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At least 19 recordsLinked to original sources
PubMed2025

ChIP-Rx: Arabidopsis Chromatin Profiling Using Quantitative ChIP-Seq.

Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is widely used to probe the chromatin landscape of transcription factors, chromatin components, and associated proteins. Conventional ChIP normalization procedures robustly allow estimating differences in local enrichment across genomic regions. Yet, inter-sample comparisons can be biased by technical variability and biological differences. This is notably the case when samples display large differences in the abundance of the target protein or its enrichment at chromatin. For example, epigenome defects are improperly detected or quantified upon large-effect genetic or chemical inhibition of chromatin modifiers. To circumvent these caveats and robustly determine biological variations while minimizing technical variability, ChIP adaptations using an external reference have flourished. Here, we describe a step-by-step protocol employing a reference exogenous chromatin (ChIP-Rx) that allows absolute comparisons of epigenome variations in Arabidopsis samples displaying drastic differences in chromatin mark abundance. In contrast to the originally published ChIP-Rx approach, which assumes that exogenous spike-in references are constant across samples, the method detailed here involves the sequencing of each input sample to account for technical variability in initial reference chromatin contents. We also report a detailed computational workflow with an accompanying Github resource to help in calculating spike-in normalization factors, applying them to normalize epigenome tracks, and performing spike-in normalized inter-sample differential analyses. We propose two ways of computing the spike-in factor: a classically used method based on raw counts and a noise-corrected method using peak detection on the exogenous genome.

Arabidopsis↗
PubMed1993

Aquaporin CHIP: the archetypal molecular water channel.

Despite longstanding interest by nephrologists and physiologists, the molecular identities of membrane water channels remained elusive until recognition of CHIP, a 28-kDa channel-forming integral membrane protein from human red blood cells originally referred to as "CHIP28." CHIP functions as an osmotically driven, water-selective pore; 1) expression of CHIP conferred Xenopus oocytes with markedly increased osmotic water permeability but did not allow transmembrane passage of ions or other small molecules; 2) reconstitution of highly purified CHIP into proteoliposomes permitted determination of the unit water permeability, i.e., 3.9 x 10(9) water molecules.channel subunit-1 x s-1. Although CHIP exists as a homotetramer in the native red blood cell membrane, site-directed mutagenesis studies suggested that each subunit contains an individually functional pore that may be reversibly occluded by mercurial inhibitors reacting with cysteine-189. CHIP is a major component of both apical and basolateral membranes of water-permeable segments of the nephron, where it facilitates transcellular water flow during reabsorption of glomerular filtrate. CHIP is also abundant in certain other absorptive or secretory epithelia, including choroid plexus, ciliary body of the eye, hepatobiliary ductules, gall bladder, and capillary endothelia. Distinct patterns of CHIP expression occur at these sites during fetal development and maturity. Similar proteins from other mammalian tissues and plants were later shown to transport water, and the group is now referred to as the "aquaporins." Recognition of CHIP has provided molecular insight into the biological phenomenon of osmotic water movement, and it is hoped that pharmacological modulation of CHIP function may provide novel treatments of renal failure and other clinical problems.

Amino Acid Sequence↗
PubMed1995

Quantification of Aquaporin-CHIP water channel protein in microdissected renal tubules by fluorescence-based ELISA.

