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PubMed1985

Structure and function of factor IX: defects in haemophilia B.

The genetics of haemophilia B and the structure-function relationships of factor IX interactions with cofactors and substrates have been reviewed. Emphasis has been placed on contributions to our understanding made by analysis of variants. Amino acid substitutions at or near the site of activation lead to inactive factor IX or to factor IX species with decreased clotting activity. Release of the activation peptide is necessary for optimal interaction of factor IX with its cofactors and substrates. Abnormalities in the calcium binding region, whether Gla independent or dependent, also decrease clotting activity. The defects in haemophilia Bm variants somehow affect factor VII-tissue factor interactions with factor X. Other mutations may affect the factor IX heavy chain, probably at or near the active site. Amino acid substitutions may cause conformational changes in factor IX that interfere with other interactions such as with antithrombin III and factor VIII. Recombinant DNA techniques have been employed to analyse normal and abnormal factor IX genes. DNA sequence analysis of factor IX cDNA clones revealed the primary structure of the mature protein and a predicted leader peptide. Knowledge of the primary sequence of factor IX allowed identification of the specific defect in the factor IX Chapel Hill variant. Analysis of normal factor IX genomic clones has determined that the 35 kb gene is composed of eight coding exons and seven intervening sequences. Sequence analysis of the CRM+ variants will identify mutations disrupting the normal interactions of factor IX. Southern analysis of CRM- variants has revealed gross factor IX gene deletions in some cases. Such deletions have been employed for carrier deletion in some families. Restriction fragment length polymorphisms in the factor IX gene have also proven useful for carrier identification. Manipulations of the cloned factor IX gene to make specific mutations in vitro and improvements in the technology for expression of deliberately modified genes will further elucidate the relationships between factor IX structure and function.

Amino Acid Sequence↗
PubMed1990

Phenotypic and molecular biological analysis of human butyrylcholinesterase variants.

Our laboratory has recently shown that several variant forms of human butyrylcholinesterase, associated with unusual sensitivity to succinylcholine, are caused by specific mutations within the structural DNA coding for this enzyme. Atypical (dibucaine-resistant) butyrylcholinesterase is caused by a point mutation at nucleotide position 209(GAT-- greater than GGT), which changes aspartate 70 to glycine. One fluoride-resistant variant family has a point mutation at nucleotide 728(ACG-- greater than ATG), which changes threonine 243 to methionine. Another type of fluoride-resistant variant has a point mutation at nucleotide 1169(GGT-- greater than GTT), which changes glycine 390 to valine. One type of silent phenotype is due to a frame-shift mutation at nucleotide position 351(GGT-- greater than GGAG). A polymorphic site at nucleotide position 1615 (GCA/ACA), coding for Ala/Thr, accounts for the quantitative K-variant, which causes an approximate one-third reduction of activity, if Thr occupies that position at codon 539. Examples are given to illustrate the advantages of using a combination of the new DNA analytical techniques, including: the use of allele-specific probes, with the standard serum cholinesterase phenotyping methods. More accurate typing of patients with certain variants is now possible; pedigree analysis will be aided by the improved methodology.

Alleles↗
PubMed2025

Dissecting the shared genetic architecture of schizophrenia with ventricular subregion volumes.

Schizophrenia is characterized by cerebral ventricular enlargement as an early and consistent structural anomaly. While genetic factors significantly influence both schizophrenia and cerebral ventricular enlargement, the shared genetic etiology between them requires further investigation. Using summary statistics from recent large genome-wide association studies on schizophrenia and 9 ventricular subregion volumes phenotypes. Gaussian causal mixture modeling was applied to characterize the genetic architecture and overlap between schizophrenia and ventricular subregion volumes phenotypes. Local genetic correlation was investigated with Local Analysis of Variant Association. The conjunctional false discovery rate framework was used to identify the specific shared genetic loci, annotated with FUMA. Gaussian causal mixture modeling estimated schizophrenia to be more polygenic more polygenic (9574 trait-influencing variants) than ventricular subregion volumes phenotypes (157-1267 trait-influencing variants). Conjunctional false discovery rate analysis identified 42 shared genetic loci, 17 loci were identified as novel for both schizophrenia and the ventricular subregion volumes phenotypes. Local Analysis of Variant Association revealed that 11 distinct loci demonstrated significant differences, among which 4 loci were situated in the Major Histocompatibility Complex region. Annotated genes in shared loci were enriched in molecular signaling pathways involved in inflammation and the brain structure. The shared loci between them were annotated and enriched in Major Histocompatibility Complex and inflammation-related pathways, highlighting new opportunities for future investigation.

