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Paget's disease of bone in the French population: novel SQSTM1 mutations, functional analysis, and genotype-phenotype correlations.

UNLABELLED: Mutation screening of the SQSTM1 gene in 94 French patients with PDB revealed two novel point-mutations (A381V and L413F) and two new compound heterozygous genotypes (P392L/A381V and P392L/A390X). Functional analysis showed an increased level of SQSTM1/p62 protein in PDB patients and truncated forms of the protein encoded by the A390X allele. Clinical data indicate that PDB patients with SQSTM1 mutation are younger at PDB diagnosis and have more extensive bone lesions. INTRODUCTION: Paget's disease of bone (PDB) is a common chronic disease of the skeleton, with a strong genetic component. A recurrent mutation (P392L) was first identified on chromosome 5, in the Sequestosome 1 (SQSTM1) gene. Several other mutations of the SQSTM1 gene have been described in PDB patients, affecting the ubiquitin-associated domain (UBA) of the SQSTM1/p62 protein. The objectives of this study were to evaluate the frequency of the SQSTM1 mutations in French PBD patients, to study the expression of the SQSTM1/p62 protein, and to search for genotype-phenotype correlations. MATERIALS AND METHODS: Blood was obtained from 94 unrelated French PDB patients and 100 controls for mutation screening of exons 7 and 8, encoding for the UBA domain of SQSTM1. Epstein-Barr virus (EBV)-immortalized B-cell lymphocytes were established from 13 patients, giving access to functional analysis of the gene and the SQSTM1/p62 expressions using real-time PCR and Western blot. RESULTS: Mutations of the SQSTM1 gene were identified in 12 of the 94 PDB patients (13%). Eight patients carried P392L. Two novel missense mutations were identified: L413F and A381V. This A381V mutation and A390X were found in distinct patients already carriers of P392L. The SQSTM1/p62 protein expression in PDB patients increased when zero, one, or two mutations were present, and SQSTM1 truncated forms were associated with the A390X mutation. The mean age of PDB diagnosis was younger in patients with the SQSTM1 mutation. PDB was more extensive in patients who carried a SQSTM1 mutation. CONCLUSIONS: Mutations of SQSTM1 are present in the French population. PDB patients with and without the SQSTM1 mutation have an increased level of SQSTM1/p62, caused by overproduction of the protein, probably involved in the pathophysiology of PDB. The presence of the SQSTM1 mutation may be a worsening factor for PDB.

Adaptor Proteins, Signal Transducing↗

Functional analysis and occupational standards: their role in curriculum development.

National Vocational Qualifications and national occupational standards have been criticized by many academics and professionals, seemingly without a true knowledge of the processes and principles that underpin their development. This paper attempts to clarify the role that functional analysis and occupational standards can play in meeting the demands of central government and purchasers in providing educational programmes that meet individual, organizational and society's needs. An overview of the processes and principles relating to functional analysis and occupational standards is provided, and issues arising from their incorporation into professional education programmes are debated.

Benchmarking↗

Functional analysis of separate topographies of aberrant behavior.

We conducted a functional analysis of distinct topographies of aberrant behavior displayed by 4 clients. We first analyzed the behaviors in an aggregate fashion and then separated the behaviors to formulate hypotheses about the maintaining variables for each behavior. The procedures were used in a two-phase experiment. During Phase 1, two extended functional analyses were completed, one in an inpatient unit and one in a special education classroom. During Phase 2, two brief functional analyses were completed in an outpatient clinic. Results indicated that hypotheses of separate functions for distinct behaviors can be generated using both extended and brief functional analyses when the results are graphed in the aggregate and are separated by response topography. The results also suggest that these methods can improve the accuracy of data interpretation and treatment selection.

Adult↗

Coherence function analysis of the higher-order aberrations of the human eye.

We measured the wavefront aberrations of the eyes of five subjects with a Shack-Hartmann sensor sampling at 21.2 Hz and decomposed the measurements into Zernike aberration terms up to and including the fifth radial order. Coherence function analysis was used to determine the common frequency components between the aberrations within subjects. We found the results to be highly subject dependent. The coherence values were typically <0.4. Possible reasons for this are discussed. Coherence function analysis is a useful tool that can be used in future investigations to determine correlations between the aberration dynamics of the eye and other physiological mechanisms.

Adult↗

Convective-dispersive characteristics of tracer transport calculated from transfer function analysis of biological indicator-dilution curves.

A solution to the convection-dispersion model of tracer transport in biological systems is presented. This solution provides for the characterization of tracer transport through a network of blood vessels based on the tracer transients recorded at the inlet and outlet points of the circulation under investigation. Fourier transformations of the transients are used to produce a transfer function from which the mean transit time as well as other transport characteristics can be calculated. The practical aspects of applying transfer function analysis to retrieve transport characteristics under experimental conditions are also presented. The application demonstrates the efficacy of the transfer function analysis method independent of tracer recirculation effects and a priori knowledge of actual tracer concentrations.