Several transporters have been localized along the nephron by physiological methods or immunocytochemistry. However, the actual abundance of these molecules has not been established. To accomplish this goal, we have developed a fluorescence-based ELISA method and have used it to quantitate Aquaporin-CHIP (AQP-CHIP) water channel protein in rat kidney tubules. Microdissected tubules (2 mm/sample, permeabilized with 0.5% Triton X-100) or purified AQP-CHIP standards (0-200 fmol) were utilized in a fluorescence ELISA protocol after covalent immobilization on epoxy-activated Sepharose beads. The lower limit of detection was 2.4 fmol of AQP-CHIP. Preabsorption with excess purified AQP-CHIP or use of nonimmune serum eliminated the signal. In proximal segments, the measured AQP-CHIP was linearly related to tubule length (1-10 mm). The measured AQP-CHIP was (mean +/- SE, fmol/mm): S-1 proximal, 10.8 +/- 2.1; S-2, 10.0 +/- 2.3; S-3, 21.3 +/- 3.1; type 1 thin descending limb (DTL), 12.9 +/- 4.6; type 2 DTL, 86.5 +/- 19.5; type 3 DTL, 43.0 +/- 11.2. In thin ascending limbs, thick ascending limbs, distal convoluted tubules, connecting tubules, and collecting ducts, the AQP-CHIP signal was indistinguishable from zero. Based on the unit water conductance of single CHIP molecules, our calculations show that the content of AQP-CHIP is sufficient to explain water permeability measured in isolated proximal tubules and DTL segments.

Animals↗
PubMed1975

[Investigations on the shape and size of bone-chips produced during boring and grinding (author's transl)].

Examinations of the shape and size of chips produced during boring and grinding of dry macerated and fresh temporal bone by various drills and grinders at different revolutions show that rose trepans mainly scrape fresh bone, producing large rolled-up chips, but knock off dry macerated bone, producing more compact chips of bizarre shape. In either case the chip waste also contains plenty of fine and finest compact chips which are broken off and splinter during the removal or knocking-off of the chips from solid bone. The size of the chip depends on the size of the drill head. Diamond cutting heads produce fine and finest compact bone chips. Bone milling produces plenty of scrapes even from dry macerated temporal bone. The rate of revolutions (10,000-80,000 per min) had no influence on the shape and size of chips. Clinically the scraped chip seems to be the most favourable in the drilling of bone because it causes least damage. The use of a drill head with sharp-edged, intact cutting surfaces seems important for this, with continuous rinsing during the boring process to prevent soiling of the interspaces between the cutters and to ensure full performance in accordance with their construction.

Humans↗
PubMed1995

Distribution of mRNA encoding the FA-CHIP water channel in amphibian tissues: effects of salt adaptation.

A water channel, the frog aquaporin-CHIP (FA-CHIP) was recently cloned from Rana esculenta urinary bladder. The 28.9 kDa encoded protein shows 78.8%, 77.4%, 42.4% and 35.6% identity with rat CHIP28, human CHIP28, rat WCH-CD and gamma-TIP, other members of the new transmembrane water channel family (Aquaporin-CHIP). We have now studied membranes from different frog (R. esculenta) organs employing semiquantitative PCR using FA-CHIP specific primers and an internal standard to quantify the PCR products. The FA-CHIP mRNA was abundantly expressed in the frog urinary bladder, skin, lung and gall bladder, while a lower expression was detected in the colon, liver and oviduct. FA-CHIP mRNA was not detected in the frog kidney, erythrocytes and brain but its expression was observed in the toad (Bufo arenarum) urinary bladder and skin, showing that FA-CHIP is probably a general amphibian water channel. Salt acclimation is known to increase the water permeability of frog and toad epithelia. We have now observed that salt acclimation for 1, 3, 4 or 5 days markedly increased skin and urinary bladder FA-CHIP mRNA expression. It is generally accepted that water permeability is controlled in these tissues by the rate of water channel transfer from subapical vesicles (aggrephores) to the apical membrane. Our results indicate that water permeability is also regulated at the level of the FA-CHIP transcription.

Adaptation, Physiological↗
PubMed2025

Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations.

