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PubMed2003

Relative risk of prostate cancer for men with affected relatives: systematic review and meta-analysis.

An increased risk of prostate cancer associated with a family history of prostate cancer has been documented in multiple published reports. Risk has been shown to vary by degree of relationship and age of onset of disease in the affected relative. Several studies, using various designs, have estimated the relative risk (RR) for these associations. The purpose of our study was to identify and summarize published reports on the relationship between risk of prostate cancer and family history, which is defined as having a father, brother, any first- or second-degree relative or other relative affected with prostate cancer. A Medline and manual search from 1982 to 2000 identified 24 studies that reported RR and confidence intervals (CI) and satisfied inclusion criteria. Pooled RR estimates based upon a weighted average model were as follows: any affected family member RR = 1.93, CI 1.65-2.26; affected first-degree relative RR = 2.22, CI 2.06-2.40; affected second-degree relative RR = 1.88, CI 1.54-2.30; father with prostate cancer RR = 2.12, CI 1.82-2.51; and brother with prostate cancer RR = 2.87, CI 2.21-3.73). Statistical comparison of pooled data demonstrated that the RR is significantly higher for affected brother than for affected father (p < 0.03). A sensitivity analysis demonstrated that these results are robust with respect to population bias. This meta-analysis confirms that risk of prostate cancer is associated with family history of disease and improves the quantification of this risk.

Humans↗
PubMed2004

Humoral immune response against melanoma antigens induced by vaccination with cytokine gene-modified autologous tumor cells.

Although the existence of a humoral response against tumor-associated antigens is well appreciated, a systematic analysis of its possible induction by the tumor remains missing. We compared the specific IgG response of Stage IV melanoma patients during vaccination. Patients had been treated within 2 clinical trials with autologous tumor cells gene-modified for IL-7 or IL-12. A panel of 27 tumor-associated antigens (HD-MM-01 to HD-MM-27) was isolated by a SEREX screening of a testis cDNA library using a pool of 5 sera from patients after vaccination. All antigens were retested with individual sera of 12 patients both pre- and post-vaccination. A serological response was induced during vaccination against 18 antigens. Remarkably, induction was detected only in patients included in the screening pool. The low overlap between sero-reactivity of the 12 patients suggested a very individualized immunological reaction. Two of 5 sera included in the screening pool exhibited a high frequency of induced humoral responses. The same patients had been shown to have a high Karnovsky index and had generated lytic cytotoxic T cells against the tumor. Besides 2 known cancer-germline genes (SCP-1 and PLU-1), the other isolated antigens were expressed in a non-tumor-specific fashion as analyzed by virtual Northern blot or RT-PCR. The properties of homologues to several of the identified tumor-antigens, especially PLU-1, SCP-1, DNEL2, CLOCK, and PIASx-alpha, suggest further investigation of their possible function in malignant melanoma. We conclude that a strong humoral response against tumor-associated antigens is inducible by tumor cells and that this response is very individual.

Antibodies, Neoplasm↗
PubMed2005

A novel high-specificity approach for colorectal neoplasia: Detection of K-ras2 oncogene mutation in normal mucosa.

There is an important need for a high-specificity approach to colorectal cancer. Approximately 50% of colorectal tumors contain K-ras gene mutations, which occur as an early step in carcinogenesis. K-ras mutations were detectable not only in tumors but also in microscopically normal colorectal mucosa close to carcinomas in some patients with colorectal cancer. This is the first systematic analysis of K-ras mutations in normal colonic mucosa at multiple consistently-selected locations. A total of 480 normal colonic mucosal samples were obtained from 80 subjects, including 65 patients with sporadic colorectal cancer and 15 controls in whom a colorectal neoplasm was ruled out endoscopically. Normal mucosal samples were obtained at multiple consistently-selected locations using biopsy forceps during colonoscopy. Mutant allele-specific amplification (MASA)-PCR was performed; this could detect a K-ras mutation in normal colonic mucosa even though it was only sparsely present. The K-ras mutation was found in histologically normal mucosa from colorectal cancer patients (20 of 65 cases; 41 of 390 loci) by MASA-PCR, especially frequent (51%; 19 of 37 cases) when the tumor showed a K-ras mutation. In contrast, no mutation was found in normal mucosa from 15 controls (90 loci). K-ras mutation in normal mucosa showed a significant association with the presence of colorectal cancer (p = 0.008). The specificity of the MASA-PCR method for colorectal neoplasms was thus 100%. We conclude that detection of K-ras mutations in normal colonic mucosa might serve as a high-specificity approach to colorectal cancer.

