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PubMed1993

[Genetics in movement disorders].

Genetic considerations in movement disorders are described. 1) Familial parkinsonisms are heterogeneous; genes for two of them, 'Lubag' and Waisman syndrome have been mapped to X chromosome, though genes for others do not have been mapped. 2) The responsible gene for Huntington's disease has been cloned recently and named huntingtin. A (CAG)n repeat longer than the normal range was observed in huntingtin gene. The (CAG)n repeat appears to be located within the coding sequence of a predicted approximately 348 kD protein that is widely expressed but unrelated to any known gene. The expansion of an unstable trinucleotide CAG repeat are also the causes of hereditary neurodegenerative diseases such as X-linked bular and spinal muscular atrophy and spinocerebellar ataxia type 1. 3) There are various forms in hereditary dystonia. Although the responsible gene for idiopathic torsion dystonia, inherited as an autosomal dominant pattern, has been mapped to 9q 32-34, genes for others do not have been mapped. 4) The Gilles des la Tourette syndrome (GTS) is a hereditary, neuropsychiatric-neurobehavioral disorder with childhood onset that is characterized by motor and vocal tics. About 80% of the human genome could be excluded as possible site for the GTS gene by studies with over 600 DNA markers in an international collaborative effort, but actual localization has not yet been accomplished.

Chromosome Mapping↗
PubMed1994

Cloning of a novel alpha 2,3-sialyltransferase that sialylates glycoprotein and glycolipid carbohydrate groups.

Sialyltransferases are a family of 10-12 enzymes that catalyze the transfer of sialic acid to carbohydrate groups of glycoproteins and glycolipids. Three sialyltransferase cDNAs have been cloned, revealing a highly conserved sialylmotif in the catalytic domain of these enzymes. Using a polymerase chain reaction-based approach, we cloned a 150-base pair fragment of a new sialymotif from human placenta mRNA, which was then used as a probe to clone the complete coding sequence of the corresponding gene from a cDNA library. Like the other members of the sialyltransferase gene family cloned to date, the new cDNA coded for a protein predicted to have an NH2-terminal signal-anchor sequence and had the sialylmotif located in the center of the molecule. Comparison with the three other cloned sialyltransferases revealed extensive sequence homology that was not recognized earlier. Expression of a soluble recombinant form of the protein in COS-1 cells produced an active sialyltransferase, which used oligosaccharide, glycoprotein, and glycolipid acceptor substrates with terminal galactose in the Gal beta 1,3GalNAc and Gal beta 1, 4GlcNAc sequences but not the Gal beta 1,3GlcNAc sequence. The sialylated products were sensitive to digestion with the Newcastle disease virus sialidase, which is specific for sialic acid-galactose linkages in the alpha 2,3 linkage. The results suggest that this new member of the sialyltransferase gene family is the enzyme previously described as a glycolipid sialyltransferase activity (SAT-3), which forms the terminal sequences NeuAc alpha-2,3Gal beta 1,3GalNAc-R and NeuAc alpha 2,3Gal beta 1, 4GlcNAc-R.

Adult↗
PubMed1993

Human ABR encodes a protein with GAPrac activity and homology to the DBL nucleotide exchange factor domain.

We have previously cloned a segment of a gene, ABR, homologous to the BCR gene, which encodes a protein consisting of three distinct functional domains. In the present study, genomic ABR sequences were used to isolate human ABR cDNAs. Surprisingly, the two types of ABR cDNAs identified differed only in their most 5' coding sequences. These are predicted to encode proteins of 93.5 and 92.3 kDa molecular mass. ABR showed a differential expression pattern in various mouse tissues, analogous to that of BCR, and the highest level was found in brain. Similar to BCR, ABR contains a region with homology to DBL, vav, and CDC24, which are likely to or have been shown to encode GTP exchange factors. A domain of ABR with similarity to GAPrho was expressed as a fusion protein in Escherichia coli and was shown to have GAP activity toward rac. Although both ABR and BCR have GAP activity, ABR lacks homology to the serine/threonine kinase domain of BCR. Therefore, ABR is likely to have cellular functions overlapping with but also distinct from those of BCR.

