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PubMed1997

Efficient modelling protocols for oligosaccharides: from vacuum to solvent.

The determination of conformational preferences of oligosaccharides is best approached by describing their preferred conformations on potential energy surfaces as a function of the glycosidic linkage phi, psi torsional angles. For proper molecular mechanics modelling the flexibility of the rotatable pendant groups must also be considered. The so called adiabatic maps partially mimic the flexibility within the 10 dimensional conformational space of the pendant groups of the given disaccharide. These molecular mechanics maps are considered to be the state-of-the art of the phi, psi potential energy surface of disaccharides recently calculated. The RAMM (RAndom Molecular Mechanics) method was shown to be able to calculate such profiles automatically. Additionally, based on the continuum solvent approach, RAMM allows the calculation of the effects of solvent on conformational energy profiles. Molecular dynamics simulations are also useful tools to study the influence of solvent on conformational behaviour of oligosaccharides. The capability of the RAMM calculational protocol to locate low-energy conformers on the multidimensional potential energy hypersurfaces of disaccharides is illustrated and compared with molecular dynamics simulations with and without inclusion of the solvent.

Carbohydrate Conformation↗

PubMed2003

Myocardin mRNA is augmented in the failing myocardium: expression profiling in the porcine model and human dilated cardiomyopathy.

The implication of myocardin and homeodomain only protein (HOP) in combinatorial molecular pathways that guide heart development and cardio-specific gene expression has recently been reported. However, expression of these genes in the failing heart has not yet been investigated. This study was designed to elaborate a molecular profile of myocardin and HOP expression in the failing ventricular myocardium through the use of both explanted human heart samples and heart biopsies from neonatal piglets with doxorubicin-induced cardiomyopathy (Dox-CM). Myocardin and HOP mRNA levels were estimated by both northern blot hybridization and semiquantitative RT-PCR in human ventricular preparations in end-stage failure due to dilated cardiomyopathy (DCM), as well as in nonfailing donor hearts. Similar experiments were performed with ventricular samples from normal and Dox-treated neonatal piglets. The gene expression of brain natriuretic peptide (BNP) was used as a molecular marker of myocardial damage and failure. The study revealed the following novel findings: (1) myocardin transcripts are detected in neonatal human and pig hearts at lower levels than in mature cardiac tissues, (2) the myocardin transcript pool is significantly augmented in the failing human and porcine myocardium as compared to that in nonfailing heart samples, (3) in the failing human myocardium, increased levels of myocardin mRNA are associated with a diminished HOP transcript content, and (4) the inverse proportion in cardiac myocardin/HOP mRNA pools observed in explanted human hearts is also traceable in normal human heart and aorta. A possible dual consequence of increased myocardin and decreased HOP expression levels on serum response factor-dependent cardiac-specific expression in the normal heart and at heart failure is discussed. Therefore, increased abundance of the myocardin mRNA pool is judged to be a novel CM-related feature which, alone or in association with decreased HOP transcript levels, can be responsible for dysregulation of myocardin-mediated gene expression in failing myocardium.

Amino Acid Sequence↗

PubMed2001

Validation of tissue microarrays for immunohistochemical profiling of cancer specimens using the example of human fibroblastic tumors.

Tissue microarrays allow high-throughput molecular profiling of cancer specimens by immunohistochemistry. Phenotype information of sections from arrayed biopsies on a multitissue block needs to be representative of full sections, as protein expression varies throughout the entire tumor specimen. To validate the use of tissue microarrays for immunophenotyping, we studied a group of 59 fibroblastic tumors with variable protein expression patterns by immunohistochemistry for Ki-67, p53, and the retinoblastoma protein (pRB). Data on full tissue sections were compared to the results of one, two, and three 0.6-mm core biopsies per tumor on a tissue array. Ki-67 and p53 staining was read as two categories (positive or negative). Concordance for this staining between tissue arrays with triplicate cores per tumor and full sections were 96 and 98%, respectively. For pRB staining was read as three categories (high, moderate, or negative), where concordance was 91%. The use of three cores per tumor resulted in lower numbers of lost cases and lower nonconcordance with standard full sections as compared to one or two cores per tumor. Correlations between phenotypes and clinical outcome were not significantly different between full section and array-based analysis. Triplicate 0.6-mm core biopsies sampled on tissue arrays provide a reliable system for high-throughput expression profiling by immunohistochemistry when compared to standard full sections. Triplicate cores offer a higher rate of assessable cases and a lower rate of nonconcordant readings than one or two cores. Concordance of triplicate cores is high (96 to 98%) for two category distinction and decreases with the complexity of the phenotypes being analyzed (91%).

