Peptides generated ex vivo from serum proteins by tumor-specific exopeptidases are not useful biomarkers in ovarian cancer

BACKGROUND: The serum peptidome may be a valuable source of diagnostic cancer biomarkers. Previous mass spectrometry (MS) studies have suggested that groups of related peptides discriminatory for different cancer types are generated ex vivo from abundant serum proteins by tumor-specific exopeptidases. We tested 2 complementary serum profiling strategies to see if similar peptides could be found that discriminate ovarian cancer from benign cases and healthy controls. METHODS: We subjected identically collected and processed serum samples from healthy volunteers and patients to automated polypeptide extraction on octadecylsilane-coated magnetic beads and separately on ZipTips before MALDI-TOF MS profiling at 2 centers. The 2 platforms were compared and case control profiling data analyzed to find altered MS peak intensities. We tested models built from training datasets for both methods for their ability to classify a blinded test set. RESULTS: Both profiling platforms had CVs of approximately 15% and could be applied for high-throughput analysis of clinical samples. The 2 methods generated overlapping peptide profiles, with some differences in peak intensity in different mass regions. In cross-validation, models from training data gave diagnostic accuracies up to 87% for discriminating malignant ovarian cancer from healthy controls and up to 81% for discriminating malignant from benign samples. Diagnostic accuracies up to 71% (malignant vs healthy) and up to 65% (malignant vs benign) were obtained when the models were validated on the blinded test set. CONCLUSIONS: For ovarian cancer, altered MALDI-TOF MS peptide profiles alone cannot be used for accurate diagnoses.

Use and abuse of mathematical models: an illustration from the 2001 foot and mouth disease epidemic in the United Kingdom

Foot and mouth disease (FMD) is a major threat, not only to countries whose economies rely on agricultural exports, but also to industrialised countries that maintain a healthy domestic livestock industry by eliminating major infectious diseases from their livestock populations. Traditional methods of controlling diseases such as FMD require the rapid detection and slaughter of infected animals, and any susceptible animals with which they may have been in contact, either directly or indirectly. During the 2001 epidemic of FMD in the United Kingdom (UK), this approach was supplemented by a culling policy driven by unvalidated predictive models. The epidemic and its control resulted in the death of approximately ten million animals, public disgust with the magnitude of the slaughter, and political resolve to adopt alternative options, notably including vaccination, to control any future epidemics. The UK experience provides a salutary warning of how models can be abused in the interests of scientific opportunism.

Risk of foot and mouth disease associated with proximity in space and time to infected premises and the implications for control policy during the 2001 epidemic in Cumbria

An analysis was made that calculated the risk of disease for premises in the most heavily affected parts of the county of Cumbria during the foot-and-mouth disease epidemic in the UK in 2001. In over half the cases the occurrence of the disease was not directly attributable to a recently infected premises being located within 1.5 km. Premises more than 1.5 km from recently infected premises faced sufficiently high infection risks that culling within a 1.5 km radius of the infected premises alone could not have prevented the progress of the epidemic. A comparison of the final outcome in two areas of the county, south Penrith and north Cumbria, indicated that focusing on controlling the potential spread of the disease over short distances by culling premises contiguous to infected premises, while the disease continued to spread over longer distances, may have resulted in excessive numbers of premises being culled. Even though the contiguous cull in south Penrith appeared to have resulted in a smaller proportion of premises becoming infected, the overall proportion of premises culled was considerably greater than in north Cumbria, where, because of staff and resource limitations, a smaller proportion of premises contiguous to infected premises was culled

Factors required for the uridylylation of the foot-and-mouth disease virus 3B1, 3B2, and 3B3 peptides by the RNA-dependent RNA polymerase (3D(pol)) in vitro

