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At least 397 records · Page 22Linked to original sources
PubMed2004

Assessment of ciliates in the sheep rumen by DGGE.

AIMS: This work was carried out to develop a rapid molecular profiling technique to screen ciliate populations in the rumen of sheep. METHODS AND RESULTS: DGGE was used to study the ciliate diversity in the rumen of sheep. There was considerable variation between sheep which were co-housed, and fed the same diet. However, no difference in the major banding patterns was detected, when samples were collected from a single sheep sampled at different points. Following dietary changes, use of a pair-wise comparison of lanes, demonstrated that although there was still diversity between the ciliate population of sheep, the effects as a result of dietary changes were greater. CONCLUSIONS: The technique generated molecular profiles which are sufficiently different to allow comparison between samples, and to permit molecular ecological studies on the rumen ciliate population. SIGNIFICANCE AND IMPACT OF THE STUDY: The outcome of this study means that ciliate diversity in the rumen may now be studied by those unfamiliar with morphological identification of these organisms.

Animal Feed↗
PubMed2006

Profiling of molecular interactions in real time using acoustic detection.

Acoustic sensors that exploit resonating quartz crystals to directly detect the binding of an analyte to a receptor are finding increasing utility in the quantification of clinically relevant analytes. We have developed a novel acoustic detection technology, which we term resonant acoustic profiling (RAP). This technology builds on the fundamental basics of the "quartz crystal microbalance" or "QCM" with several key additional features including two- or four-channel automated sample delivery, in-line referencing and microfluidic sensor 'cassettes' that are pre-coated with easy-to-use surface chemistries. Example applications are described for the quantification of myoglobin concentration and its interaction kinetics, and for the ranking of enzyme-cofactor specificities.

Biosensing Techniques↗
PubMed2002

Single-cell antisense RNA amplification and microarray analysis as a tool for studying neurological degeneration and restoration.

Neurodegenerative diseases typically affect subpopulations of neurons. Characterizing these vulnerable cells and identifying the factors that make them susceptible to damage while neighboring cells remain resistant are essential to the understanding of molecular pathogenesis that underlies neurodegenerative diseases. Classically, molecular analysis of the central nervous system involves the identification and isolation of an anatomic region of interest; next, the relevant tissue is pulverized, and the resulting homogenate is analyzed. Although this method provides useful data, its effectiveness diminishes when used in areas of high cellular diversity or in instances in which one cell type is lost as a consequence of selective cell death or quiescence. A technique that affords the ability to assess molecular events in a very precise anatomical site would provide a powerful tool for this research discipline. In this review, we discuss the amplification of messenger RNA from single neural cells and the subsequent use of the RNA to probe DNA microarrays in an effort to create cell-specific molecular profiles. Specifically, recent work in single-cell expression profiling in Alzheimer's and Huntington's diseases is discussed. We also review some new work with neural stem cells and their application to restorative neurobiology. Finally, we discuss the use of cell-specific molecular profiles to better understand the basics of neuronal cell biology.

Animals↗
PubMed2026

Molecular and Clinical Determinants of Targeted Therapy Treatment in Biliary Tract Cancer.

PURPOSE: Actionable genomic alterations occur in all anatomic subsets of biliary tract cancer; however, targeted therapies have not shown a survival advantage over cytotoxics, and resistance mechanisms require further characterization. EXPERIMENTAL DESIGN: We analyzed a prospectively maintained cohort of 1,254 patients with histologically confirmed biliary tract cancer who underwent molecular profiling using an FDA-authorized targeted next-generation sequencing (NGS) assay. We defined actionable alterations across anatomic subsets, compared outcomes with targeted therapy versus cytotoxics, and evaluated genomic correlates of resistance using longitudinal samples. RESULTS: Overall, 59% of patients harbored at least one OncoKB alteration, and 32.2% (intrahepatic 40%, extrahepatic 15%, and gallbladder 22%) had a level 1/2 alteration. Emerging targets included KRAS alterations (17%), MTAP deletions (12.8%), MDM2 amplification (6.5%), and MET amplification (1.5%). Targeted therapy was associated with improved progression-free survival but not overall survival. Co-occurring TP53/RAS pathway and SMAD4 alterations were associated with inferior outcomes in IDH1/FGFR2-and ERBB2-driven tumors, respectively. Longitudinal profiling demonstrated ERBB2 loss in ERBB2-driven tumors, whereas IDH-, FGFR-, BRAF-, and NTRK-driven tumors retained the primary oncogenic driver. Acquired resistance was associated with alterations in RAS, MEK, MET, MYC, and CDKN2A. CONCLUSIONS: This comprehensive molecular profiling study illustrates the real-world utility and limitations of targeted NGS of biliary tract cancer and affirms the use of precision medicine in patients with these diseases. Genomic heterogeneity and therapeutic resistance observed in this study has the potential to inform ongoing drug development efforts for biliary tract cancer.

