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Results for “Functional potential”

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PubMed2004

GEISHA, a whole-mount in situ hybridization gene expression screen in chicken embryos.

Despite the increasing quality and quantity of genomic sequence that is available to researchers, predicting gene function from sequence information remains a challenge. One method for obtaining rapid insight into potential functional roles of novel genes is through gene expression mapping. We have performed a high throughput whole-mount in situ hybridization (ISH) screen with chick embryos to identify novel, differentially expressed genes. Approximately 1,200 5' expressed sequence tags (ESTs) were generated from cDNA clones of a Hamburger and Hamilton (HH) stage 4-7 (late gastrula) chick embryo endoderm-mesoderm library. After screening to remove ubiquitously expressed cDNAs and internal clustering and after comparison to GenBank sequences, remaining cDNAs (representing both characterized and uncharacterized genes) were screened for expression in HH stage 3-14 embryos by automated high throughput ISH. Of 786 cDNAs for which ISH was successfully performed, approximately 30% showed ubiquitous expression, 40% were negative, and approximately 30% showed a restricted expression pattern. cDNAs were identified that showed restricted expression in every embryonic region, including the primitive streak, somites, developing cardiovascular system and neural tube/neural crest. A relational database was developed to hold all EST sequences, ISH images, and corresponding BLAST report information, and to enable browsing and querying of data. A user interface is freely accessible at http://geisha.biosci.arizona.edu. Results show that high throughput whole-mount ISH provides an effective approach for identifying novel genes that are differentially expressed in the developing chicken embryo.

Animals↗

PubMed2006

Analysis of immunoglobulin heavy and light chain variable genes in post-transplant lymphoproliferative disorders.

Post-transplant lymphoproliferative disorders (PTLD) derive from antigen-experienced B-cells and represent a major complication of solid organ transplantation. We characterized usage, mutation frequency and mutation pattern of immunoglobulin variable (IGV) gene rearrangements in 50 PTLD (polymorphic PTLD, n=10; diffuse large B-cell lymphoma, n=35; and Burkitt/Burkitt-like lymphoma, n=5). Among PTLD yielding clonal IGV amplimers, a functional IGV heavy chain (IGHV) rearrangement was found in 40/50 (80.0%) cases, whereas a potentially functional IGV light chain rearrangement was identified in 36/46 (78.3%) PTLD. By combining IGHV and IGV light chain rearrangements, 10/50 (20.0%) PTLD carried crippling mutations, precluding expression of a functional B-cell receptor (BCR). Immunohistochemistry showed detectable expression of IG light chains in only 18/43 (41.9%) PTLD. Failure to detect a functional IGV rearrangement associated with lack of IGV expression. Our data suggest that a large fraction of PTLD arise from germinal centre (GC)-experienced B-cells that display impaired BCR. Since a functional BCR is required for normal B-cell survival during GC transit, PTLD development may implicate rescue from apoptosis and expansion of B-cells that have failed the GC reaction. The high frequency of IGV loci inactivation appears to be a peculiar feature of PTLD among immunodeficiency-associated lymphoproliferations.

Apoptosis↗

PubMed2000

Molecular interactions of neural chondroitin sulfate proteoglycans in the brain development.

Aggrecan family proteoglycans, phosphacan/RPTPzeta/beta, and neuroglycan C (NGC) are the major classes of chondroitin sulfate proteoglycan in the developing mammalian brain. A multidomain is a common structural feature of these proteoglycans which can interact with various molecules including growth factors, cell adhesion molecules, and extracellular matrix molecules. Individual proteoglycans are distributed in the developing brain in a distinct temporal and spatial pattern, suggesting that they are involved in distinct phases of the brain development through multiple molecular interactions. This review mainly summarizes recent studies on the involvement of these three classes of proteoglycan in cell-cell and cell-substratum interactions during the brain development. Their expressions and proposed functional roles in injured brains are also mentioned. In addition, this review briefly covers potential functions of other neural chondroitin sulfate proteoglycans such as decorin, testican, NG2 proteoglycan, and amyloid precursor protein (APP) in developing and injured brains.

