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Inefficient membrane targeting, translocation, and proteolytic processing by signal peptidase of a mutant preproparathyroid hormone protein.

A preproparathyroid hormone allele from a patient with familial isolated hypoparathyroidism was shown to have a single point mutation in the hydrophobic core of the signal sequence. This mutation, changing a cysteine to an arginine codon at the -8 position of the signal peptide, was associated with deleterious effects on the processing of preproparathyroid hormone to proparathyroid hormone in vitro. To examine the biochemical consequence(s) of this mutation, proteins produced by cell-free translation of wild-type and mutant cRNAs were used in assays that reconstitute the early steps of the secretory pathway. We find that the mutation impairs interaction of the nascent protein with signal recognition particle and the translocation machinery. Moreover, cleavage of the mutant signal sequence by solubilized signal peptidase is ineffective. The consequence of this mutation on processing and secretion of parathyroid hormone is confirmed in intact cells by pulse-chase experiments following transient expression of the mutant protein in COS-7 cells. The inability of the mutant signal sequence, however, to interfere with the targeting and processing of other secreted proteins does not support obstruction of the translocation apparatus as the mechanism underlying the dominant mode of inheritance of hypoparathyroidism in this family.

Alleles↗

Concordant loss of imprinting of the human insulin-like growth factor II gene promoters in cancer.

The human insulin-like growth factor II (IGFII) gene has been shown to be imprinted for the promoters P2, P3, and P4 but not for the promoter P1 in liver and chondrocytes. Loss of imprinting of the IGFII gene has been found in a variety of human tumors including rhabdomyosarcoma and lung cancer. In this report, we determined whether loss of imprinting in tumors displays a promoter-specific pattern. We examined allelic expression of all four IGFII promoters in rhabdomyosarcoma, lung cancer, and normal skeletal muscle. We demonstrate that the imprinting of all IGFII promoters is relaxed in rhabdomyosarcoma and lung cancer. These data suggest that loss of imprinting of IGFII gene promoters may be regulated coordinately by a common mechanism in these tumors. Unexpectedly, we also found that P1, in addition to P2, P3, and P4 is monoallelically expressed in three informative adult skeletal muscle tissues. This indicates that imprinting of the IGFII promoter P1 occurs in a tissue-specific manner.

Adult↗

Localization of filamin in smooth muscle.

The distribution of contractile and cytoskeletal proteins in smooth muscle has been mapped by immunocytochemical methods, with special reference to the localization of the actin-binding protein, filamin. Immunolabeling of ultrathin sections of polyvinylalcohol-embedded smooth muscle distinguished two domains in the smooth muscle cell: (a) actomyosin domains, made up of continuous longitudinal arrays of actin and myosin filaments, and (b) longitudinal, fibrillar, intermediate filament domains, free of myosin but containing actin and alpha-actinin-rich dense bodies. Filamin was found to be localized specifically in the latter intermediate filament-actin domains, but was excluded from the core of the dense bodies. Filamin was also localized close to the cell border at the inner surface of the plasmalemma-associated plaques. In isolated cells the surface filamin label showed a rib-like distribution similar to that displayed by vinculin. It is speculated that the two domains distinguished in these studies may reflect the existence of two functionally distinct systems: an actomyosin system required for contraction and an intermediate filament-actin system, with associated gelation proteins, that is responsible, at least in part, for the slow relaxation and tone peculiar to smooth muscle.

Animals↗

Identification of mutations associated with peroxisome-to-mitochondrion mistargeting of alanine/glyoxylate aminotransferase in primary hyperoxaluria type 1.

