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PubMed2000

Regulation of Id gene expression during embryonic stem cell-derived hematopoietic differentiation.

To elucidate the role of helix-loop-helix (HLH) Id proteins in hematopoietic differentiation, we used a model of embryonic stem (ES) cell differentiation in vitro which gives access not only to hematopoietic myeloid progenitor cells but also to the more primitive blast colony-forming cell (BL-CFC), the in vitro equivalent of the hemangioblast that gives rise to blast cell colonies in the presence of VEGF. We first demonstrated that ES cell-derived blast cell colonies could be used as a model to study hematopoietic differentiation and maturation. We next established the expression profile of Id genes in this model. Transcripts of the four Id genes were present in ES cells. Id1, Id3 and Id4 gene expression was down-regulated during the development of blast cell colonies while that of Id2 was maintained. Thus, Id1, Id3, and Id4 proteins are candidates for being negative regulators of hematopoiesis in the model of hematopoietic ES cell differentiation in vitro.

Animals↗
PubMed2001

Expression of ID family genes in the synovia from patients with rheumatoid arthritis.

Rheumatoid arthritis (RA) is a chronic inflammatory disease characterized by aggressive proliferation of synovial tissue leading to destruction of cartilage and bone. To identify molecules which play a crucial role for the pathogenesis, we compared mRNA expression pattern of RA synovium with that of osteoarthritis (OA), using the differential display. From the panel of differentially expressed genes, ID1 (inhibitor of differentiation 1) was considered to be particularly relevant to the pathogenesis of RA, because Id family genes have been shown to play a role in cell proliferation and angiogenesis. To examine whether the up-regulation of these genes is consistently observed in the patients with RA, mRNA levels of ID1 and ID3 in the synovial tissues from 13 patients with RA and 6 patients with OA were semi-quantitatively analyzed by RT-PCR. Mean mRNA levels of ID1 and ID3 were significantly elevated in RA synovia compared with OA by 8.6-fold (P = 0.0044) and 3.3-fold (P = 0.0085), respectively. Immunohistochemistry revealed striking staining of Id1 and Id3 in the endothelial cells, suggesting a possible role of Id in severe angiogenesis observed in RA. The expression of Id family genes in the synovium constitutes a new finding of particular interest. Their functional role as well as their contribution to the genetic susceptibility to RA requires further investigation.

Aged↗
PubMed1999

Differential biological activities of mammalian Id proteins in muscle cells.

Id proteins are helix-loop-helix (HLH) transcription factors that lack DNA-binding domains. These proteins form inactive heterodimers with basic HLH (bHLH) factors, inhibiting their DNA-binding and transcriptional activities. Consistent with a proposed role for Id proteins as inhibitors of terminal differentiation, Id1 and Id3 have been shown to negatively regulate myogenesis in cultured muscle cells. Here we have investigated the possibility that Id2 and/or Id4 can act in a similar manner. Surprisingly, while overexpression of Id2 resulted in inhibition of differentiation of Sol 8 myoblast cells, overexpression of Id4 did not. Sol 8 cells stably transfected with Id4 showed no apparent changes in expression of muscle-specific genes upon differentiation. DNA-binding activities present at the muscle creatine kinase (MCK) enhancer E-box and transcription of the MCK enhancer were not altered in Id4-overexpressing cells, compared with vector-transfected cells. Id2 is also a more potent inhibitor of protein/DNA complex formation at the MCK-R enhancer E-box than Identified in vitro. Therefore, our data support the notion that members of the Id family might be involved in the regulation of distinct developmental pathways.

Animals↗
PubMed1982

Evaluation of Gram-stain screen and Micro-ID methods for direct identification of Enterobacteriaceae from urines.

