus persica (L.) Batsch) trees from two locations in northern New Mexico exhibited leaf deformity and stunting, dark green venation, slight mottling, and branch dieback. Preliminary viral diagnostic screening was performed by Agdia (Elkhart, IN) on one symptomatic tree and it was negative for all viruses tested. Three trees from two different orchards tested positive for X. fastidiosa by ELISA and PCR analysis using X. fastidiosa-specific primer sets HL (1) and RST (2). Bacterial colonies were also cultured from these samples onto periwinkle wilt media. Eight colonies obtained from these three plants tested PCR positive using the X. fastidiosa-specific primers. The 16S ribosomal and 16S-23S rRNA internal transcribed spacer (ITS) region (557 nucleotides) (GenBank Accession No. HQ292776) along with the gyrase region (400 nucleotides) (GenBank Accession No. HQ292777) was amplified from the peach total DNA samples and the bacterial colonies. Sequencing analysis of these regions indicate that the X. fastidiosa found in peach is 100% similar to other X. fastidiosa multiplex isolates including isolates from peach, pecan, sycamore, and plum trees and 99% similar to the X. fastidiosa isolates previously found in New Mexico. Further analysis of the 16S ribosomal and 16S-23S rRNA ITS sequences with maximum likelihood phylogenetic analysis using Paup also groups the peach isolates into the X. fastidiosa multiplex subspecies. The gyrase sequence could not be used to differentiate the peach isolates into a subspecies grouping because of the lack of variability within the sequence. This X. fastidiosa multiplex subspecies could possibly be a threat to the New Mexico pecan industry since pecan infecting X. fastidiosa isolates belong to the same bacterial subspecies. It is not known if X. fastidiosa subspecies multiplex isolates from peach are capable of infecting pecans but they are closely genetically related. It is interesting to note that the isolates from peach are different than previously described X. fastidiosa isolates in New Mexico that were infecting chitalpa and grapes (3). X. fastidiosa has previously been described in peach; the disease is called "phony peach". The peach trees exhibited stunting and shortened internodes as reported for "phony peach". They also exhibited slight mottling and branch dieback that may be due to the environment in New Mexico or perhaps they are also exhibiting mineral deficiency symptoms in association with the X. fastidiosa disease. To our knowledge, this is the first report of X. fastidiosa in peach in New Mexico. References: (1) M. H. Francis et al. Eur. J. Plant Pathol. 115:203, 2006. (2) G. V. Minsavage et al. Phytopathology 84:456, 1994. (3) J. J. Randall et al. Appl. Environ. Microbiol. 75:5631, 2009.

Quantitative imaging of mixing dynamics in microfluidic droplets using two-photon fluorescence lifetime imaging

Droplet-based microfluidic systems enable miniaturization of chemical reactions in femtoliter to picoliter volume compartments. Quantifying mixing dynamics of the reagents in droplets is critical to determine the system performance. In this Letter, we developed a two-photon excitation fluorescence lifetime imaging technique to quantitatively image the mixing dynamics in microfluidic droplets. A cross/autocorrelation method was used to reconstruct a high-quality fluorescence lifetime image of the droplet. The fluorescence decay was analyzed for accurate determination of the mixing ratio at each pixel of the image.

Competitive electroporation formulation for cell therapy

Established cell transfection via nucleofection relies on nucleofection buffers with unknown and proprietary makeup due to trade secrecy, inhibiting the possibility of using this otherwise effective method for developing cell therapy. We devised a three-step method for discovering an optimal formulation for the nucleofection of any cell line. These steps include the selection of the best nucleofection program and known buffer type, selection of the best polymer for boosting the transfection efficiency of the best buffer and the comparison with the optimal buffer from an established commercial vendor (Amaxa). Using this three-step selection system, competitive nucleofection formulations were discovered for multiple cell lines, which are equal to or surpass the efficiency of the Amaxa nucleofector solution in a variety of cells and cell lines, including primary adipose stem cells, muscle cells, tumor cells and immune cells. Through the use of scanning electron microscopy, we have revealed morphological changes, which predispose for the ability of these buffers to assist in transferring plasmid DNA into the nuclear space. Our formulation may greatly reduce the cost of electroporation study in laboratory and boosts the potential of application of electroporation-based cell therapies in clinical trials.

