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PubMed2006

Frequent alterations in the expression of serine/threonine kinases in human cancers.

Protein kinases constitute a large family of regulatory enzymes involved in the homeostasis of virtually every cellular process. Subversion of protein kinases has been frequently implicated in malignant transformation. Within the family, serine/threonine kinases (STK) have received comparatively lesser attention, vis-a-vis tyrosine kinases, in terms of their involvement in human cancers. Here, we report a large-scale screening of 125 STK, selected to represent all major subgroups within the subfamily, on nine different types of tumors ( approximately 200 patients), by using in situ hybridization on tissue microarrays. Twenty-one STK displayed altered levels of transcripts in tumors, frequently with a clear tumor type-specific dimension. We identified three patterns of alterations in tumors: (a) overexpression in the absence of expression in the normal tissues (10 kinases), (b) overexpression in the presence of expression by normal tissues (8 kinases), and (c) underexpression (3 kinases). Selected members of the three classes were subjected to in-depth analysis on larger case collections and showed significant correlations between their altered expression and biological and/or clinical variables. Our findings suggest that alteration in the expression of STK is a relatively frequent occurrence in human tumors. Among the overexpressed kinases, 10 were undetectable in normal controls and are therefore ideal candidates for further validation as potential targets of molecular cancer therapy.

DNA, Complementary↗
PubMed2001

Identification of small molecule binding sites within proteins using phage display technology.

Affinity selection of peptides displayed on phage particles was used as the basis for mapping molecular contacts between small molecule ligands and their protein targets. Analysis of the crystal structures of complexes between proteins and small molecule ligands revealed that virtually all ligands of molecular weight 300 Da or greater have a continuous binding epitope of 5 residues or more. This observation led to the development of a technique for binding site identification which involves statistical analysis of an affinity-selected set of peptides obtained by screening of libraries of random, phage-displayed peptides against small molecules attached to solid surfaces. A random sample of the selected peptides is sequenced and used as input for a similarity scanning program which calculates cumulative similarity scores along the length of the putative receptor. Regions of the protein sequence exhibiting the highest similarity with the selected peptides proved to have a high probability of being involved in ligand binding. This technique has been employed successfully to map the contact residues in multiple known targets of the anticancer drugs paclitaxel (Taxol), docetaxel (Taxotere) and 2-methoxyestradiol and the glycosaminoglycan hyaluronan, and to identify a novel paclitaxel receptor [1]. These data corroborate the observation that the binding properties of peptides displayed on the surface of phage particles can mimic the binding properties of peptides in naturally occurring proteins. It follows directly that structural context is relatively unimportant for determining the binding properties of these disordered peptides. This technique represents a novel, rapid, high resolution method for identifying potential ligand binding sites in the absence of three-dimensional information and has the potential to greatly enhance the speed of development of novel small molecule pharmaceuticals.

Bacteriophages↗
PubMed1999

Human papillomavirus is a necessary cause of invasive cervical cancer worldwide.

A recent report that 93 per cent of invasive cervical cancers worldwide contain human papillomavirus (HPV) may be an underestimate, due to sample inadequacy or integration events affecting the HPV L1 gene, which is the target of the polymerase chain reaction (PCR)-based test which was used. The formerly HPV-negative cases from this study have therefore been reanalyzed for HPV serum antibodies and HPV DNA. Serology for HPV 16 VLPs, E6, and E7 antibodies was performed on 49 of the 66 cases which were HPV-negative and a sample of 48 of the 866 cases which were HPV-positive in the original study. Moreover, 55 of the 66 formerly HPV-negative biopsies were also reanalyzed by a sandwich procedure in which the outer sections in a series of sections are used for histological review, while the inner sections are assayed by three different HPV PCR assays targeting different open reading frames (ORFs). No significant difference was found in serology for HPV 16 proteins between the cases that were originally HPV PCR-negative and -positive. Type-specific E7 PCR for 14 high-risk HPV types detected HPV DNA in 38 (69 per cent) of the 55 originally HPV-negative and amplifiable specimens. The HPV types detected were 16, 18, 31, 33, 39, 45, 52, and 58. Two (4 per cent) additional cases were only HPV DNA-positive by E1 and/or L1 consensus PCR. Histological analysis of the 55 specimens revealed that 21 were qualitatively inadequate. Only two of the 34 adequate samples were HPV-negative on all PCR tests, as against 13 of the 21 that were inadequate ( p< 0.001). Combining the data from this and the previous study and excluding inadequate specimens, the worldwide HPV prevalence in cervical carcinomas is 99.7 per cent. The presence of HPV in virtually all cervical cancers implies the highest worldwide attributable fraction so far reported for a specific cause of any major human cancer. The extreme rarity of HPV-negative cancers reinforces the rationale for HPV testing in addition to, or even instead of, cervical cytology in routine cervical screening.