Amino Acid Sequence↗
PubMed1993

Germ-line mutations in the first 14 exons of the adenomatous polyposis coli (APC) gene.

The first 14 exons of the APC gene have been screened by the denaturation gradient gel electrophoresis method in 160 unrelated patients with familial adenomatous polyposis coli (APC) syndrome. Four polymorphic variants corresponding to silent mutations not associated with the disease phenotype were observed. Mutations predicted to alter the coding property of the APC gene were observed in 26 patients. All these mutations are expected to lead either to aberrant splicing, to synthesis of a truncated APC protein because of the emergence of a stop codon, or to a change in the translation reading frame. Single-base-pair substitutions were observed on 21 occasions. The most frequent mutation (eight cases) was a C-to-T change which exclusively occurred on the nontranscribed strand within a CG dinucleotide.

Adenomatous Polyposis Coli↗
PubMed1993

[Huntington's disease--advances in gene mapping].

Huntington's disease (HD) is a progressive neurodegenerative disorder characterized by motor disturbance, cognitive loss, and psychiatric manifestations. It is inherited in an autosomal dominant fashion. The genetic defect causing HD was assigned to chromosome 4 in 1983 using polymorphic DNA markers in humans. Thereafter, a location cloning approach was pursued to isolate and characterize the HD gene. Recently, the Huntington's disease collaborative research group has isolated a new gene, IT 15, in 4p 16.3. IT 15 contains a polymorphic trinucleotide repeat that is expanded and unstable on HD chromosomes. A (CAG)n repeat longer than the normal range was observed on HD chromosomes from disease families. The (CAG)n repeat appears to be located within the coding sequence of a predicted 348 kd protein that is unrelated to any known gene.

Amino Acid Sequence↗
PubMed1993

A novel cloning strategy reveals the gene for the yeast homologue to Escherichia coli ribosomal protein S12.

Using a novel technique designed to identify genes of Saccharomyces cerevisiae which carry introns, we have cloned two genes encoding ribosomal protein S28. Although the genes differ by 15 nucleotides within their coding regions, they are predicted to encode identical proteins of 145 amino acids. The predicted amino acid sequence of S28 contains significant homology to ribosomal protein S25 of Tetrahymena thermophila and to ribosomal protein S12 of several archaebacteria, suggesting a relationship to S12 of Escherichia coli. Dot matrix analysis confirmed that regions of S12, especially those implicated in the accuracy of translation, have been conserved in S28 of S. cerevisiae. Either RPS28A or RPS28B alone can support growth, but heterozygous disruption of both genes abolishes the ability to sporulate. Haploids harboring a disruption of both genes cannot survive without an intact gene on a plasmid. RPS28A maps to the right arm of chromosome VII and RPS28B to the right arm of chromosome XVI.

Amino Acid Sequence↗
PubMed1996

Is Marlatt's relapse taxonomy reliable or valid?

The Relapse Replication and Extension Project (RREP) has failed to provide empirical support for Marlatt's relapse taxonomy. Neither the reliability of the original Marlatt coding system nor its predictive or construct validity was supported by this group of studies. The present commentary explores a number of possible reasons for the generally negative outcomes. These findings should certainly lead to a re-evaluation of Marlatt's relapse taxonomy and its operationalization. Nevertheless, despite the negative results, there are a number of reasons why the general Relapse Prevention concept is likely to survive in some form: it has been widely adopted and imitated clinically, key elements of the taxonomy are often focal points of treatment, and clinical research studies have repeatedly supported some elements of the taxonomy (e.g. negative emotional states, social pressure, interpersonal conflict, positive emotional states and temptations/urges). The RREP also evaluated some modifications of the original taxonomy as well as the use of more structured assessment instruments, and some of these provided more promising results. Further developments will need to take into account both research needs for greater precision, most likely through the use of more structured assessment instruments, and clinical needs for richness of detail and sensitivity to a wide variety of life circumstances.

Alcoholism↗
PubMed2002

Feasibility, reliability and validity of the Spanish version of Psychiatric Assessment Schedule for Adults with Developmental Disability: a structured psychiatric interview for intellectual disability.