Biological Transport↗

Time autocorrelation function analysis of master equation and its application to atomic clusters.

We derive the energy fluctuation Delta(2)E, and the time autocorrelation kappa(tau) and its Fourier transformation--the fluctuation spectra S(omega)--of the master-equation transition matrix. The contribution from each eigenmode of the transition matrix to these fluctuation quantities reveals the relevant importance of the individual mode in the relaxation processes. The time scales associated with these relaxation processes are determined by the corresponding eigenvalues. Unlike traditional time evolution analysis, the autocorrelation function and fluctuation spectra analysis does not involve an arbitrary initial population. It is also more suitable for analyzing the underlying dynamic, kinetic behavior near the equilibrium and the behavior of the long-time-scale rare events. We utilize our technique to analyze the solid-liquid phase coexistence of the 13-atom Morse cluster and the fcc-to-icosahedral structure transition of the 38-atom Lennard-Jones cluster. For the processes studied, the fluctuation spectra from the master equation simplify the analysis of the transition matrix, and the important relaxation modes are easily extracted.

Chemistry, Physical↗

Functional analysis of the regulatory region of polyoma mutant F9-1 DNA.

Functional analysis of the transcriptional control region of the polyoma (Py) mutant F9-1 reveals that the mutation is located in a region of Py DNA required for at least two functions. First, an enhancer element which includes the F9-1 mutation was characterized by deletion analysis. This element, described previously as enhancer B is essential for viral early gene expression in F9 stem cells whereas enhancer A is unnecessary for transcriptional activity in embryonal carcinoma (EC) cells. Second, a CCACCC motif, present twice in the 3' part of enhancer B is also required in cis for the response to a heterologous enhancer. This suggests that a promoter element is present in this region of the polyoma genome which overlaps Py enhancer B. We also demonstrate the enhancement of the polyoma early promoter activity in F9 stem cells by MSV sequences. The significance of these observations is discussed.

Acetyltransferases↗

Applying functional analysis to psychological rehabilitation following spinal cord injury.

There have been numerous attempts to categorize the responses of individuals to spinal trauma on the basis of generalized stage theories of grief reaction, and personality theory. A number of these studies are critically appraised and a behavioral model, based on functional analysis, is proposed as a more constructive framework for future research. Such an approach is applied clinically to the activities and development of the Clinical Psychology Service provided to the Mersey Regional Spinal Injuries Centre in Southport, England. A number of examples of clinical and research practice are included, highlighting the applicability of functional analysis to individual and systems level investigations.

Adaptation, Psychological↗

Mechanisms for renal blood flow control early in diabetes as revealed by chronic flow measurement and transfer function analysis.

The purpose of this study was to establish the roles of the myogenic response and the TGF mechanism in renal blood flow (RBF) control at the very earliest stages of diabetes. Mean arterial pressure (MAP) and RBF were measured continuously, 18 h/d, in uninephrectomized control and diabetic rats, and transfer function analysis was used to determine the dynamic autoregulatory efficiency of the renal vasculature. During the control period, MAP averaged 91 +/- 0.5 and 89 +/- 0.4 mmHg, and RBF averaged 8.0 +/- 0.1 and 7.8 +/- 0.1 ml/min in the control and diabetic groups, respectively. Induction of diabetes with streptozotocin caused a marked and progressive increase in RBF in the diabetic rats, averaging 10 +/- 6% above control on day 1 of diabetes and 22 +/- 3 and 34 +/- 1% above control by the end of diabetes weeks 1 and 2. MAP increased approximately 9 mmHg during the 2 wk in the diabetic rats, and renal vascular resistance decreased. Transfer function analysis revealed significant increases in gain to positive values over the frequency ranges of both the TGF and myogenic mechanisms, beginning on day 1 of diabetes and continuing through day 14. These very rapid increases in RBF and transfer function gain suggest that autoregulation is impaired at the very onset of hyperglycemia in streptozotocin-induced type 1 diabetes and may play an important role in the increase in RBF and GFR in diabetes. Together with previous reports of decreases in chronically measured cardiac output and hindquarter blood flow, this suggests that there may be differential effects of diabetes on RBF versus nonrenal BF control.

Albuminuria↗

Ciliary function analysis for the diagnosis of primary ciliary dyskinesia: advantages of ciliogenesis in culture.