Photosensitization of carbon nanotubes using dye aggregates

Ordered assemblies of dye molecules, dye aggregates, possess significantly larger molar optical absorptivity than dye monomers. Yet, aggregates have not been utilized for photosensitizing nanoscale electronic devices. We find that single-walled carbon nanotubes, which are cleaned down to the atomic scale, template the growth of squaraine dye aggregates and these aggregates effectively photosensitize nanotubes. Templating of aggregates by nanotubes and functionalization of nanotubes with ordered molecular films are reported for the first time. The sensitivity achieved by aggregate-functionalized nanotube network devices is approximately an order of magnitude better than those of similar nanotube devices functionalized with dye monomers and photoactive polymers.

Is radiation therapy superior to conservative management in men with localized prostate cancer?

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Background: Radiation therapy is commonly employed for localized prostate cancer; however, there is little data regarding the comparative effectiveness of radiation therapy (RAD) vs. conservative management (CM).

Methods: We performed a population-based cohort study, using Medicare claims data linked to the Surveillance, Epidemiology, and End Results data, to evaluate outcomes in 42,039 men aged 65-85 years treated with either primary RAD or CM for T1-T2 prostate cancer diagnosed in 1992-2005. To overcome potential biases associated with unmeasured confounding variables, we used instrumental variable analysis (IVA), a pseudo-randomization technique that captures the randomness associated with geographic variations in the use of RAD, to control for overt and hidden confounders.

Results: The majority of patients (57%) had low-risk disease (Gleason score ≤7, PSA <10, and T stage ≤T2a), and RAD was commonly used (60%) with considerable geographic variations. With median age 74 years and median follow-up 119 months, higher RAD use was not associated with improved survival in low-risk patients (10-year disease-specific survival differed by −0.9%, 94.9% vs. 95.8% in the highest and lowest tertile RAD use areas respectively; 95% C.I. −.1 to 0.6%). Among high-risk patients (Gleason score >7 or PSA >20), highest tertile RAD areas showed a borderline improved (2.7%) 10-year disease-survival (83.9% vs. 81.2% in the highest and lowest tertile radiation use areas; 95% C.I. −1.1% to 7.0%). The results in the moderate-risk group were between that of the low- and high-risk group. Primary RAD did not reduce future ADT use (odds ratios 0.95 for low-risk, 1.02 for moderate-risk, and 1.07 for high-risk with corresponding P values of 0.50, 0.86, and 0.51, respectively).

Conclusions: In patients aged over 65 years old with low-risk prostate cancer, primary RAD is unlikely to improve 10-year disease-specific survival or prevent future ADT use. Weighing the potential risks and benefits of radiation therapy is critical for decision making.

No significant financial relationships to disclose.

TNIP1, SLC15A4, ETS1, RasGRP3 and IKZF1 are associated with clinical features of systemic lupus erythematosus in a Chinese Han population

Systemic lupus erythematosus (SLE) is an autoimmune disease with heterogeneous clinical manifestations influenced by genetic and environmental factors. Five novel susceptibility genes (TNIP1, SLC15A4, ETS1, RasGRP3 and IKZF1) for SLE have been identified in a recent genome-wide association study of a Chinese Han population. This study investigated their relationships with disease subphenotypes, including renal nephritis, photosensitivity, antinuclear antibody (ANA), age at diagnosis, malar rash, discoid rash, immunological disorder, oral ulcer, hematological disorder, neurological disorder, serositis, arthritis and vasculitis. Significant associations were found for the single nucleotide polymorphism rs10036748 of TNIP1 with photosensitivity (odds ratio (OR) = 0.87, p = 0.01) and vasculitis (OR = 1.18, p = 0.04); rs10847697 of SLC15A4 with discoid rash (OR = 1.18, p = 0.02); rs6590330 of ETS1 with SLE of age at diagnosis <20 years (OR = 1.24, p = 8.91 x 10(-5)); rs13385731 of RasGRP3 with malar rash (OR = 1.20, p = 0.01), discoid rash (OR = 0.78, p = 0.02) and ANA (OR = 0.72, p = 0.004); rs4917014 of IKZF1 with renal nephritis (OR = 1.13, p = 0.02) and malar rash (OR = 0.83, p = 0.00038), respectively. The study suggested that these susceptibility genes might not only play important roles in the development of SLE, but also contribute to the complex phenotypes of SLE.