Animals↗

PubMed2003

Usp9y (ubiquitin-specific protease 9 gene on the Y) is associated with a functional promoter and encodes an intact open reading frame homologous to Usp9x that is under selective constraint.

Sequences complementary to the X-linked ubiquitin-specific protease gene Usp9x (Dffrx) have been shown to map to the Sxr(b) interval of the mouse Y Chromosome (chr) and to be expressed in a testis-specific manner. In humans, ubiquitously expressed functional homologues (USP9Y and USP9X DFFRY/DFFRX) are present on both sex chromosomes, whereas in mouse it remains to be demonstrated that the Y-linked sequences encode a functional protein. In this paper, it is shown that the Usp9y gene encodes a potentially functional ubiquitin-specific protease possessing a core promoter region that shares several features characteristic of other testis-specific genes. Analysis of synonymous and nonsynonymous nucleotide changes suggests that there is constraint on the amino acid sequence of both the mouse Usp9x and Usp9y genes, a finding that mirrors similar analysis of the human orthologs. Thus, in both mouse and human, selection is acting to maintain the amino acid sequence of the X and Y-linked genes. This indicates that in both species the genes on each sex chromosome continue to encode an important function.

Amino Acid Sequence↗

PubMed1999

Genetic variations in human fetal globin gene microsatellites and their functional relevance.

Short tandem repeats are abundantly present within the genome. They are commonly used as polymorphic markers but their potential functional role is poorly documented. Several of these microsatellites have been described within the beta-globin locus and some could be involved in controlling gene expression. Our purpose was to investigate the extent and significance of the (TG)n(CG)m dinucleotide repeat polymorphisms in the two gamma-globin gene IVS2s. Two groups of subjects were studied: a group of 63 beta-thalassaemic patients presenting either with a severe Cooley's anaemia (n=50) or with thalassaemia intermedia (TI, n=13), and a control group of 60 unrelated healthy individuals. A high heterogeneity of the polymorphic repeats was demonstrated, extending the range of the published alleles from 13 to 22 and allowing a first attempt at making a phenotype/genotype correlation. One specific allele, (TG)13 in the Agamma-gene, was highly enriched in the TI patients (46.1% vs 2.9% of the Cooley's anaemia cases, P < 0.0002, and 23.3% in the normal controls, P < 0.008) and preferentially observed in TI patients with a high haemoglobin F (Hb F). Transient transfection assays in K562 cells, with the growth hormone gene as a reporter, showed a positive regulatory action mediated by a (TG)13-containing 243 nt IVS2 fragment. Finally, a first set of mobility shift experiments with erythroid (K562 and MEL) and nonerythroid (HeLa) cell lines showed binding of erythroid component(s) in this DNA region and the binding pattern was modified upon induction of MEL cells by DMSO. Thus, our in vivo and in vitro data raise the question of a possible contribution of the gamma-gene IVS2s polymorphic microsatellites to the variable Hb F synthesis in the major haemoglobinopathies: a well known, puzzling and still unanswered question.

Cell Line↗

PubMed1994

Granulated metrial gland cells: hypotheses concerning possible functions during murine gestation.

Granulated metrial gland (GMG) cells are morphologically distinctive lymphoid cells found in the murine uterus only during gestation. The life history of GMG cells suggests that they have important roles during mammalian gestation but these roles have been difficult to define. Genetic and immunologic data suggest that GMG cells may be a specialized subset of natural killer (NK) lymphocytes. This has directed research on GMG cell functions towards questions of effector cell-target cell interactions. A broader range of potential functions is discussed and shifts in functional roles played by GMG cells are proposed over the course of gestation.

Animals↗

PubMed2002

Mini-Mental State Examination, cognitive FIM instrument, and the Loewenstein Occupational Therapy Cognitive Assessment: relation to functional outcome of stroke patients.