Adolescent↗

PubMed2006

Laser capture microdissection.

Laser capture microdissection (LCM) is a technique for isolating pure cell populations from a heterogeneous tissue section or cytological preparation via direct visualization of the cells. This technique is applicable to molecular profiling of diseased and disease-free tissue, permitting correlation of cellular molecular signatures with specific cell populations. DNA, RNA, or protein analysis can be performed with the microdissected tissue by any method with adequate sensitivity. The principle components of LCM technology are (1) visualization of the cells of interest via microscopy, (2) transfer of laser energy to a thermolabile polymer with formation of a polymer-cell composite, and (3) removal of the cells of interest from the heterogeneous tissue section. LCM is compatible with a variety of tissue types, cellular staining methods, and tissue-preservation protocols that allow microdissection of fresh or archival specimens. LCM platforms are available as a manual system (PixCell; Arcturus Bioscience) or as an automated system (AutoPix).

Cell Separation↗

PubMed2001

Role of transcription factors in the pathogenesis of pituitary adenomas: a review.

The diversity inherent in every organ has its roots in gene-expression variation and is revealed through distinctions in the molecular profile and hence the identity of individual cell type. Study into the molecular mechanisms of the development of individual cell type within the pituitary, which is under the control of transcription factors, has provided a basis for a deeper insight into the molecular mechanisms underlying the pathogenesis of a variety of hormone-producing pituitary tumors. Identification of some of these transcription factors in pituitary adenomas further supports their role in the pathogenesis of pituitary adenomas. Understanding the molecular mechanisms of regulation of proliferation of pituitary cell types by transcription factors offers a basis for hope that rational genetic or pharmacologic therapies for pituitary tumors can be designed in the future.

Adenoma↗

PubMed1982

A 94,000-dalton glycoprotein expressed by human melanoma and carcinoma cells.

The IgG2a monoclonal antibody (MoAb) 376.96S, secreted by a hybridoma derived from a mouse immunized with cultured human melanoma cells COLO 38, reacts with a single 94,000-dalton glycoprotein that is peripherally associated with the plasma cell membrane of cultured melanoma cells. Indirect immunofluorescence analysis with cryostat thin sections of human tissues showed that this antigen is absent from a large variety of normal tissues but is readily detectable on melanomas, nevi, and several different carcinomas. The MoAb 376.96S binds with cultured melanoma and carcinoma cell lines to a similar extent and can mediate both complement-dependent and cell-dependent lysis of these cells. The 94,000-dalton glycoprotein detected by MoAb 376.96S is distinct in its tissue distribution, antigenicity, and molecular profile from several structures previously identified with monoclonal antibodies that have similar molecular weights.

Antibodies, Monoclonal↗

PubMedDate not supplied

Molecular prognostic markers in ovarian cancer: toward patient-tailored therapy.

In ovarian cancer the ceiling seems to be reached with chemotherapeutic drugs. Therefore a paradigm shift is needed. Instead of treating all patients according to standard guidelines, individualized molecular targeted treatment should be aimed for. This means that molecular profiles of the distinct ovarian cancer subtypes should be established. Until recently, most studies trying to identify molecular targets were single-marker studies. The prognostic role of key components of apoptotic and prosurvival pathways such as p53, EGFR, and HER2 has been extensively studied because resistance to chemotherapy is often caused by failure of tumor cells to go into apoptosis. However, it is more than likely that different ovarian cancer subtypes with extensive molecular heterogeneity exist. Therefore, exploration of the potential of specific tumor-targeted therapy, based on expression of a prognostic tumor profile, may be of interest. Recently, new profiling techniques, such as DNA and protein microarrays, have enabled high-throughput screening of tumors. In this review an overview of the current status of prognostic marker and molecular targeting research in ovarian cancer, including microarray studies, is presented.

Antineoplastic Agents↗

PubMed1997

Enhancement of resolution of low molecular weight RNA profiles by staircase electrophoresis.

Stable low molecular weight (LMW) RNA comprises molecules used in the taxonomy of microorganisms and in studies on the microbial diversity of populations. However, the use of electrophoretic techniques has been hampered due to the low resolution obtained with techniques used for the separation of this kind of molecule. In this work we develop an electrophoretic method (staircase electrophoresis) that increases the resolution of the technique. This improvement in the resolution adequately resolves the three zones that integrate the profiles of LMW RNA: ribosomic 5S RNA (5S rRNA), class 2 transfer RNA (tRNA), and class 1 transfer RNA, allowing the technique to be applied to taxonomic studies (diagnostic, the identification of the individuals), phylogenetic studies and studies on naturally occurring microbial populations.