Antibodies, Viral↗
PubMed1983

Pedigree discriminant analysis: a method to identify monogenic segregation.

We describe a method for obtaining a linear discriminant function to identify monogenic segregation in multivariate pedigree data. It differs from Fisher's linear discriminant function in that it does not assume that the genotype of each individual in the pedigree already known. The method consists of finding that linear function of the variables that maximizes the likelihood of a set of pedigree data, under the hypothesis of single gene segregation, subject to the constraint that the total sample variance of the function remains constant. To simplify the computation the variables are first transformed to their standardized principal components. Reanalysis of a set of pedigree data suggests that age and powers of age should be considered as extra variables from which the principal components are obtained, and virtually all of the variance should be accounted for by the principal components used to obtain the discriminant function.

Age Factors↗
PubMed2004

Sensitivity of diagnostic examinations for colorectal polyps.

The removal of adenomatous polyps of the large bowel reduces mortality from colorectal cancer (CRC). Faecal occult blood testing only reveals 20.40% of polyps. The flexible rectosigmoidoscope explores less than half of the large bowel. Its use should always be coupled with faecal occult blood testing which, if positive, requires a total colonoscopy. The sensitivity of double-contrast barium enema for the search of polyps is 35%. Colonoscopy does not reach the caecum in about 10% of cases. It misses 15-20% of polyps with diameter <10 mm and about 6% of polyps with diameter >10 mm. Virtual colonoscopy has substantially the same sensitivity as optical colonoscopy for polyps > or =7 mm in diameter.

Adenomatous Polyps↗
PubMed2003

Proteomic and postproteomic characterization of keratan sulfate-glycanated isoforms of thyroglobulin and transferrin uniquely elaborated by papillary thyroid carcinomas.

Previous studies have suggested that surface components of papillary thyroid carcinoma (PTC) cells may be aberrantly glycanated, but the precise nature of these molecules has not been unveiled nor documented to be of clinical relevance. A monoclonal antibody was raised against a unique keratan sulfate (KS) determinant and used to differentially screen benign and malignant thyroid tissue for the expression of components carrying these moieties. In a total of 349 cases of benign and malignant thyroid lesions, 100% of the 115 PTC cases examined (including various histological subtypes) were found to contain KS-bearing molecules, whereas these were virtually absent from benign tissues and other thyroid tumors, with the exception of 21% of the follicular carcinoma cases analyzed. A composite immunoaffinity chromatography, immunochemistry, and mass spectrometric approach revealed that the PTC-specific KS-bearing macromolecules were unique glycoforms of thyroglobulin and transferrin. Combined, reciprocal immunoprecipitation and Western blotting further indicated that the former glycoform predominated and that most of the transferrin produced by PTC was glycanated with KS moieties. Fluorescent keratanase II-based fingerprinting of the KS moieties bound to these isoforms further demonstrated several PTC-specific peculiarities: 1) that a considerable portion of the moieties was covalently attached via a novel core protein linkage structure; 2) they had an unusual extended average length; 3) an unusual relative ratio of highly sulfated disaccharides terminating with alpha (2-3)-linked N-acetylneuraminic acid capping residues; and 4) a novel unidentified oligosaccharide moiety at the nonreducing terminus. Comparative analysis of the relative distribution of transferrin in benign versus PTC tissues highlighted a marked malignancy-associated abundance of the molecule, with a >75% frequency in expression in PTC. These findings demonstrate that PTC cells synthesize unique post-translationally modified thyroglobulin and transferrin variants in situ that may be directly exploitable for diagnosis, through histological and noninvasive cytological procedures; for devising novel strategies for antibody-guided imaging of this tumor in vivo; and for postsurgery follow-up of PTC patients.