Schizophrenia↗
PubMed1994

Dual-color detection of DNA sequence variants by ligase-mediated analysis.

Genetic screening for sequence variants associated with disease is assuming increasing importance in clinical medicine as well as in research. We describe an efficient method for such analyses, comprising a combination of practical features: (1) Amplified DNA samples are analyzed for their ability to serve as templates in standardized allele-specific ligation reactions between oligonucleotide probes; (2) Two allele-specific probes, differentially labeled with either of two lanthanide labels, compete for ligation to a third oligonucleotide (the signal from the two labeled probes can thus be directly compared in a sensitive time-resolved fluorescence detection reaction); and (3) Large sets of analyses are processed in parallel using a 96-pin capture manifold, serving to reduce pipetting steps and the risk of contamination. We present here the basis of the technique and its application to the screening for two common mutations causing cystic fibrosis and alpha 1-antiytrypsin deficiency.

Base Sequence↗
PubMed2026

Parkinson Disease Pathogenic Variants: Cross-Ancestry Analysis and Microarray Data Validation.

BACKGROUND AND OBJECTIVES: Known pathogenic variants (PVs) in Parkinson disease (PD) contribute to disease development but have yet to be fully explored by arrays on a large scale. This study evaluated genotyping success of the NeuroBooster array (NBA) and determined the frequencies of PVs across ancestries. METHODS: We analyzed the presence and allele frequency of PVs in 28,710 PD cases, 9,614 other neurodegenerative disorder cases, and 15,821 controls across 11 ancestries within the Global Parkinson's Genetics Program (GP2) data set. Cluster plots were used to assess the quality of PVs genotyped on NBA. RESULTS: Genes previously predicted to have high or very high confidence of causing PD tend to have more PVs and are present across ancestry groups. Of 34 known PD gene PVs assessed, 25 were typed by NBA and classified as "good" (n = 12), "medium" (n = 4), or "bad" (n = 9) quality variants. DISCUSSION: Our results confirm the likelihood that established PD genes are pathogenic and highlight the importance of ancestrally diverse research in PD. We also show the usefulness of the NBA as a reliable tool for the genotyping of rare variants of PD.

Journal Article↗
PubMed1990

Classification of glucose-6-phosphate dehydrogenase variants by multivariate statistical analysis.

Using principal component analysis a two-dimensional presentation of kinetic parameters from various G6PD-variants was obtained from which similarities between individual enzymes became detectable. Conclusions could be drawn as to how far the kinetic parameters contribute to the discrimination between different variants. An objective classification of G6PD-variants was achieved by application of cluster analysis. The proposed methods provide an effective means for differential elucidation of G6PD-variants and other heterogeneous enzymopathies.

Cluster Analysis↗
PubMed1989

Analysis of isotype switch variants of a Qa-5 specific hybridoma.

Qa-5 is a Class I MHC Ag expressed on mature T cells and natural killer (NK) cells of mice, and is defined by specific reactivity with an IgM secreting hybridoma (B16-167). The availability of IgG antibodies with Qa-5 specificity would greatly facilitate in vivo studies of Qa-5 positive NK cells. Using a sequential subline technique in conjunction with ELISA screening, several isotype variants of the B16-167 parent line were selected and cloned. An IgG2a, an IgG2b, and two IgG1 switch variants were selected, and it was demonstrated that one of these cloned lines produced both IgM and IgG1 simultaneously. Binding of the variant antibodies to Qa-5+ cells was not detected by flow cytometry analysis, nor by the ability to deplete NK activity from Qa-5+ large granular lymphocytes (LGL). However, all of the variant lines appeared to use the same VH region genes by Southern blot analysis. Furthermore, IgG2a from the switch variants inhibited binding of the parental IgM anti-Qa-5 when used in excess, and reduction of the parental IgM anti-Qa-5 to monomeric form abolished its binding capacity. These data together indicate that the weak binding by the IgG variants may be due to loss of an innate low affinity/high avidity binding of the parent IgM. Therefore, the isotype switch detection procedure is a useful technique for selection of antibodies with various effector functions, provided the initial antibody is an antibody with sufficient binding affinity.