OBJECTIVES: To compare 3 cognitive tests, used on admission, for predicting discharge functional outcome and to assess the efficacy of these tests in predicting functional outcome at discharge in stroke patients undergoing rehabilitation. DESIGN: Cohort study. SETTING: Geriatric rehabilitation department of a tertiary care hospital in Israel. PATIENTS: Sixty-six patients undergoing acute inpatient comprehensive rehabilitation after first clinical stroke. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASUREMENTS: Cognitive status was assessed with the Loewenstein Occupational Therapy Cognitive Assessment (LOTCA), the Mini-Mental State Examination (MMSE), and the cognitive subscale of the FIM instrument. The FIM motor subscale was used to assess functional outcome status. Functional gain was determined by the motor FIM gain (efficacy), and the relative (to potential) functional gain was determined by the Montebello Rehabilitation Factor Score. Efficiency was calculated by efficacy divided by the length of hospital stay. RESULTS: A significant increase in total FIM scores (34.8 points) occurred during rehabilitation mainly because of improvement in motor functioning (31.5 points). Significant improvement in global cognitive status was documented by all 3 tests. Intertest correlation coefficients ranged between.47 and.67. The LOTCA showed somewhat higher correlation coefficients with most of the parameters of functional motor outcomes. Correlation between the MMSE and FIM cognitive subscale and these outcome parameters were nearly identical. CONCLUSION: The LOTCA is slightly better than the MMSE and the FIM cognitive subscale in predicting functional status change after stroke rehabilitation but it is a time-consuming and exhausting instrument to use. The FIM cognitive subscale requires a better overall understanding of the patient's situation at time of administration and therefore is less convenient for the initial assessment. The similar correlation of all 3 tests with functional outcomes and the simplicity of administration of the MMSE suggests its use in the initial assessment of stroke patients.

Activities of Daily Living↗

PubMed1997

Transglutaminase-catalyzed cross-linking of osteopontin is inhibited by osteocalcin.

Osteocalcin, the most abundant noncollagenous protein of bone matrix, has been demonstrated to inhibit bone growth by gene knockout experiments (Ducy, P., Desbois, C., Boyce, B., Pinero, G., Story, B., Dunstan, C., Smith, E., Bonadio, J., Goldstein, S., Gundberg, C., Bradley, A., and Karsenty, G. (1996) Nature 382, 448-452). Its specific functional mechanism in bone metabolism is, however, largely unknown. In this study, we provide evidence that osteocalcin has an inhibitory effect on tissue transglutaminase activity, as measured by cross-linking of osteopontin, another bone matrix protein. Using a set of synthetic peptides, we found that the inhibitory activity resided within the first 13 N-terminal amino acid residues of osteocalcin. An N-terminal peptide also inhibited cross-linking of another tissue transglutaminase substrate, beta-casein. The inhibitory peptide was shown to have affinity for the substrates of transglutaminase rather than for the enzyme. Since the N terminus of osteocalcin exhibits homology to the substrate recognition site sequences of two transglutaminases, we conclude that the inhibitory effect is most likely due to competition with the enzyme for the transglutaminase-binding region of the substrates, osteopontin and beta-casein, which prevents access of the enzyme to them to perform its function. The interference of osteocalcin with osteopontin cross-linking gives osteocalcin a new potential function as the first protein inhibitor of tissue transglutaminase. This suggests a specific role and a plausible mechanism for it as a modulator of maturation, stabilization, and calcification of bone matrix.

Amino Acid Sequence↗

PubMed2002

Do nonhuman primates comprise appropriate experimental models for studying the function of human leukocyte antigen-G?

The expression and function of the human major histocompatibility complex (MHC) class Ia genes, human leukocyte antigen (HLA)-A, -B, and -C, is well-established; they are expressed in most nucleated cells and present endogenous peptides to CD8+ T cells. However, MHC class Ib genes are poorly characterized and have unknown functions. In humans, the best-characterized class Ib gene is HLA-G. This gene has a restricted tissue expression of the mRNA and a unique pattern of protein expression; it is expressed mainly in the extravillous cytotrophoblast cells in the placenta. The function of HLA-G is not clear, but its presence at the maternal-fetal interface suggests a role in protection of the semiallogeneic fetus. Whereas functional studies using in vitro models and transgenic mice provide useful insights regarding the potential function of this molecule, in vivo studies cannot be performed in humans. Nonhuman primates that are closely related to humans phylogenetically contain homologues of HLA-G. The MHC-G loci in nonhuman primates appear to have diverged from the human HLA-G. However, in the rhesus monkey (Macaca mulatta) and olive baboon (Papio anubis), a novel class Ia-related locus has been described. This gene encodes glycoproteins with characteristics that resemble those of HLA-G, including restricted tissue distribution, alternative splicing of mRNA, truncated cytoplasmic domain, and limited polymorphism. Thus, this molecule may be the functional homologue of HLA-G, and these two species may comprise appropriate models for elucidating the function of HLA-G.

