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PubMed2004

Development of a protein chip: a MS-based method for quantitation of protein expression and modification levels using an immunoaffinity approach.

Protein chip technology permits analysis of the expression and modification status of numerous targeted proteins within a single experiment, mainly through the use of antibody-based microarrays. Despite recent improvements in these protein chips, their applications are still limited for a variety of reasons, which include technical challenges in fabrication of the antibody chips as well as the very low specificity achieved by current detection methods. We have developed a unique approach for relative and/or absolute quantitation of protein expression and modification based on the capture of epitope peptides on affinity beads, which can be used to develop a mass-spectrometry-based protein chip technology. This new method, which utilizes antibodies immobilized on beads for the capture of target peptides, instead of proteins, eliminates many of the problems previously associated with protein chips. We present here several proof-of-principle experiments examining model peptides by this technique. These experiments show that the method is capable of (i). detecting peptides bound to a single antibody bead, (ii). detecting peptides at low (fmol) levels, (iii). producing MS/MS data of suitable quality for protein identification via database searching or de novo sequencing, (iv). quantitating peptides affinity-bound to antibody beads, (v). specifically detecting target peptides in complex mixtures over wide dynamic ranges, and (vi) is compatible with a microarray format for high-throughput analysis. Because our novel method uses antibody beads instead of a derivatized capture surface, and peptides instead of proteins for affinity capture, it can overcome many of the pitfalls of previous protein chip fabrications. Therefore, this method offers an improved approach to protein chip technology that should prove useful for diagnostics and drug development applications.

Antibodies↗
PubMed2003

Effect of bone chip orientation on quantitative estimates of changes in bone mass using digital subtraction radiography.

OBJECTIVES: To assess the effect of the orientation of arbitrarily shaped bone chips on the correlation between radiographic estimates of bone loss and true mineral loss using digital subtraction radiography. METHODS: Twenty arbitrarily shaped bone chips (dry weight 1-10 mg) were placed individually on the superior lingual aspect of the interdental alveolar bone of a dry dentate hemi-mandible. After acquiring the first baseline image, each chip was rotated 90 degrees and a second radiograph was captured. Follow-up images were created without the bone chips and after rotating the mandible 0, 1, 2, 4, and 6 degrees around a vertical axis. Aluminum step tablet intensities were used to normalize image intensities for each image pair. Follow-up images were registered and geometrically standardized using projective standardization. Bone chips were dry ashed and analyzed for calcium content using atomic absorption. RESULTS: No significant difference was found between the radiographic estimates of bone loss from the different bone chip orientations (Wilcoxon: P > 0.05). The correlation between the two series of estimates for all rotations was 0.93 (Spearman: P < 0.05). Linear regression analysis indicated that both correlates did not differ appreciably ( and ). CONCLUSION: It is concluded that the spatial orientation of arbitrarily shaped bone chips does not have a significant impact on quantitative estimates of changes in bone mass in digital subtraction radiography. These results were obtained in the presence of irreversible projection errors of up to six degrees and after application of projective standardization for image reconstruction and image registration.

Alveolar Process↗
PubMed2000

Dentine chips produced by nickel-titanium rotary instruments.

This study aimed to compare the cross-sectional shape of two nickel-titanium rotary instruments, namely ProFile and Quantec files, both ISO 25, 0.06 taper, and sought to relate this to the chips produced by cutting dentine. A limited comparison was made with stainless steel engine reamers. First, five files of each type were sectioned transversely at 12 mm, 8 mm and 4 mm from the tip and examined by scanning electron microscopy. The cutting angles were assessed by a direct measurement technique which allowed for the inclination of a cutting edge to the root canal. Second, eight samples of cutting debris were collected from instrumentation by each type of nickel-titanium file and four samples from the engine reamers. The major and minor axis, area and roundness of the dentine chips in each sample were measured using computerized particle analysis. The results demonstrated that all files had a negative cutting angle which varied at the different levels (ProFiles range 69.4 degrees to 58.4 degrees and Quantec range 74.8 degrees to 56.8 degrees). The consistency within files of the same type was good as demonstrated by low standard deviations, except for Quantec files at the 4 mm level where higher standard deviations of 4.1 degrees and 5.5 degrees for the two blades were found. The chip analysis showed significant differences between chips produced by ProFile and Quantec files (P < 0.05). The latter were larger and rounder. The chips from the ProFile and the engine reamer chips were similar in dimension (P > 0.05). No simple relationship existed between file geometry and the dentine chips produced during instrumentation.