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used to study the genomic localization of DNA-associated proteins. However, conventional protocols include multiple manual steps that can introduce inconsistency and limit scalability, thereby restricting the inclusion of appropriate replicates and controls. Although the introduction of liquid handling platforms has improved reproducibility, most existing efforts have automated only a subset of the workflow, and extending automation to efficiently map non-histone proteins, such as chromatin regulators, remains challenging. Here, we present a fully automated implementation of our previously developed single-pot ChIP-seq protocol (Texari et al. 2021), named spa-ChIP-seq, which enables scalable processing of 8 to 96 ChIP-seq samples from crosslinked cells to sequencing-ready library in approximately three days with an estimated cost of $70 per sample. Benchmarking spa-ChIP-seq against manual ChIP-seq performed in parallel demonstrates comparable signal-to-noise ratio between the two workflows. Using spa-ChIP-seq, we systematically evaluate multiple parameters including shearing and crosslinking conditions, buffer compositions, and the ratio of antibody to cell-number. We find, for the first time to our knowledge, that weaker genomic localization signals are sensitive to changing the antibody to cell-number ratio, whereas the stronger signals remain unaffected. This finding underscores the importance of maintaining consistent antibody-to-cell-number ratio for comparative studies, such as treatment responses or chromatin-QTL mapping. The spa-ChIP-seq protocol is publicly available, including deck setups, operational parameters, and scripts. We envision that this robust, cost-efficient protocol will facilitate high-throughput, reproducible ChIP-seq analyses, supporting large-scale studies of antibody validation, compound screening, population genomics, and diagnostic frameworks.

Journal Article↗
PubMed1982

[On vibration hazards of chipping-hammer operators in an iron foundry. Part 2. Results of the hygienic control].

We previously reported that the working and health conditions of vibrating tool operators in an iron foundry were investigated in 1975 and vibration hazards were observed to occur frequently in workers operating chipping-hammers powered by compressed air. After that, we instituted medical treatment for the afflicted workers and improvement of working conditions in the foundry, and have performed annual medical examinations for four years. In this paper, the course of hygienic control and the change in the medical findings of twenty-four chipping-hammer operators are reported. 1. The following measures were taken to improve the working conditions of chipping-hammer operators and therapy for patients (Table 1): (1) The operating time of vibrating tools, including chipping-hammer, was limited to two hours per day. The casting process was improved to diminish the flashes that are the objects of chipping-hammer operation. For the purpose of reducing the vibration transmitted to the operator, a servo-arm that has a servomechanism for the chipping-hammer was developed and introduced. (2) Infrared lamps in the foundry and air curtains at the doorway were installed for keeping the chipping-hammer operating area warm. A warm room was set up in the foundry for providing warmth during rest periods and protective clothing against the cold was provided. (3) Workers who displayed health disturbances by medical examinations were treated during the cold season from November to April by periodic visits to the clinic or extended hospitalization, or transferred to job without vibration exposure, according to their stage of disease. Preventive treatment with vasodilator and bubble bath was performed in winter for the chipping-hammer operators. 2. In order to estimate the effect of these countermeasures, annual medical examinations were conducted in March 1975, March 1976, April 1977 and March 1978. Such subjective symptoms as Raynaud's phenomenon, finger numbness, finger listlessness, heavy-headedness, forgetfulness, irritability and hearing disorder showed a tendency for improvement, but other complaints did not (Tables 2-4). The improvement of Raynaud's phenomenon is considered to be due not merely to the countermeasures but also to reducing the chance of provocation and therefore the countermeasures should not be overestimated as a factor of recovery of vibration hazards. Of the functional tests, a tendency for improvement was recognized in sensory functions and peripheral circulatory functions, but not in motor functions (Tables 5, 6). However, the course of recovery was not fast and some advanced cases, especially those using chipping-hammers for more than ten years, showed less improvement after hospital treatment (Table 7, Fig. 1). This indicates the importance of hygienic control which enables vibration hazards patients to have early diagnosis and treatment. Furthermore, in order to eradicate the vibration hazards in the cast metal industry, a drastic reform of the finishing process is considered to be necessary.

Adult↗
PubMed1994

The three-dimensional structure of human erythrocyte aquaporin CHIP.