A rapid method of urine screening and enterobacterial identification was evaluated. Results indicated that an average of 13.5 bacteria/oil immersion field (threshold value greater than or equal to 1) was observed in unsedimented urine of patients with significant bacteriuria, with an average of less than 1 bacterium/field in urines of patients without significant bacteriuria. In centrifuged urines, numbers of bacteria divided by amount of urine sedimented yielded similar results. Of 1758 urines studied, 136 yielded greater than or equal to 10(5) bacteria/ml, and 58 greater than 10(4) but less than 10(5) bacteria/ml, by conventional techniques. Gram-screening of unsedimented specimens gave sensitivity rates of 94.1%, specificity of 97.7%, and predictive positive and negative values of 78.5%, 99.5%, respectively; similar values were obtained with sedimented urines. Sensitivity rates of both screening methods for the 58 urines with greater than 10(4) but less than 10(5) bacteria/ml were 9.0%, 10.0%, respectively. Total correct enteric identification in 113 urines with positive screens and significant bacteriuria (greater than or equal to 10(5)/ml) was 82.3% and 90.3% with direct saline and broth Micro-ID methods, respectively. In 99 urines yielding pure or predominantly pure growth of 1 species of Enterobacteriaceae identification by direct saline and broth Micro-ID corresponded with isolated colony identification in 85.9%, 94.9% of cases, respectively. Gram-stain screening (together with back-up conventional plating in certain patient categories) and enterobacterial identification by direct broth Micro-ID, of urines with pure stains suggestive of greater than or equal to 10(5) Gram-negative rods/ml has been shown to be useful in laboratories without automated equipment for urine screening.

Bacteriological Techniques↗
PubMed2000

Isotope dilution inductively coupled plasma mass spectrometry (ID ICP-MS) for the certification of lead and cadmium in environmental standard reference materials.

Lead (Pb) and cadmium (Cd) have been determined in six new environmental standard reference materials (SRMs) using isotope dilution inductively coupled plasma mass spectrometry (ID ICP-MS). The SRMs are the following: SRM 1944, New York-New Jersey Waterway Sediment, SRMs 2583 and 2584, Trace Elements in Indoor Dust, Nominal 90 mg/kg and 10,000 mg/kg Lead, respectively, SRMs 2586 and 2587, Trace Elements in Soil Containing Lead from Paint, Nominal 500 mg/kg and 3,000 mg/kg Lead, respectively, and SRM 2782, Industrial Sludge. The capabilities of ID ICP-MS for the certification of Pb and Cd in these materials are assessed. Sample preparation and ratio measurement uncertainties have been evaluated. Reproducibility and accuracy of the established procedures are demonstrated by determination of gravimetrically prepared primary standard solutions and by comparison with isotope dilution thermal ionization mass spectrometry (ID TIMS). Material heterogeneity was readily demonstrated to be the dominant source of uncertainty in the certified values.

Cadmium↗
PubMed2006

Evaluation of S. aureus ID, a chromogenic agar medium for the detection of Staphylococcus aureus.

BACKGROUND: Screening for staphylococci among various patient populations has become important for appropriate therapeutic management and for control of nosocomial infections. The purpose of this study is to evaluate the in vitro sensitivity and specificity of a chromogenic agar medium, S. aureus ID (bioMérieux, France), for the identification of Staphylococcus aureus. MATERIALS AND METHODS: A well-defined collection of S. aureus and coagulase-negative staphylococci (CNS) was used. The methicillin-resistant S. aureus (MRSA) isolates were collected in The Netherlands and all had a unique typing pattern. The methicillin-susceptible S. aureus (MSSA) and CNS were isolated from cultures of blood. The isolates were inoculated on Columbia agar plates with 5% sheep blood and incubated for 24 h at 35 degrees C. From the resulting cultures, a suspension of 0.5 McFarland was made and subsequently 10 mul was streaked on a S. aureus ID plate using a sterile loop. The results were read after 24 h and 48 h of incubation at 35 degrees C. Growth of colonies showing green coloration was considered to be positive (indicating S. aureus). RESULTS: A total of 519 S. aureus strains were tested (249 MSSA, 270 MRSA). The sensitivity to detect S. aureus was 96.5% (501/519) after 24 h and 97.5% (506/519) after 48 h. A total of 478 CNS were tested. The specificity was 98.5% (471/478) after 24 h and 98.3% (470/478) after 48 h. The differences between 24 h and 48 h incubation were not statistically significant. CONCLUSION: S. aureus ID is highly sensitive and specific to differentiate between S. aureus and CNS in vitro. Since the performance does not significantly differ between 24 h or 48 h of incubation, samples need only 1 day of incubation before optimal results can be obtained.

