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Mutations of the human polycystic kidney disease 2 (PKD2) gene.

Autosomal dominant polycystic kidney disease (ADPKD) is an inherited nephropathy, usually of late onset (onset between third to seventh decade), primarily characterized by the formation of fluid-filled cysts in the kidneys. It is one of the most frequent inherited conditions affecting approximately 1:1,000 Caucasians. Two major genes have been identified and characterized in detail: PKD1 and PKD2, mapping on chromosomes 16p13.3 and 4q21-23, respectively. A third gene, PKD3, has been implicated in selected families. Polycystic kidney disease of types 1 or 2 follows a very similar course of symptoms, both being multisystem pleiotropic disorders of indistinguishable picture on clinical grounds. The only difference is that patients with PKD2 mutations run a milder course compared to PKD1 carriers, with an average 10-20 years later age of onset and lower probability to reach end-stage-renal failure. The proteins polycystin-1 and -2 are trans-membranous glycoproteins hypothesized to participate in a common signaling pathway, interacting with each other and with other proteins, and coordinately expressed in normal and cystic tissue. Renal cysts most probably arise after a second somatic event, which inactivates the inherited healthy allele of the same gene, or perhaps one of the alleles of the other gene counterpart, generating a trans-heterozygous state. This article reviews the reported mutations in PKD2. Mutations of all kinds have been reported over the entire sequence of the PKD2 gene, with no apparent significant clustering and with some evidence of genotype/phenotype correlation. Most families harbor their own private mutations but a few recurrent events have been reported in unrelated families.

Genotype↗

Isolation of caudal, a Drosophila homeo box-containing gene with maternal expression, whose transcripts form a concentration gradient at the pre-blastoderm stage.

We report the isolation and characterization of caudal (cad), a previously unknown Drosophila homeo box-containing gene from the 38E region on the left arm of the second chromosome. This homeo box has diverged from the prototype sequence in Antennapedia, but contains subregions which are highly homologous. By Northern analysis and in situ hybridization experiments two transcripts of 2.4 kb were found to accumulate in nurse cells and in the oocyte during oogenesis. These transcripts generate a transient concentration gradient along the antero-posterior axis at the syncytial blastoderm stage. At the cellular blastoderm stage transcripts accumulate in a single band from 13-19% egg length at the posterior end. One zygotic transcript of 2.6 kb is detected. At later stages this transcript is localized in ectodermally and endodermally derived tissues such as the proctodeum, the Malpighian tubules and the posterior midgut. The 2.6-kb transcript is detectable until the onset of metamorphosis.

Journal Article↗

A human phosphatidylinositol 3-kinase complex related to the yeast Vps34p-Vps15p protein sorting system.

Phosphoinositide (PI) 3-kinases have been characterized as enzymes involved in receptor signal transduction in mammalian cells and in a complex which mediates protein trafficking in yeast. PI 3-kinases linked to receptors with intrinsic or associated tyrosine kinase activity are heterodimeric proteins, consisting of p85 adaptor and p110 catalytic subunits, which can generate the 3-phosphorylated forms of phosphatidylinositol (PtdIns), PtdIns4P and PtdIns(4,5)P2 as potential second messengers. Yeast Vps34p kinase, however, has a substrate specificity restricted to PtdIns and is a PtdIns 3-kinase. Here the molecular characterization of a new human PtdIns 3-kinase with extensive sequence homology to Vps34p is described. PtdIns 3-kinase does not associate with p85 and phosphorylates PtdIns, but not PtdIns4P or PtdIns(4,5)P2. In vivo PtdIns 3-kinase is in a complex with a cellular protein of 150 kDa, as detected by immunoprecipitation from human cells. Protein sequence analysis and cDNA cloning show that this 150 kDa protein is highly homologous to Vps15p, a 160 kDa protein serine/threonine kinase associated with yeast Vps34p. These results suggest that the major components of the yeast Vps intracellular trafficking complex are conserved in humans.

Amino Acid Sequence↗

Fat-suppressed three-dimensional MR angiography technique with elliptical centric view order and no prolonged breath-holding time.