The gold standard for the diagnosis of primary ciliary dyskinesia (PCD) is a dynein deficiency shown with transmission electron microscopy. However, there are many cases of PCD without dynein deficiency. When considering ciliary function, there are similar problems of sensitivity in diagnosis and there is also a major lack of specificity. Based on the normal ciliary function and ultrastructure and the absence of secondary abnormalities after ciliogenesis in sequential monolayer-suspension culture, the diagnostic value of ciliary function analysis after ciliogenesis was investigated in more than 70 PCD and 640 non-PCD cases. In biopsies, ciliary immotility was found in 66% of PCD cases but was also found in 8% of non-PCD cases. PCD was later confirmed in 61% of the biopsies with ciliary immotility. Normal ciliary beat frequency (CBF) was found in 20% of PCD biopsies. Coordinated ciliary activity was observed in 10% of PCD cases. After ciliogenesis in culture, ciliary immotility was present in 78% of the PCD cases but never in non-PCD cases. CBF was normal after ciliogenesis in 7% of the PCD cases and was always found in non-PCD cases. Absence of coordinated ciliary activity was found in 100% of PCD cases and 0% of non-PCD cases. In conclusion, while ciliary function analysis in a biopsy never proves, nor excludes the diagnosis of PCD, after ciliogenesis in culture CBF measurement can be diagnostic for PCD and reaches 100% specificity and sensitivity when considering coordinated ciliary activity, making it the single 100% diagnostic parameter for PCD.

Biopsy↗

High-efficiency identification of genes by functional analysis from a retroviral cDNA expression library.

Retroviral gene transfer efficiently delivers genes of interest stably into target cells, and expression cDNA cloning has been shown to be highly successful. Considering these two advantages, we now report a method by which one can identify genes stimulating cell growth through functional analysis. The first step requires the construction of a retroviral cDNA expression library and the optimization of transfection of vector DNA into virus packaging cells. The second step involves the cocultivation of target cells with libraries of retrovirus-producing cells, resulting in the amplification of target cells transduced with a gene(s) stimulating cell growth. Under standardized conditions of transfection, we detected an average of 4,000 independent clones per dish, among which expression of a retroviral beta-galactosidase gene at an abundance of 0.2% could be detected. Next, we demonstrated the augmentation of the sensitivity of the assay by retroviral infection and functional analysis. We did this by cocultivating factor-dependent (FD) cells with dishes of GP/E cells transfected with plasmids containing various molar ratios of pN2-IL3 DNA and retroviral library cDNA and by determining the highest dilution of pN2-IL3 which still resulted in the conversion of FD cells to factor independence. The retroviral interleukin-3 gene at an abundance as low as 0.001% could be detected. Indeed, we were able to detect from FD cells the development of factor-independent colonies with different phenotypes after retroviral transfer of cDNAs from an immortalized hemopoietic stem cell line. Thus, the combination of a standardized high-efficiency DNA transfection and retrovirus-mediated gene transfer should facilitate the identification of genes capable of conferring to target FD cells a detectable new function or phenotype. By scaling up the size of the experiment realistically during screening, the assay can detect cDNA at an abundance of lower than 0.0001%.

Animals↗

One-step synthesis of labeled sugar nucleotides for protein O-GlcNAc modification studies by chemical function analysis of an archaeal protein.

Herein we present the chemical function analysis of a recombinant sugar nucleotidyltransferase from the hyperthermophile Pyrococcus furiosus and its use in the one-pot synthesis of chloroacetyl- and alkyne-tagged analogues of uridinediphospho-N-acetylglucosamine (UDP-GlcNAc). The gene was originally annotated as a glucose-1-phosphate deoxythymidylyltransferase; however, kinetic analysis of a panel of sugar-1-phosphates with the protein shows that it is better described as a bifunctional protein that synthesizes UDP-GlcNAc from glucosamine-1-phosphate and acetyl coenzyme A (CoA). A new mass-spectrometry-based assay for the rapid analysis of the acyltransferase activity demonstrates that the enzyme can also accept cheaper truncated N-acetylcysteamine thioester substrates in place of the natural acetyl CoA. The enzyme can tolerate alkyne or chloride substitutions in the acyl moiety, thereby allowing the facile synthesis of tagged sugar nucleotides for future use in protein O-GlcNAc modification studies.

Archaeal Proteins↗

Molecular cloning and functional analysis of zebrafish neutral ceramidase.