We have previously shown that in some patients with primary hyperoxaluria type 1 (PH1), disease is associated with mistargeting of the normally peroxisomal enzyme alanine/glyoxylate aminotransferase (AGT) to mitochondria (Danpure, C.J., P.J. Cooper, P.J. Wise, and P.R. Jennings. J. Cell Biol. 108:1345-1352). We have synthesized, amplified, cloned, and sequenced AGT cDNA from a PH1 patient with mitochondrial AGT (mAGT). This identified three point mutations that cause amino acid substitutions in the predicted AGT protein sequence. Using PCR and allele-specific oligonucleotide hybridization, a range of PH1 patients and controls were screened for these mutations. This revealed that all eight PH1 patients with mAGT carried at least one allele with the same three mutations. Two were homozygous for this allele and six were heterozygous. In at least three of the heterozygotes, it appeared that only the mutant allele was expressed. All three mutations were absent from PH1 patients lacking mAGT. One mutation encoding a Gly----Arg substitution at residue 170 was not found in any of the control individuals. However, the other two mutations, encoding Pro----Leu and Ile----Met substitutions at residues 11 and 340, respectively, cosegregated in the normal population at an allelic frequency of 5-10%. In an individual homozygous for this allele (substitutions at residues 11 and 340) only a small proportion of AGT appeared to be rerouted to mitochondria. It is suggested that the substitution at residue 11 generates an amphiphilic alpha-helix with characteristics similar to recognized mitochondrial targeting sequences, the full functional expression of which is dependent upon coexpression of the substitution at residue 170, which may induce defective peroxisomal import.

Alanine Transaminase↗

The DMPK gene of severely affected myotonic dystrophy patients is hypermethylated proximal to the largely expanded CTG repeat.

Using methylation-sensitive restriction enzymes, we characterized the methylation pattern on the 5' side of the CTG repeat in the DMPK gene of normal individuals and of patients affected with myotonic dystrophy, showing expansions of the repetitive sequence. The gene segment analyzed corresponds to the genomic SacI-HindIII fragment carrying exons 11-15. There is constitutive methylation in intron 12 at restriction sites of SacII and HhaI, localized 1,159-1,232 bp upstream of the CTG repeat, whereas most, if not all, of the other sites of SacII, HhaI, and HpaII in this region are unmethylated, in normal individuals and most of the patients. In a number of young and severely affected patients, however, complete methylation of these restriction sites was found in the mutated allele. In most of these patients, the onset of the disease was congenital. Preliminary in vivo footprinting data gave evidence for protein-DNA contact in normal genes at an Sp1 consensus binding site upstream of the CTG repeat and for a significant reduction of this interaction in cells with a hypermethylated DMPK gene.

Adolescent↗

Increased frequency of genomic alterations in Staphylococcus aureus during chronic infection is in part due to phage mobilization.

We assessed the nature and frequency of genome alterations in Staphylococcus aureus during chronic lung infection in patients with cystic fibrosis (CF) and during colonization of the nares in healthy individuals. Only individuals harboring the same S. aureus clone on consecutive samplings were included in the present study. Clone definition was based on pulsed-field gel electrophoresis (PFGE) analysis. Minor fragment variations in consecutive clones were interpreted as genome alterations. The frequency of genome alterations was significantly higher in S. aureus derived from patients with CF (mean time, 1.03 years) than in isolates derived from healthy individuals (mean time, 13.4 years). In total, 19 S. aureus strain pairs showing genome alterations were available for molecular analysis to clarify the nature of recombinational events in the host environment. In 8 cases, genome alteration could be linked to phage mobilization. Phage conversion of beta-toxin production was evident in 7 pairs. In 1 strain pair, changes in the PFGE pattern were accompanied by deletion of a phage similar to ETA. Obviously, phage mobilization plays an important role in vivo. During long-term lung infection in patients with CF, the specific host response and/or the regular exposure to antibiotics exercises strong selective pressure on the pathogen. Genome plasticity may facilitate the adaptation to various host conditions.

Bacterial Typing Techniques↗

Interferon-alpha 2 variants in the human genome.