BACKGROUND: Over 30% of people with intellectual disability (ID) have a comorbid psychiatric disorder. However, there are few assessment instruments available for international use and cross-cultural validation studies of these instruments are rare. The aim of the present study was to standardize the Spanish version of the Psychiatric Assessment Schedule for Adults with Developmental Disability (PAS-ADD-10), a semi-structured interview for people with ID. METHODS: After a conceptual translation, feasibility (i.e. applicability, acceptability and practicality) and reliability analyses were carried out. The predictive validity of the PAS-ADD-10 CATEGO-5 codings was also examined (i.e. positive and negative predictive values). Four independent raters with wide-ranging experience in quantitative evaluation and psychiatric assessment of ID evaluated a sample of 80 subjects with ID and borderline intellectual functioning at the AFANAS occupational centre in Jerez, Southern Spain. The ICD-10 codes were used for psychiatric diagnosis. RESULTS: The practicality of the PAS-ADD-10 is limited because of the need for previous standardization of SCAN interviews. Nevertheless, its overall feasibility was judged adequate by raters and the PAS-ADD-10 was considered extremely useful for training. Test-retest and inter-rater reliability kappa values were moderate to high. The CATEGO coding showed limited validity because of overdiagnosis of anxiety disorders and underdiagnosis of mood and psychotic disorders (positive predictive value = 74%, negative predictive value = 76%). CONCLUSIONS: The PAS-ADD-10 is a useful tool for standard psychiatric assessment of people with ID; however, CATEGO codings show low validity and a series of modifications should be considered before this instrument is used extensively in Spain. In this regard, a study on the clinical usefulness of the PAS-ADD-10 in patients with ID and severe mental disorders has been undertaken.

Adolescent↗
PubMed1983

Spontaneous activation of a human proto-oncogene.

It has been recently shown that malignant activation of the c-has/bas proto-oncogene in T24 human bladder carcinoma cells was mediated by a single point mutation. A deoxyguanosine located at position 35 of the first exon of this proto-oncogene was substituted by thymidine. These findings predicted that the resulting oncogene would code for a structurally altered p21 protein containing valine instead of glycine as its 12th amino acid residue. We now report the spontaneous activation of the human c-has/bas proto-oncogene during transfection of NIH/3T3 cells. As in T24 cells, this in vitro activated oncogene also acquired malignant properties by a single point mutation. In this case we have detected a G leads to A transition, which occurred at the same position as the mutation responsible for the activation of the T24 oncogene. These results predict that the p21 protein coded for by the spontaneously activated c-has/bas gene will incorporate aspartic acid as its 12th amino acid residue. Computer analysis of the secondary structure of c-has/bas encoded p21 proteins indicates that substitution of the glycine residue located at position 12, not only by aspartic acid or valine but also by any other amino acid, would result in the same structural alteration. These findings indicate that a specific conformational change is sufficient to confer transforming properties to this p21 protein. Moreover, they predict that any mutation affecting the coding properties of the 12th codon of the c-has/bas proto-oncogene will lead to its malignant activation.

Amino Acid Sequence↗
PubMed1990

Common structures of the 5' non-coding RNA in enteroviruses and rhinoviruses. Thermodynamical stability and statistical significance.

A total of 4051 suboptimal secondary structures are predicted by folding the 5' non-coding region of ten polioviruses, five human rhinoviruses and three coxsackieviruses using our new suboptimal folding algorithm for the prediction of both optimal and suboptimal RNA secondary structures. A comparative analysis of these RNA secondary structures reveals the conservation of common secondary structure that can be supported by phylogenetic data. The thermodynamic stability and statistical significance of these predicted, conserved helical elements are assessed and significant structure motifs in the 5' non-coding region are proposed. The possible roles of these structure motifs in the virus life cycle are discussed.

Base Sequence↗
PubMed2003

Efficient mapping of California mortality fields at different spatial scales.