Animals↗

PubMed1994

Purification of the 230-kD bullous pemphigoid antigen (BP230) from bovine tongue mucosa: structural analyses and assessment of BP230 tissue distribution using a new monoclonal antibody.

In the epidermis the autoantigen BP230 is a component of the hemidesmosomal plaque. We have developed a procedure for the isolation of BP230 from bovine tongue mucosa using chromatographic means. The identity of the isolated protein was confirmed by its recognition by bullous pemphigoid autoantibodies. A monoclonal antibody (MoAb230), generated against the purified protein, localizes to the region of the plaque of the hemidesmosome with which keratin bundles interact. Furthermore, the tissue distribution of BP230, assessed using MoAb230, suggests that BP230 or an immunologically related protein is a component of all hemidesmosomes. Ultrastructural analyses of the BP230 preparation reveal that the BP230 molecules assemble into macromolecular aggregates. The few images of individual intact molecules that we have observed in platinum replicas of rotary shadowed BP230 preparations suggest that BP230 is an elongate rod-shaped molecule. This is consistent with predictions based on the primary sequence of BP230 deduced from BP230 cDNAs reported by others. We discuss our results in relation to the potential function of BP230. Isolation of BP230 should now allow more rigorous biochemical analyses of potential protein-protein interactions of BP230 in the hemidesmosome.

Animals↗

PubMed2006

The cytoplasmic domain of NrCAM binds to PDZ domains of synapse-associated proteins SAP90/PSD95 and SAP97.

NrCAM, a member of the L1 family of cell adhesion molecules, serves important functions during the development of the nervous system, e.g. in adhesion-dependent processes such as neurite outgrowth and axonal pathfinding. Complex homo- and heterophilic binding and several extracellular ligands of NrCAM have been described, but less is known about intracellular interaction partners. The cytoplasmic carboxy-terminus of NrCAM contains a typical sequence motif for binding to PDZ domains, making interactions with PDZ domain-containing scaffolding proteins quite conceivable. In this study, we identified specific interactions of the intracellular domain of NrCAM with class I PDZ domains of the membrane-associated guanylate kinases SAP90/PSD95 and SAP97. In contrast to NrCAM, the intracellular domains of the other mammalian L1 family molecules, e.g. L1, CHL1 and Neurofascin, did not interact with these PDZ domains. In transfected COS-7 cells, NrCAM-mediated recruitment of SAP97 to the plasma membrane was dependent on the PDZ binding motif. We show that NrCAM and SAP97 are colocalized, e.g. within photoreceptor terminals of the mammalian retina. In summary, our results confirm a functional PDZ domain binding motif at the carboxy-terminus of NrCAM and support potential functions of NrCAM during the assembly of highly organized protein complexes at the cell membrane.

Adaptor Proteins, Signal Transducing↗

PubMed1981

Re-evaluation of viability testing of cadaveric kidneys for transplantation.

Twenty-three human cadavers kidneys were studied during hypothermic pulsatile perfusion prior to transplantation. The accumulation of laevo-lactate and lactate dehydrogenase, alterations in pH and perfusion flow rate were measured and compared with organ function following transplantation. No parameter measured was found to be an accurate index of potential function.

Cadaver↗

PubMed1994

Identification of functional domains of the aryl hydrocarbon receptor nuclear translocator protein (ARNT).