Electrophoresis↗

PubMed2006

Transcending the biomarker mindset: deciphering disease mechanisms at the single cell level.

The application of proteomics to disease research promises to enhance the understanding and treatment of many human maladies through the identification of molecular profiles associated with each disease. However, although much is made of the utility of molecular signatures as markers of disease state, insufficient emphasis is often placed on the simultaneous need for biological mechanism inquiry. Focused and detailed analyses of disease-associated signaling networks have the potential to be more mechanistically informative than large-scale proteomic profiling approaches, providing insight into the cellular processes involved in pathogenesis, disease progression and therapeutic resistance; while still providing diagnostic or clinical management direction. Phospho-specific flow cytometry provides a method for the analysis of pathological signaling networks, enabling the investigation of disease mechanisms at the single-cell level.

Biomarkers↗

PubMed2001

Carcinogenesis of cancer of the papilla and ampulla: pathophysiological facts and molecular biological mechanisms.

BACKGROUND: Ampullary cancer has one of the highest resectability rates and best prognoses among neoplasms arising in the periampullary region. DISCUSSION: Early diagnosis due to early symptoms can partially explain the better prognosis as compared to other cancers of the periampullary region, but biologic factors should also be taken in account. In the past few years, the molecular mechanisms underlying this disease have been investigated and alterations of genes that regulate different cell functions have been described. Mutations of K-ras and of the tumor suppressor genes APC, p16 and p53 indicate a major disturbance in cell cycle regulation. CONCLUSIONS: If the molecular profile of ampullary cancer is examined in terms of rate and type of molecular changes, it seems to be more similar to intestinal than to pancreatic cancer. Furthermore, the fact that many ampullary carcinomas arise from adenomas and the frequent finding of ampullary tumors in patients affected by polyposis syndromes also suggest that ampullary and colon cancers share common molecular mechanisms of carcinogenesis.

Ampulla of Vater↗

PubMedDate not supplied

Urinary bladder tumor markers.

Bladder cancer is amenable to biomarker development because many tumor-associated molecules are secreted in urine. Tumor cells are shed in urine, and, therefore, tests that detect tumor cell-surface markers have also been developed to diagnose bladder cancer and monitor its recurrence. Several bladder tumor markers show higher sensitivity than cytology, but most have lower specificity. In addition to markers that use conventional technologies such as enzyme-linked immunosorbent assay, point-of-care devices, reverse transcriptase polymerase chain reaction, fluorescent in situ hybridization, and immunocytochemistry, proteomic and gene profiling approaches are being used to find new biomarkers to assist in the molecular profiling of bladder cancer. This review describes both new and well-studied bladder tumor markers.

Biomarkers, Tumor↗

PubMed2004

Molecular stratification of diagnostically challenging high-grade gliomas composed of small cells: the utility of fluorescence in situ hybridization.

PURPOSE: There is considerable morphologic overlap between various entities of high-grade gliomas, and, therefore, a further planning of their optimal treatment is a controversial issue. The aim of this study was molecular stratification of morphologically ambiguous high-grade gliomas composed from small cells. Fluorescence in situ hybridization (FISH) with commercially available probes was used for this purpose. EXPERIMENTAL DESIGN: We analyzed a set of 114 high-grade small-cell gliomas that were difficult to interpret diagnostically because of their distinct cytological origin. FISH assay with locus probes for EGFR, p16, PTEN, and 1p and 19q was done. RESULTS: Morphologically uniform high-grade gliomas composed of small cells varied greatly in terms of molecular features and clinical outcome. Four clinically relevant subsets of patients whose tumors showed distinctly different molecular profiles were identified as follows: (a) 13 patients whose tumors exhibited no discernable molecular alterations (5-year survival rate, 83%); (b) 20 patients whose tumors harbored either 1p/19q codeletion or isolated deletion of 19q unaccompanied by other molecular abnormalities (5-year survival rate, 59%); (c) 35 patients whose tumors showed p16 and/or PTEN deletions unaccompanied by EGFR amplification (5-year survival rate, 8%); and (d) 46 patients whose tumors harbored EGFR amplification (5-year survival rate, 0). CONCLUSIONS: The FISH method provides clinically useful information in the molecular analysis of morphologically ambiguous malignant small-cell gliomas that could potentially enhance the quality of patient care.

Adolescent↗

PubMed2006

Separate populations of receptor cells and presynaptic cells in mouse taste buds.