Dental Alloys↗
PubMed2003

Polymer microfluidic chip for online monitoring of microarray hybridizations.

A disposable single use polymer microfluidics chip has been developed and manufactured by micro injection molding. The chip has the same outer dimensions as a standard microscope slide (25 x 76 x 1.1 mm) and is designed to be compatible with existing microscope slide handling equipment like microarray scanners. The chip contains an inlet, a 10 microL hybridization chamber capable of holding a 1000 spot array, a waste chamber and a vent to allow air to escape when sample is injected. The hybridization chamber ensures highly homogeneous hybridization conditions across the microarray. We describe the use of this chip in a flexible setup with fluorescence based detection, temperature control and liquid handling by computer controlled syringe pumps. The chip and the setup presented in this article provide a powerful tool for highly parallel studies of kinetics and thermodynamics of duplex formation in DNA microarrays. The experimental setup presented in this article enables the on-chip microarray to be hybridized and monitored at several different stringency conditions during a single assay. The performance of the chip and the setup is demonstrated by on-line measurements of a hybridization of a DNA target solution to a microarray. A presented numerical model indicates that the hybridization process in microfluidic hybridization assays is diffusion limited, due to the low values of the diffusion coefficients D of the DNA and RNA molecules involved.

Automation↗
PubMed2000

Chip interacts with diverse homeodomain proteins and potentiates bicoid activity in vivo.

The Drosophila protein Chip potentiates activation by several enhancers and is required for embryonic segmentation. Chip and its mammalian homologs interact with and promote dimerization of nuclear LIM proteins. No known Drosophila LIM proteins, however, are required for segmentation, nor for expression of most genes known to be regulated by Chip. Here we show that Chip also interacts with diverse homeodomain proteins using residues distinct from those that interact with LIM proteins, and that Chip potentiates activity of one of these homeodomain proteins in Drosophila embryos and in yeast. These and other observations help explain the roles of Chip in segmentation and suggest a model to explain how Chip potentiates activation by diverse enhancers.

Animals↗
PubMed2001

CHIP is a U-box-dependent E3 ubiquitin ligase: identification of Hsc70 as a target for ubiquitylation.

Proper folding of proteins (either newly synthesized or damaged in response to a stressful event) occurs in a highly regulated fashion. Cytosolic chaperones such as Hsc/Hsp70 are assisted by cofactors that modulate the folding machinery in a positive or negative manner. CHIP (carboxyl terminus of Hsc70-interacting protein) is such a cofactor that interacts with Hsc70 and, in general, attenuates its most well characterized functions. In addition, CHIP accelerates ubiquitin-dependent degradation of chaperone substrates. Using an in vitro ubiquitylation assay with recombinant proteins, we demonstrate that CHIP possesses intrinsic E3 ubiquitin ligase activity and promotes ubiquitylation. This activity is dependent on the carboxyl-terminal U-box. CHIP interacts functionally and physically with the stress-responsive ubiquitin-conjugating enzyme family UBCH5. Surprisingly, a major target of the ubiquitin ligase activity of CHIP is Hsc70 itself. CHIP ubiquitylates Hsc70, primarily with short, noncanonical multiubiquitin chains but has no appreciable effect on steady-state levels or half-life of this protein. This effect may have heretofore unanticipated consequences with regard to the chaperoning activities of Hsc70 or its ability to deliver substrates to the proteasome. These studies demonstrate that CHIP is a bona fide ubiquitin ligase and indicate that U-box-containing proteins may comprise a new family of E3s.