Amino Acid Sequence↗
PubMedDate not supplied

Design of libraries to explore receptor sites.

Despite rapid progress in both combinatorial chemistry and high-throughput screening, the number of molecules that could potentially be made and tested for biological activity still far exceeds the capacity for synthesis or screening. Consequently, it is potentially valuable to select and synthesize sublibraries that contain rationally selected subsets. When the structure of the protein receptor site is known, this may be used to impose restrictions of the selection on molecules. This paper describes a method for rapid analysis of large virtual libraries to select a subset that can exhibit at least one conformer which wil interact strongly with the receptor and fit within the receptor site.

Binding Sites↗
PubMed2006

Interaction forces in thin liquid films stabilized by hydrophobically modified inulin polymeric surfactant. 1. Foam films.

Using the interferometric method of Scheludko-Exerowa for investigation of foam films, we have obtained results using a hydrophobically modified inulin polymeric surfactant (INUTEC SP1). Measurements were carried out at constant INUTEC SP1 concentration of 2 x 10(-)(5) mol.dm(-)(3) and at various NaCl concentrations (in the range 1 x 10(-)(4) to 2 mol.dm(-)(3)). At constant capillary pressure of 50 Pa, the film thickness decreased gradually with an increase in NaCl concentration up to 10(-)(2) mol.dm(-)(3) NaCl above which the film thickness remains virtually constant at about 16 nm. This reduction in film thickness with an increase in NaCl concentration is due to the compression of the double layer and at the critical electrolyte concentration (C(el,cr) = 10(-)(2) mol.dm(-)(3)) the electrostatic component of the disjoining pressure is completely screened and the remaining pressure is due to the steric interaction between the adsorbed polymer layers. Disjoining pressure-thickness (Pi-h) isotherms were obtained at C(el) < C(el,cr) (10(-)(4) - 10(-)(3) mol.dm(-)(3)) and C(el) > C(el,cr) (0.5, 1, and 2 mol.dm(-)(3)). In the first case, the disjoining pressure isotherms could be fitted using the classical DLVO theory, Pi = Pi(el) + Pi(vw), and using the constant charge model. At C(el) > C(el,cr), the main repulsion is due to the steric interaction between the polyfructose loops that exist at the air-water interface, i.e., Pi = Pi(st) + Pi(vw). Under these conditions, there is a sharp transition from DLVO to non-DLVO forces. In the latter case, the interaction could be described using the de Gennes' scaling theory. This gave an adsorbed layer thickness of 6.5 nm which is in reasonable agreement with the values obtained at the solid-solution interface. The Pi-h isotherms showed that these foam films are not very stable and they tend to collapse above a critical capillary pressure (of about 1 x 10(3) Pa), and these results could be used to predict the foam stability.

Electrolytes↗
PubMed2003

Transposable elements as tools for genomics and genetics in Drosophila.

The P-element has been the workhorse of Drosophila genetics since it was developed as a tool for transgenesis in 1982; the subsequent development of a variety of systems based on the transposon have provided a range of powerful and flexible tools for genetics and genomics applications. P-element insertions are frequently used as starting-points for generating chromosomal deletions to remove flanking genes, either by screening for imprecise excision events or by selecting for male recombination events. Elements that utilise the yeast FLP/FLP recombination target (FRT) site-specific recombination system have been widely used to generate molecularly marked mitotic clones for mosaic analysis, extending the reach of this powerful genetic tool to virtually all areas of developmental biology. P-elements are still widely used as traditional mutagenesis reagents and form the backbone of projects aimed at generating insertions in every predicted gene in the fly genome. In addition, vectors based on the FLP/FRT system are being used for genome-wide applications, including the development of molecularly-mapped deletion and duplication kits. In addition to these 'traditional' genetic approaches, a variety of engineered elements have been developed for a wide range of transgenic applications, including enhancer trapping, gene-tagging, targeted misexpression, RNA interference (RNAi) delivery and homologous recombination/gene replacement. To complement the use of P-elements, alternative transposon vectors have been developed. The most widely used of these are the lepidopteran element piggyBac and a Drosophila hydei transposon, Minos. In total, a range of transposon vectors offers the Drosophila biologist considerable flexibility and sophistication in manipulating the genome of the fly and has allowed rapid advances in all areas of developmental biology and genome science.