Alkylation↗
PubMed1995

Latent phenotype analysis of three deletion variants of herpes simplex virus type 1 (HSV-1) in mouse model.

Latency analysis of three herpes simplex virus type 1 (HSV-I) strain 17 syn+ deletion variants (1704, 1705 and 1706) showed that they established, maintained and reactivated from latency. The kinetics of reactivation of 1705 and 1706 were similar to the parent HSV-1, 17 syn+, in which reactivation occurred 5-6 days post-explanation, but 1704 reactivated with delayed kinetics i.e. on the 12th day post-explantation. Since 1704 has deleted both copies of the latency associated transcripts (LATs) promoter region and one copy of the LAT coding region in internal inverted repeat sequence of long region (IRL), it was concluded that the LATs play a part in latency reactivation of 1704 from dorsal root ganglia (DRG) of spinal cord in mouse model. Restoration of the deleted sequences in the variant 1704 by marker rescue with the wild type BamHI b fragment resulted in a wild type genotype. This virus was designated as 1704R. Latency studies of 1704R revealed that the rate and frequency of reactivation was intermediate between 17 syn+ and 1704, suggesting a secondary undetected mutation affecting latency phenotype. Isolation of 1704LP-, during the same marker rescue experiment in which both copies of promoter region of the LAT are deleted and reactivation of this virus from latency with delayed kinetics confirms that the LATs play a role in reactivation from latency.

Amino Acid Sequence↗
PubMed1978

Principal clinical features and prognosis in chronic lymphocytic leukemia.

A prospective study of 102 patients with chronic lymphocytic leukaemia (CLL) on 30 parameters subdivided into 77 variables was analyzed by correspondence analysis, a variant of principal component analysis, which allows simultaneous graphical representation of patients and variables. This statistical method clearly defined three principal clinical features recognized at the time of diagnosis: lymph node proliferation, lymphoid infiltration and cytopenia. Cytopenia was clearly subdivided into peripheral and central types. Each of these clinical features were derived from clinical and laboratory observations which agreed with each other. Simple examination permitted an evaluation of these three syndromes. They seemed to be independent of each other except for a relationship between central cytopenia and lymphoid infiltration. Thus clinical staging at the moment of diagnosis must record three scales of severity corresponding to the three independant clinical features. Prognosis was essentially related to cytopenia, whatever the mechanism. In a further analysis of the subsequent progress of the disease, a "common path" for patients was found terminating in a region of the graph where marked splenomegaly and cytopenia were plotted. We conclude that it is necessary to consider the three clinical features independently in a clinical staging. This study emphasizes the poor prognosis of cytopenia and splenomegaly and indicates that follow up and treatment should take this feature into account.

Anemia↗
PubMed1977

Correspondence analysis of HLA gene frequency data from 124 population samples.

Correspondence analysis, a variant of principal components analysis, is used to interpret and compare gene frequencies of the HLA system for 124 samples from different populations studied in the Fifth and Sixth International Histocompatibility Workshops. The major advantage of this analysis is that populations and HLA genes are represented simultaneously with respect to the same axes in multidimensional space. This permits the visual interpretation of genetic differences between populations, the relative participation of each gene in the dispersion, and the correspondence between populations and genes. By this method a clear separation of ethnic groups in the world is obtained. Furthermore, within Europe the separation of samples from different countries is concordant with their geographical distances. The HLA system appears sufficiently polymorphic to define a population by its gene frequencies.