The 5' terminus of picornavirus genomic RNA is covalently linked to the virus-encoded peptide 313 (VTg). Foot-and-mouth disease virus (FMDV) is unique in encoding and using 3 distinct forms of this peptide. These peptides each act as primers for RNA synthesis by the virus-encoded RNA polymerase 3D(pol). To act as the primer for positive-strand RNA synthesis, the 3B peptides have to be uridylylated to form VPgpU(pU). For certain picornaviruses, it has been shown that this reaction is achieved by the 3D(pol) in the presence of the 3CD precursor plus an internal RNA sequence termed a cis-acting replication element (cre). The FMDV ere has been identified previously to be within the 5' untranslated region, whereas all other picornavirus cre structures are within the viral coding region. The requirements for the in vitro uridylylation of each of the FMDV 313 peptides has now been determined, and the role of the FMDV ere (also known as the 3B-uridylylation site, or bus) in this reaction has been analyzed. The poly(A) tail does not act as a significant template for FMDV 3B uridylylation.

Antiproliferative activity of Titanocene Y against tumor colony-forming units

Bis-[(p-methoxybenzyl)cyclopentadienyl] titanium dichloride, better known as Titanocene Y, is a newly synthesized titanium-based anticancer drug. We studied the antitumor activity of Titanocene Y with concentrations of 2.1, 21 and 210 μmol/l against a range of freshly explanted human tumors, using an in-vitro soft agar cloning system. The sensitivity against Titanocene Y was highly remarkable in the case of renal cell, ovarian, nonsmall cell lung and colon cancer. In particular the surprisingly good response of nonsmall cell lung cancer and colon cancer against Titanocene Y at its lowest concentration of 2.1 μmol/l was well comparable or better with respect to cisplatin, given at a concentration of 1.0 μmol/l. Further clinical development of Titanocene Y appears to be warranted because of the broad cytotoxic activity shown and the specific activity of Titanocene Y against renal cell cancer.

Anti-tumor activity of Titanocene Y in xenografted Caki-1 tumors in mice

The benzyl-substituted unbridged titanocene bis-[(p-methoxybenzyl)cyclopentadienyl] titanium(IV) dichloride (Titanocene Y) was tested in vitro against human renal cancer cells (Caki-1), in which it showed an IC50 value of 36 x 10(-6) mol/l. Titanocene Y was then given in vivo in doses of 10, 20, 30, 40 and 50 mg/kg on 5 consecutive days to Caki-1-bearing mice, and it showed concentration-dependent and statistically significant tumor growth reduction with respect to a solvent-treated control cohort. The maximum tolerable dose of Titanocene Y was determined to be 40 mg/kg and it showed significantly better tumor volume growth reduction than cisplatin given at a dose of 2 mg/kg. This superior activity of Titanocene Y with respect to cisplatin will hopefully lead to clinical tests against metastatic renal cell cancer in the near future.

Antitumor activity of Titanocene Y against freshly explanted human breast tumor cells and in xenografted MCF-7 tumors in mice

Bis-[(p-methoxybenzyl)cyclopentadienyl] titanium dichloride, better known as Titanocene Y, is a newly synthesized transition metal-based anticancer drug. We studied the antitumor activity of Titanocene Y with concentrations of 2.1, 21 and 210 mu mol/l against a freshly explanted human breast cancer, using an in-vitro soft agar cloning system. The sensitivity against Titanocene Y was highly remarkable in the breast cancer tumor in the full concentration range. Titanocene Y showed cell death induction at 2.1 mu mol/l, well comparable to cisplatin, given at a concentration of 1.0 mu mol/l. A further preclinical development of Titanocene Y was warranted and therefore an MCF-7 human breast cancer xenograft nonobese diabetic/severe combined immunodeficient mouse model was used. Titanocene Y was given for 21 days at 30 mg/kg/ day (75% of the maximum tolerable dose of Titanocene Y), which resulted in the reduction of the tumor volume to around one-third, whereas no mouse was lost because of the surprisingly low toxicity of Titanocene Y.