Water-permeable membranes of several plant and mammalian tissues contain specific water channel proteins, the 'aquaporins'. The best characterized aquaporin is CHIP, a 28 kDa red blood cell channel-forming integral protein. Isolated CHIP and Escherichia coli lipids may be assembled into 2-D crystals for structural analyses. Here we present (i) a structural characterization of the solubilized CHIP oligomers, (ii) projections of CHIP arrays after negative staining or metal-shadowing, and (iii) the 3-D structure at 1.6 nm resolution. Negatively stained CHIP oligomers exhibited a side length of 6.9 nm with four-fold symmetry, and a mass of 202 +/- 3 kDa determined by scanning transmission electron microscopy. Reconstituted into lipid bilayers, CHIP formed 2-D square lattices with unit cell dimensions a = b = 9.6 nm and a p422(1) symmetry. The 3-D map revealed that CHIP tetramers contain central stain-filled depressions about the fourfold axis. These cavities extend from both sides into the transbilayer domain of the molecule leaving only a thin barrier to be penetrated by the water pores. Although CHIP monomers behave as independent pores, we propose that their particular structure requires tetramerization for stable integration into the bilayer.

Aquaporin 1↗
PubMed1994

Examination of rat salivary glands for the presence of the aquaporin CHIP.

The aquaporin CHIP, AQP-CHIP, is a 28-kDa integral membrane protein that functions as a water channel in kidney and red blood cells. We have examined rat salivary glands for the presence of this molecule. In Northern blot analyses an AQP-CHIP cDNA hybridized to rat kidney mRNA approximately 20-fold more than to mRNA from the rat parotid gland. Western blot analyses, using antisera against human AQP-CHIP, showed that AQP-CHIP was present in crude membranes from rat salivary glands to a much lesser extent than in rat kidney membranes. A 2.8 kb cDNA encoding AQP-CHIP was also isolated from an adult rat parotid gland cDNA library. Immunolocalization studies using thin and ultrathin cryosections and light and electron microscopy, however, revealed that no glandular epithelium was labeled. In contrast, significant immunolabeling was present in microvascular endothelial cells. Non-fenestrated endothelia of capillaries and venules exhibited labeling on both their apical and basolateral membranes. The present study demonstrates that AQP-CHIP is not involved directly in fluid secretion from salivary epithelial cells. Further, this study provides strong evidence that AQP-CHIP is an endothelial cell water channel found within salivary gland tissue which may contribute to water permeability in the capillary beds.

Animals↗
PubMed1994

Human red cell Aquaporin CHIP. II. Expression during normal fetal development and in a novel form of congenital dyserythropoietic anemia.

Channel-forming integral protein (CHIP) is the archetypal member of the Aquaporin family of water channels. Delayed CHIP expression was shown recently in perinatal rat (Smith, B. L., R. Baumgarten, S. Nielsen, D. Raben, M. L. Zeidel, and P. Agre. 1993. J. Clin. Invest. 92:2035-2041); here we delineate the human patterns. Compared with adult, second and third trimester human fetal red cells had lower CHIP/spectrin ratios (0.72 +/- 0.12, 0.94 +/- 0.22 vs 1.18 +/- 0.11) and reduced osmotic water permeability (0.029, 0.026 vs 0.037 cm/s); CHIP was already present in human renal tubules by the second trimester. A patient with a novel form of congenital dyserythropoietic anemia (CDA) with persistent embryonic and fetal globins and absent red cell CD44 protein was studied because of reduced CHIP-associated Colton antigens. Novel CDA red cells contained < 10% of the normal level of CHIP and had remarkably low osmotic water permeability (< 0.01 cm/s), but no mutation was identified in Aquaporin-1, the gene encoding CHIP. These studies demonstrate: (a) unlike rat, human CHIP expression occurs early in fetal development; (b) red cell water channels are greatly reduced in a rare phenotype; and (c) disrupted expression of red cell CHIP and CD44 suggests an approach to the molecular defect in a novel form of CDA.