Animals↗
PubMed1995

Identification of male germ cells undergoing apoptosis in adult rats.

The possible role of apoptosis in spontaneous or induced germ cell death was investigated by treating adult male rats with either a GnRH antagonist (112.5 micrograms kg-1 day-1 for 14 days) or methoxyacetic acid (650 micrograms kg-1; single dose) or sham-treated with either of the vehicles (n = 3 per group). The antagonist virtually abolished gonadotrophin secretion, while methoxyacetic acid reduced serum testosterone concentrations and slightly increased those of FSH (neither significantly). Bands of low molecular mass characteristic of apoptotically degraded DNA were detected by electrophoresis in both treatment groups but not in the controls. Sectioned, Carnoy-fixed testes were screened for degenerating cells with periodic acid-Schiff's base and haemalaun or examined for apoptotic cells using a modified in situ end-labelling procedure. Periodic acid-Schiff's-stained dying cells were found in low numbers in control animals with a distribution and frequency that matched that of apoptotic cells. Degenerating germ cells identified by histology were present at certain stages of spermatogenesis after 2 weeks of antagonist treatment. A comparison of their distribution with that of end-labelled cells identified the cell death as apoptotic. Methoxyacetic acid caused a massive depletion of spermatocytes at stages IX-II, which was also found to be apoptotic. It is concluded that spontaneous germ cell death in adult rats is apoptotic and that both gonadotrophin ablation and administration of methoxyacetic acid can cause apoptosis in the germ cells of adult male rats, but via different routes.

Acetates↗
PubMed1992

Aspects of breast cancers.

Breast cancer is the commonest killing malignant disease of women in the European Community. The average annual age standardised mortality rate among the 12 EEC countries ranges from 28.5 to 13.7 per 100,000 females. In Ireland, breast cancer is treated primarily by general surgeons. At our Breast Institute at St. Vincent's Hospital where we see 100 patients with breast diseases weekly it is policy to recommend quadrantectomy, total axillary dissection and radiotherapy (QU.A.R.T.) for patients with T1 and T2 tumours if they are peripherally placed within the breast. Complete axillary dissection in early breast cancer provides accurate staging and virtually eliminates axillary recurrence and the dissection is standardised and audited in our unit. Audit of axillary dissection improves the lymph node yield and enhances the completeness of the procedure. Sophisticated mammography improves the detection of small tumours but even excellent mammography may fail to identify malignant disease. Screening programmes for early breast cancer detection should be based on clinical examination in addition to mammography and some 15% of our patients with palpable breast cancer had falsely negative mammograms. Before operation, extensive scintigraphy and sonography is carried out before primary treatment is undertaken. After treatment, clinical and biochemical surveillance is carried out. We have found the lysosomal protease, Cathepsin D to be a useful marker of progressive disease and prognosis in patients with breast cancer. Routine postoperative CEA and CA15.3 are also valuable markers and a high or rising CA15.3 often precedes clinical or investigative evidence of recurrence. In addition, assay of c-erB-2 protein by ELISA is also a simple, rapid quantitative prognostic guide in patients with breast cancer.

Biomarkers, Tumor↗
PubMed2003

From extreme environments to biologically active exopolysaccharides.