PURPOSE: To determine the appropriate rate of fat-suppression pulses (using spec IR-spectral selective inversion recovery) for fat-suppressed 3D magnetic resonance angiography (MRA) with an elliptical centric view order. MATERIALS AND METHODS: In abdominal 3D fast spoiled gradient echo (fast SPGR) with an elliptical centric view order, the spec IR pulse rate was changed from zero to one every 15 repetitions (in nine steps) in eight volunteers. In the equilibrium phase, abdominal contrast-enhanced 3D MRA was obtained by 3D fast SPGR using an elliptical centric view order without fat-suppression and with two spec IR, and by fat-suppressed 3D fast SPGR with a sequential-centric view order (efgre3D) in 18 cases. Fat and vascular signals were estimated. RESULTS: Although 3D fast SPGR using an elliptical centric view order with spec IR placed every 15 TR and efgre3D effectively decreased fat signals, these sequences lengthened the breath-hold by 4-6 seconds compared with non-fat-suppressed sequence. 3D fast SPGR using an elliptical centric view order and two spec IR reduced the fat signal by 30% and provided good 3D MR angiography without substantial prolongation of breath-hold. CONCLUSION: Two spec IR can be used for generation of partially fat-suppressed abdominal 3D MRA without prolongation of the breath-hold when performing 3D fast SPGR using an elliptical centric view order.

Abdomen↗

The identification and characterization of two promoters and the complete genomic sequence for the Wiskott-Aldrich syndrome gene.

The Wiskott-Aldrich syndrome (WAS) is an X-linked disorder characterized by immunodeficiency, eczema and thrombocytopenia. The gene responsible for WAS was identified through positional cloning, and the function of the encoded protein (WASP) is still the subject of much speculation. WASP is currently thought to be involved in the regulation of actin polymerization in hematopoietic cells. To study the elements that regulate the WASP gene, we have identified the sites for transcription initiation. We found that two promoters were responsible for controlling WASP expression. Multiple transcription initiation sites were found immediately adjacent to the translation start site, however an alternate exon with a second promoter region was identified 6 kb upstream. Examination of the 5' sequence adjacent to the initiation sites in both promoters failed to reveal a TATA or CCAAT box, but numerous putative transcription factor binding sites including Sp1, Ets, c-Myb and PU.1 were apparent. Reporter constructs generated from each promoter showed functional activity in the Jurkat T-cell and HEL erythro-megakaryocytic cell lines. Although the alternate exon sequence was extremely GC rich and contained several potential binding elements, the primary promoter was stronger than the upstream promoter in the cell lines assayed. The transcription factor binding site profiles within each promoter suggested that they may play different roles in regulating WASP expression depending on the stage of differentiation and development, and the cell lineage. In this study we have also reported the complete nucleotide sequence of the coding and intervening sequences for the WASP gene. A comprehensive knowledge of the genomic structure and the further characterization of WASP gene expression will facilitate the continued investigation of mutations in WAS patients, and the eventual prospect of gene therapy.

Base Sequence↗

Cloning, in vitro expression, and novel phylogenetic classification of a channel catfish estrogen receptor.

We obtained two channel catfish estrogen receptor (ccER) cDNA from liver of female fish using RT-PCR. The two fragments were identical in sequence except that the smaller one had an out-of-frame deletion in the E domain, suggesting the existence of ccER splice variants. The larger fragment was used to screen a cDNA library from liver of a prepubescent female. A cDNA was obtained that encoded a 581-amino-acid ER with a deduced molecular weight of 63.8 kDa. Extracts of COS-7 cells transfected with ccER cDNA bound estrogen with high affinity (Kd = 4.7 nM) and specificity. Maximum parsimony and Neighbor Joining analyses were used to generate a phylogenetic classification of ccER on the basis of 18 full-length ER sequences. The tree suggested the existence of two major ER branches. One branch contained two clearly divergent clades which included all piscine ER (except Japanese eel ER) and all tetrapod ERalpha, respectively. The second major branch contained the eel ER and the mammalian ERbeta. The high degree of divergence between the eel ER and mammalian ERbeta suggested that they also represent distinct piscine and tetrapod ER. These data suggest that ERalpha and ERbeta are present throughout vertebrates and that these two major ER types evolved by duplication of an ancestral ER gene. Sequence alignments with other members of the nuclear hormone receptor superfamily indicated the presence of 8 amino acids in the E domain that align exclusively among ER. Four of these amino acids have not received prior research attention and their function is unknown. The novel finding of putative ER splice variants in a nonmammalian vertebrate and the novel phylogenetic classification of ER offer new perspectives in understanding the diversification and function of ER.

