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Restricted polymorphism of the mannose-binding lectin gene of indigenous Australians.

Mannose-binding lectin (MBL) is an important complement-activating protein of the human innate immune system. Deficiency of MBL is associated with an increased risk of various infections and arises from three structural gene mutations in exon 1 (variants B, C and D) and/or the presence of a low efficiency promoter. The C allele is found in sub-Saharan Africa whereas the B allele is found elsewhere, suggesting that these mutations occurred after the suggested hominid migration out of Africa [100-150 000 years before present (BP)]. Paradoxically, these alleles may have a selective advantage in protection against intracellular pathogens and occur at particularly high frequencies in sub-Saharan Africa (C variant) and South America (B variant). Since hominids reached Australia at least 50 000 years ago, a study of MBL polymorphisms in the indigenous population was of interest. Using heteroduplex technology we found a paucity of MBL structural gene mutations in two population groups from geographically distinct regions. Of 293 individuals tested, 289 were wild-type and four were heterozygous for either the B or D allele. In each individual with an MBL mutation the HLA haplotype profile suggested some Caucasian admixture. We also found a restricted range of MBL promoter haplotypes and the serum MBL levels were higher than those of any other ethnic group studied to date (median 3.07 microg/ml). Our data suggest that the B mutation probably arose between 50 000 and 20 000 BP. Its absence from the founder gene pool of indigenous Australians may also partly explain their vulnerability to intracellular infections such as tuberculosis.

Alleles↗

Major histocompatibility genes in egg-laying hens.

A common base population of White Leghorn was "synthesized" for a joint project on the genetics of egg-laying, undertaken by animal breeding geneticists in 4 Scandinavian countries. After 6 to 7 generations of line selection for various egg-laying parameters, MHC typing was undertaken of both the selection lines in Denmark, Norway, and Sweden and the respective control lines representing the common base population. Ten MHC haplotypes were defined which jointly accounted for about 95% of the MHC gene pool of the base population. The 2 haplotypes which were predominant in the base population, B15 and B19, responded very differently to the selection pressures applied.

Animals↗

A complete hlyCABD-like RTX operon marks a virulence-associated subset of trh-positive Vibrio parahaemolyticus from Hangzhou Bay, China.

Vibrio parahaemolyticus remains a major cause of seafood-associated gastroenteritis, yet routine surveillance still relies largely on the canonical hemolysin markers thermostable direct hemolysin (tdh) and tdh-related hemolysin (trh). To determine whether this framework overlooks accessory virulence determinants in trh-positive lineages, we analyzed 193 V. parahaemolyticus isolates collected between 2022 and 2025 from clinical, environmental, and seafood-associated sources in the Hangzhou Bay region of China. Serotyping identified 45 serotypes, with O10:K4 predominating among clinical isolates. Both clinical and non-clinical populations showed open pan-genomes, although the non-clinical group carried a larger accessory gene pool. We identified a complete hlyCABD-like RTX operon in 10 trh-positive isolates with T3SS2-associated virulence backgrounds. These RTX-positive isolates were distributed across seven sequence types and three of five phylogenetic groups. This distribution was lineage-restricted but non-clonal. In the representative hybrid-assembled genome, the operon occurred within a mosaic genomic region containing additional virulence- and mobility-associated genes, indicating a composite pathogenicity island-like element. In the tested subset, RTX-positive isolates showed significantly greater hemolytic activity than RTX-negative trh-positive isolates. This significant difference was consistently observed in both plate-based and liquid assays, and within the RTX-positive subset, hlyA expression correlated with hemolytic activity, whereas the trh gene and the tlh (thermolabile hemolysin) gene did not. A complete hlyCABD-like RTX operon therefore identifies a hemolysis-associated subset of trh-positive V. parahaemolyticus and supports its further evaluation as an additional target for food safety surveillance.

Vibrio parahaemolyticus↗

Inheritance of partial resistance against Colletotrichum lindemuthianum in Phaseolus vulgaris and co-localization of quantitative trait loci with genes involved in specific resistance.