A meaningful characterization of epidemiologic fields (mortality, incidence rate, etc.) often involves the assessment of their spatiotemporal variation at multiple scales. An adequate analysis should depend on the scale at which the epidemiologic field is considered rather than being limited by the scale at which the data are available. In many studies, for example, data are available at a larger scale (say, counties), whereas the epidemiologist is interested in a smaller-scale analysis (say, residential neighborhoods). We propose a mathematically rigorous and epidemiologically meaningful multiscale approach that uses the well-known BME theory to study important scale effects and generate informative scale-dependent maps. The approach is applied to a real-world case study involving daily mortality counts in the state of California. The approach accounts for scale effects and produces mortality predictions at the zip-code scale by downscaling data from the county scale. The multiscale approach is tested by means of a verification data set with detailed mortality information at the zip-code level for 1 day. A measure of mapping accuracy is used to demonstrate that the multiscale approach offers more accurate mortality predictions at the local scale than existing approaches, which do not account for scale effects.

California↗
PubMed1995

Ancient splice junction shadows with relation to blocks in protein structure.

Splice junction shadows (ancient exon-exon junctions) presumably reflect the existence of amino acid primary blocks which were used in the course of evolution for the construction of new proteins. The lengths of such blocks (i.e. regions between splice junctions), as the lengths of corresponding inserted or duplicated ancient exons, should be divisible by three in order to store the preexisting coding frame in the course of evolution. In this paper, we will test the hypothesis of intron-mediated recombination in a model of block molecular evolution (exon shuffling) by revealing corresponding blocks in existing database-contained coding sequences. For this purpose, we use a weight matrix prediction of ancient splice junction shadows in coding regions of the nucleotide sequences in current databases. The usage of splice junction shadows allows us to test the block evolution hypothesis in better detail in comparison with previous methods which were based only on currently existing recent exons. Our result of block length distribution at the nucleotide level shows a clear tendency to be divisible by three. At the protein level, several unexpected favorable block lengths, which are six, nine, 12 and 15 amino acids in length, were observed. Further refinements in our method for revealing splice junction shadows (structural block boundaries) might reveal peptides which probably maintain stable folds in different structures. The latter can in turn be used for protein structure prediction.

Biological Evolution↗
PubMed1989

Cuticle collagen genes of Haemonchus contortus and Caenorhabditis elegans are highly conserved.

Several genes and partial cDNAs encoding cuticle collagens have been isolated from the sheep parasitic nematode Haemonchus contortus. DNA sequencing and Southern blot hybridization studies reveal that H. contortus collagens comprise a large family of related, but non-identical genes. The genes appear to be dispersed throughout the genome. The predominant size of collagen mRNA in molting worms was found to be between 1.0 and 1.2 kb. The one complete gene that was sequenced contains two short introns and encodes a protein of about 300 amino acids. The predicted protein sequence contain several (Gly-X-Y)n triple helix-coding domains that are interrupted by short stretches of non-helix-coding amino acids. The size of the predicted protein and the organization of the triple-helix coding domains are similar to that of Caenorhabditis elegans collagens. All the H. contortus genes studied show a striking homology to the C. elegans collagen gene subfamily represented by col-1. In particular, the amino acid sequence of the carboxy-terminal non-(Gly-X-Y)n region and the positions of cysteine residues flanking the (Gly-X-Y)n domains were found to be highly conserved in the collagens of these two nematodes.

Amino Acid Sequence↗
PubMed2026

Identification and Classification of Expressed Orphan Genes, Spurious Orphan Genes, and Conserved Genes in the Human Gut Microbiome.

Orphan genes (OGs)-genes lacking detectable homologs outside a species-are widespread in microbial genomes and are thought to contribute to their adaptation and molecular innovation. However, not all predicted OGs may represent novel functional coding sequences. False positive OGs, also called spurious OGs, can arise from gene prediction errors. We reason that OGs lacking detectable expression are more likely to be spurious. To test this, we combined large-scale metatranscriptomic profiling of the human gut microbiome with machine learning to distinguish expressed OGs from spurious ones and compare them with conserved genes (CGs) found in multiple species. Using nearly 5,000 metatranscriptome libraries, we identified ∼218,000 OGs supported by expression evidence, while ∼330,000 predicted OGs lacked detectable expression and were classified as spurious. We extracted 154 features for sequence, structural, and evolutionary properties for each gene and trained XGBoost classifiers while accounting for genomic representation. The models achieved an area under the receiver operating characteristic curve (AUC) of 0.82 in distinguishing expressed OGs from spurious OGs and an AUC of 0.93 in distinguishing expressed OGs from CGs. Interpretation based on SHAP (SHapley Additive exPlanations) revealed clear biological signals. Particularly, expressed orphans were present in more genomes than spurious ones, and expressed OGs were shorter than CGs. This work improves OG discovery and suggests that expressed OGs differ systematically from CGs and spurious OGs in sequence composition, structural constraints, and evolutionary signals.