Animals↗
PubMed2003

Chaperone-dependent regulation of endothelial nitric-oxide synthase intracellular trafficking by the co-chaperone/ubiquitin ligase CHIP.

Endothelial nitric-oxide synthase (eNOS), the enzyme responsible for production of endothelial NO, is under tight and complex regulation. Proper cellular localization of eNOS is critical for optimal coupling of extracellular stimulation with NO production. In addition, the molecular chaperone Hsp90 interacts with eNOS and positively regulates eNOS activity. Hsp90 is modulated by physical interaction with its co-chaperones. CHIP (carboxyl terminus of Hsp70-interacting protein) is such a co-chaperone that remodels the Hsp90 heterocomplex and causes protein degradation of some Hsp90 substrates through the ubiquitin-protein isopeptide ligase activity of CHIP. Here we show that CHIP incorporated into the eNOS.Hsp90 complex and specifically decreased soluble eNOS levels in transiently transfected COS cells. Surprisingly, in contrast to the effects of the Hsp90 inhibitor geldanamycin, which induces eNOS ubiquitylation and its subsequent protein degradation, CHIP did not target eNOS for ubiquitylation and proteasome-dependent degradation. Instead, CHIP partitioned soluble eNOS into an insoluble and inactive cellular compartment, presumably through its co-chaperone activity. This effect seems to be due to displacement of eNOS from the Golgi apparatus, which is otherwise required for trafficking of eNOS to the plasmalemma and subsequent activation. Consistent with observations from overexpression studies, eNOS localization to the membrane and activity were increased in mouse lung endothelial cells lacking CHIP. Taken together, these results demonstrate a novel co-chaperone-dependent mechanism through which eNOS trafficking is regulated and suggest a potentially generalized role for CHIP in protein trafficking through the Golgi compartment.

Animals↗
PubMed1998

Study III: development and concurrent validity of the Children's Interview for Psychiatric Syndromes--parent version (P-ChIPS).

OBJECTIVE: To assess concurrent validity for the newly developed parent version of the Children's Interview for Psychiatric Syndromes (P-ChIPS). METHOD: ChIPS and P-ChIPS were administered to 36 children 6 to 13 years of age and their parents. P-ChIPS results were compared with clinicians' diagnoses for 21 of those children. Either a standard or rare kappa coefficient and percentage agreement were used to assess concordance. Questions on P-ChIPS have a one-to-one correspondence with questions on the ChIPS, with the only change being from first to third person (e.g. "Have you ever . ." is replaced by "Has your child ever . . ."). RESULTS: There were moderate levels of agreement between the parent and child versions of the instrument, consistent with other reports of parent and child concordance on structured interviews in the literature. Likewise, there were moderate levels of agreement between the parent interview and clinician diagnoses, again consistent with other reports of parent and clinician concordance in the literature. Sensitivity averaged 87% across diagnostic categories, and average specificity was 76%. CONCLUSION: P-ChIPS has adequate psychometric properties for use in clinical settings.

Adolescent↗
PubMed2001

CHIP is a chaperone-dependent E3 ligase that ubiquitylates unfolded protein.

The ubiquitin-proteasome system catalyses the immediate destruction of misfolded or impaired proteins generated in cells, but how this proteolytic machinery recognizes abnormality of cellular proteins for selective elimination remains elusive. Here, we report that the C-terminus of Hsc70-interacting protein (CHIP) with a U-box domain is an E3 ubiquitin-ligase collaborating with molecular chaperones Hsp90 and Hsc70. Thermally denatured firefly luciferase was multiubiquitylated by CHIP in the presence of E1 and E2 (Ubc4 or UbcH5c) in vitro, only when the unfolded substrate was captured by Hsp90 or Hsc70 and Hsp40. No ubiquitylating activity was detected in CHIP lacking the U-box region. CHIP efficiently ubiquitylated denatured luciferase trapped by the C-terminal region of Hsp90, which contains a CHIP binding site. CHIP also showed self-ubiquitylating activity independent of target ubiquitylation. Our results indicate that CHIP can be regarded as 'a quality-control E3' that selectively ubiquitylates unfolded protein(s) by collaborating with molecular chaperones.