Anthracnose, one of the most important diseases of common bean (Phaseolus vulgaris), is caused by the fungus Colletotrichum lindemuthianum. A "candidate gene" approach was used to map anthracnose resistance quantitative trait loci (QTL). Candidate genes included genes for both pathogen recognition (resistance genes and resistance gene analogs [RGAs]) and general plant defense (defense response genes). Two strains of C. lindemuthianum, identified in a world collection of 177 strains, displayed a reproducible and differential aggressiveness toward BAT93 and JaloEEP558, two parental lines of P. vulgaris representing the two major gene pools of this crop. A reliable test was developed to score partial resistance in aerial organs of the plant (stem, leaf, petiole) under controlled growth chamber conditions. BAT93 was more resistant than JaloEEP558 regardless of the organ or strain tested. With a recombinant inbred line (RIL) population derived from a cross between these two parental lines, 10 QTL were located on a genetic map harboring 143 markers, including known defense response genes, anthracnose-specific resistance genes, and RGAs. Eight of the QTL displayed isolate specificity. Two were co-localized with known defense genes (phenylalanine ammonia-lyase and hydroxyproline-rich glycoprotein) and three with anthracnose-specific resistance genes and/or RGAs. Interestingly, two QTL, with different allelic contribution, mapped on linkage group B4 in a 5.0 cM interval containing Andean and Mesoamerican specific resistance genes against C. lindemuthianum and 11 polymorphic fragments revealed with a RGA probe. The possible relationship between genes underlying specific and partial resistance is discussed.

Chromosome Mapping↗

Clonal reproduction by males and females in the little fire ant.

Sexual reproduction can lead to major conflicts between sexes and within genomes. Here we report an extreme case of such conflicts in the little fire ant Wasmannia auropunctata. We found that sterile workers are produced by normal sexual reproduction, whereas daughter queens are invariably clonally produced. Because males usually develop from unfertilized maternal eggs in ants and other haplodiploid species, they normally achieve direct fitness only through diploid female offspring. Hence, although the clonal production of queens increases the queen's relatedness to reproductive daughters, it potentially reduces male reproductive success to zero. In an apparent response to this conflict between sexes, genetic analyses reveal that males reproduce clonally, most likely by eliminating the maternal half of the genome in diploid eggs. As a result, all sons have nuclear genomes identical to those of their father. The obligate clonal production of males and queens from individuals of the same sex effectively results in a complete separation of the male and female gene pools. These findings show that the haplodiploid sex-determination system provides grounds for the evolution of extraordinary genetic systems and new types of sexual conflict.

Alleles↗

Genetic engineering and coagulation factors.

It is unfortunate that we cannot report, in the area of coagulation, advances that have been seen in related fields such as thrombolytic therapy. The reported progress (Gold et al, 1984; Van de Werf et al, 1984) with human recombinant tissue plasminogen activator (Pennica et al, 1983) augers well for the application of recombinant technology to the problems faced by patients with coagulation defects. While plasminogen activator is being assessed in an acute therapeutic setting, its use signals a beginning of the application of the technology to abnormalities of the haemostatic mechanism. Chronic administration of coagulation factors for prophylaxis and replacement therapy would appear to be just one more step down the pathway illuminated by the biochemists, microbiologists and cell biologists who have preceded the clinicians in this promising area. There is no record of the use of genetically engineered materials in the treatment of coagulation defects, primarily because the body of knowledge and refined techniques have only recently been acquired. For this reason we have had to project developments in other areas onto the problems that exist for the haemostatically compromised patient. In describing the potential usefulness of these technologies, it is difficult to ascertain where the logical projection, from a fully investigated model system, diverges from flights of imaginative fancy. Cloning projects considered overly ambitious and grandiose at the beginning of this decade are already accomplished feats. The feasibility of gene therapy in the mammalian system has been demonstrated, and trade publications now discuss governmental approval for investigative use of this procedure in 1985. Panels of physicians, scientists and even politicians now seriously contemplate and promulgate views and regulations pertaining to the efficacy and ethics of the use of genetic engineering in the treatment of human disease. The haemophilias will certainly be among the first genetic diseases to be approached with the techniques of recombinant DNA technology. Diagnostic testing, using cloned DNA, is already underway and therapeutic trials are predicted for the near future. Every observer of this rapidly growing field has to define for himself when the future is. For the potential carrier of haemophilia B, the future is now. For the physician managing the patient with a haemophilic inhibitor, the future can't come soon enough. And, for those who are concerned with man's tampering with the gene pools of living things, from viruses to humans, the future comes too quickly to be dealt with in a rational and understanding way.

