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At least 703 records · Page 39Linked to original sources
PubMed2004

Photoaptamer arrays applied to multiplexed proteomic analysis.

Multiplexed photoaptamer-based arrays that allow for the simultaneous measurement of multiple proteins of interest in serum samples are described. Since photoaptamers covalently bind to their target analytes before fluorescent signal detection, the arrays can be vigorously washed to remove background proteins, providing the potential for superior signal-to-noise ratios and lower limits of quantification in biological matrices. Data are presented here for a 17-plex photoaptamer array exhibiting limits of detection below 10 fM for several analytes including interleukin-16, vascular endothelial growth factor, and endostatin and able to measure proteins in 10% serum samples. The assays are simple, scalable, and reproducible. Affinity of the capture reagent is shown to be directly correlated to the limit of detection for the analyte on the array.

Antibodies↗
PubMed2006

Genome-wide microRNA profiling in human fetal nervous tissues by oligonucleotide microarray.

OBJECTS: Our objective was to develop an oligonucleotide DNA microarray (OMA) for genome-wide microRNA profiling and use this method to find miRNAs, which control organic development especially for nervous system. MATERIALS AND METHODS: Eighteen organic samples included cerebrum and spinal cord samples from two aborted human fetuses. One was 12 gestational weeks old (G12w) and the other was 24 gestational weeks old (G24w). Global miRNA expression patterns of different organs were investigated using OMA and Northern blot. CONCLUSION: The OMA revealed that 72-83% of miRNAs were expressed in human fetal organs. A series of microRNAs were found specifically and higher-expressed in the human fetal nervous system and confirmed consistently by Northern blot, which may play a critical role in nervous system development.

Age Factors↗
PubMed2004

Structural determinants of heparan sulfate interactions with Slit proteins.

We have previously demonstrated that the Slit proteins, which are involved in axonal guidance and related processes, are high-affinity ligands of the heparan sulfate proteoglycan glypican-1. Glypican-Slit protein interactions have now been characterized in greater detail using two approaches. The ability of heparin oligosaccharides of defined structure (ranging in size from disaccharide to tetradeccasaccharide) to inhibit binding of a glypican-Fc fusion protein to recombinant human Slit-2 was determined using an ELISA. Surface plasmon resonance (SPR) spectroscopy, which measures the interactions in real time, was applied for quantitative modeling of heparin-Slit binding on heparin biochips. Heparin was covalently immobilized on these chips through a pre-formed albumin-heparin conjugate, and the inhibition of Slit binding by heparin, LMW heparin, and heparin-derived oligosaccharides (di-, tetra-, hexa-, and octa-) was examined utilizing solution competition SPR. These competition studies demonstrate that the smallest heparin oligosaccharide competing with heparin binding to Slit was a tetrasaccharide, and that in the ELISA maximum inhibition (approximately 60% at 2 microM concentration) was attained with a dodecasaccharide.

Amino Acid Sequence↗
PubMed2004

Correlation of Wnt-2 expression and beta-catenin intracellular accumulation in Chinese gastric cancers: relevance with tumour dissemination.

Wnt/beta-catenin signalling pathway is integrally associated with human tumour development and progression. Aberrant beta-catenin intracellular distribution has been found in gastric cancer, but the pattern of Wnt expression in stepwise gastrocarcinogenesis and its potential influence in beta-catenin distribution are still lesser known. By the methods of frozen tissue array-based immunohistochemistry, Western blot analysis and RT-PCR, a paralleled study was conducted to check Wnt2 expression and beta-catenin intracellular distribution in two major subtypes of gastric cancers (intestinal gastric cancer, i-GC and diffuse gastric cancer, d-GC) and their premalignant (intestinal metaplasia, IM and chronic gastritis, CG) and noncancerous counterparts. According to the results obtained and the clinical data collected, correlation of Wnt2 expression with beta-catenin translocalisation and their links with tumour dissemination were elucidated. The results demonstrated (1) that Wnt2 expression and cytoplasmic/nuclear beta-catenin accumulations appeared in most gastric cancers irrespective to their morphological phenotypes, (2) that over-expressed Wnt and nuclear translocalisation of beta-catenin were found in 68 and 58% of i-GCs and in 47 and 47% of d-GCs in a closely related pattern (P<0.01) and (3) that co-existence of Wnt2 up-regulation/beta-catenin nuclear translocalisation were positively associated with lymph node metastasis (P<0.05) as well as T-stage. These data indicate that Wnt/beta-catenin signalling pathway is activated in most of gastric cancers, which may play pivotal roles either in gastric cancer formation or in tumour invasion and dissemination.