Colon↗
PubMed2005

CXCR4 expression reflects tumor progression and regulates motility of bladder cancer cells.

Transitional cell carcinoma of the urinary bladder remains life threatening due to the high occurrence of metastases. Emerging evidence suggests that chemokines and their receptors play a critical role in tumor metastases. In our study, we performed a systematic analysis of the mRNA and protein expression levels of all 18 chemokine receptors in normal urothelium and bladder cancer. CXCR4 was the only chemokine receptor whose mRNA expression level was upregulated in bladder cancer cell lines as well as in invasive and locally advanced bladder cancer tissue samples (pT2-pT4). In contrast, superficial bladder tumors (pTa and pT1) displayed low CXCR4 expression levels and normal urothelial cells were negative for CXCR4. Immunohistochemistry of a bladder cancer tissue microarray (TMA) confirmed that a subgroup of invasive bladder cancers revealed a high CXCR4 protein expression, while superficial bladder tumors showed low immunoreactivity. To investigate the functional significance of CXCR4 expression, we performed migration and invasion assays. Exposure of CXCR4-positive bladder cancer cells to CXCL12 in a Boyden chamber type assay provoked a significant increase in migration as well as invasion across a Matrigel barrier. Enhanced migration and invasion were inhibited by a CXCR4-specific blocking antibody. In contrast, normal urothelial cells did not respond to CXCL12 and lacked chemotactic migration. In conclusion, bladder cancer cells express CXCR4 progressively with advanced tumorigenesis and this receptor interacts with CXCL12 to mediate tumor chemotaxis and invasion through connective tissue. These properties identify CXCR4 as a potential target for the attenuation of bladder cancer metastases.

Breast Neoplasms↗
PubMed1992

Nuclease resistant ribozymes with high catalytic activity.

Hammerhead ribozymes are efficient RNA enzymes characterized by a typical hammerhead secondary structure and a number of conserved bases. Little is known about the role of the ribose-phosphate backbone, although it is obviously important since a DNA molecule with the same base sequence is not a catalyst. Here we describe the synthesis of artificial ribozymes where modified (2'-O-allyl- and 2'-O-methyl-) ribonucleotides substitute for the corresponding ribonucleotides. A systematic analysis of partially substituted polymers identified a minimum set of six non-contiguous positions where insertion of modified ribonucleotides strongly affects catalytic activity. Surprisingly, ribozymes completely substituted except for these six ribonucleotides are still very active. These molecules efficiently cleave in trans target RNAs in a sequence-specific way, but, unlike RNA ribozymes, are very resistant to nuclease degradation and are very stable in serum. These properties make such synthetic polymers potentially useful for in vivo gene expression studies and therapeutic applications.

Base Sequence↗
PubMedDate not supplied

Cell specificity of aquaporins 0, 3, and 10 expressed in the testis, efferent ducts, and epididymis of adult rats.

Aquaporins (AQPs) are transmembrane protein channels that allow the rapid passage of water across an epithelium at a low energy requirement, though some also transport glycerol, urea, and solutes of various sizes. At present, 11 members of the AQP family of proteins have been described in mammals, with several being localized to the testis (AQP-7 and AQP-8), efferent ducts (AQP-1 and AQP-9), and epididymis (AQP-1 and AQP-9) of adult rats. With the discovery of expression of multiple AQPs in different tissues, we undertook a systematic analysis of several other members of the AQP family on Bouin-fixed tissues of the male reproductive tract employing light microscope immunocytochemistry. In the testis, AQP-0 expression in the seminiferous epithelium was restricted to Sertoli cells and to Leydig cells of the interstitial space; no reaction was observed in the efferent ducts or epididymis. In Sertoli cells, a semicircular pattern of staining was noted, with only one fourth or one half of the Sertoli cells of a given tubule showing a reaction product. Furthermore, while Sertoli cells at stages VI-VIII of the cycle showed intense staining, those at stages IX-XIV were least reactive, with Sertoli cells at stages I-V showing intermediate levels of reaction product. The epithelial expression of AQP-10 was restricted to the microvilli of the nonciliated cells and the cilia of the ciliated cells of the efferent ducts; however, the endothelial cells of vascular channels of the efferent ducts and epididymis were also intensely reactive. AQP-3 expression was localized exclusively to the epididymis, where intense staining was noted exclusively over basal cells. Examination of orchidectomized rats revealed that AQP-3 expression was abolished over basal cells and that it was greatly diminished after efferent duct ligation. As the reaction was not fully restored in orchidectomized animals supplemented with high levels of testosterone, we suggest that AQP-3 expression in basal cells is regulated in part by testosterone, in addition to a luminal factor emanating from the testis. Together, the data indicate a cell- and tissue-specific expression for AQP-0, AQP-3, and AQP-10 in the testis, efferent ducts, and epididymis, as well as differential regulating factors for the expression of AQP-3 in basal cells.