Taste buds are aggregates of 50-100 cells, only a fraction of which express genes for taste receptors and intracellular signaling proteins. We combined functional calcium imaging with single-cell molecular profiling to demonstrate the existence of two distinct cell types in mouse taste buds. Calcium imaging revealed that isolated taste cells responded with a transient elevation of cytoplasmic Ca2+ to either tastants or depolarization with KCl, but never both. Using single-cell reverse transcription (RT)-PCR, we show that individual taste cells express either phospholipase C beta2 (PLCbeta2) (an essential taste transduction effector) or synaptosomal-associated protein 25 (SNAP25) (a key component of calcium-triggered transmitter exocytosis). The two functional classes revealed by calcium imaging mapped onto the two gene expression classes determined by single-cell RT-PCR. Specifically, cells responding to tastants expressed PLCbeta2, whereas cells responding to KCl depolarization expressed SNAP25. We demonstrate this by two methods: first, through sequential calcium imaging and single-cell RT-PCR; second, by performing calcium imaging on taste buds in slices from transgenic mice in which PLCbeta2-expressing taste cells are labeled with green fluorescent protein. To evaluate the significance of the SNAP25-expressing cells, we used RNA amplification from single cells, followed by RT-PCR. We show that SNAP25-positive cells also express typical presynaptic proteins, including a voltage-gated calcium channel (alpha1A), neural cell adhesion molecule, synapsin-II, and the neurotransmitter-synthesizing enzymes glutamic acid decarboxylase and aromatic amino acid decarboxylase. No synaptic markers were detected in PLCbeta2 cells by either amplified RNA profiling or by immunocytochemistry. These data demonstrate the existence of at least two molecularly distinct functional classes of taste cells: receptor cells and synapse-forming cells.

Animals↗

PubMed2006

DNA fingerprinting elicited evolutionary trend of oral Candida tropicalis isolates from diverse geographic locales.

PURPOSE: To study molecular profiles of oral Candida tropicalis isolates from five different geographic locales to determine the molecular diversity, clonality and evolutionary trends of this opportunistic pathogen. METHODS: A total of 36 strains from five countries (China, Canada, Scotland, Japan and Tanzania) were genotyped by PCR fingerprinting with 11 separate primers. Of these, primers RSG9, RSG8, T3B and RSD12 generated complex fingerprinting patterns. RESULTS: Three significantly dissimilar profiles were derived from the primer T3B and particularly focused on tDNA suggested the prevalence of genetic subtypes within the species. Comparison of tDNA and rDNA (RSD12) fingerprints of C. tropicalis suggested that rDNA is much more heterogeneous than the relatively distinct tDNA. Further analysis of similarity coefficient (SAB) of gel profiles derived from computer-generated dendrograms indicated some degree of similarity in isolates from five-disparate geographic locales as well as the presence of unique isotypes in each region. CONCLUSIONS: This study demonstrates the evolutionary divergence of distinct genetic subgroups within Candida tropicalis .

AIDS-Related Opportunistic Infections↗

PubMed2002

Molecular heterogeneity of fluconazole-resistant and -susceptible oral Candida albicans isolates within a single geographic locale.

The emergence of drug-resistant Candida albicans in immunocompromised patients is common. A disconcerting aspect of this phenomenon is the rapid emergence of C. albicans strains that are resistant to a widely used azole drug, fluconazole (FLZ). To understand the origin of FLZ-resistant yeast isolates, we investigated molecular profiles of 20 geographically related oral C. albicans isolates using three genotyping methods: randomly amplified polymorphic DNA-PCR, with six different primers (OBU1, OBU2, OBU3 RSD6, RSD11 and RSD12); electrophoretic karyotyping by pulsed-field gel electrophoresis; and HinfI restriction fragment analysis. Of the 20 isolates studied, 10 were FLZ- resistant and originated from patients with oral candidosis with a history of FLZ therapy, and the remainder were FLZ susceptible from individuals with oral candidosis, but without a history of FLZ therapy. A composite genotype was generated for each strain by combining molecular types derived from the three independent molecular methods. The composite profiles indicated genetic diversity amongst both the FLZ-resistant as well as -sensitive isolates, and no specific features emerged distinguishing the drug-resistant and -sensitive groups. These observations cast doubt on the theory of a clonal origin of FLZ-resistant C. albicans isolates.

Antifungal Agents↗

PubMed2006

Distribution and origins of polycyclic aromatic hydrocarbons (PAHs) in riverine, estuarine, and marine sediments in Thailand.