Animals↗

Biochemical genetic relationships among Tunisian hares (Lepus sp.), South African cape hares (L. capensis), and European brown hares (L. europaeus).

Tunisian hares (n = 45), currently assigned to Lepus capensis, were assayed for allelic variation at 40 allozyme loci, and allele frequencies at 32 loci were directly compared with earlier data of South African cape hares (L. capensis, n = 9) and European brown hares (L. europaeus, n = 244) to reveal genetic relationships among them. European mountain hares (L. timidus, n = 200) were used for outgroup comparison. In the Tunisian hares 27.5% of the loci were polymorphic with 2-4 alleles. Among all alleles at polymorphic loci, 15.1% occurred exclusively in Tunisian hares, 5.7% exclusively in cape hares, and 7.5% exclusively in brown hares at low frequencies. Not a single locus showed alternately fixed alleles between the samples of the L. capensis/L. europaeus complex. Levels of absolute and relative genetic differentiation among the samples of the L. capensis/L. europaeus complex were low, relative to pairwise comparisons involving mountain hares. Diverse cluster analyses and multidimensional scaling of various pairwise genetic distance matrices concordantly grouped Tunisian hares with brown hares, and South African cape hares clustered only slightly farther apart, whereas mountain hares were distinctly separate. These results suggest regionally distinct phylogenetic units within an overall cohesive gene pool in the L. capensis/L. europaeus complex, supporting Petter's view that all North African hares belong to L. capensis except for one local population of savanna hares, and that cape hares and brown hares are conspecific.

Animals↗

The Odyssean personality. A survival advantage for carriers of genes predisposing to schizophrenia?

To explain the persistence of schizophrenia in human populations at relatively high and constant rates, it is proposed that the schizoid-paranoid personality (designated as the Odyssean personality) which characterizes so many nonpsychotic relatives of schizophrenics, represents a selective advantage. It is assumed that odyssean relatives carry the gene or genes predisposing to schizophrenia, but not in sufficient quantity for the development of the psychosis. It is suggested that because of their schizoid-paranoid out-look, Odysseans have an increased probability of contributing to the gene pool of succeeding generations since, in a world plagued by terror, strife, and war, they, rather than their trusting peers, are the ones more likely to survive long enough to ensure the survival of their progeny.

Adaptation, Psychological↗

Phylogenetic star contraction applied to Asian and Papuan mtDNA evolution.

In the past decade, mitochondrial DNA (mtDNA) of 826 representative East Asians and Papuans has been typed by high-resolution (14-enzyme) restriction fragment length polymorphism (RFLP) analysis. Compared with mtDNA control region sequencing, RFLP typing of the complete human mitochondrial DNA generally yields a cleaner phylogeny, the nodes of which can be dated assuming a molecular clock. We present here a novel star contraction algorithm which rigorously identifies starlike nodes (clusters) diagnostic of prehistoric demographic expansions. Applied to the Asian and Papuan data, we date the out-of-Africa migration of the ancestral mtDNA types that founded all Eurasian (including Papuan) lineages at 54,000 years. While the proto-Papuan mtDNA continued expanding at this time along a southern route to Papua New Guinea, the proto-Eurasian mtDNA appears to have drifted genetically and does not show any comparable demographic expansion until 30,000 years ago. By this time, the East Asian, Indian, and European mtDNA pools seem to have separated from each other, as postulated by the weak Garden of Eden model. The east Asian expansion entered America about 25,000 years ago, but was then restricted on both sides of the Pacific to more southerly latitudes during the Last Glacial Maximum around 20,000 years ago, coinciding with a chronological gap in our expansion dates. Repopulation of northern Asian latitudes occurred after the Last Glacial Maximum, obscuring the ancestral Asian gene pool of Amerinds.

Algorithms↗

Historical genetics in Uruguay: estimates of biological origins and their problems.