Animals↗
PubMed1982

Parameters for crystal growth of ribosomal subunits.

A systematic analysis of the parameters that control the crystal growth of the large subunit of ribosomes from B stearothermophilus has been carried out. Several parameters have been identified and classified according to their significance. It was found that only biologically active particles can crystallize and that the critical period for the crystallization process is the first few days, during which changes in the volume and content of the crystallization drop are of importance for both nucleation and crystal growth. Consequently, an experimental procedure for fine control of these variables has been developed. As a result of these studies, the reproducibility of crystal formation was increased, and larger and more stable crystals have been obtained.

Bacillus↗
PubMed1992

Candidate biomarkers for application as intermediate end points of lung carcinogenesis.

The need for validated intermediate end point markers to facilitate lung cancer chemointervention research is compelling. Three major classes of lung markers are relevant for this application. Since lung cancer includes four distinct histologies, markers that map degrees of histologic differentiation are important. Many of the markers for squamous differentiation overlap with the candidates for application in the study of head and neck cancer. Production of tissue-specific cell products especially for surfactant or CEA is of interest, because the gene structure is known and many differentiation-related polymorphisms exist. This strategy would be useful for adenomatous type tissue. A second type of marker is the broad group of differentiation markers. The carbohydrate or blood group-like antigens comprise a representative example. Carbohydrate structures are expressed in a specific sequence during fetal processes, and this sequence appears to reverse with the development of a cancer. Retrodifferentiation of specific differentiation markers is the basis of a major effort to effect earlier lung cancer detection using sputum immunocytochemistry. The final class includes markers which affect either positive or negative aspects of growth. Candidates in this area include growth factors or their receptors, or genes that regulate growth. If the intermediate end point marker reflects tumor biology and that biology is in the causal path of tumor progression, serial observation of that parameter should indicate the success of the intervention. In all three of these examples, the clinical material to be analyzed could be sputum specimens, bronchial biopsies or resected lung tissue. Systematic analysis of these markers in context of intervention trials is required to validate their utility.(ABSTRACT TRUNCATED AT 250 WORDS)

Adenoma↗
PubMed1994

Towards an understanding of nuclear morphogenesis.

In the age of "virtual reality," the imperfect microscopic silhouettes of cells and organelles are gradually being replaced by calligraphic computer drawings. In this context, textbooks and introductory slides often depict the cell nucleus as a smooth-shaped, featureless object. However, in reality, the nuclei of different cells possess distinct sizes and morphological features which develop in a programmed fashion as each cell differentiates. To dissect this complex morphogenetic process, we need to identify the basic elements that determine nuclear architecture and the regulatory factors involved. Recently, clues about the identity of these components have been obtained both by systematic analysis and by serendipity. This review summarizes a few recent findings and ideas that may serve as a first forum for future discussions and, I hope, for further work on this topic.

Adaptation, Physiological↗
PubMed2002

Ab initio prediction of helical segments in polypeptides.

An ab initio method has been developed to predict helix formation for polypeptides. The approach relies on the systematic analysis of overlapping oligopeptides to determine the helical propensity for individual residues. Detailed atomistic level modeling, including entropic contributions, and solvation/ionization energies calculated through the solution of the Poisson-Boltzmann equation, is utilized. The calculation of probabilities for helix formation is based on the generation of ensembles of low energy conformers. The approach, which is easily amenable to parallelization, is shown to perform very well for several benchmark polypeptide systems, including the bovine pancreatic trypsin inhibitor, the immunoglobulin binding domain of protein G, the chymotrypsin inhibitor 2, the R69 N-terminal domain of phage 434 repressor, and the wheat germ agglutinin.