Adult↗
PubMed1988

Pharmacokinetics of cis-dichloro-trans-dihydroxy-bis-isopropylamine platinum IV (iproplatinum, CHIP) in patients with normal and impaired renal function and following intraperitoneal administration.

CHIP is a quadrivalent platinum (Pt) complex, introduced clinically as a less toxic alternative to cis-platinum. The drug's major route of excretion is via the kidneys, and in this study the pharmacokinetics of unchanged CHIP, filterable Pt and total Pt have been determined following intravenous administration to patients with a range of renal function. Total Pt and filterable Pt in plasma decayed biexponentially and was fitted to a two-compartment model, whereas unchanged CHIP declined monoexponentially and was best fitted to a one-compartment model, according to Akaike's information criteria. There is a correlation between the unchanged CHIP clearance and 51Cr-EDTA clearance. The pharmacokinetics of CHIP was determined following intraperitoneal (i.p.) administration (dose, 150-300 mg m-2 4 h dwell time) and a regional advantage (peritoneal peak concentration/plasma peak concentration) of approximately 30 fold was seen. It is likely that the dose of CHIP will need to be reduced in patients with impaired renal function, and the use of i.p. CHIP in ovarian carcinoma warrants further study.

Female↗
PubMed1990

[Histopathological studies of periodontal tissue reactions following apical plugging with autogenous dentin chips].

After treating the infected canals, we investigated to determine the influence of autogenous dentin chips accidentally applied as filling in the root apexes. Materials were 15 mandibular premolars and molars obtained from healthy, mature dogs. According to standard procedures, after pulp extirpation, canals were temporarily filled with sandarac cotton pellets and left otherwise untreated for 4 weeks. At this time, the degree of infection was ascertained. After root-canal enlargement, root canals were filled with No. 55 gutta-percha points; and a sealer (Neotriozinc Paste, AH26, or Sealapex) was applied. The animals were sacrificed at the conclusion of either a short term (2 weeks) or a long term (16 weeks), and histological studies were performed. Conclusions In short-term specimens, no formation of new hard tissue was observed at the apical dentino-cemental junction; and inflammatory changes in the periapical soft tissue were remarkable. In long-term specimens, hard-tissue formation had resulted in apical closure in 6 out of 8 instances; and periapical inflammatory changes had decreased. Relations between dentin-chip density and histopathological conditions were as follows: In most of the specimens that were evaluated as good, dentin chips were very densely applied. Insufficient numbers of dentin chips produced poor results. In other words, dense applications of dentin chips result in good prognoses. Consequently, when root-canal enlargement has been adequately performed, application of dentin chips to the apex of infected canals stimulates hard-tissue formation resulting in biological apical closure. In infected canals, however, the degree to which dentin chips are infected can be a major factor.

Animals↗
PubMed1994

Molecular structure of the water channel through aquaporin CHIP. The hourglass model.

Aquaporin channel-forming integral protein (CHIP) is the first characterized water channel protein (genome symbol AQP1), but the molecular structure of the aqueous pathway through CHIP remains undefined. The two halves of CHIP are sequence-related, and each has three bilayer-spanning domains with the motif asparagine-proline-alanine (NPA) at residues 76-78 (in cytoplasmic loop B) and 192-194 (in extracellular loop E). The NPA motifs are oriented 180 degrees to each other, and the second NPA is near cysteine 189, the known site where mercurials inhibit osmotic water permeability (Pf). When expressed in Xenopus oocytes, the double mutant A73C/C189S exhibited high, mercurial-sensitive Pf similar to wild-type CHIP. Conservative substitutions of slightly greater mass in or near NPA motifs in loop B or loop E in CHIP caused reduced Pf and failure of the protein to localize at the plasma membrane. Certain nonfunctional loop E mutants complemented the truncation mutant D237Z. Formation of mixed oligomers was demonstrated by velocity sedimentation, immunoprecipitation, and analysis of dimeric-CHIP polypeptides. Cellular distributions of individual mutants or complementing pairs of mutants were verified by plasma membrane isolation and confocal microscopy. An hourglass structural model is proposed in which a cytoplasmic chamber (loop B) connects within the membrane to an extracellular chamber (loop E) forming a single, narrow aqueous pathway through each of the CHIP subunits; subunit oligomerization may provide the vertical symmetry necessary for residence within the lipid bilayer.