Almost all observations on the functions of neutral ceramidase have been carried out at cellular levels but not at an individual level. Here, we report the molecular cloning of zebrafish neutral ceramidase (znCD) and its functional analysis during embryogenesis. We isolated a cDNA clone encoding znCD by 5' and 3' rapid amplification of cDNA ends-PCR. It possessed an open reading frame of 2,229 base pairs encoding 743 amino acids. A possible signal/anchor sequence near the N terminus and four potential O-glycosylation and eight potential N-glycosylation sites were found in the putative sequence. The enzyme activity at neutral pH increased markedly after transformation of Chinese hamster CHOP and zebrafish BRF41 cells with the cDNA. The overexpressed enzyme was found to be distributed in endoplasmic reticulum/Golgi compartments as well as the plasma membranes. The antisense morpholino oligonucleotide (AMO), which was designed based on the sequence of znCD mRNA, successfully blocked the translation of znCD in a wheat germ in vitro translation system. The knockdown of znCD with AMO led to an increase in the number of zebrafish embryos with severe morphological and cellular abnormalities such as abnormal morphogenesis in the head and tail, pericardiac edema, defect of blood cell circulation, and an increase of apoptotic cells, especially in the head and neural tube regions, at 36 h post-fertilization. The ceramide level in AMO-injected embryos increased significantly compared with that in control embryos. Simultaneous injection of both AMO and synthetic znCD mRNA into one-cell-stage embryos rescued znCD activity and blood cell circulation. These results indicate that znCD is essential for the metabolism of ceramide and the early development of zebrafish.

Amidohydrolases↗

Functional analysis and treatment of severe pica.

A two-phase functional analysis of a profoundly retarded 19-year-old male's pica facilitated the design of an effective intervention containing no aversive components. In the first analysis, frequent staff-client interaction resulted in 25% and 66% less pica than limited and no interaction, respectively. Paradoxical effects were obtained in the second analysis, where no protective helmet resulted in 38% and 26% less pica than the helmet with face shield and helmet without face shield, respectively. On the basis of these analyses, limited interaction and no helmet conditions were combined in an effective, staff-implemented treatment at a medium-sized institution.

Adult↗

Vaccinia as a tool for functional analysis in regenerating limbs: ectopic expression of Shh.

Axolotls, with their extensive abilities to regenerate as adults, provide a useful model in which to study the mechanisms of regeneration in a vertebrate, in hopes of understanding why other vertebrates cannot regenerate. Although the expression of many genes has been described in regeneration, techniques for functional analysis have so far been limited. In this paper we demonstrate a new method for efficient overexpression of foreign genes in axolotls. Using vaccinia virus expressing beta-galactosidase microinjected into regenerating limbs, we show that vaccinia can infect both dividing and nondividing limb cells. The site of infection remains discrete and there is no secondary spread of infection to nearby cells. beta-Gal is expressed at high levels in blastema cells for about a week and in differentiated cells for longer. Blastemas that have been injected with vaccinia at different stages regenerate normally. As a test of the utility of vaccinia for functional analysis in regeneration, we constructed a virus expressing Shh and injected it into the anterior of regenerating limbs. Ectopic Shh expression caused extra digits, carpals, and tarsals in the hands and feet of regenerating limbs, suggesting that despite differences in the timing of expression and the eventual pattern, the function of Shh appears to be similar to that in the developing limbs of other vertebrates. Our results demonstrate that vaccinia virus is an excellent vector for ectopically expressing genes for secreted proteins and is a useful tool to study the function of signaling molecules during the process of regeneration in urodeles.

Ambystoma↗

Functional analysis of eight open reading frames on chromosomes XII and XIV of Saccharomyces cerevisiae.

Deletion, together with basic functional and bioinformatic analyses has been carried out on eight novel ORFs discovered during the sequencing of the Saccharomyces cerevisiae genome. Six ORFs (YLL049w, YLL051c, YLL052c, YLL053c, YLL054c and YLL055w) located on the left arm, and one (YLR130c) on the right arm, of chromosome XII, and an eighth ORF (YNL331c) on the left arm of the chromosome XIV, have been investigated. ORFs were deleted by the SFH-PCR gene-replacement strategy. Basic functional analysis revealed no obvious phenotype for any of the eight ORFs. Bioinformatic analysis, however, revealed possible functions for seven of the ORFs on the basis of the amino acid sequence similarity of their predicted protein products to those of proteins with known functions. ORF YLL051c (FRE6) shows similarity to iron transport proteins, such as ferric reductase. YLL052c and YLL053c appear to be aquaporins. The product of YLL054c (Yll054p) is highly similar to the oleate-specific transcriptional activator protein (Pip2p), which is involved in the peroxisomal induction pathway (pip). ORF YLL055w is similar to Dal5p, allantoate permease, and may play role in allantoin transport. YLR130c (ZRT2) is a low-affinity zinc transporter protein. YNL331c is also named AAD14, which is induced by chemicals that induce oxidative stress by depleting the cell of glutathione.

Chromosomes, Fungal↗

Computational methods for protein function analysis.

Two recent advances have had the greatest impact on protein function analysis so far: the complete sequences of genomes and mRNA expression level profiles. The former has spurred the development of novel techniques to study protein function: phylogenetic profiles and gene clusters. The latter has introduced a method, not based on sequence homology, that enables one to group together functionally related genes.

Animals↗