Agar↗
PubMed1993

HLH forced dimers: tethering MyoD to E47 generates a dominant positive myogenic factor insulated from negative regulation by Id.

Basic-helix-loop-helix (bHLH) class transcription factors bind DNA as hetero- and homodimers. In murine myogenic cells the HLH network includes multiple members of the E protein, MyoD, and Id families; changes in the network characterize muscle determination and differentiation and have been proposed as causal for these developmental transitions. To test the importance of HLH partner choice in these cellular decisions, we have designed a strategy in which the identity of a bHLH dimer is specified by joining two monomers via a flexible polypeptide linker. A MyoD-E47 polyprotein avidly bound the same DNA targets as its unlinked counterpart, but, unlike intermolecular dimers that are very sensitive to inhibition by Id, MyoD-E47 was resistant to Id challenge. In cells MyoD-E47 acted as a dominant positive myogenic factor, capable of initiating myogenic determination and also substantially bypassing negative regulation of differentiation by serum growth factors.

3T3 Cells↗
PubMed1996

A homology model of the Id-3 helix-loop-helix domain as a basis for structure-function predictions.

The function of the dominant negative Id (inhibitor of differentiation) helix-loop-helix (HLH) proteins is to dimerize with, and prevent the DNA binding of basic HLH (bHLH) transcription factors. A three-dimensional homology model was constructed for the HLH domain of human Id3 based on the X-ray crystal structures of the E47, MyoD, and Max bHLH proteins. The model showed that, in contrast to bHLH proteins, Id proteins appear able to dimerize without DNA stabilization because of better packing of the hydrophobic core, and the absence of destabilizing polar loop residues and of repulsive positive charges in the monomer interface at the base of the four alpha-helix bundle. This prediction was tested by in vitro protein-binding experiments, which showed that Id3 did indeed self-associate. It also showed that the inability of Id proteins to bind DNA arises from the non-basic, poorly defined, random coil structure of the region corresponding to that responsible for bHLH DNA-binding. A model of the Id1 protein was constructed and revealed a potential site of charge-charge repulsion in the hypothetical homodimer interface that may explain its observed inability to form homodimers.

Amino Acid Sequence↗
PubMed1988

ID sequence-binding protein factors during development of mice.

The ID repetitive sequence has been reported to be transcribed as small RNA in both a brain-specific and a developmental stage-specific manner. Several brain-specific proteins required for transcription, along with RNA polymerase III, may be involved in controlling the gene activity throughout development. We analyzed extracts from the brains and livers of mice in an electrophoretic mobility shift assay. Of ID sequence-binding proteins, we detected a protein factor(s) that interacts specifically with the region between two promoter sequences for RNA polymerase III. This protein factor seems to be relevant to postnatal accumulation of the small RNA transcripts of ID sequences, since its time course of expression is consistent with that of the synthesis of the small RNA during development. A penta-nucleotide direct repeat (GCAAG) and its inverted complement (CTTGC) are both present in that region and may be involved in the binding site for the protein factor. The biological significance of the binding site and interacting protein factor(s) is discussed.

Aging↗
PubMed1994

Structural organisation and chromosomal mapping of the human Id-3 gene.

The helix-loop-helix (HLH) family of transcription factors plays a central role in the regulation of cell growth, differentiation and tumourigenesis. Members of the Id (inhibitor of DNA binding) class of these nuclear proteins are able to heterodimerise with and thereby antagonise the functions of other transcription factors of this family. We report here on the genomic organisation of the human Id3 (HLH 1R21/heir1) gene. Comparison with the two other mammalian Id genes, Id1 and Id2, reveals a highly conserved protein coding gene organisation consistent with evolution from a common, ancestral Id-like gene. In addition, by using a yeast artificial chromosome (YAC) clone of Id3, we have fine-scale mapped the gene to chromosome band 1p36.1 by fluorescence in situ hybridisation (FISH) and, using the same FISH technique, we have detected heterogeneity in tumour-associated 1p36 chromosome translocations.

Adenocarcinoma↗
PubMed1995

Role of computational chemistry in support of hazard identification (ID): mechanism-based SARs.