Asian People↗
PubMed2026

Comparative genomics of the monophasic variant of Salmonella Typhimurium: analysis of Colombian genomes and their relationship with international lineages.

The monophasic variant of Salmonella enterica serovar Typhimurium (STVM) represents a growing threat to global public health owing to its wide dissemination, capacity to adapt to multiple hosts, and antimicrobial resistance. In this study, 98 STVM isolates recovered in Colombia (57 from humans and 41 from pig farms and abattoirs) were genomically characterized between 2015 and 2022 and compared with 102 representative genomes of international lineages by whole-genome sequencing (WGS) and phylogenomic analysis. Phylogenomic analysis revealed the existence of two well-defined endemic lineages in Colombia (Clusters 1 and 2), arising from independent introduction events and subsequent local stabilization. Both lineages comprise isolates of human and swine origin without clear phylogenetic separation by host species, suggesting active zoonotic cocirculation and closely integrated interspecies transmission dynamics. Marked differences were observed in the accessory genome, including the differential presence of prophages (e.g., Gifsy-2, Fels-2, SW9), virulence plasmids, and resistance profiles. The Colombian lineages exhibited a high frequency of the pSTV plasmid (85%, n = 84/98) and a substantial burden of resistance determinants to quinolones (such as qnrB19, 74.5%; gyrA S83F mutation, 19.4%), phenicols (floR), tetracyclines (tetA, tetB), β-lactams (blaTEM-1B), and heavy metals. In contrast, the Colombian genomes clustered with the European ST34 lineage lacked pSTV but retained resistance and heavy metal operons. These findings demonstrate that international and endemic lineages coexist in Colombia with independent evolutionary trajectories, underscoring the need to strengthen genomic surveillance under the "One Health" approach to anticipate emerging threats and develop integrated control strategies.IMPORTANCEThe monophasic variant of Salmonella Typhimurium (STVM) has emerged as a predominant serovar in both humans and swine internationally. In Colombia, a fundamental question driving this study was whether local isolates belonged to international lineages or represented endemic strains. This study provides the first comprehensive genomic characterization demonstrating that two Colombian endemic lineages circulate simultaneously between humans and pigs without phylogenetic separation by host species, confirming active zoonotic transmission. The results demonstrate the coexistence of both lineages, each with distinctive repertoires of mobile genetic elements and specific antimicrobial resistance profiles. Understanding these transmission dynamics and evolutionary patterns is crucial for public health, as it demonstrates how zoonotic pathogens can establish locally adapted lineages with distinct resistance patterns. The genomic evidence of sustained interspecies circulation highlights the critical need for integrated surveillance strategies under the "One Health" framework. This will enable anticipating emerging threats, tracing transmission routes, and developing targeted interventions in food production systems.

One Health↗
PubMed1988

[Genetic polymorphism of alpha 1-antitrypsin in green monkeys studied by isoelectric focusing and family analysis].

24 variants of alpha 1-antitrypsin (alpha 1-AT) were recognized in sera of 120 wild and capture-born African green monkeys by isoelectrofocusing in Ampholine PAG-plates (pH 4-6.5) and western blotting with antihuman alpha 1-AT serum. All variants had much more cathodal position than human alpha 1-AT and revealed very high microheterogeneity which was slightly different from the observed in human alpha 1-AT. The alpha 1-AT banding pattern allowed to postulate existence of 10 codominant alleles in the Pi locus of African green monkeys. The reality of 8 alleles was proved by family analysis which included 45 monkey birth cases. Two other alleles were absent in the parents available. Thus, alpha 1-AT is the most polymorphic among the known serum proteins of African green monkeys. The latter can be useful for molecular systematics of these primates.

Alleles↗
PubMed1992

Behavioral analysis of Vibrio parahaemolyticus variants in high- and low-viscosity microenvironments by use of digital image processing.