In the course of the discovery of novel polysaccharides of biotechnological interest, it is now widely accepted that extremophilic microorganisms will provide a valuable resource not only for exploitation in novel biotechnological processes but also as models for investigating how biomolecules are stabilized when subjected to extreme conditions. Microbes isolated from extreme environments offer a great diversity in chemical and physical properties of their EPS as compared to anywhere else in the biosphere. Bacteria from remote areas still remain virtually unexplored and there is not doubt that extreme environments are a rich source of microorganisms of biotechnological importance. A number of interesting and unique bacterial polysaccharides have been isolated from these ecosystems and are expected to find applications in the very near future in different industrial. Further screenings are underway as well as research into understanding the structure-function relationships of these unusual polymers.

Alteromonas↗
PubMed2004

[Rendu-Osler-Weber syndrome--a complex systemic disease].

Hereditary hemorrhagic teleangiectasia (HHT or Rendu-Osler-Weber Syndrome) is an inherited autosomal dominant disorder of the vascular connective tissue. The resulting vascular malformations can occur in virtually any organ. Nosebleeds can massively impact on the quality of life of those afflicted. However, visceral manifestations are likely to be more serious, and may be comparable with a "ticking time bomb". Most commonly affected are the vascular systems of the lungs, liver, brain and gastrointestinal tract. Screening is recommended--at least with regard to the lungs. Difficult constellations of this complex condition may be successfully managed by an interdisciplinary approach.

Adult↗
PubMed1990

Behavioral risks for human immunodeficiency virus infection in adolescent medical patients.

This paper is an examination of the extent to which adolescents in primary care indicated behavioral risk for human immunodeficiency virus infection, and the degree to which their clinic records reflected either awareness of such conditions or interventions for them. Levels of risk were assigned to the youths based on known risk factors in adult populations and arbitrarily selected natural breaks in the frequency of sexual behaviors. Of the sample, 3% were at high risk for human immunodeficiency virus infection because the adolescents engaged in prostitution, injectable drug use, male homosexual behavior, or had a sexually transmitted disease associated with genital ulcers or sores; 16% were at moderate risk because the youths had more than six sexual partners in the year preceding the interview or had nonulcerative forms of sexually transmitted disease; and the remainder were at low risk. Fewer than half of the youths at risk for human immunodeficiency virus infection sought or received help for any of their problem behaviors, while virtually all sought and received help for sexually transmitted diseases. Because a high proportion of the youths engaging in risky behaviors had sexually transmitted diseases, the most promising approach for prevention of human immunodeficiency disease infection is through health clinics that treat sexually transmitted diseases. These clinics could screen the youths for associated behavioral risk factors, and then offer preventive or interventive services.

Adolescent↗
PubMed1982

Expression and excretion of human fibroblast beta 1 interferon in monkey cells after transfection with a recombinant SV40 plasmid vector.

We have constructed a eukaryotic expression vector designed to express a gene under late SV40 transcriptional control. From this chimeric plasmic-SV40 vector, virtually all the sequences which code for the major capsid protein VP1 have been deleted and instead, the human fibroblast interferon beta 1 cDNA gene has been inserted. After transfection of monkey cells with this recombinant, substantial quantities of human beta 1 interferon (up to 2 x 10(-4) IU/ml) were excreted in the culture medium. Transfection of nonpermissive mouse L cells or rat cells yielded virtually undetectable quantities of human beta 1 interferon (5 x 10(3) to 10(4) times less than that in monkey cells). The recombinant SV40 vector may serve as a model vehicle for the efficient expression of other eukaryotic genes and might also be used as a direct screening vector for cloning of eukaryotic or prokaryotic cDNA genes.

DNA, Recombinant↗
PubMed1999

Operating theater blood transaction system. A "virtual" blood transfusion service that brings the blood bank to the operating table.