Amino Acid Sequence↗

Identification of appropriate primitive polynomials to avoid cross-contamination in multifocal electroretinogram responses.

Abstract-The basis of the multifocal/electroretinogram is the use of a decimated m-sequence for simultaneous and independent stimulation of many areas of the visual pathway. The purpose of this study was to investigate the effects of cross-contamination from higher orders of the response. A series of primitive polynomials were found by construction of finite fields. The first-order ERG response was formed by cross-correlation of m-sequence with the physiological response. A second-order response was formed by investigation of particular flash sequences of the stimulation sequence and cross-correlation of a second-order m-sequence with the physiological response. Zech logarithms were used to identify cross-contamination between the various first and second-order sequences. Tables of good and bad primitive polynomials were constructed for degrees 12-16, and the effects of window length and decimation length were examined. When the sequence was decimated into 128 areas, and a window of length 16 was examined, cross-contamination occurred in all sequences generated from primitive polynomials of degree less than or equal to 12, but in only 26% of degree 14, and 5.6% of degree 16. A photodiode (artificial eye) was used in an experiment to construct trace arrays showing responses from 61 individual areas. Additional waveforms were present on the trace array when the experiment was carried out with a bad primitive polynomial. The use of finite field theory to generate primitive polynomials and Zech logarithm analysis allowed prediction of which primitive polynomials were suitable for m-sequence generation for multifocal electroretinography. Practical investigations supported the theoretical analysis. This has important implications for developers of multifocal electrophysiology systems.

Artifacts↗

Familial hyperproinsulinaemia due to a mutation substituting histidine for arginine at position 65 in proinsulin: identification of the mutation by restriction enzyme mapping.

UNLABELLED: Familial hyperproinsulinaemia is a rare genetic disorder characterized by point mutations in the insulin gene which impair the conversion of proinsulin to insulin. We report here three members of a two-generation Caucasian family in whom this syndrome was identified by unexplained hyperinsulinism associated with normal glucose tolerance and normal insulin sensitivity. Plasma insulin immunoreactivity showed a reduced affinity for the insulin receptor and eluted mainly, on Biogel chromatography, at the position of proinsulin. Analysis of the PCR-amplified insulin gene by restriction enzyme mapping revealed a new recognition site for the enzyme Nla III, indicating a Arg65 to His mutation. Sequence analysis of exon 3 confirmed this mutation in one allele of the gene. CONCLUSION: This study reports a two-generation European-Caucasian family with hyperproinsulinaemia due to a substitution of His for Arg at position 65 in proinsulin, the seventh now identified worldwide and the second from Europe. The mutation generated a new restriction site on the insulin gene suggesting the usefulness of restriction enzyme mapping as a screening procedure.

Adult↗

Towards an auditory account of speech rhythm: application of a model of the auditory 'primal sketch' to two multi-language corpora.

The world's languages display important differences in their rhythmic organization; most particularly, different languages seem to privilege different phonological units (mora, syllable, or stress foot) as their basic rhythmic unit. There is now considerable evidence that such differences have important consequences for crucial aspects of language acquisition and processing. Several questions remain, however, as to what exactly characterizes the rhythmic differences, how they are manifested at an auditory/acoustic level and how listeners, whether adult native speakers or young infants, process rhythmic information. In this paper it is proposed that the crucial determinant of rhythmic organization is the variability in the auditory prominence of phonetic events. In order to test this auditory prominence hypothesis, an auditory model is run on two multi-language data-sets, the first consisting of matched pairs of English and French sentences, and the second consisting of French, Italian, English and Dutch sentences. The model is based on a theory of the auditory primal sketch, and generates a primitive representation of an acoustic signal (the rhythmogram) which yields a crude segmentation of the speech signal and assigns prominence values to the obtained sequence of events. Its performance is compared with that of several recently proposed phonetic measures of vocalic and consonantal variability.