Variants in the BRCA1/Fanconi-Anemia Repair Pathway and Taxane-Induced Neuropathy in SWOG S0221

Background: Taxane-induced peripheral neuropathy is a dose-limiting side effect that leads to suboptimal cancer treatment and diminished quality of life. The mode of taxane neurotoxicity is unclear, but may be through stabilization of microtubules and induction of spindle checkpoint, leading to cell cycle arrest at G2/M. Fanconi Anemia (FA) genes, including FANCD2, and FANCA, appear to be involved in G2/M phase checkpoint maintenance as well as spindle checkpoint in response to internal and external signals, such as taxane treatment. Thus, we hypothesized that variants in FA genes could impact severity of taxane-induced neuropathies.Methods: Using DNA extracted from blood collected from 893 breast cancer patients participating in a trial evaluating metronomic dosing of cyclophosphamide, doxorubicin and paclitaxel (S0221), we genotyped for single nucleotide polymorphisms (SNPs) that represent all of the variability across FANCA (44 SNPs) and FANCD2 (24 SNPs) in all race/ethnicity groups, as well as a panel of ancestry informative markers to control for potential population stratification, using Illumina GoldenGate platform. SNPs with minor allele frequency (MAF) less than 0.10 and those out of Hardy Weinberg Equilibrium (HWE) proportions (p&lt;0.001) were removed from analyses. Ordinal regression was used to test for allelic and haplotypic association with grade 3 or 4 toxicities relative to 0, 1, and 2 toxicities, adjusting for age, genetic admixture index and treatment arm. To adjust for multiple testing, permutation analyses were performed on both single SNP and haplotype models.Results: Eighteen SNPs in FANCD2 and 38 SNPs in FANCA passed MAF and HWE proportion requirements. For FANCD2, 4 SNPs spanning 67.5 Kb (rs7648104, rs2272125 [coding SNP], rs6786638 and rs644215), were significantly associated with taxane-induced neuropathy (p&lt;0.001) after controlling for multiple testing, with each SNP resulting in approximately a twofold increase in odds of severe taxane-induced neuropathy. Haplotype estimation showed that all 18 SNPs comprise a single haplotype. Two major (&gt;1% frequency) haplotypes were found. The frequencies of the risk haplotype in cases (patients with grade 3 or 4 neuropathy) and controls (patients with ≤ grade 2 neuropathy) were 0.25 and 0.15, respectively. Ordinal regression analyses were highly significant (p&lt;0.0005); patients with at least one copy of the risk haplotype had more than a twofold increased risk of grade 3 or 4 taxane-induced neuropathy (OR=2.2, 95% CI 1.44, 3.44). For FANCA, no SNPs or haplotypes were significantly associated with grade 3 or 4 neurotoxicity, either prior to or after correction for multiple testing.Conclusions: These results indicate that the Fanconi-Anemia pathway may be important for neurological sensitivity to taxanes, and that genotypic markers might be able to be used to identify patients at increased risk for severe taxane-induced neuropathy. Further studies will elucidate potential associations with survival outcomes.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 2001.

LPS mediated injury to oligodendrocytes is mediated by the activation of nNOS: relevance to human demyelinating disease

Loss of oligodendrocytes and the destruction of myelin form the core features of inflammatory demyelinating disease. Although many of the inflammatory and cellular mediators of tissue injury are known, recent studies have suggested an important role for nitric oxide NO and other reactive nitrogen species in oligodendrocyte injury. The human transformed oligodendrocyte cell line, MO3.13 cells, express Toll like receptor genes (TLR) genes and are activated by lipopolysaccharide (LPS). We determined the activation and consequences of neuronal nitric oxide synthase (nNOS) following stimulation with LPS in the MO3.13 cell line. Our studies show that MO3.13 cells induce nNOS following stimulation with LPS. Most importantly, these studies show a susceptibility of MO3.13 cells to NO mediated cell death by the activation of nNOS but not of inducible NOS (iNOS). MO3.13 cells show increased susceptibility to peroxynitrite mediated cellular injury to mitochondrial proteins and decreased cell survival in the presence of LPS. Our studies suggest that the presence and activation of nNOS in oligodendrocytes can directly mediate oligodendrocyte (OC) injury and reduce cell viability.