The activated aryl hydrocarbon receptor (AHR) and the AHR nuclear translocator (ARNT) bind DNA as a heterodimer. Both proteins represent a novel class of basic helix-loop-helix (bHLH)-containing transcription factors in that (i) activation of AHR requires the binding of ligand (e.g., 2,3,7,8-tetrachlorodibenzo-p-dioxin [TCDD]), (ii) the xenobiotic responsive element (XRE) recognized by the AHR/ARNT heterodimer differs from the recognition sequence for nearly all other bHLH proteins, and (iii) both proteins contain a PAS homology region, which in the Drosophila PER and SIM proteins functions as a dimerization domain. A cDNA for mouse ARNT has been cloned, and potential functional domains of ARNT were investigated by deletion analysis. A mutant lacking all regions of ARNT other than the bHLH and PAS regions is unimpaired in TCDD-dependent dimerization and subsequent XRE binding and only modestly reduced in ability to complement an ARNT-deficient mutant cell line, c4, in vivo. Both the first and second alpha helices of the bHLH region are required for dimerization. The basic region is required for XRE binding but not for dimerization. Deletion of either the A or B segments of the PAS region slightly affects TCDD-induced heterodimerization, while deletion of the complete PAS region severely affects (but does not eliminate) dimerization. Thus, ARNT possesses multiple domains required for maximal heterodimerization. Mutants deleted for PAS A, PAS B, and the complete PAS region all retain some degree of XRE binding, yet none can rescue the c4 mutant. Therefore, both the PAS A and PAS B segments, besides contributing to dimerization, apparently fulfill additional, unknown functions required for biological activity of ARNT.

Amino Acid Sequence↗

PubMed1996

Regulation of 4-aminopyridine-sensitive, delayed rectifier K+ channels in vascular smooth muscle by phosphorylation.

Voltage-gated, delayed rectifier K+ current (KV) that is sensitive to 4-aminopyridine (4AP) block has been identified in all vascular smooth muscle tissues studied to date. These channels conduct outward, hyperpolarizing K+ current that influences resting membrane potential and contributes to repolarization of action potentials. Smooth muscle cells in most arterial resistance vessels regulate Ca2+ influx and contractile tone by low amplitude, tonic changes in membrane potential. Block of KV with 4-aminopyridine leads to contraction and an enhanced myogenic response to increased intravascular pressure. We investigated the modulation of KV currents in isolated, freshly dispersed smooth muscle cells from rabbit portal vein and coronary arteries in whole-cell voltage clamp experiments. Our findings indicate that KV channels are regulated by signal transduction mechanisms involving vasoactive agonists that activate cAMP-dependent protein kinase (PKA) or protein kinase C (PKC). In this paper, the properties and potential function of KV channels in vascular smooth muscle are reviewed. Further, the regulation and potential role of alterations in KV due to beta-adrenoceptor agonists, adenylyl cyclase and PKA, as well as angiotensin II, diacylglycerol, and PKC are discussed.

4-Aminopyridine↗

PubMed2002

Increased frequency of the uncommon tumor necrosis factor -857T allele in British and Dutch patients with sarcoidosis.

Interindividual variation in the expression of tumor necrosis factor (TNF)-alpha suggests the existence of functionally distinct TNF alleles, which might play a role in sarcoidosis. We investigated five potentially functional biallelic TNF promoter polymorphisms at nucleotide positions -1,031(T/C), -863(C/A), -857(C/T), -307(G/A), and -237(G/A) in two clinically well-defined groups of white patients (British [UK] and Dutch [NL]) with sarcoidosis, each with their own control subjects. Polymorphisms were determined using SSP-PCR. A total of 772 individuals were studied (96 UK patients, 354 UK control subjects, 100 NL patients, 222 NL controls). A significant increase in the rarer TNF -857T allele was found in both sarcoidosis populations. In total 25.5% of the sarcoid patients carried the TNF -857T allele versus 14.1% of the control subjects (p = 0.003, p(c) = 0.02). In the sarcoidosis group the allele frequency of this polymorphism was 13.5% versus 7.3% in the control subjects (p = 0.0003, p(c) = 0.002). Subgroup analysis showed a significant increase in the rarer TNF -307A (TNF-2) allele in patients with Löfgren's syndrome (p = 0.006, p(c) = 0.03). Our finding does not necessarily imply that the two polymorphisms relate to different functions; it may be that one or both are in linkage disequilibrium with the causal site. This requires further studies of functionality and linkage disequilibrium.

Gene Frequency↗

PubMed2006

Embryonic pig pancreatic tissue transplantation for the treatment of diabetes.