Variants of human leukocyte interferon alpha 2 (IFN-alpha 2a, alpha 2b, and alpha 2c) differ from each other by changes in their coding regions at nucleotide positions 137 and 170. As a result of these nucleotide variations, the DNA sequences of the three variants can be distinguished by selective restriction enzyme analysis. Human genomic DNA obtained from over 28,000 normal healthy individuals was used as templates in the polymerase chain reaction (PCR) to amplify the human IFN-alpha 2 gene sequence. The resulting PCR products were analyzed with restriction nucleases to identify the specific IFN-alpha 2 variant sequences present in the genomic DNA of the population examined. The results show that IFN-alpha 2b was detected as the predominant species and IFN-alpha 2c as a very minor species (< 0.1%). The IFN-alpha 2a gene was not detected in this population.

Alleles↗

Interferon-alpha 8b is the only variant of interferon-alpha 8 identified in a large human population.

Three variants of human interferon (IFN)-alpha 8a gene, that is, IFN-alpha 8b, and IFN-alpha 8c, have been reported previously. They differ from each other by changes in their coding region at nucleotide positions 359-360, 372, and 550. Human genomic DNA obtained from over 28,000 healthy blood donors and from 4 human cell lines was used in the polymerase chain reaction (PCR) designed for specific amplification of the IFN-alpha 8 gene fragments. The resulting PCR product was analyzed by (1) restriction endonuclease digestion, (2) DNA sequencing, and (3) allele-specific secondary PCR amplification. Only one sequence for IFN-alpha 8 was identified, and that was for IFN-alpha 8b. The sequences for IFN-alpha 8a and IFN-alpha 8c were not detected after PCR amplification either in the pooled leukocytes obtained from > 28,000 individuals or in cell lines tested. These data suggest that the naturally occurring variant or allele for IFN-alpha 8 in the population is IFN-alpha 8b. IFN-alpha 8a and IFN-alpha 8c variants were consistently below the level of detection of the assays and, if present at all in the population, are very rare.

Alleles↗

Determination of interferon-alpha2 allele composition in the genomic DNA from healthy volunteers and leukemic patients in Japan.

The three interferon-alpha2 (IFN-alpha2) sequences identified to date differ from each other in just two nucleotide positions, both of which result in changes in amino acids. Thus, the mature IFN-alpha2a protein product is characterized by a lysine residue at position 23 (AAA) and a histidine at position 34 (CAA), IFN-alpha2b has an arginine at position 23 (AGA) and histidine at position 34 (CAT), and IFN-alpha2c has arginine residues at both positions 23 (AGA) and 34 (CGT). These nucleotide variations in the DNA sequence can be distinguished by selective restriction enzyme analysis. We studied the distributions of the three IFN-alpha2 variants by analyzing chromosomal DNA from 103 Japanese volunteers and 33 patients with hematologic disorders. Fragments of 238 bp and 617 bp of the IFN-alpha2 gene containing codons 23 and 34 were amplified by PCR using specific primers, and the PCR products were analyzed with specific restriction nucleases to identify the IFN-alpha2 variant sequences. Only IFN-alpha2b gene was detected in normal volunteers, and no IFN-alpha2a gene was detected in Japanese subjects. However, IFN-alpha2c was detected in 4 of 33 (12.1%) patients with leukemia.

Adult↗

Mining SARS-CoV protease cleavage data using non-orthogonal decision trees: a novel method for decisive template selection.

MOTIVATION: Although the outbreak of the severe acute respiratory syndrome (SARS) is currently over, it is expected that it will return to attack human beings. A critical challenge to scientists from various disciplines worldwide is to study the specificity of cleavage activity of SARS-related coronavirus (SARS-CoV) and use the knowledge obtained from the study for effective inhibitor design to fight the disease. The most commonly used inductive programming methods for knowledge discovery from data assume that the elements of input patterns are orthogonal to each other. Suppose a sub-sequence is denoted as P2-P1-P1'-P2', the conventional inductive programming method may result in a rule like 'if P1 = Q, then the sub-sequence is cleaved, otherwise non-cleaved'. If the site P1 is not orthogonal to the others (for instance, P2, P1' and P2'), the prediction power of these kind of rules may be limited. Therefore this study is aimed at developing a novel method for constructing non-orthogonal decision trees for mining protease data. RESULT: Eighteen sequences of coronavirus polyprotein were downloaded from NCBI (http://www.ncbi.nlm.nih.gov). Among these sequences, 252 cleavage sites were experimentally determined. These sequences were scanned using a sliding window with size k to generate about 50,000 k-mer sub-sequences (for short, k-mers). The value of k varies from 4 to 12 with a gap of two. The bio-basis function proposed by Thomson et al. is used to transform the k-mers to a high-dimensional numerical space on which an inductive programming method is applied for the purpose of deriving a decision tree for decision-making. The process of this transform is referred to as a bio-mapping. The constructed decision trees select about 10 out of 50,000 k-mers. This small set of selected k-mers is regarded as a set of decisive templates. By doing so, non-orthogonal decision trees are constructed using the selected templates and the prediction accuracy is significantly improved.