Stress echocardiography: risk stratification, prognosis, patient outcomes and cost-effectiveness

The utilization of stress echocardiography has undergone considerable expansion and evolution over the past three decades. Although stress echocardiography was first conceived as a noninvasive diagnostic tool for determining the presence or absence of coronary artery disease (CAD), its prognostic value is now well established. Thus, identification of patients at risk for future cardiac events has become a primary objective in the noninvasive evaluation of patients with chest pain syndromes and among patients with known CAD. In particular, the ability of stress echocardiography to identify patients at low (<1%), intermediate (1-5%) or high (>5%) risk for future cardiac events is essential to patient management decisions. Moreover, previous studies have conclusively demonstrated the incremental prognostic value of stress echocardiography over clinical and treadmill exercise data, in predicting future cardiac events. This review addresses the current role and summarizes current literature with respect to the use of stress echocardiography in determining patient risk for cardiac events and the cost-effective integration of such information into patient management decisions.

Outcomes of conservatively managed localized prostate cancer

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Background: The natural history of screen-detected prostate cancer has not been well described. Methods: Cancer-specific and overall mortality, assessed through competing risk analyses, were determined for 14,516 men aged 65 years or older diagnosed between 1992–2002 and did not receive surgery or radiation within 6 months of cancer diagnosis. The population-based cohort was identified from US cancer registries, which had 98% completeness in case ascertainment. Results: Compared to earlier era studies, survival has improved considerably for conservatively managed patients diagnosed in the contemporary prostate specific antigen (PSA) era ( Table ). Conclusions: Men diagnosed with prostate cancer in the PSA era have survival outcomes significantly better than those in the past. Patients and healthcare providers may need to reassess some treatment options in light of these data.

[Table: see text]

No significant financial relationships to disclose.

A phase I dose-escalation study of the safety, pharmacokinetics (PK), and pharmacodynamics (PD) of SCH 727965, a novel cyclin-dependent kinase inhibitor, administered weekly in subjects with advanced malignancies

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Background: SCH 727965 is a potent and selective inhibitor of the cyclin-dependent kinases CDK1,2,5 and 9 with IC50's of < 5nM. SCH 727965 induces apoptosis in a broad array of tumor cell lines, causes tumor growth inhibition or regression in various xenograft models, and has a greater therapeutic index than flavopiridol in an in vivo screening model. SCH 727965 was advanced into clinical trials. Methods: SCH 727965 was administered by 2-hour IV infusion on days 1, 8 and 15 of a 28-day cycle. Doses were escalated with an accelerated titration algorithm to define the maximally administered dose (MAD) and the recommended phase 2 dose (RPTD). PD assessments included an ex vivo PHA lymphocyte stimulation assay, skin biopsies for IHC measurement of retinoblastoma protein phosphorylation, and functional imaging using FDG-PET/CT scans. PK and PD data were obtained during Cycle 1. Results: 43 subjects have been treated at doses ranging from 0.33 to 14 mg/m2. The most common treatment-emergent adverse events were nausea, anemia, and fatigue. The MAD was 14 mg/m2 defined by a DLT of grade 3 hypotension in one subject and transient grade 4 hyperuricemia in another subject. The RPTD was 12 mg/m2. Grade 3 or 4 treatment related adverse events were uncommon. Grade 3 or 4 neutropenia was seen in only 3 subjects. SCH 727965 inhibition of lymphocyte proliferation was dose-dependent, indicating a PD effect, and was sustained up to 8 hours post-dose at the RPTD. Drug exposure was dose-proportional. SCH 727965 was rapidly eliminated with a terminal half-life of 1.5 to 3 hours. No objective responses by RECIST criteria have yet been observed although PET SUV signal decreases as large as >30% have been observed in some subjects. Conclusions: SCH 727965 is safe and well tolerated at the recommended phase 2 dose of 12 mg/m2. The AE profile of weekly dosing differed from that seen in an every -21 day dosing schedule, and plasma concentrations at the RPTD or lower doses were above those required for in vivo efficacy in xenograft tumor models. PD activity was verified in an ex vivo lymphocyte proliferation assay, and preliminary changes on PET/CT suggest drug related modulation of tumor metabolic activity.