Blotting, Western↗
PubMed2005

Oriented immobilization of antibodies by a self-assembled monolayer of 2-(biotinamido)ethanethiol for immunoarray preparation.

Orientation of antibodies is very important in the preparation of immunoarrays to keep the activity of antibodies on solid surfaces. Thus, we synthesized a new bifunctional compound, 2-(biotinamido)ethanethiol, and investigated whether the thiol compound is useful to analyze antibody-antigen interactions on immunoarrays with a spectral SPR biosensor. The synthesized organic thiol was characterized by nuclear magnetic resonance spectroscopy and mass spectrometry. 2-(Biotinamido)ethanethiol formed a monolayer on a gold surface and properly immobilized antibodies via streptavidin and biotinylated protein G. Optimal molar ratio of 2-(biotinamido)ethanethiol and mercaptohexanol for antigen-antibody interactions was 1:2. Thus, 2-(biotinamido)ethanethiol is an useful bifunctional linker in the preparation of immunoarrays on gold surfaces.

Antibodies, Immobilized↗
PubMed2005

Examination of the molecular signature associated with islet dysfunction.

The aim of this study was to identify the molecular signatures that are predictive of nonfunctional islet preparations. We examined functional outcomes of six islet preparations accepted for research purposes from human donors. Islet were maintained on culture in M-SFM media for 7 to 14 days then transplanted into NOD-SCID mice. At the time of transplant, RNA was extracted from a second aliquot of cultured islets for expression analysis. We also performed gene expression analysis using high-density Affymetrix U133A GeneChips on these preparations. Among 1833 genes selected, hierarchical clustering was performed using the GeneSpring software package (Silicon Genetics, Inc.), where 754 genes (higher in nonfunctional) and 177 genes (lower in nonfunctional) were differentially expressed with tight pattern of expression. Islets with low functionality showed high relative levels of expression of hypoxia-induced genes and increased frequency of expression of proinflammatory and proangiogenic genes, such as vascular endothelial growth factor. Conversely, nonfunctional islets had low levels of insulin-processing message. The general profile of these low-functionality islets shows attempted recovery from hypoxic assault and little effort directed toward insulin production and secretion. Further identification of the molecular signature of nonfunctional islets could allow the development of a potency assay for human transplantation.

Cadaver↗
PubMed2002

Differential expression and biodistribution of cytokeratin 18 and desmoplakins in non-small cell lung carcinoma subtypes.

Adenocarcinoma (AC), squamous cell carcinoma (SCC) and adenosquamous carcinoma (ASC) of the lung are morphologically distinguished in part by cyto-architectural features. However, little is known about the relative expression and distribution of cyto-architectural proteins among AC, SCC and ASC. Initial microarray analysis revealed significant differences in expression of two cyto-architectural genes in AC, SCC and ASC. Desmoplakin (DP) 1 and 2, which link desmosomes to intermediate filaments, was strongly expressed in SCC relative to AC and ASC. Cytokeratin 18 (CK18), an intermediate filament that is commonly linked to desmoplakin, was strongly expressed in AC and ASC relative to SCC. Western blot analysis demonstrated that AC and ASC had abundant CK18 protein, whereas CK18 was weakly detected in SCC. DP 1 and 2 are strongly expressed in SCC and minimally expressed in AC and ASC. However, the ratio of one to the other is the same in SCC and AC, but DP2 is lost in ASC. Microscopic analysis with fluorescence-labeled antibodies for CK18 and DP 1 and 2 revealed abundant membrane localization of DP and minimal perinuclear localization of CK18 in SCC. In contrast, in both AC and ASC, the CK18 protein was diffusely distributed within the cytoplasm, and DP showed both membranous and cytoplasmic localization. In conclusion, the data here shows that AC, SCC and ASC each have specific patterns of DP 1 and 2 and CK18 gene expression, protein content and biodistribution.

Biomarkers, Tumor↗
PubMed1988

Mesangial IgA in IgA nephropathy arises from the mucosa.