Characterization and classification of tumor lesions using computerized fractal-based texture analysis and support vector machines in digital mammograms

Objective: This paper presents a detailed study of fractal-based methods for texture characterization of mammographic mass lesions and architectural distortion. The purpose of this study is to explore the use of fractal and lacunarity analysis for the characterization and classification of both tumor lesions and normal breast parenchyma in mammography. Materials and methods: We conducted comparative evaluations of five popular fractal dimension estimation methods for the characterization of the texture of mass lesions and architectural distortion. We applied the concept of lacunarity to the description of the spatial distribution of the pixel intensities in mammographic images. These methods were tested with a set of 57 breast masses and 60 normal breast parenchyma (dataset1), and with another set of 19 architectural distortions and 41 normal breast parenchyma (dataset2). Support vector machines (SVM) were used as a pattern classification method for tumor classification. Results: Experimental results showed that the fractal dimension of region of interest (ROIs) depicting mass lesions and architectural distortion was statistically significantly lower than that of normal breast parenchyma for all five methods. Receiver operating characteristic (ROC) analysis showed that fractional Brownian motion (FBM) method generated the highest area under ROC curve (A z = 0.839 for dataset1, 0.828 for dataset2, respectively) among five methods for both datasets. Lacunarity analysis showed that the ROIs depicting mass lesions and architectural distortion had higher lacunarities than those of ROIs depicting normal breast parenchyma. The combination of FBM fractal dimension and lacunarity yielded the highest A z value (0.903 and 0.875, respectively) than those based on single feature alone for both given datasets. The application of the SVM improved the performance of the fractal-based features in differentiating tumor lesions from normal breast parenchyma by generating higher A z value. Conclusion: FBM texture model is the most appropriate model for characterizing mammographic images due to self-affinity assumption of the method being a better approximation. Lacunarity is an effective counterpart measure of the fractal dimension in texture feature extraction in mammographic images. The classification results obtained in this work suggest that the SVM is an effective method with great potential for classification in mammographic image analysis.

Efficient production of foot-and-mouth disease virus empty capsids in insect cells following down regulation of 3C protease activity

Foot-and-mouth disease virus (FMDV) is a significant economically and distributed globally pathogen of Artiodactyla. Current vaccines are chemically inactivated whole virus particles that require large-scale virus growth in strict bio-containment with the associated risks of accidental release or incomplete inactivation. Non-infectious empty capsids are structural mimics of authentic particles with no associated risk and constitute an alternate vaccine candidate. Capsids self-assemble from the processed virus structural proteins, VP0, VP3 and VP1, which are released from the structural protein precursor P1-2A by the action of the virus-encoded 3C protease. To date recombinant empty capsid assembly has been limited by poor expression levels, restricting the development of empty capsids as a viable vaccine. Here expression of the FMDV structural protein precursor P1-2A in insect cells is shown to be efficient but linkage of the cognate 3C protease to the C-terminus reduces expression significantly. Inactivation of the 3C enzyme in a P1-2A-3C cassette allows expression and intermediate levels of 3C activity resulted in efficient processing of the P1-2A precursor into the structural proteins which assembled into empty capsids. Expression was independent of the insect host cell background and leads to capsids that are recognised as authentic by a range of anti-FMDV bovine sera suggesting their feasibility as an alternate vaccine.

Perception of thickness, mouth-coating and mouth-drying of dairy beverages by younger and older volunteer

Sensory perception has been found to change during ageing. The perception of mouth feel by older adults, and the role of ageing on the sensory perception of texture attributes is uncertain. . This study investigated perception of the textural attributes of thickness, mouth-coating and mouth-drying, in the context of dairy beverages, by older and younger adults. Just noticeable differences (JND) of a starch thickener and for cream concentration within milk were established for thickness and mouth-coating perception, finding no age-related differences between participant groups. Mouth-drying was assessed through the directional paired comparison of a mouth-drying milk beverage to a skimmed milk sample. The older adults were found to be more sensitive to mouth-drying (p=0.03) than the younger adults. This study found no age-related decline in texture perception with older adults finding perception of some attributes such as mouth-drying enhanced by ageing.