Animals↗
PubMed2004

The impact of S-CHIP enrollment on physician participation in Medicaid in Alabama and Georgia.

OBJECTIVE: To assess whether increasing enrollment in State Children's Health Insurance Programs (S-CHIPs) has an impact on the number of office physicians participating in Medicaid and the extent of their participation. Effects are measured for a freestanding S-CHIP program with an open provider panel and an S-CHIP program that uses the state's Medicaid provider panel. DATA SOURCES: Children's Medicaid claims data for primary care services were used to measure physician participation in the program; census and enrollment data were used to describe market area characteristics. Study Design. This is a time series study of communities in two states, measuring physician Medicaid participation quarterly between 1998 and 2001, controlling for changes in community characteristics and children's program enrollment as well as other factors by quarter. DATA COLLECTION/EXTRACTION: Office physician participation is measured by practice site. Claims data are aggregated to the level of the community and reflect the number of limited practice sites, the ratio of Medicaid office sites to the number of primary care physicians in the community as reported by the American Medical Association (AMA), and the mean number of Medicaid office visits made to physician sites in the community in the quarter. FINDINGS: In Alabama, the state with a freestanding S-CHIP program, there is little association between increased S-CHIP enrollment and physician participation in Medicaid. In Georgia, where the same provider network serves both programs, increases in S-CHIP enrollment are associated with a decline in office-based physician participation in Medicaid in urban areas. CONCLUSION: Linkage of S-CHIP and Medicaid programs through the use of the same provider network, in the absence of market conditions that encourage the expansion of the network, can lead to a negative impact on access for Medicaid enrollees.

Adolescent↗
PubMed2005

CHIP, a cochaperone/ubiquitin ligase that regulates protein quality control, is required for maximal cardioprotection after myocardial infarction in mice.

Limitation of damage after ischemia and reperfusion injury to the myocardium remains an elusive clinical goal. Previous studies have suggested that molecular chaperones, which include members of the heat shock protein (Hsp) family, may have cardioprotective effects, although the protective role of endogenous chaperones has not been well documented. CHIP (carboxyl terminus of Hsp70-interacting protein) is a cochaperone/ubiquitin ligase that integrates the response to stress at multiple levels. We tested the response of CHIP(-/-) mice to in vivo ischemia and reperfusion injury induced by left anterior descending coronary artery ligation. Compared with wild-type littermates, CHIP(-/-) mice had decreased survival and increased incidence of arrhythmias during reperfusion. The size of myocardial infarction, as assessed by the ratio of infarct area to area at risk, was 50% greater in CHIP(-/-) mice. Increased infarct size was accompanied by impaired upregulation of the chaperone Hsp70 after ischemia-reperfusion injury. In situ analysis also indicated that hearts of CHIP(-/-) mice were more prone to develop apoptosis in cardiomyocytes and especially endothelial cells of intramural vessels. Previous studies have found that CHIP plays a central role in maintaining protein quality control and coordinating the response to stress. The present data indicate that these functions of CHIP provide a critical cardioprotective effect in the setting of ischemia-reperfusion injury due in part to increased apoptosis in cardiac cells. Quality control mechanisms therefore may be underappreciated clinical targets for maximizing myocardial protection after injury.

Adaptor Proteins, Signal Transducing↗
PubMed1993

Concurrent expression of erythroid and renal aquaporin CHIP and appearance of water channel activity in perinatal rats.