Humans↗
PubMed2004

Gene expression profiling for molecular characterization of inflammatory breast cancer and prediction of response to chemotherapy.

Inflammatory breast cancer (IBC) is a rare but aggressive form of breast cancer with a 5-year survival limited to approximately 40%. Diagnosis, based on clinical and/or pathological criteria, may be difficult. Optimal systemic neoadjuvant therapy and accurate predictors of pathological response have yet to be defined for increasing response rate and survival. Using DNA microarrrays containing approximately 8,000 genes, we profiled breast cancer samples from 81 patients, including 37 with IBC and 44 with noninflammatory breast cancer (NIBC). Global unsupervised hierarchical clustering was able to some extent to distinguish IBC and NIBC cases and revealed subclasses of IBC. Supervised analysis identified a 109-gene set the expression of which discriminated IBC from NIBC samples. This molecular signature was validated in an independent series of 26 samples, with an overall performance accuracy of 85%. Discriminator genes were associated with various cellular processes possibly related to the aggressiveness of IBC, including signal transduction, cell motility, adhesion, and angiogenesis. A similar approach, with leave-one-out cross-validation, identified an 85-gene set that divided IBC patients with significantly different pathological complete response rate (70% in one group and 0% in the other group). These results show the potential of gene expression profiling to contribute to a better understanding of IBC, and to provide new diagnostic and predictive factors for IBC, as well as for potential therapeutic targets.

Adult↗
PubMed2003

Gliogenic and neurogenic progenitors of the subventricular zone: who are they, where did they come from, and where are they going?

The subventricular zone (SVZ) of the perinatal forebrain gives rise to both neurons and glia. The mechanisms governing the phenotypic specification of progenitors within this heterogeneous germinal zone are unclear. However, the characterization of subpopulations of SVZ cells has given us a better understanding of the basic architecture of the SVZ and presents us with the opportunity to ask more detailed questions regarding phenotype specification and cell fate. Recent work demonstrating the embryonic origins of SVZ cells is summarized, and a model describing the formation of the perinatal SVZ, noting contributions of cells from pallial as well as subpallial germinal zones, is presented. We further address differences among classes of SVZ cells based on molecular profile, phenotype, and migration behavior and present a model summarizing the organization of perinatal SVZ cells along coronal, sagittal, and horizontal axes. A detailed description of the SVZ in the adult, outlining classes of cells based on morphology, molecular profile, and proliferative behavior, was recently reported by Doetsch et al. (Proc Natl Acad Sci USA 93:14895-14900, 1997). Potential relationships among cells within the perinatal and adult SVZ will be discussed. GLIA 43:52-61, 2003.

Animals↗
PubMed2002

Hashimoto's thyroiditis shares features with early papillary thyroid carcinoma.

Neoplastic transformation is a multistep process that results in a continuous spectrum from the normal (physiological) state to a fully established neoplasm. The gold standard for diagnosis of papillary thyroid carcinoma is conventional histology, the essential element being the characteristic nuclear features, regardless of whether papillary structures are present or not. However, other criteria are being used increasingly in the diagnosis of neoplasms, including immunohistochemical staining and molecular profile. The RET/PTC gene rearrangement is highly specific for papillary thyroid carcinoma and is associated with the characteristic nuclear features seen in papillary thyroid carcinoma. There is an overlap in the morphological features, immunohistochemical staining pattern, and most importantly, molecular profile between papillary thyroid carcinoma and Hashimoto's thyroiditis. Although considered a 'benign' condition, Hashimoto's thyroiditis almost always harbours a genetic rearrangement that is strongly associated with and is highly specific for papillary thyroid carcinoma. Submicroscopic foci of papillary thyroid carcinoma must be present in Hashimoto's thyroiditis, although the clinical behaviour is still benign. Further studies are required to predict which foci will progress to papillary thyroid carcinoma.

Carcinoma, Papillary↗
PubMed2006

Relationship between genetic alterations and prognosis in sporadic colorectal cancer.