Amino Acid Sequence↗
PubMed1994

Localization of aquaporin CHIP in the human eye: implications in the pathogenesis of glaucoma and other disorders of ocular fluid balance.

PURPOSE: The existence of integral membrane proteins that serve as selective water channels has been postulated to explain the movement of water across plasma membranes. Aquaporin CHIP (channel-forming integral membrane protein of 28 kd) is the first such channel to be characterized and is abundant in human erythrocytes and a variety of secretory and absorptive epithelia of the rat. Because disturbances in the movement of water characterize several ocular diseases, the distribution of CHIP in the human eye was studied. METHODS: Affinity-purified antibodies against purified CHIP protein were used for the indirect immunofluorescence localization of CHIP in human eye structures. Labeling was confirmed by immunoblot analyses of membrane preparations from eye structures. RESULTS: CHIP immunolabeling was found in the corneal endothelium, the lens epithelium, the nonpigmented epithelium of the ciliary process, the iris epithelium, and the endothelium of the trabecular meshwork and the canal of Schlemm. CONCLUSIONS: The presence of CHIP water channels in the secretory and absorptive tissues of the human eye provides a mechanism for transcellular water movement and may be important for understanding diseases of the eye that involve excess or insufficient movement of ocular fluid such as glaucoma, cataracts, and Fuch's dystrophy. In addition, the existence of CHIP in the outflow pathways of the human eye provides a novel explanation for the movement of water out of the eye.

Adolescent↗
PubMed1988

Microorganisms associated with mouldiness of dried yam chips and their prevention.

The broad objective of this study was to isolate and identify the microorganisms causing mouldiness of stored yam chips and to look for ways of preventing the problem. Microorganisms isolated included Aspergillus flavus, A. glaucus, A. nidulans, A. niger, A. ochraceous, A. tamarii, A. candidus, Penicillium oxalicum, Trichoderma longibrachyatum, Rhizopus nigricans, Cylindrocarpon radicicola, Neurospora crassa, Botryodiplodia theobromae, Bacillus subtilis, Bacillus cereus, Erwinia carotovora and Serratia marcescens. Some of these microorganisms are transient invaders. Of the calcium-based chemicals used to prevent mouldiness, only CaCO3 and Ca(OH)2 proved effective and also prevented infestation of the chips by storage pests throughout the period of study. Whereas the product of the untreated yam chips was preferred in terms of colour, the product of CaCO3- and Ca(OH)2-treated yam chips were preferred in terms of taste and texture. As for physiological reaction after eating the products of the treated chips, Ca(OH)2- treated chips seemed to be more preferred by the members of the tasting panel.

Calcium Chloride↗
PubMed1991

Processing and quality evaluation of sweet potato chips.

A study was conducted to develop a process for producing sweet potato chips. Sweet potato tubers sliced to 0.5 by 0.5 cm size were dehydrated at 70 degrees C for various times (0, 90, 105, 120, 135, 150, 165 min). Determination of the moisture content of the dehydrated chips and sensory evaluation of the dehydrated and fried chips were carried out to establish optimum dehydration time and moisture which corresponded to optimum quality. Blanching the slices in water and 1% sodium metabisulfite solution respectively prior to the dehydration significantly (P greater than 0.05) improved the color and general acceptability of the chips over those immersed in water. The process development resulted in about 26 to 76% decrease in the ascorbic acid content of the chips. Significant changes also occurred in the total and reducing sugars of the chip following partial dehydration.

Cooking↗