Animals↗
PubMed2006

Performance of DFT in modeling electronic and structural properties of cobalamins.

Computational modeling of the enzymatic activity of B12-dependent enzymes requires a detailed understanding of the factors that influence the strength of the Co--C bond and the limits associated with a particular level of theory. To address this issue, a systematic analysis of the electronic and structural properties of coenzyme B12 models has been performed to establish the performance of three different functionals including B3LYP, BP86, and revPBE. In particular the cobalt-carbon bond dissociation energies, axial bond lengths, and selected stretching frequencies have been analyzed in detail. Current analysis shows that widely used B3LYP functional significantly underestimates the strength of the Co--C bond while the nonhybrid BP86 functional produces very consistent results in comparison to experimental data. To explain such different performance of these functionals molecular orbital analysis associated with axial bonds has been performed to show differences in axial bonding provided by hybrid and nonhybrid functionals.

Computer Simulation↗
PubMedDate not supplied

Low-mode docking search in iGluR homology models implicates three residues in the control of ligand selectivity.

Homology models of the ionotropic rat kainate receptor iGluR6, based on the ligand binding domains of iGluR2, were constructed. A systematic analysis by low-mode docking searches of kainic acid in homology models of the native iGluR6 receptor, chimeric (iGluR2 and iGluR6) receptors and mutant receptors have identified three residues which influence the conformation of kainic acid in the binding core and hence the affinity for kainic acid. These residues are Leu650, Thr649 and Leu704, all located in domain 2. Leu650 has previously been implicated in the control of selectivity of iGluR2. However, this is the first report that suggests that Thr649 and Leu704 play a role in receptor selectivity.

Amino Acid Sequence↗
PubMed2001

Proteomics: the move to mixtures.

Proteomics can be defined as the systematic analysis of proteins for their identity, quantity and function. In contrast to a cell's static genome, the proteome is both complex and dynamic. Proteome analysis is most commonly accomplished by the combination of two-dimensional gel electrophoresis (2DE) and mass spectrometry (MS). However, this technique is under scrutiny because of a failure to detect low-abundance proteins from the analysis of whole cell lysates. Alternative approaches integrate a diversity of separation technologies and make use of the tremendous peptide separation and sequencing power provided by MS/MS. When liquid chromatography is combined with tandem mass spectrometry (LC/MS/MS) and applied to the direct analysis of mixtures, many of the limitations of 2DE for proteome analysis can be overcome. This tutorial addresses current approaches to identify and characterize large numbers of proteins and measure dynamic changes in protein expression directly from complex protein mixtures (total cell lysates).

Electrophoresis, Gel, Two-Dimensional↗
PubMed2005

Optimized sample preparation for isotopic analyses of CO2 in air: systematic study of precision and accuracy dependence on driving variables during CO2 purification process.

A systematic analysis of efficiency, reproducibility and accuracy of cryogenic purification of CO(2) from air samples for isotopic analyses is presented. The technical characteristics of the cryogenic line are given in detail. To study the cryogenic process, three different operating parameters are considered: flow rate of the gas entering the line, pressure of the gas in the line, and CO(2)-trap shape. Experimental results demonstrate that efficiency, reproducibility and accuracy strongly depend on the CO(2)trap shape. Moreover, a dependence of reproducibility and accuracy on the flow rate of the gas is found, but not on its pressure. High precision (< or =0.02 per thousand for delta(13)C and < or =0.05 per thousand for delta(18)O) and good accuracy (<0.09 per thousand for delta(13)C and <0.14 per thousand for delta(18)O) is achieved after applying the N(2)O correction.

Journal Article↗
PubMed2003

Imaging of the varicella zoster virion in the viral highways: comparison with herpes simplex viruses 1 and 2, cytomegalovirus, pseudorabies virus, and human herpes viruses 6 and 7.