Because chromosomal chromosomal instability (CIN) and microsatellite instability (MSI) are important genetic alterations in colorectal cancers, we classified the sporadic colorectal cancers (CRC) on the status of the CIN and MSI and explored their molecular profiles. A total of 213 colorectal tumors were collected for analysis of DNA ploidy, MSI, loss of heterozygosity (LOH), mutation of p53 (exons 5 to 9), Ki-ras (exons 1 and 2) and BRAF (V599E). Relationships between clinicopathological variables and molecular analyses were analyzed with the chi(2) test (Yates' correction). Kaplan-Meier survival curves were compared using log-rank test. Variables with p < 0.1 were entered into the Cox regression hazard model for multivariate analysis. High microsatellite instability (MSI-H) existed in 19 tumors (8.9%), which were more likely to be right-sided (31.6%) with poor differentiation (26.3%). Seventy-one (33.3%) tumors were diploid and 142 (66.7%) were aneuploid. Mutations in p53, Ki-ras and BRAF were found in 45.1%, 41.8% and 4.2% of tumors, respectively. Based on MSI, and CIN, 3 classes were defined: (i) High microsatellite instability MSI-H tumors: young age, high carcinoembryonic antigen (CEA) level, right colon, poorly differentiated, mucin production, high BRAF mutation, lower allelic loss and relatively good prognosis; (ii) Microsatellite stability (MSS) diploid tumors: right colon, poorly differentiated, less infiltrative tumor, mucin production, lower allelic loss and low p53, BRAF mutation; (iii) MSS aneuploid tumors: more infiltrative invasion, greater allelic loss and high p53 mutation. According to multivariate analysis, tumor stage and p53 mutation were significantly associated with disease progression. The MSS diploid and MSS aneuploid CRCs could be subtyped with p53 mutation and had different prognostic outcome and molecular profiles. The 4-year disease-free survival (DFS) of patients with MSS-diploid, wild-type p53 tumors was 67% and significantly higher than those of patients with MSS-diploid, mutant p53 CRC (30%, p = 0.003). The same trend was found in patients with MSS-aneuploid CRC(wild p53 vs. mutant p53, 64% vs. 41%, p = 0.009). We concluded that CIN, MSI and p53 mutation status might be used as a multiple parameter profile for the prognosis of sporadic colorectal cancer.

Aged↗
PubMed2004

Molecular signatures of lymphoma.

Hematologic malignancies have historically been characterized by morphologic, immunophenotypic, molecular, and genetic features. However, morphologically identical tumors can have clearly distinct clinical outcomes, suggesting underlying biological heterogeneity. Recent advances in microarray technology have helped the classification of lymphoid malignancies evolve to a new refined level. In addition to the discovery of new disease subclasses defined by unique molecular profiles, gene expression patterns can be correlated with specific genetic abnormalities and prognoses. Furthermore, the discovery of new disease subtypes has provided further insight into lymphoma biology and pathogenesis. Unique gene signatures can highlight key deregulated pathways that are active in molecular disease categories, and in some cases these findings have elucidated new targets for novel therapeutic approaches. This review summarizes the current status of molecular profiling in non-Hodgkin lymphomas. In this review, we have endeavored to include data from multiple investigator groups and tried to cover the breadth of lymphoid tumors, excluding acute and chronic leukemias.

Biomarkers, Tumor↗
PubMed2002

Identification of end points relevant to detection of potentially adverse drug reactions.

Expectations are high that the use of proteomics, gene arrays and metabonomics will improve risk assessment and enable prediction of toxicity early in drug development. These molecular profiling techniques may be used to classify compounds and to identify predictive markers that can be used to screen large numbers of chemicals. One of the challenges for the scientific community is to discriminate between changes in gene/protein expression and metabolic profiles reflecting physiological/adaptive responses, and changes related to pathology and toxicology. In these proceedings we provide a brief overview of the technologies with focus on proteomics and the possible applications to mechanistic and predictive toxicology. The discussion also includes strengths and limitations of molecular profiling technologies.

Animals↗
PubMed1999

Molecular genotoxicity profiles of apoptosis-inducing vanadocene complexes.