Humans↗

[Tryptic hydrolysis extended to the level of aspartyl bonds].

A quantitative modification of free carboxyl groups in peptides and proteins can be obtained, under mild conditions, by reacting them with ethylenediamine in the presence of N-ethyl-N'-(3-dimethylaminopropyl)-Carbodimide. Aminoethylasparagine and aminoethylglutamine side chains are thus generated in place of the corresponding carboxylic ones. The first kind of residue because of its structure closer to that of lysine, is a point of greater potential trypsic cleavage than the second one. The specificity and yields of this enzymatic cleavage reaction and its possible application in sequence studies are discussed.

Amino Acid Sequence↗

Probing the dimeric structure of porcine aminoacylase 1 by mass spectrometric and modeling procedures.

Aminoacylase 1 is a zinc-binding metalloprotease catalyzing the hydrolysis of N(alpha)-acylated l-amino acids; it presents altered expression levels in different renal and small cell lung carcinomas. A description of its redox and oligomerization state was achieved by combined biochemical and mass spectrometric procedures. A topological analysis of the enzyme structural architecture was derived from limited proteolysis and selective chemical modification experiments, using a broad range of proteases and chemical reagents. The analysis of the reaction products by different mass spectrometric techniques identified 26 amino acids as being accessible on the molecular surface, defining polypeptide regions exposed in the structure of the dimeric protein. The nature of the intermolecular contact zone between monomers was investigated by cross-linking reaction and mass mapping experiments. The cross-linked dimer was isolated, and the intermolecular cross-linked peptides were characterized, thus demonstrating the spatial proximity of Lys220 and Lys231 at the dimerization interface. Standard modeling procedures based on automatic alignment on the structure of members of the M20 peptidase family failed to produce a dimeric model consistent with experimental data. Discrepancies were observed mainly at the dimer interface and at loop regions. Therefore, a refined model for this dimeric protease was calculated by selecting the one able to generate a structure fully compatible with experimental findings, among all possible suboptimal sequence alignments. According to this model, each aminoacylase monomer consists of two domains: a globular catalytic subunit (residues 1-188 and 311-399) consisting of a beta-sheet sandwiched between alpha-helices and a second beta-sheet located on the surface, and the dimerization domain (residues 189-310) folding into a beta-sheet flanked on one side by two alpha-helices. These results indicate that reliable approaches such as limited proteolysis, selective chemical modification, and cross-linking coupled to mass spectrometry can be used to test and optimize molecular models of multimeric proteins and highlight problems in automatic model building.

Amidohydrolases↗

Ca2+ shuttling between endoplasmic reticulum and mitochondria underlying Ca2+ oscillations.

Although many cell functions are regulated by Ca(2+) oscillations induced by a cyclic release of Ca(2+) from intracellular Ca(2+) stores, the pacemaker mechanism of Ca(2+) oscillations remains to be explained. Using green fluorescent protein-based Ca(2+) indicators that are targeted to intracellular Ca(2+) stores, the endoplasmic reticulum (ER) and mitochondria, we found that Ca(2+) shuttles between the ER and mitochondria in phase with Ca(2+) oscillations. Following agonist stimulation, Ca(2+) release from the ER generated the first Ca(2+) oscillation and loaded mitochondria with Ca(2+). Before the second Ca(2+) oscillation, Ca(2+) release from the mitochondria by means of the Na(+)/Ca(2+) exchanger caused a gradual increase in cytoplasmic Ca(2+) concentration, inducing a regenerative ER Ca(2+) release, which generated the peak of Ca(2+) oscillation and partially reloaded the mitochondria. This sequence of events was repeated until mitochondrial Ca(2+) was depleted. Thus, Ca(2+) shuttling between the ER and mitochondria may have a pacemaker role in the generation of Ca(2+) oscillations.

Calcium↗

Discrimination of suballeles present at the TNFd microsatellite locus using induced heteroduplex analysis.