Major phenotypic changes occur in red cell membranes during the perinatal period, but the underlying molecular explanations remain poorly defined. Aquaporin CHIP, the major erythroid and renal water channel, was studied in perinatal rats using affinity-purified anti-CHIP IgG for immunoblotting, flow cytometry, and immunofluorescence microscopy. CHIP was not detected in prenatal red cells but was first identified in circulating red cells on the third postnatal day. Most circulating red cells were positive for CHIP by the seventh postnatal day, and this proportion rose to nearly 100% by the 14th day. The ontogeny of red cell CHIP correlated directly with acquisition of osmotic water permeability and inversely with Arrhenius activation energy. Only minor alterations in the composition of red cell membrane lipids occurred at this time. Immunohistochemical analysis of perinatal kidneys demonstrated a major induction of CHIP in renal proximal tubules and descending thin limbs at birth, coincident with the development of renal concentration mechanisms. Therefore, water channels are unnecessary for oxygen delivery or survival in the prenatal circulation, however CHIP may confer red cells with the ability to rehydrate rapidly after traversing the renal medulla, which becomes hypertonic after birth.

Aging↗
PubMed2006

Deletion of the ubiquitin ligase CHIP leads to the accumulation, but not the aggregation, of both endogenous phospho- and caspase-3-cleaved tau species.

Accumulation of the microtubule-associated protein tau into neurofibrillary lesions is a pathological consequence of several neurodegenerative diseases, including Parkinson's disease and Alzheimer's disease. Hereditary mutations in the MAPT gene were shown to promote the formation of structurally distinct tau aggregates in patients that had a parkinsonian-like clinical presentation. Whether tau aggregates themselves or the soluble intermediate species that precede their aggregation are neurotoxic entities in these disorders has yet to be resolved; however, recent in vivo evidence supports the latter. We hypothesized that depletion of CHIP, a tau ubiquitin ligase, would lead to an increase in abnormal tau. Here, we show that deletion of CHIP in mice leads to the accumulation of non-aggregated, ubiquitin-negative, hyperphosphorylated tau species. CHIP-/- mice also have increased neuronal caspase-3 levels and activity, as well as caspase-cleaved tau immunoreactivity. Overexpression of mutant (P301L) human tau in CHIP-/- mice is insufficient to promote either argyrophilic or "pre-tangle" structures, despite marked phospho-tau accumulation throughout the brain. These observations are supported in post-developmental studies using RNA interference for CHIP (chn-1) in Caenorhabditis elegans and cell culture systems. Our results demonstrate that CHIP is a primary component in the ubiquitin-dependent degradation of tau. We also show that hyperphosphorylation and caspase-3 cleavage of tau both occur before aggregate formation. Based on these findings, we propose that polyubiquitination of tau by CHIP may facilitate the formation of insoluble filamentous tau lesions.

Animals↗
PubMed1999

[Wood chip alveolitis].

A 52 year old farmer was referred to us for investigation of suspected farmer's lung. For many years the farmer had been exposed to hay, straw, pigeons, and fuel chip dust. Under exertion he suffered from shortness of breath. In the farmer's own fuel chips we could identify Aspergillus fumigatus, Paecilomyces species and Mucor species. In the farmer's blood we found IgG-antibodies against his own fuel chips, thermophilic actinomycetes, Penicillium species, Mucor species and Aspergillus fumigatus. We did not detect any IgG-antibodies against pigeon serum or pigeon faeces. In order to determine the responsible allergen we performed two challenge tests. In the first test the farmer had to inhale his own hay and straw dust for one hour. This provocation was negative. A second one-hour inhalative challenge was carried out 16 days later using his own fuel chips. This time he experienced significant pulmonary and systemic reactions: body temperature rose by 3.3 degrees C, leucocytes by 12,200/mm3; PO2 fell by 39.4 mmHg, vital capacity by 52%, DLCO by 36%. After the challenge the farmer complained of coughing and dyspnoea. Rales could be heard on auscultation, and an interstitial infiltrate was seen to develop on chest x-rays. After the challenge the patient had to be treated with oxygen and systemic corticosteroids. We diagnosed a fuel chip-induced exogenous allergic alveolitis (EAA). Eight days later the parameters were back to normal and the farmer was discharged from our hospital with further corticosteroid medication. This method of inhalative provocation is very important in diagnosing an EAA. Problems arise when the mode and duration of exposure to substances has to be chosen. Because of the risk of severe reactions, inhalative provocations relating to EAAs should only be performed in special centres with an intensive care unit. In this paper we present a diagnosis of fuel chip lung, which is rarely seen in Germany. However, with the rising use of fuel chips as heating material it is necessary to consider this use as a cause of EAA among farmers.