Algorithms↗

A complete and a truncated U1 snRNA gene of Drosophila melanogaster are found as inverted repeats at region 82E of the polytene chromosomes.

A phage containing two sequences homologous to U1 snRNA was isolated from a Drosophila melanogaster genomic library, and identified with a previously cloned D. melanogaster U1 snRNA gene. DNA sequence analysis showed that complete and truncated U1 snRNA genes are present, both of which have base substitutions relative to U1 snRNA. These genes show conservation of 5' and 3' flanking regions relative to other U1 and U2 snRNA genes of Drosophila. Intramolecular renaturation experiments and electron microscope mapping demonstrates that the two U1 snRNA sequences are present as inverted repeats about 2.7kb apart, separated by a smaller pair of inverted repeats of an unrelated sequence. These U1 snRNA sequences were located by in situ hybridization at 82E, and related sequences were found at 21D and 95C on the polytene chromosome map. The results are discussed with reference to the origin and function of snRNAs.

Animals↗

Detection of a specific mitochondrial DNA deletion in tissues of older humans.

Using PCR, we found that normal heart muscle and brain from adult human individuals contain low levels of a specific mitochondrial DNA deletion, previously found only in patients affected with certain types of neuromuscular disease. This deletion was not observed in fetal heart or brain. Experimental tests support the idea that the deletion exists in vivo in adult mitochondria and is not an in vitro artifact of PCR. Our data provide direct experimental support for the idea that accumulation of mitochondrial DNA deletions may be important in aging.

Adult↗

euHCVdb: the European hepatitis C virus database.

The hepatitis C virus (HCV) genome shows remarkable sequence variability, leading to the classification of at least six major genotypes, numerous subtypes and a myriad of quasispecies within a given host. A database allowing researchers to investigate the genetic and structural variability of all available HCV sequences is an essential tool for studies on the molecular virology and pathogenesis of hepatitis C as well as drug design and vaccine development. We describe here the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes. The annotations include genome mapping of sequences, use of recommended nomenclature, subtyping as well as three-dimensional (3D) molecular models of proteins. A WWW interface has been developed to facilitate database searches and the export of data for sequence and structure analyses. As part of an international collaborative effort with the US and Japanese databases, the European HCV Database (euHCVdb) is mainly dedicated to HCV protein sequences, 3D structures and functional analyses.

Databases, Protein↗

Mapping the chicken genome.

Most economically important traits are genetically complex and controlled by numerous genes. A quality genetic map is a prerequisite for identifying quantitative trait loci (QTL) that contain the genes involved in these traits. Currently, there are two internationally recognized reference families that are used to build genetic maps. In this paper, the East Lansing (EL) genetic map is described in detail. Presently, the EL genetic map contains 617 genetic markers, of which 589 are resolved into 41 linkage groups. The map coverage within linkage groups is over 2,700 cM, which is about the estimated size of the chicken genome. There are 322 microsatellite markers, which greatly enhances the utility of this genetic map for genome-wide QTL searches. Also, 101 genes have been mapped, which will aid in the development of a comparative map. Further efforts to improve the genetic map and the potential for the map to identify QTL are discussed.

Animals↗

Mutation analysis and association studies of the UCHL1 gene in German Parkinson's disease patients.