Polymorphism at the TNFd locus has been implicated in a number of disease association studies. The TNFd locus consists of three regions of (GA)(n) repeats separated by an imperfect repeat of two guanine bases. TNFd alleles are genotyped by the number of repeats in the first (GA)(n) repeat region, and until now the second repeat region had been thought to be nonpolymorphic. We report the existence of suballeles present within the TNFd microsatellite locus, detected using induced heteroduplex generator (IHG) technology. These alleles cannot be detected using conventional typing strategies as they represent altered distribution of the (GA)(n) repeats or sequence variation within the repeat. The suballeles affect the frequencies of the conventional d3 and d4 alleles leading to significantly altered allele frequencies. Some studies have associated the d3 and d4 alleles with disease outcome. We re-analysed one such study cohort using IHG technology and demonstrated a high proportion of incorrectly assigned TNFd3 alleles.

Base Sequence↗

Fighting fruit flies: a model system for the study of aggression.

Despite the importance of aggression in the behavioral repertoire of most animals, relatively little is known of its proximate causation and control. To take advantage of modern methods of genetic analysis for studying this complex behavior, we have developed a quantitative framework for studying aggression in common laboratory strains of the fruit fly, Drosophila melanogaster. In the present study we analyze 73 experiments in which socially naive male fruit flies interacted in more than 2,000 individual agonistic interactions. This allows us to (i) generate an ethogram of the behaviors that occur during agonistic interactions; (ii) calculate descriptive statistics for these behaviors; and (iii) identify their temporal patterns by using sequence analysis. Thirty-minute paired trials between flies contained an average of 27 individual agonistic interactions, lasting a mean of 11 seconds and featuring a variety of intensity levels. Only few fights progressed to the highest intensity levels (boxing and tussling). A sequential analysis demonstrated the existence of recurrent patterns in behaviors with some similarity to those seen during courtship. Based on the patterns characterized in the present report, a detailed examination of aggressive behavior by using mutant strains and other techniques of genetic analysis becomes possible.

Aggression↗

Formation of a functional ribosome-membrane junction during translocation requires the participation of a GTP-binding protein.

The requirement for ribonucleotides and ribonucleotide hydrolysis was examined at several distinct points during translocation of a secretory protein across the endoplasmic reticulum. We monitored binding of in vitro-assembled polysomes to microsomal membranes after removal of ATP and GTP. Ribonucleotides were not required for the initial low salt-insensitive attachment of the ribosome to the membrane. However, without ribonucleotides the nascent secretory chains were sensitive to protease digestion and were readily extracted from the membrane with either EDTA or 0.5 M KOAc. In contrast, nascent chains resisted extraction with either EDTA or 0.5 M KOAc and were insensitive to protease digestion after addition of GTP or nonhydrolyzable GTP analogues. Translocation of the nascent secretory polypeptide was detected only when ribosome binding was conducted in the presence of GTP. Thus, translocation-competent binding of the ribosome to the membrane requires the participation of a novel GTP-binding protein in addition to the signal recognition particle and the signal recognition particle receptor. The second event we examined was translocation and processing of a truncated secretory polypeptide. Membrane-bound polysomes bearing an 86-residue nascent chain were generated by translation of a truncated preprolactin mRNA. Ribonucleotide-independent translocation of the polypeptide was detected by cleavage of the 30-residue signal sequence after puromycin termination. Nascent chain transport, per se, is apparently dependent upon neither ribonucleotide hydrolysis nor continued elongation of the polypeptide once a functional ribosome-membrane junction has been established.

Adenosine Triphosphate↗

The SONB(NUP98) nucleoporin interacts with the NIMA kinase in Aspergillus nidulans.