Agricultural Workers' Diseases↗
PubMed2002

[Effect of probe purification on the reutilization of gene chip].

OBJECTIVE: To investigate the effect of probe purity on the reutilization of gene chips. METHODS: Purified and unpurified probes were respectively hybridized with the gene chip and after being scanned with Scanarry lite, a laser scanning device, the gene chip was treated with stripping solution to wash off the probes. After another round of scanning under the same condition to obtain the images, the gene chip was recycled for another hybridization. RESULTS: Hybridization of unpurified probes resulted in high background noise and obscure positive signals, which were present even after wash with stripping solution for 4 times. Hybridization using purified probes, in contrast, presented low background noise that was completely eliminated after the gene chip was washed twice before it was used again. CONCLUSION: The purity of probes is of great importance to the recycling of the gene chips, and hybridization with unpurified probes renders the chips impossible for reutilization.

DNA, Complementary↗
PubMed2003

Genotyping and species identification of Fritillaria by DNA chips.

AIM: To investigate the genetic polymorphism of several species of Fritillaria and to develop a DNA chip for the genotyping and identification of the origin of various species of Fritillaria at molecular level. METHODS: Genomic DNA from bulbs of several Fritillaria species was extracted and the polymorphisms of the D2 and D3 regions inside the 26S rDNA gene were identified by direct sequencing. Oligonucleotide probes specific for these polymorphisms were designed and printed on the poly-lysine coated slides to prepare the DNA chip. PCR products from the Fritillaria species were labeled with fluorescence by incorporation of dye-labeled dideoxyribonucleotides and hybridized to the immobilized probes on the chip. RESULTS: The polymorphisms were used as markers for discrimination among various species. Specific oligonucleotide probes were designed and immobilized on a DNA chip. Differentiation of the various Fritillaria species was accomplished based on hybridization of fluorescent labeled PCR products with the DNA chip. CONCLUSION: The results demonstrated the reliability of using DNA chips to identify different species of Fritillaria, and the DNA chip technology can provide a rapid, high throughput tool for genotyping and quality assurance of the plant species verification.

Base Sequence↗
PubMed2003

A new tool for routine testing of cellular protein expression: integration of cell staining and analysis of protein expression on a microfluidic chip-based system.

The key benefits of Lab-on-a-Chip technology are substantial time savings via an automation of lab processes, and a reduction in sample and reagent volumes required to perform analysis. In this article we present a new implementation of cell assays on disposable microfluidic chips. The applications are based on the controlled movement of cells by pressure-driven flow in microfluidic channels and two-color fluorescence detection of single cells. This new technology allows for simple flow cytometric studies of cells in a microfluidic chip-based system. In addition, we developed staining procedures that work "on-chip," thus eliminating time-consuming washing steps. Cells and staining-reagents are loaded directly onto the microfluidic chip and analysis can start after a short incubation time. These procedures require only a fraction of the staining reagents generally needed for flow cytometry and only 30,000 cells per sample, demonstrating the advantages of microfluidic technology. The specific advantage of an on-chip staining reaction is the amount of time, cells, and reagents saved, which is of great importance when working with limited numbers of cells, e.g., primary cells or when needing to perform routine tests of cell cultures as a quality control step. Applications of this technology are antibody staining of proteins and determination of cell transfection efficiency by GFP expression. Results obtained with microfluidic chips, using standard cell lines and primary cells, show good correlation with data obtained using a conventional flow cytometer.

Antibodies↗