A mechanism-based structure-activity relationship (SAR) study examines the structural basis for a chemical/biological activity by targeting a single or a few stages in a postulated mechanism of action. Computational chemistry approaches provide a valuable complement to experiment for probing such associations, but require a highly focused viewpoint that neglects much of the full biological and chemical interaction problem. Research questions are formulated in terms of fundamental structure and reactivity properties and are designed to test key assumptions of a postulated mechanism of activity. The results of such studies can aid in the generation of new hypotheses, suggest new experiments, and provide scientific rationale for extrapolation in hazard identification (ID). Toxicologists and computational chemists bring very different, yet complementary viewpoints, approaches, and expertise to bear on the hazard ID problem. However, improved communication and interaction between these two groups is needed to most productively address hazard ID issues.

Algorithms↗
PubMedDate not supplied

RGSS-ID: an approach to new radiologic reporting system.

RGSS-ID is a developmental computer system that applies artificial intelligence (AI) methods to a reporting system. The representation scheme called Generalized Finding Representation (GFR) is proposed to bridge the gap between natural language expressions in the radiology report and AI methods. The entry process of RGSS-ID is made mainly by selecting items; our system allows a radiologist to compose a sentence which can be completely parsed by the computer. Further RGSS-ID encodes findings into the expression corresponding to GFR, and stores this expression into the knowledge data base. The final printed report is made in the natural language.

Artificial Intelligence↗
PubMed2006

Carcinoembryonic antigen (CEA) mimicry by an anti-idiotypic scFv isolated from anti-Id 6.C4 hybridoma.

Since carcinoembryonic antigen (CEA) is expressed during embryonic life, it is not immunogenic in humans. The use of anti-idiotypic (Id) antibodies as a surrogate of antigen in the immunization has been considered a promising strategy for breaking tolerance to some tumor associated antigens. We have described an anti-Id monoclonal antibody (MAb), designated 6.C4, which is able to mimic CEA functionally. The anti-Id MAb 6.C4 was shown to elicit antibodies that recognized CEA in vitro and in vivo. In the present study, we sought to verify whether a single chain (scFv) antibody obtained, the scFv 6.C4, would retain the ability to mimic CEA. Two scFv containing the variable heavy and light chain domains of 6.C4 were constructed with a 15-amino acid linker: one with and another without signal peptide. DNA immunization of mice with both forms of scFv individually elicited antibodies able to recognize CEA.

Adenocarcinoma↗
PubMed2026

Individual Differences in Cognitive Aging Rodent Datasets (ID-CARD): A collaborative platform for behavioral analysis across the lifespan.

Understanding cognitive aging requires approaches that capture individual variability while enabling integration across studies. In rodent models, behavioral data are central to this effort, yet cross-laboratory differences in experimental design limit comparability and constrain secondary analysis. To address this gap, we developed the Individual Differences in Cognitive Aging Rodent Datasets (ID-CARD), a first-of-its-kind collaborative repository aggregating trial-level Morris water maze data from multiple laboratories. ID-CARD is designed to support large-scale, integrative analyses and to facilitate secondary use of existing behavioral data in alignment with emerging data-sharing and transparency initiatives. Rather than imposing retrospective harmonization of experimental protocols, we implemented a normalization and modeling framework that enables comparison of learning trajectories while preserving meaningful variation across studies. Behavioral data from > 5000 rats spanning common strains, both sexes, and multiple ages were normalized in training and performance domains and fit with a logarithmic function to derive an error accumulation rate coefficient (EARC) as a measure of spatial learning. Age was strongly associated with increased EARC, indicating attenuated learning, even after adjusting for non-spatial cue performance. Analyses of goodness of fit revealed systematic structure in learning dynamics, where age was associated with reduced learning-curve conformity after accounting for overall performance. Inter-individual variability in spatial learning also increased with age, with strain-specific interactions. These findings demonstrate that integrated analysis of heterogeneous behavioral datasets can yield robust, individual-level insights into cognitive aging. ID-CARD provides a scalable resource and analytic framework to advance discovery in behavioral neuroscience by enabling reuse, integration, and comparative analysis of existing data.

Cognitive aging↗
PubMed2003

Relationship between angiotensin-converting enzyme ID polymorphism and VO(2max) of Chinese males.