Humans↗
PubMed1981

Nucleotide sequence of the transforming early region E1b of adenovirus type 12 DNA: structure and gene organization, and comparison with those of adenovirus type 5 DNA.

The nucleotide sequence of the entire transforming early region of E1b of the highly oncogenic adenovirus type 12 (Ad12) DNA has been determined. The total sequence (3860 base pairs) encompasses the entire transforming early region E1 of Ad12 DNA. From the sequence for the E1b region of Ad12, and the transcription map of the E1b region (1, 2, 3, and this paper) the structure and gene organization of the early region E1b of Ad12 DNA were analyzed and compared with those of the E1b region in the non-oncogenic Ad5 DNA (4, 5). Most of the sequences in the E1b region of Ad12 was highly homologous to that of Ad5. It is predicted that the Ad12 region E1b codes for polypeptides of 53.9, 19.1, and 8.9 kd. This situation is identical with that of the Ad5 region E1b which codes for polypeptides of 54.9, 20.6, and 8.3 kd. The function of these predicted polypeptides encoded by the E1b regions in cell transformation is discussed.

Adenoviridae↗
PubMed1997

A potential new gene (tccA) on IncP plasmid RK2 and transposon Tn1721: relationship of its product to the TrwC relaxase/helicase of IncW plasmid R388.

Computational analysis of the fully sequenced 60-kb genome of broad-host-range IncP alpha plasmid RK2 revealed a previously unreported potential protein-coding sequence, an 80-codon open reading frame (tccA), located in the region between the vegetative origin of replication (oriV) and the tetR gene of the tetracycline resistance determinant. The coding region is also present in the transposon Tn1721 tet region, which is nearly identical to the tet region of RK2. Remarkably, the predicted polypeptide product of the coding region displays 56% identity and 72% similarity with the C-terminal domain of the TrwC relaxase/helicase protein of IncW plasmid R388.

Amino Acid Sequence↗
PubMed1999

Prediction of human cDNA from its homologous mouse full-length cDNA and human shotgun database.

We propose a prediction method for human full-length cDNA by comparing sequence data between human genome shotgun sequence and mouse full-length cDNA. The human genome which is homologous to the mouse full-length cDNA is selected by a homology search program, and the predicted exons are connected at the exon-intron junction which gives the best homology score to the mouse full-length cDNA. The accuracy of the predicted human full-length coding region is 83.3%, and the false positive rate is 16.7%. Five human full-length proteins out of 20 proteins are correctly predicted.

Animals↗
PubMed2025

A high-quality chromosome-scale genome assembly of Xingan mandarin (Citrus reticulata 'Xingan'), a primitive Mandarin type.

Mandarin (Citrus reticulata) is broadly recognized as one of the foremost citrus crops globally. Our study identified the Xingan mandarin (Citrus reticulata 'Xingan') as a primitive type found near Maoer Mountain. This report provides a high-resolution, chromosome-scale genome assembly for the Xingan mandarin. The total size of the genome assembly is an impressive 325.12 Mb, including contig N50 and scaffold N50 values of 29.32 Mb and 29.62 Mb, respectively. Notably, we successfully anchored approximately 93.08% of the assembled sequences onto nine pseudochromosomes. Our predictions identified 30,581 protein-coding genes, 166 miRNAs, 415 tRNAs, 728 rRNAs, 325 snRNAs, and 659 snoRNAs. We were able to predict the functions of 27,242 genes, constituting 89.08% of the total protein-coding genes. A notable finding of our study was the high degree of genome synteny between the Xingan mandarin and the Mangshan mandarin (Citrus reticulata 'Mangshan'), reinforcing their genetic similarity. The acquisition of the chromosome-level genome for the Xingan Mandarin represents a significant milestone, laying an indispensable foundation for rigorous molecular investigations of this species. Moreover, it is poised to invigorate advanced research in comparative genomics within the Citrus genus.

Citrus↗