Numerous studies have attempted to elucidate the pathogenetic mechanisms of IgA nephropathy, analyzing kidney, serum, lymphocytes, and lymphoid tissue of patients with this glomerulonephritis. Based on studies of the molecular characteristics of the mesangial IgA, clinical features, and immunologic analysis of the mucosal tissue, a wide array of findings suggest that mesangial IgA indeed arises from the mucosa. These three areas of research are discussed, as well as the hypothesis of a systemic origin for the mesangial IgA.

Glomerular Mesangium↗
PubMed2001

Overexpression of c-erbB2 protein correlates with disease-stage and chromosomal gain at the c-erbB2 locus in non-small cell lung cancer.

Overexpression of the c-erbB2 protein is observed in a variety of malignancies including non-small cell lung cancer (NSCLC). We aimed to determine the rate of c-erbB2-overexpression in our tumour collection and to clarify its correlation with the chromosomal status at the c-erbB2 locus 17q21 in NSCLC. Eighty-nine NSCLC were analysed immunohistochemically using a polyclonal c-erbB2 antibody (DAKO). The staining was scored according to the guidelines of the Clinical Trial Assay recommendations (0-3+). Of these, 44 cases were also analysed by comparative genomic hybridisation (CGH). Overexpression was observed in 37% of the cases (score>1) which was associated with higher disease stages and a positive nodal status in adenocarcinomas. Chromosomal gains at 17q21 were clearly correlated with overexpression of the gene (P=0.009). In addition, there was a highly significant correlation between the c-erbB2 expression comparing the whole section immunostaining analysis and a 127 lung tumour tissue array which included 74 of the 89 cases that were analysed by the classical procedure. We conclude that c-erbB2 is a marker of tumour progression in NSCLC which can be observed on protein level and reflects chromosomal alterations at 17q21.

Adult↗
PubMed2005

Interactive domains for chaperone activity in the small heat shock protein, human alphaB crystallin.

Protein pin arrays identified seven interactive sequences for chaperone activity in human alphaB crystallin using natural lens proteins, beta(H) crystallin and gammaD crystallin, and in vitro chaperone target proteins, alcohol dehydrogenase and citrate synthase. The N-terminal domain contained two interactive sequences, (9)WIRRPFFPFHSP(20) and (43)SLSPFYLRPPSFLRAP(58). The alpha crystallin core domain contained four interactive sequences, (75)FSVNLDVK(82) (beta3), (113)FISREFHR(120), (131)LTITSSLS(138) (beta8), and (141)GVLTVNGP(148) (beta9). The C-terminal domain contained one interactive sequence, (157)RTIPITRE(164), that included the highly conserved I-X-I/V motif. Two interactive sequences, (73)DRFSVNLDVKHFS(85) and (131)LTITSSLSDGV(141), belonging to the alpha crystallin core domain were synthesized as peptides and assayed for chaperone activity in vitro. Both synthesized peptides inhibited the thermal aggregation of beta(H) crystallin, alcohol dehydrogenase, and citrate synthase in vitro. Five of the seven chaperone sequences identified by the pin arrays overlapped with sequences identified previously as sequences for subunit-subunit interactions in human alphaB crystallin. The results suggested that interactive sequences in human alphaB crystallin have dual roles in subunit-subunit assembly and chaperone activity.

Alcohol Dehydrogenase↗
PubMed2006

Fabrication of antibody arrays using thermally responsive elastin fusion proteins.

A general method has been developed to immobilize antibodies onto an array surface by employing fusion proteins consisting of an elastin domain with tunable hydrophobic properties and an antibody-binding domain with high binding affinity and specificity for antibodies. Antibodies conjugated with the elastin fusion proteins can be directly printed on a self-assembled monolayer-modified glass slide in a functionally active orientation with a spatially defined pattern. An antibody array sensor for detection of tumor markers was fabricated to demonstrate the utility of the method. We expect that the method presented here could be a simple and universal platform to immobilize antibodies for the fabrication of a variety of antibody array sensors.

Animals↗
PubMed2003

Mechanisms of sarcoma development.

Sarcomas are a rare and diverse group of tumours that are derived from connective tissues, including bone, muscle and cartilage. Although there are instances of hereditary predisposition to sarcomas, the overwhelming majority of such tumours are sporadic. In the past decade, we have gained much insight into the genetic abnormalities that seem to underlie the pathogenesis of these tumours. This information has already led to new classification of many sarcomas, as well as to successful therapies that are targeted at specific genetic abnormalities. It is likely that this approach will lead to continued refinements in classification and treatment of these tumours.