Several studies have shown that the angiotensin-converting enzyme (ACE) I allele is associated with enhanced physical performance. We investigated whether this phenomenon is observed in a cohort of 67 Chinese men in Singapore. Angiotensin-converting enzyme ID polymorphism was typed with PCR method and maximal oxygen uptake (VO(2max)) of the DD, ID, and II genotypes was compared. Analysis of covariance revealed that VO(2max) was significantly higher (p<0.05) for the DD genotype (57.86 +/- 3.5 ml.kg.(-1)min(-1)) versus the ID (50.58 +/- 1.80 ml.kg.(-1)min(-1)) or II (50.48 +/- 1.58 ml.kg.(-1) min(-1)) genotype. Our findings suggest that the ACE DD genotype in young adult Chinese males is associated with higher levels of VO(2max).

Adult↗
PubMed2004

A role for Id proteins in mammary gland physiology and tumorigenesis.

Id helix-loop-helix (HLH) proteins are regulators of cell growth and differentiation in embryonic and adult tissues. They are members of the basic HLH family of transcription factors but lack a DNA binding domain. By binding to basic HLH transcription factors, Id proteins regulate gene expression. Id1 and Id3 have extensive sequence homology and similar patterns of expression during embryogenesis and in adult tissues. They are also expressed at high levels in the endothelial cells of tumor-infiltrating blood vessels, and breast tumors spontaneously arising in MMTV-neu mice demonstrate impaired angiogenesis when growing in an Id1- and/or Id3-deficient background. These lesions are typically cystic with a small rim of viable tumor cells surrounding an acellular necrotic core. Id2 plays a critical role in breast differentiation and lactation. Id4 regulates BRCA1 expression and may be involved in hormone-dependent regulation of BRCA1 homeostasis. Thus, all four members of the Id protein family play pivotal roles in distinct aspects of normal and malignant breast biology, the subject of this review.

Animals↗
PubMed1999

Use of the RAPID ID 32 A system for rapid identification of Clostridium species important in food hygiene.

The identification of Clostridium species using conventional biochemical reactions or commercially available miniaturized ready-to-use test kits often yields uncertain results. One of these test kits, the RAPID ID 32 A identification system for anaerobes (bioMérieux, Marcy-l'Etoile, France), is based on the evaluation of the action of preformed bacterial enzymes and allows classification to the species level within 4 h. This study intended to assess the suitability and reliability of this system for the rapid identification of Clostridium species relevant to food hygiene. For this purpose, 122 test strains of 18 different Clostridium species were examined via RAPID ID 32 A. Of these, 110 (90.2%) were correctly identified to the species level within 4 h. In addition, six strains were successfully classified after examination with supplementary biochemical reactions suggested by the manufacturer, which required an overall examination time of 72 h. The identity of five Clostridium strains could not be determined and in one case the test kit yielded a wrong species classification. Altogether, a correct identification was possible for 116 (95.1%) of the isolates, the total error rate was 4.9%. Using the RAPID ID 32 A system a great number of Clostridium species which are relevant to food hygiene and are often difficult to identify can be correctly and reliably classified within 4 h. Nevertheless, the test system has to be regarded as not yet completely satisfactory, e.g., because C. tyrobutyricum isolates were only insufficiently identified. Further improvements of the system are desirable in order to make it universally applicable in food microbiology.

Clostridium↗
PubMed1997

A zebrafish Id homologue and its pattern of expression during embryogenesis.

We describe the cloning, sequencing and pattern of transcript distribution during embryogenesis of a zebrafish Id homologue that we have called Id6. Transcription of the gene is spatially regulated, and its pattern of transcription shows considerable overlaps with those of other zebrafish genes with homology to Drosophila neurogenic genes, such as Notch and Delta. Since all these genes are coexpressed in particular cells, they may function together in a single genetic circuit in zebrafish as they do in Drosophila. A zebrafish homologue of Drosophila AS-C proteins can activate transcription of a CAT reporter gene by binding to an E-box in mouse 3T3 cells, either alone or in conjunction with ZfE12. The activation of transcription is inhibited in the presence of Id6. This indicates that the zebrafish gene described here is a genuine member of the Id family, and suggests that it may serve a function similar to that of the Drosophila gene emc and mammalian Ids during development.

Amino Acid Sequence↗