BACKGROUND: Transplantation of embryonic pig pancreatic tissue as a source of insulin has been suggested for the cure of diabetes. However, previous limited clinical trials failed in their attempts to treat diabetic patients by transplantation of advanced gestational age porcine embryonic pancreas. In the present study we examined growth potential, functionality, and immunogenicity of pig embryonic pancreatic tissue harvested at different gestational ages. METHODS AND FINDINGS: Implantation of embryonic pig pancreatic tissues of different gestational ages in SCID mice reveals that embryonic day 42 (E42) pig pancreas can enable a massive growth of pig islets for prolonged periods and restore normoglycemia in diabetic mice. Furthermore, both direct and indirect T cell rejection responses to the xenogeneic tissue demonstrated that E42 tissue, in comparison to E56 or later embryonic tissues, exhibits markedly reduced immunogenicity. Finally, fully immunocompetent diabetic mice grafted with the E42 pig pancreatic tissue and treated with an immunosuppression protocol comprising CTLA4-Ig and anti-CD40 ligand (anti-CD40L) attained normal blood glucose levels, eliminating the need for insulin. CONCLUSIONS: These results emphasize the importance of selecting embryonic tissue of the correct gestational age for optimal growth and function and for reduced immunogenicity, and provide a proof of principle for the therapeutic potential of E42 embryonic pig pancreatic tissue transplantation in diabetes.

Abatacept↗

PubMed1992

Changes in actin state and chemotactic peptide receptor expression in granulocytes during cytokine administration after autologous bone marrow transplantation.

We studied the changes in actin state and chemotactic peptide receptor expression in granulocytes from patients receiving different cytokines following high dose chemotherapy and autologous bone marrow transplantation (ABMT). The F-actin content in granulocytes was higher in all patients following ABMT. However, in patients receiving granulocyte colony-stimulating factor (G-CSF) and macrophage colony-stimulating factor (M-CSF) the increase in F-actin content was much greater than in those not receiving these cytokines (159, 149, and 90% for G-CSF, M-CSF, and noncytokine group, respectively). Patients receiving granulocyte-macrophage colony-stimulating factor (GM-CSF) had only a 62% increase in the F-actin content, which was not statistically significant from patients undergoing ABMT without any cytokines. Although the basal level of F-actin was high following ABMT, granulocytes from all patients showed an additional increase in F-actin content after stimulation with either the chemotactic peptide N-formyl-methionyl-leucyl-phenylalanine (FMLP) or phorbol myristate acetate (PMA). The chemotactic peptide receptor expression was significantly higher in patients treated with ABMT alone or ABMT plus G-CSF. These observations suggest that the granulocytes generated following ABMT and cytokine administration may have different functional potential depending on the cytokine administered. Further studies to evaluate these potential differences are essential to devise optimal therapeutic protocols for maximizing the granulocyte protective function in this clinical setting.

Actins↗

PubMed1992

Differential function of intestinal intraepithelial lymphocyte subsets.

It has been proposed that intestinal intraepithelial lymphocytes (I-IEL) perform immune surveillance of the epithelial layer (1) and regulate mucosal humoral responses to exogenous Ag (2). To better understand the functional potential of this unique population, purified murine I-IEL were analyzed phenotypically and functionally. Initial studies determined that I-IEL could be distinguished based on several phenotypic characteristics including: TCR (TCR-alpha beta vs TCR-gamma delta); Thy-1, CD45R/B220, CD5, and CD8 (CD8 alpha alpha vs CD8 alpha beta) expression. Using anti-TCR mAb, individual I-IEL subsets were activated and examined functionally. Both TCR-alpha beta and TCR-gamma delta I-IEL were found to synthesize an array of lymphokines that included IL-2, IL-3, and IL-6 but not IL-4 or IL-5. Additionally, a number of lymphokines were detected that directly influence epithelial function (IFN-gamma, TNF-alpha, and TGF-beta 1). However, the majority of the I-IEL function was localized within the Thy-1+, CD45R/B220- I-IEL subset. In addition those TCR-alpha beta I-IEL expressing the CD8 alpha beta heterodimer were more easily activated. Thus, a subset of I-IEL have the capacity to respond to TCR-mediated stimuli. The functional activities of these cells may influence both local immune cell populations as well as epithelial differentiation.

Animals↗