Metallocene complexes containing vanadium induce apoptosis in human cancer cells by an as yet unknown mechanism and may therefore be useful as a new class of cytotoxic anticancer drugs. Ultrastructural studies showing the formation of metallocene-DNA complexes prompted the hypothesis that their mechanism of action may resemble the DNA damage induced by cisplatin. Molecular genotoxicity testing provides insights into the mechanisms of action of new chemotherapeutic agents. Therefore, we determined the effects of three cytotoxic vanadocene complexes, vanadocene dichloride, vanadocene dithiocyanate, and vanadocene dioxycyanate, on genomic stability using the yeast DEL recombination assay and transcriptional activation of genotoxic stress-specific promoters in human HepG2 cells using the CAT-Tox(L) assay. Cisplatin caused an 11-fold increase of recombination frequency in yeast and induced transcriptional activation of the DNA damage-associated promoters such as the minimum promoter containing p53 response elements and the GADD45 promoter in addition to activating the promoters for c-fos, heat shock protein 70, metallothionine IIa, and the minimum promoter containing nuclear factor kappa(kappa)B response elements. In contrast to cisplatin, vanadocene complexes did not increase the DEL recombination frequency in yeast nor did they activate any of the DNA damage-associated promoters in HepG2 cells. Vanadocene complexes triggered activation of the c-fos promoter without affecting the minimum promoter containing p53 response elements or the GADD45 promoter. These results indicate that the apoptotic signal of vanadocene complexes is not triggered by primary DNA damage and it does not require p53 induction, thereby disproving the hypothesis that it mechanistically resembles the cytotoxic action of cisplatin.

Antineoplastic Agents↗
PubMed2006

Microarrays in breast cancer research and clinical practice--the future lies ahead.

Molecular profiling for classification and prognostic purposes has demonstrated that the genetic signatures of tumors contain information regarding biological properties as well as clinical behavior. This review highlights the progress that has been made in the field of gene expression profiling of human breast cancer. Breast cancer has become one of the most intensely studied human malignancies in the genomic era; several hundred papers over the last few years have investigated various clinical and biological aspects of human breast cancer using high-throughput molecular profiling techniques. Given the grossly heterogeneous nature of the disease and the lack of robust conventional markers for disease prediction, prognosis, and response to treatment, the notion that a transcriptional profile comprising multiple genes, rather than any single gene or other parameter, will be more predictive of tumor behavior is both appealing and reasonable. Promising results have emerged from these studies, correlating gene expression profiles with prognosis, recurrence, metastatic potential, therapeutic response, as well as biological and functional aspects of the disease. Clearly, the integration of genomic approaches into the clinic lies in the near future, but prospective studies based on larger patient cohorts representing the whole spectrum of breast cancer, oncogenic pathway-based studies, attendant care in bioinformatic analyses and validation studies are needed before the full promise of gene expression profiling can be realized in the clinical setting.

Biomedical Research↗
PubMed2026

Clinical and Genomic Characteristics of Mexican Patients with Early Onset Gastric Adenocarcinoma.

BACKGROUND: Gastric cancer is a leading cause of cancer-related deaths in Mexico, with a rising incidence of early onset gastric cancer (EOGC) in young adults. This single-center study aimed to describe the clinical and mutational characteristics associated with EOGC in Mexican patients, based on an age cutoff of 50 years. METHODS: Clinical information was retrieved from electronic records and compared between EOGC and late-onset gastric cancer (LOGC). Whole exome sequencing data from 50 patients were analyzed and compared between both groups to elucidate the genomic overview of EOGC. RESULTS: Clinical data from 2,034 patients were analyzed. Of those, 35.69% had EOGC, with higher proportions of women (52.50%), diffuse histology (74.38%), signet ring cells (79.90%), and advanced stages (IVB: 79.58%; all p <0.001). Multivariate analysis in young patients identified ECOG (hazard ratio [HR]: 1.49) and clinical stage (HR: 1.78) as independent prognostic factors that increased mortality risk. However, the presence of Helicobacter pylori (HR: 0.76) and participation in genetic counseling (HR: 0.61) were independent prognostic factors that decreased the mortality risk. The molecular profile of Mexican patients demonstrated a high prevalence of CDH1 mutations and SBS44 mutational signatures. CONCLUSION: Mexican patients demonstrated higher rates of EOGC compared to other ethnicities. Genetic counseling enhances the overall survival of patients with EOGC; efforts should be made to incorporate it into routine practice. Molecular profiling revealed high CDH1 and SBS44 prevalence; however, sample size limitations warrant caution.

Humans↗
PubMed2004

On lung endothelial cell heterogeneity.