To assess the status of polycyclic aromatic hydrocarbon (PAH) contamination in coastal and riverine environments in Thailand, we collected 42 surface sediment samples from canals, a river, an estuary, and coastal areas in Thailand in 2003 and analyzed them for PAHs with 3-7 benzene rings by gas chromatography-mass spectrometry (GC-MS). The total concentration of PAHs ranged from 6 to 8399 ng/g dry weight. The average total PAH concentrations were 2290+/-2556 ng/g dry weight (n=8) in canals, 263+/-174 (n=11) in the river, 179+/-222 (n=9) in the estuary, and 50+/-56 (n=14) in coastal areas. Comparison of the concentration range with a worldwide survey of sedimentary PAH concentrations ranked PAH contamination in Thai sediments as low to moderate. The ratio of the sum of methylphenanthrenes to phenanthrene (MP/P ratio) allows discrimination of PAH sources between petrogenic (>2) and pyrogenic (<0.5) origins. Sediments from urban canals in Bangkok showed the highest PAH concentrations and petrogenic signatures (MP/P=1.84+/-0.98 [n=6] in canal sediments) with abundant alkylated PAHs, indicating major sources of petrogenic PAHs in the city. To identify the sources of the petrogenic inputs in Thailand, we analyzed triterpanes, biomarkers of petroleum pollution, in the sediment samples and in potential source materials. Hopane profiles were remarkably uniform throughout the nation, suggesting a diffuse single source (e.g. automobiles). Molecular profiles of hopanes and PAHs in sediments from the urban canals were similar to those in street dust, indicating that street dust is one of the major sources of petrogenic PAHs in the urban area. On the other hand, low levels of PAHs (approximately 50 ng/g) with a pyrogenic signature (MP/P ratio approximately 0.5) were widely recorded in remote areas of the coast and the Chao Phraya River. These pyrogenic PAHs may be atmospherically transported throughout the nation. Middle and lower reaches of the Chao Phraya River, the river mouth, and the upper Gulf of Thailand showed intermediate concentrations and profiles of PAHs, indicating mixtures of petrogenic and pyrogenic origins. Perylene was abundant in sediments, representing up to approximately 60% of total identified PAHs. High inputs of soil due to frequent heavy rains could contribute to the high perylene abundance in the sediments. Sedimentary PAH concentrations decreased offshore with a half distance of approximately 10 km in the upper Gulf off the mouth of the Chao Phraya River. This is probably due to active deposition of laterally transported riverborne particles.

Environmental Monitoring↗

PubMed2000

Growth factors, receptors, and molecular alterations in pancreatic cancer. Putting it all together.

Because of the dismal prognosis of advanced ductal pancreatic adenocarcinoma, recent investigational strategies have focused on improved detection and therapeutic intervention in early-stage pancreatic cancer. The obvious cost constraints of screening populations at risk but with a low tumor yield will restrict screening protocols to only the highest risk groups (hereditary pancreatitis = age 50, certain hereditary pancreatic cancer kindreds). The vast majority of patients, either lacking or exhibiting an inherited predisposition to pancreatic cancer, will continue to present with disease not resectable for cure. The authors believe that the best hope for these patients lies in the further delineation of the integrative pathophysiology driving tumor growth; this would facilitate the future development of a computer program or other modality that would predict the dominant pathways driving the growth and spread of each tumor based on its "molecular profile." This article reviews the authors' current knowledge regarding the growth factors, receptors, and molecular alterations driving uncontrolled proliferation, local invasion, and metastatic spread of these tumors. The current and potential contributions of studies in cohorts with an inherited predisposition to pancreatic cancer to this pathophysiologic model are also discussed. The future strategy for incorporating this information into a working pathophysiologic road map with clinical relevance is subsequently outlined.

Adenocarcinoma↗

PubMed2004

Multidisciplinary approach to breast cancer management.

The 21st Annual Miami Breast Cancer Conference took place in Miami Beach, Florida, United States, February 25-28, 2004. This meeting aimed to provide practicing surgical and medical oncologists with a multidisciplinary approach to the practice of breast cancer management with incorporation of molecular biologic translation from laboratory to bedside. The expanding knowledge in molecular biology has given rise to the potential for the use of gene expression profiles, molecular fingerprinting and biomarkers for clinical decision making. The theme of this year's meeting was stated to be, "What can you learn that you can use Monday morning and what can you look forward to on Friday?" It is the focus on the most recent practical advances that attracted more than 450 international participants to this 3-day meeting. More than half of all presentations explored recent advances in early breast cancer biology, predictive and prognostic markers, prevention and early diagnosis. This report will collate various presentations to attempt to present a coherent picture of the advances in this area.

Antineoplastic Agents↗