Recently, an Ile93Met substitution has been identified in the ubiquitin carboxy-terminal hydrolase L1 (UCHL1) gene in a single German PD family with autosomal dominant inheritance. To determine whether mutations in the UCHL1 gene are causative for Parkinson's disease (PD) a detailed mutation analysis was performed in a large sample of German sporadic and familial PD patients. We found no disease-causing mutation in the coding region of the UCHL1 gene. Direct sequencing revealed six intronic polymorphisms in the UCHL1 gene. Analysis of an S18Y polymorphism in exon 3 of the UCHL1 gene in sporadic PD patients and controls showed carriers of allele 2 (tyrosine) significantly less frequent in patients with a reduced risk of 0.57 (CI = 0.36-0.88; p = 0.012, p(c) = 0.047, chi2 = 6.31). Our study shows that sequence variations in the coding region of UCHL1 are a rare event. A protective effect of a certain UCHL1 variant in the pathogenesis of sporadic PD is suggested, underlining the relevance of UCHL1 in neurodegeneration.

Aged↗

A critical review of clinical applications of topographic mapping of brain potentials.

A brief review of several aspects of topographic mapping of brain potentials is presented. Some general factors of importance for the construction of brain maps are considered, namely, how to sample in space and how to deal with the influence of the reference electrode. The issue of what is a representative map is examined for the cases of both steady and dynamic states. Special attention is paid to the methodology of assessing whether a brain map may be considered "normal" or "abnormal" on the basis of multivariate statistical considerations. Besides being used to visualize statistical comparisons between sets of EEG data, brain maps may be used as a first step for a model-based analysis in order to estimate the localization of equivalent dipolar sources of the electrical activity within the brain. The question of whether brain maps may yield added value to multivariate quantitative EEG analysis is examined for the following clinical cases: (1) developmental disorders; (2) space-occupying lesions; (3) epilepsy; (4) cerebrovascular diseases; (5) dementia; and (6) psychiatric diseases. It is concluded that brain mapping may be valuable as a comprehensive and attractive form of data reduction to represent a complex set of multichannel (optimally at least 64) EEG signals, but only if the user is well aware of the pitfalls involved. Brain mapping might supplement quantitative topographic analysis if it can be used as the basis for solving the inverse problem in EEG. More extensive and well-controlled studies are necessary in order to establish the clinical value of complementing a routine EEG examination with brain mapping.

Brain↗

Identification of "premyelination" by diffusion-weighted MRI.

OBJECTIVE: The purpose of this study was to compare white matter maturation as demonstrated with diffusion-weighted MRI and with myelin-sensitive histological staining. MATERIALS AND METHODS: The diffusion-, T1-, and T2-weighted SE MRI at 4.7 T was performed weekly in a total of 16 rat pups, aged from 5 days to 8 weeks, 2 animals evaluated per week. Heavily diffusion-weighted sequences were obtained with the diffusion-sensitizing gradient switched alternately in two orthogonal directions. To enhance signal intensity of anisotropic structures, a synthesized image (referred to as the "anisotropy index map") was constructed from the ratio of pairs of images acquired with diffusion sensitization of identical magnitude but orthogonal direction sensitivity. The anisotropy index maps were used for comparison with T1-weighted and heavily T2-weighted SE sequences and histological sections, respectively. RESULTS: The first evidence of diffusion anisotropy on anisotropy index maps preceded initial myelin as well as neurofibril staining by 5-12 days and T2 shortening by 2 weeks. The T1-weighted sequences did not yield visible changes and were not helpful for the assessment of ongoing white matter maturation in this model. CONCLUSION: Magnetic resonance imaging signal intensity changes based on anisotropic water diffusion were demonstrated in regions of unmyelinated cerebral white matter tracts of albino rat pups before the onset of histologically detectable myelin. The ability of in vivo mapping of premyelinating white matter maturation indicates a new diagnostic use of MRI in evaluating cerebral white matter maturation.

Animals↗