[Table: see text]

Analysis of six synthetic adulterants in herbal weight-reducing dietary supplements by LC electrospray ionization-MS

A liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) method was developed for the simultaneous determination of six synthetic adulterants, namely fenfluramine, phenolphthalein, N-di-desmethyl sibutramine, N-mono-desmethyl sibutramine, sibutramine, and orlistat. The method was applied to the analysis of herbal weight-reducing dietary supplements. Chromatographic separation of the analytes on a C(8) reversed-phase column was achieved using a gradient elution of solvent A: acetonitrile and solvent B: aqueous 20 mM ammonium formate solution. Sildenafil was utilized as an internal standard for quantification. The MS detector was operated in positive electrospray ionization mode. Selected-ion monitoring (SIM) was carried out for m/z 232, 319, 252, 266, 280, 496, and 475 for fenfluramine, phenolphthalein, N-di-desmethyl sibutramine, N-mono-desmethyl sibutramine, sibutramine, orlistat, and sildenafil, respectively. The method was validated for accuracy, precision, linearity, and selectivity. The limits of detection for the six synthetic adulterants ranged from 0.0018 to 0.73 microg g(-1). The proposed method was used for a small survey of 22 dietary supplements of which eleven samples were adulterated with phenolphthalein, N-mono-desmethyl sibutramine, and sibutramine at levels from 0.212 to 96.2 mg g(-1).

Ruggedness in the folding landscape of protein L

By exploring the folding pathways of the B1 domain of protein L with a series of equilibrium and rapid kinetic experiments, we have found its unfolded state to be more complex than suggested by two-state folding models. Using an ultrarapid mixer to initiate protein folding within approximately 2-4 microseconds, we observe folding kinetics by intrinsic tryptophan fluorescence and fluorescence resonance energy transfer. We detect at least two processes faster than 100 mus that would be hidden within the burst phase of a stopped-flow instrument measuring tryptophan fluorescence. Previously reported measurements of slow intramolecular diffusion are commensurate with the slower of the two observed fast phases. These results suggest that a multidimensional energy landscape is necessary to describe the folding of protein L, and that the dynamics of the unfolded state is dominated by multiple small energy barriers.

Differentiation of stem cells in the dental follicle

The dental follicle (DF) differentiates into the periodontal ligament. In addition, it may be the precursor of other cells of the periodontium, including osteoblasts and cementoblasts. We hypothesized that stem cells may be present in the DF and be capable of differentiating into cells of the periodontium. Stem cells were identified in the DF of the rat first mandibular molar by Hoechst staining, alkaline phosphatase staining, and expression of side-population stem cell markers. These cells were shown to be able to differentiate into osteoblasts/cementoblasts, adipocytes, and neurons. Treating the DF cell population with doxorubicin, followed by incubation in an adipogenesis medium, suggested that the adipocytes originated from stem cells. Thus, a possibly puripotent stem cell population is present in the rat DF.

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.

Improvements in Mixing Time and Mixing Uniformity in Devices Designed for Studies of Protein Folding Kinetics

Using a microfluidic laminar flow mixer designed for studies of protein folding kinetics, we demonstrate a mixing time of 1 +/- 1 micros with sample consumption on the order of femtomoles. We recognize two limitations of previously proposed designs: (1) size and shape of the mixing region, which limits mixing uniformity and (2) the formation of Dean vortices at high flow rates, which limits the mixing time. We address these limitations by using a narrow shape-optimized nozzle and by reducing the bend of the side channel streamlines. The final design, which combines both of these features, achieves the best performance. We quantified the mixing performance of the different designs by numerical simulation of coupled Navier-Stokes and convection-diffusion equations and experiments using fluorescence resonance energy-transfer (FRET)-labeled DNA.

Protein hydrophobic collapse and early folding steps observed in a microfluidic mixer

We demonstrate that the sub-millisecond protein folding process referred to as "collapse" actually consists of at least two separate processes. We observe the UV fluorescence spectrum from naturally occurring tryptophans in three well-studied proteins, cytochrome c, apomyoglobin, and lysozyme, as a function of time in a microfluidic mixer with a dead time of approximately 20 mus. Single value decomposition of the time-dependent spectra reveal two separate processes: 1), a spectral shift which occurs within the mixing time; and 2), a fluorescence decay occurring between approximately 100 and 300 micros. We attribute the first process to hydrophobic collapse and the second process to the formation of the first native tertiary contacts.

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

14528

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

6113

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

14551

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.