Digital image analysis and light microscopy were used to study and quantify the growth and behavior of two variants and selected flagellar mutants of Vibrio parahaemolyticus in glass flow cells under high- and low-viscosity conditions. The observations showed a series of surface-associated behaviors, including attachment, microcolony formation, migration, chemotactic movements, and aggregation, indicating a substantial degree of adaptive flexibility and multicellular behavior during growth of V. parahaemolyticus at interfaces.

Bacterial Adhesion↗
PubMed1990

Alpha 1-antitrypsin Wbethesda: molecular basis of an unusual alpha 1-antitrypsin deficiency variant.

Molecular analysis of alpha 1-antitrypsin (alpha 1AT) Wbethesda revealed that it differs from the normal M1 (Ala213) allele by a single base mutation causing an amino acid substitution Ala336 GCT----Thr ACT. Evaluation of alpha 1AT biosynthesis directed by the Wbethesda allele showed that although Wbethesda alpha 1AT mRNA was translated normally in vitro, transfection of the Wbethesda cDNA into COS-I cells was associated with human alpha 1AT secretion of 50% that of cells transfected with a normal alpha 1AT cDNA. The pattern of alpha 1AT biosynthesis was not intracellular accumulation as observed with the common Z alpha 1AT deficiency allele, but reduced intracellular alpha 1AT, suggesting intracellular degradation of the newly synthesized Wbethesda molecule. Together these observations suggest that in heterozygous combination with a Z or Null alpha 1AT allele, the Wbethesda variant causes "alpha 1AT deficiency", thus classifying it as an alpha 1AT "at risk" allele for emphysema.

Alleles↗
PubMed1978

[Characteristics of the polysaccharide-containing somatic antigens isolated from the K-1 strain of the plague microbe and its antibiotic-resistant variants].

Immunochemical analysis of 2 polysaccharide-containing structures of the lypopolysaccharide of the plague causative agent (main somatic antigen and lipopolysaccharide) isolated from K-1 strain and a number of its antibiotic resistant mutants was carried out. It was shown that development of resistance to streptomycin alone or its combination with monomycin did not cause detectable changes in the monosaccharide composition and serological properties of the cultures tested. More significant changes associated with development of complex resistance, i.e. K-1 (Strr leads to Penr leads to Tetr) were accompanied by a decrease in the content of hexozamine and serological activity of the main somatic antigen determining the O-specificity of the lipopolysaccharide. Defective changes in the monosaccharide composition and serological properties of both the main somatic antigen and the polysaccharide were observed in the yellow variant of the streptomycin resistant mutant K-1.

Anti-Bacterial Agents↗
PubMed1992

Decreased stress inducibility of the HSP68 protein in a rat hepatoma variant clone.

Analysis of the stress response of closely related rat hepatoma clones revealed that the major inducible heat-shock protein 68 (HSP68) was only slightly inducible upon stress in the glucocorticoid-resistant, dedifferentiated clone-2 cells, but strongly activated in the differentiated, glucocorticoid-sensitive Faza 967 cells from which clone 2 was derived. The decreased inducibility of HSP68 in clone-2 cells was not the consequence of altered kinetics of protein synthesis recovery, was not correlated with the deficient inducibility of other major heat-shock proteins and had no effect on the heat sensitivity of the cells. This deficiency was observed after treatment with mild and strong heat and various chemicals. The results of nuclear run-on experiments suggested that the impairment of HSP68 mRNA induction most likely occurs at the transcriptional level and is probably specific for the corresponding gene. In Faza 967 and clone-2 cells, stress activated comparable levels of heat-shock-factor binding to the heat-shock element, and the expression of a reporter gene under the control of murine HSP70.1 promoter was strongly stimulated in both cells. Therefore, our results raise the possibility that the deficient stress inducibility of HSP68 is due to some specific regulation of the endogeneous HSP68 gene, rather than to a deficiency of the heat-shock factor or mutation of the corresponding gene.

Animals↗
PubMed1985

[Rapid immunoenzyme analysis].

A variant of the immunoenzyme assay, reducing the duration of the assay procedure by 3 hours in comparison with the standard technique, is presented. This rapid variant is sufficiently sensitive and reproducible.

Antigens, Bacterial↗