Imaging by scanning electron microscopy (SEM) can provide insight into viral egress. At a low magnification level, varicella zoster virions (VZV) emerge from an infected cell surface in a distinctive pattern previously described as "viral highways." Viral highways consist of thousands of particles arranged in linear pathways across the syncytial surface. This egress pattern has not been described with other herpesviruses, but a systematic analysis has not been performed. Therefore, the characteristic arrangement of VZV egress was compared with that of six other members of the herpes virus family, including herpes simplex virus (HSV) types 1 and 2, human cytomegalovirus (CMV), pseudorabies virus (PRV), and human herpesvirus types 6 and 7 (HHV-6 and HHV-7). Only VZV-infected cells exhibited viral highways. Subsequent SEM examination of VZ virions at an ultra high-resolution revealed that more than 70% were aberrant. Further imaging of the other herpesviruses demonstrated that VZV structure was more closely related to PRV than HSV-1 or HSV-2. Finally, it is noted that the individual members of the herpesvirus family have distinguishable SEM profiles.

Animals↗
PubMed1992

Lack of detectable human T-cell lymphotropic virus type I sequences in samples from multiple sclerosis patients.

Recently, inconclusive results have followed the early data on the possible association between multiple sclerosis (MS) and human T-cell lymphotropic virus type I (HTLV-I) infection. For this reason, we examined this hypothesis using the polymerase chain reaction (PCR) to study samples of differing origin from Italian MS patients. In particular, we developed a systematic analysis of paraffin-embedded brain white matter from histologically defined lesions of 14 MS patients using PCR and primer sets specific for HTLV-I sequences; additionally, cerebrospinal fluids (CSFs) from 12 patients and peripheral blood mononuclear cells (PBMCs) from subjects at the early and late phase of the disease were investigated for free HTLV-I virions and specific proviral sequences, respectively. In agreement with some groups who reported lack of HTLV-I sequences in PBMCs of MS patients but in clear contrast with others, we failed to detect specific viral sequences using this broad approach.

Base Sequence↗
PubMed2006

The VP1 protein of human enterovirus 71 self-associates via an interaction domain spanning amino acids 66-297.

Enterovirus 71 (EV71) is a major etiological agent of hand, foot, and mouth disease (HFMD). Several recent outbreaks of HFMD in East Asia were associated with neurological complications and numerous deaths. In 2000, an outbreak in Singapore afflicted thousands of children, resulting in four fatal cases from whom EV71 was isolated. The virus possesses four structural proteins VP1, VP2, VP3, and VP4, each of which is involved in forming the pentameric icosahedral structure of the virus. Here we report that the full-length VP1 structural protein of EV71 is capable of self-association. Dimerization of VP1 was tested using the yeast two-hybrid system, fluorescence resonance energy transfer (FRET) analysis, in vitro coupled transcription-translation binding assays, and mammalian cell transcription-translation experiments. Dimerization of various truncated versions of the VP1 protein was also studied by mutational analysis. Systematic deletions of parts of VP1 revealed that the region spanning amino acids 66-132 of VP1 contains the major dimerization domain. However, the region between amino acids 132 and 297 was indispensable, and contributed largely to increasing the strength of the interaction. This ability of EV71 VP1 to self-associate and to participate significantly in forming the characteristic icosahedral capsid strongly enhances the pathogenicity and stability of the virus to withstand the environment of the gastrointestinal tract.

Amino Acids↗
PubMed2002

Exploitation of intracellular pH gradients in the cellular delivery of macromolecules.

Most cellular components such as the cytoplasm, endosomes, lysosomes, endoplasmic reticulum, Golgi bodies, mitochondria, and nuclei are known to maintain their own characteristic pH values. These pH values range from as low as 4.5 in the lysosome to about 8.0 in the mitochondria. Given these proton gradients around a neutral pH, weak acids, and bases with a pKa between 5.0 and 8.0 can exhibit dramatic changes in physicochemical properties. These compounds can be conjugated as such to macromolecules or incorporated into polymeric or liposomal formulations to promote the efficient cellular delivery of macromolecules. Mechanistically, the carrier molecules can facilitate favorable membrane partition, membrane fusion, transient pore formation, or membrane disruption. Drug carriers equipped with such pH-sensitive triggers and switches are able to significantly enhance the cellular delivery of macromolecules in vitro. However, the successful application of these molecules for efficient delivery in vivo requires the design of noncytotoxic, nonimmunogenic, serum compatible and biochemically labile carriers, systematic analysis of their mechanisms of action, and extensive animal studies.

Animals↗