The Aspergillus nidulans NIMA kinase is essential for mitotic entry. At restrictive temperature, temperature-sensitive nimA alleles arrest in G2, before accumulation of NIMA in the nucleus. We performed a screen for extragenic suppressors of the nimA1 allele and isolated two cold-sensitive son (suppressor of nimA1) mutants. The sonA1 mutant encoded a nucleoporin that is a homolog of yeast Gle2/Rae1. We have now cloned SONB, a second nucleoporin genetically interacting with NIMA. sonB is essential and encodes a homolog of the human NUP98/NUP96 precursor. Similar to NUP98/NUP96, SONB(NUP98/NUP96) is autoproteolytically cleaved to generate SONB(NUP98) and SONB(NUP96). SONB(NUP98) localizes to the nuclear pore complex and contains a GLEBS domain (Gle2 binding sequence) that binds SONA(GLE2). A point mutation within the GLEBS domain of SONB1(NUP98) suppresses the temperature sensitivity of the nimA1 allele and compromises the physical interaction between SONA(GLE2) and SONB1(NUP98). The sonB1 mutation also causes sensitivity to hydroxyurea. We isolated the histone H2A-H2B gene pair as a copy-number suppressor of sonB1 cold sensitivity and hydroxyurea sensitivity. The data suggest that the nucleoporins SONA(GLE2) and SONB(NUP98) and the NIMA kinase interact and regulate nuclear accumulation of mitotic regulators to help promote mitosis.

Amino Acid Sequence↗

A consensus linkage map for sugi (Cryptomeria japonica) from two pedigrees, based on microsatellites and expressed sequence tags.

A consensus map for sugi (Cryptomeria japonica) was constructed by integrating linkage data from two unrelated third-generation pedigrees, one derived from a full-sib cross and the other by self-pollination of F1 individuals. The progeny segregation data of the first pedigree were derived from cleaved amplified polymorphic sequences, microsatellites, restriction fragment length polymorphisms, and single nucleotide polymorphisms. The data of the second pedigree were derived from cleaved amplified polymorphic sequences, isozyme markers, morphological traits, random amplified polymorphic DNA markers, and restriction fragment length polymorphisms. Linkage analyses were done for the first pedigree with JoinMap 3.0, using its parameter set for progeny derived by cross-pollination, and for the second pedigree with the parameter set for progeny derived from selfing of F1 individuals. The 11 chromosomes of C. japonica are represented in the consensus map. A total of 438 markers were assigned to 11 large linkage groups, 1 small linkage group, and 1 nonintegrated linkage group from the second pedigree; their total length was 1372.2 cM. On average, the consensus map showed 1 marker every 3.0 cM. PCR-based codominant DNA markers such as cleaved amplified polymorphic sequences and microsatellite markers were distributed in all linkage groups and occupied about half of mapped loci. These markers are very useful for integration of different linkage maps, QTL mapping, and comparative mapping for evolutional study, especially for species with a large genome size such as conifers.

Base Sequence↗

Levalbuterol versus racemic albuterol in the treatment of acute exacerbation of asthma in children.

OBJECTIVE: To compare levalbuterol and racemic albuterol for the treatment of acute exacerbation of asthma in pediatric population. DESIGN: Prospective, double-blind, randomized research trial in a pediatric emergency department of an urban tertiary care hospital. PARTICIPANTS: Children 5 to 21 years with a history of asthma presenting to the emergency department in acute exacerbation. INTERVENTIONS: As per a computer-generated randomization sequence, patients received either 1.25 mg of levalbuterol or albuterol 2.5 mg via nebulization along with ipratropium hydrochloride. Patients received 3 back-to-back treatments as needed every 20 minutes, maximum of 3; 2 mg/kg of oral prednisone was administered to the patients after the second treatment. Baseline respiratory parameters such as oxygen saturations, respiratory rates, and peak flow rates were measured and repeated after every treatment.The decision for further treatments and or hospitalization was made by the treating emergency department physician as per his/her clinical judgement of the respiratory parameters at the end of 3 treatments. RESULTS: Seventy patients completed the study. Most of the patients were in moderate severity of asthma exacerbation. All patients in both groups showed improvement in oxygen saturations, respiratory rates, and peak flow rates. However, no statistically significant difference was observed in the 2 groups regarding the respiratory parameters (P > 0.05). CONCLUSION: Levalbuterol is not more efficacious than racemic albuterol in improving respiratory parameters in children presenting with acute exacerbation of asthma.

Adolescent↗