Heterogeneity in endothelial cell structure and function among vascular beds has been recognized for decades. However, recent findings have resolved that endothelial cells possess a functional memory based upon where they are in a blood vessel or based upon where they are isolated from within the blood vessel. Functional memory has been identified using integrated in vivo and in vitro bioassays and, most recently, through molecular profiling experiments. Memory is attributed to the epigenetic modification of phenotype that occurs in response to site-specific, cell-environment interaction during vascular development. In the embryo, Notch signal transduction is required for proper large blood vessel formation and function, whereas vascular endothelial cell growth factor (VEGF) is required for many of the processes of early vascular development including vasculogenesis and large vessel formation. Both Notch and VEGF are expressed in the developing lung, and their roles in pulmonary vascular development likely parallel those in the systemic circulation. Thus, integrated molecular profiling and transgenic technology provide new tools to investigate the interplay between epigenetic and environmental modulation of cell phenotype that controls endothelial cell behavior, and will aid in our understanding of the molecular signals required for normal and abnormal lung vascular development and function.

Animals↗
PubMed2000

Typing of non-Saccharomyces yeasts with enzymatic activities of interest in wine-making.

Enzymatic activity of potential interest in wine-making was studied for 182 non-Saccharomyces yeasts isolated from musts before and at the onset of fermentation at wine cellars operating under the La Mancha Appellation of Origin in Spain. Tests were carried out on plates containing differential substrates appropriate for each case (casein, gelatin, polygalacturonic acid, and arbutin) to determine whether each of the isolates exhibited proteolytic, polygalacturonase, and beta-glucosidase activities. Nearly 80% of the wild yeasts possessed one or more enzymes of biotechnological interest. Once the enzymatic activities of the isolates had been established, 69 of the isolates that exhibited pronounced enzymatic activity and 11 randomly selected isolates that were devoid of any activity were typed using PCR/RFLP, which gave 13 different molecular profiles. The isolates for each of the profiles were then identified by classical methods. The enzyme beta-glucosidase was linked to the species Metschnikowia pulcherrima, and polygalacturonase activity was common in most of the species identified. Proteolytic activity was observed in Pichia membranifaciens and in Metschnikowia pulcherrima. Typing revealed the possibility of intraspecific differences in Pichia membranifaciens, because six different molecular profiles with one or more shared restriction bands were recorded for that species.

Cluster Analysis↗
PubMed1975

Molecular weight profile of fat globule membrane proteins.

Fat globule membrane material, isolated by churning cream that had been washed four times, was extracted sequentially with .6 M potassium chloride and centrifuged to yield pellet and supernatant fractions. Compositional data indicated that lipid components were removed preferentially into the supernatant fractions. Electropherograms of the pellet and supernatant fraction in 10% and 5% sodium dodecyl sulfate-containing polyacrylamide gels revealed that the protein species originally present in the membrane associated into higher molecular weight species concomitant with the removal of lipid moieties. Thus, a contribution of the lipid moiety to membrane integrity is suggested. Approximately 17 protein-stained zones, ranging in molecular weight from 13,500 to 208,000 daltons, were observed in gels of the membrane material.

Animals↗
PubMed2005

Molecular characterization and biological response to respiration inhibitors of Pyricularia isolates from ctenanthe and rice plants.

The molecular profile and the biological response of isolates of Pyricularia oryzae Cavara obtained from ctenanthe to two strobilurins (azoxystrobin, kresoxim-methyl) and the phenylpyridinamine fungicide fluazinam were characterized, and compared with isolates from rice plants. Five different isozymes (alpha-esterase, lactate, malate, isocitrate and sorbitol dehydrogenases) and five random decamer primers for RAPD-PCR were used to generate molecular markers. Using unweighted pair-group with arithmetic average analysis, ctenanthe isolates were found to form a separate group distinct from that of the rice isolates for both sets of markers. Amplified polymorphic sequences of mitochondrial cytochrome b that were digested with Fnu4HI or StyI revealed no differences among Pyricularia isolates at amino acid positions 143 or 129 which confer resistance to strobilurins in several fungi. In absence of the alternative respiration inhibitor salicylhydroxamic acid (SHAM) the three fungicides showed inferior and variable efficacy, with a trend toward the rice isolate being less sensitive. The addition of SHAM enhanced the effectiveness of all fungicides against isolates regardless of their origin. Appressorium formation was the most vulnerable target of action of the respiration inhibitors and azoxystrobin the most effective. This is the first report of a comparison between the molecular profiles and sensitivities to respiration inhibitors for Pyricularia oryzae isolates from a non-gramineous host and from rice.

Acrylates↗