We describe an operating theater blood transaction system (OTBTS) that is a novel computer software system incorporating electronic crossmatch and the concept of a "self-service" blood banking system in the operating theater. Through this system, the surgeons and the anesthetists can issue blood units for intraoperative transfusion for the patients with a negative antibody screen without the need for a porter service or pneumatic tube system. Since implementation of the OTBTS, the time for obtaining compatible blood for intraoperative transfusion has been reduced from 20 to 30 minutes to around 1 minute. Furthermore, the crossmatch-transfusion ratio was reduced to 1.05. The 23% of patients who required extra blood units (i.e., more than originally anticipated) during surgery further benefited from the system. The blood stock reserved for patients undergoing surgery was reduced by 20%. Therefore, the OTBTS is a system that can greatly enhance the efficiency and safety of intraoperative transfusion and can also save workforce resources.

Blood Banks↗
PubMed2003

A surgical simulator for cleft lip planning and repair.

The objective of this project was to develop a computer-based surgical simulation system for cleft lip planning and repair. This system allows the user to interact with a virtual patient to perform the traditional steps of cleft-lip repair. The system interfaces to force-feedback (haptic) devices to track the user's motion and provide feedback during the procedure, while performing real-time soft-tissue simulation. An eleven-day old unilateral cleft-lip and palate patient was previously CT scanned for ancillary diagnostic purposes using standard imaging protocols and 1mm slices. High-resolution 3D meshes were automatically generated from this data using the ROVE software created in our lab. The resulting 3D meshes of bone and soft-tissue were instilled with physical properties of soft tissues for purposes of simulation. Once these preprocessing steps were completed, the patient's bone and soft-tissue data are presented on the computer screen in stereo and the user can freely view, rotate, and otherwise interact with the patient's data in real-time. The user is prompted to select anatomical landmarks on the patient data for preoperative planning purposes, then their locations are compared against that of a "gold standard" and a score, derived from their deviation from that standard and time required, is generated. The user can then move a haptic stylus and guide the motion of the virtual cutting tool. The soft tissues can thus be incised using this virtual cutting tool, moved using virtual forceps, and fused in order to perform any of the major procedures for cleft-lip repair. Real-time soft tissue deformation of the mesh realistically simulates normal tissues and haptic-rate (>1kHz) force-feedback is provided. The surgical result of the procedure can then be immediately visualized and the entire training process can be repeated at will. A short evaluation study was also performed. Two groups (nonmedical and plastic surgery residents) of six-people each performed the anatomical marking task of the simulator four times. Results showed that the plastic surgery residents scored consistently better than the people without medical background. Every person's score increased with practice, and the length of time needed to complete the eleven markings decreased. The data was compiled and showed which specific markers consistently took users the longest to identify as well as which locations were hardest to accurately mark. Our findings suggest that the simulator is a valuable training tool, giving residents a way to practice anatomical identification for cleft lip surgery without the risks associated with training on a live patient. Educators can also use the simulator to examine which markers are consistently problematic, and modify their training to address these needs.

Cleft Lip↗
PubMed2003

Recognition of mycobacterial epitopes by T cells across mammalian species and use of a program that predicts human HLA-DR binding peptides to predict bovine epitopes.

Bioinformatics tools have the potential to accelerate research into the design of vaccines and diagnostic tests by exploiting genome sequences. The aim of this study was to assess whether in silico analysis could be combined with in vitro screening methods to rapidly identify peptides that are immunogenic during Mycobacterium bovis infection of cattle. In the first instance the M. bovis-derived protein ESAT-6 was used as a model antigen to describe peptides containing T-cell epitopes that were frequently recognized across mammalian species, including natural hosts for tuberculosis (humans and cattle) and small-animal models of tuberculosis (mice and guinea pigs). Having demonstrated that some peptides could be recognized by T cells from a number of M. bovis-infected hosts, we tested whether a virtual-matrix-based human prediction program (ProPred) could identify peptides that were recognized by T cells from M. bovis-infected cattle. In this study, 73% of the experimentally defined peptides from 10 M. bovis antigens that were recognized by bovine T cells contained motifs predicted by ProPred. Finally, in validating this observation, we showed that three of five peptides from the mycobacterial antigen Rv3019c that were predicted to contain HLA-DR-restricted epitopes were recognized by T cells from M. bovis-infected cattle. The results obtained in this study support the approach of using bioinformatics to increase the efficiency of epitope screening and selection.

Animals↗