Animals↗
PubMed2005

Identification of VCP/p97, carboxyl terminus of Hsp70-interacting protein (CHIP), and amphiphysin II interaction partners using membrane-based human proteome arrays.

Proteins mediate their biological function through interactions with other proteins. Therefore, the systematic identification and characterization of protein-protein interactions have become a powerful proteomic strategy to understand protein function and comprehensive cellular regulatory networks. For the screening of valosin-containing protein, carboxyl terminus of Hsp70-interacting protein (CHIP), and amphiphysin II interaction partners, we utilized a membrane-based array technology that allows the identification of human protein-protein interactions with crude bacterial cell extracts. Many novel interaction pairs such as valosin-containing protein/autocrine motility factor receptor, CHIP/caytaxin, or amphiphysin II/DLP4 were identified and subsequently confirmed by pull-down, two-hybrid and co-immunoprecipitation experiments. In addition, assays were performed to validate the interactions functionally. CHIP e.g. was found to efficiently polyubiquitinate caytaxin in vitro, suggesting that it might influence caytaxin degradation in vivo. Using peptide arrays, we also identified the binding motifs in the proteins DLP4, XRCC4, and fructose-1,6-bisphosphatase, which are crucial for the association with the Src homology 3 domain of amphiphysin II. Together these studies indicate that our human proteome array technology permits the identification of protein-protein interactions that are functionally involved in neurodegenerative disease processes, the degradation of protein substrates, and the transport of membrane vesicles.

Adenosine Triphosphatases↗
PubMed2001

Unraveling human cancer in the mouse: recent refinements to modeling and analysis.

The ability to manipulate the mouse genome has made the mouse the primary mammalian genetic model organism. It has been possible to model human cancer in the mouse by overexpressing oncogenes or inactivating tumor suppressor genes, and these experiments have provided much of our in vivo understanding of cancer. However, these transgenic approaches do not always completely and accurately model human carcinogenesis. Recent developments in transgenic and knockout approaches have improved the accuracy of modeling somatic cancer in the mouse and analyzing the genomic instability that occurs in murine tumors. It is possible to use retroviral gene delivery, chromosome engineering and inducible transgenes to selectively manipulate the genome in a more precise spatial and temporal pattern. In addition, the development of powerful cytogenetic tools such as spectral karyotyping, fluorescence in situ hybridization and comparative genome hybridization have improved our ability to detect chromosomal rearrangements. Finally, global patterns of gene expression can be determined by microarray analysis to decipher complex gene patterns which occur in cancers. Several of these advances in mouse modeling of human cancer are discussed in this review.

Animals↗
PubMed2006

Altered gene expression in mice selected for high maternal aggression.

We previously applied selective breeding on outbred mice to increase maternal aggression (maternal defense). In this study, we compared gene expression within a continuous region of the central nervous system (CNS) involved in maternal aggression (hypothalamus and preoptic regions) between lactating selected (S) and nonselected control (C) mice (n= 6 per group). Using microarrays representing over 40,000 genes or expressed sequence tags, two statistical algorithms were used to identify significant differences in gene expression: robust multiarray and the probe logarithmic intensity error method. Approximately 200 genes were identified as significant using an intersection from both techniques. A subset of genes was examined for confirmation by real-time polymerase chain reaction (PCR). Significant decreases were found in S mice for neurotensin and neuropeptide Y receptor Y2 (both confirmed by PCR). Significant increases were found in S mice for neuronal nitric oxide synthase (confirmed by PCR), the K+ channel subunit, Kcna1 (confirmed by PCR), corticotrophin releasing factor binding protein (just above significance using PCR; P= 0.051) and GABA A receptor subunit 1A (not confirmed by PCR, but similar direction). S mice also exhibited significantly higher levels of the neurotransmitter receptor, adenosine A1 receptor and the transcription factors, c-Fos, and Egr-1. Interestingly, for 24 genes related to metabolism, all were significantly elevated in S mice, suggesting altered metabolism in these mice. Together, this study provides a list of candidate genes (some previously implicated in maternal aggression and some novel) that may play an important role in the production of this behavior.

Aggression↗