The relative contribution of Europeans, Africans, and Amerindians to the gene pool of two Uruguayan populations (Montevideo and Tacuarembó) was estimated using several approaches. For Montevideo 8 genetic systems were considered, and for Tacuarembó 18 systems were used. A preliminary investigation of the most probable parental groups, using genetic distances, yielded four combinations of European populations, four combinations of African populations, and five combinations of Amerindian populations. Afterward, 240 possible combinations from the possible parental groups were considered for the quantitative estimations of interethnic admixture using the gene identity method. The most inclusive combinations furnished the following admixture estimates: (1) Montevideo, 92% European, 7% African, and 1% Amerindian; (2) Tacuarembó, 65% European, 15% African, and 20% Amerindian. The modal values obtained within each ethnic category did not differ by much (2-3%), the exception being the Amerindian contribution to Tacuarembó, where a higher diversity was observed (up to 14%). Comparison with a maximum-likelihood method of admixture estimation was hampered by the fact that not all markers can be used to obtain these alternative numbers. Evaluations using six systems for Montevideo and seven for Tacuarembó yielded values that were closer to the previous estimates for Montevideo (largest difference, 7% in the Amerindian component) but somewhat higher for Tacuarembó, amounting to 11% for the European and Amerindian contributions. It is clear, however, that the two populations show significant biological heterogeneity, resulting partly from diverse patterns of historical formation.

Ethnicity↗

Molecular demonstration of SLC4A1 gene deletion in two Mexican patients with Southeast Asian ovalocytosis.

We describe the finding of two Mexican patients with a specific 27-bp deletion in the solute carrier family 4 gene (SLC4A1delta27) (also known as the band 3 gene found on chromosome 17q21-q22), characteristic of Southeast Asian ovalocytosis (SAO). The patients were asymptomatic, and the initial diagnosis was made by microscopic observation of the presence of typical stomatocytic ovalocytes. The gene deletion was confirmed by PCR and DNA sequencing. Both patients were heterozygous for the deletion. One patient is from Tabasco state, in southeastern Mexico, a malaria-endemic zone. The other patient is from Mexico City, which is not a malaria-endemic area. Their families have no non-Mexican ancestors and their previous generations were born in Mexico. Both patients carry the HLA-B*3501 subtype, characteristic of Amerindians and Asian populations. Familial and HLA data led us to conclude that these two patients are the first report of SLC4A1delta27 in Amerindians. The nucleotide analysis showing a perfect match sequence between Southeast Asian and Mexican patients suggests, but does not prove, that the Mexican gene is not a de novo mutation. Instead, this gene might be the result of migration of individuals with Asian ancestry into the Mexican gene pool. We are looking for other families with the mutation to detect, by HLA analysis, the ancient ethnic origin of these patients.

Anion Exchange Protein 1, Erythrocyte↗

Some genetic markers in Valachian (Olachian) Gypsies in Slovakia.

ABO, RH, MN, Kell, P, Lutheran, Lewis, HP, GC, ACP, PGM1, ADA and ESD markers were studied in 122 Valachian Gypsies from Vinodol in West Slovakia. The Valachian Gypsies represent about 5% of the total number of Gypsies (400,000) living in the Czech and Slovak Republic. The results show that their gene pool differs greatly from the one obtained for other Gypsy populations. Since Valachian Gypsies form an endogamous isolate with a high degree of inbreeding, genetic drift and founder effect might have contributed to this difference.

Blood Group Antigens↗

Neuronal proteins custom designed by alternative splicing.

The evolution of alternative splicing in eukaryotes greatly expanded the number of functionally distinct proteins that could be produced from a finite gene pool. Extensive in the brains of higher organisms, alternative splicing might be the primary mechanism for generating the spectrum of protein activities that support complex brain functions. Alternative splicing is controlled at the level of individual neurons to custom design proteins for optimal performance. The expression profiles of splice isoforms are modified during development and as neuronal activity changes. Alternative splicing can lead to incremental, long lasting changes in ion channel and receptor activities, independent of changes in gene transcription. Recent studies of tissue-specific splicing factors are revealing how coordinated alterations in alternative splicing of RNA transcripts control synaptic function.

Alternative Splicing↗

Y-chromosome 10 locus short tandem repeat haplotypes in a population sample from Sicily Italy.

This study reports the first data on Y-chromosome-specific short tandem repeat (STR) haplotype frequencies, in the population of the island of Sicily (Italy), based on the combination of alleles at the following 10 Y-chromosome loci DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, and DYS439. In a total of 117 males, 108 unique haplotypes were observed, with 99 of them being singletons. The 10 locus haplotypes generated a diversity value of 0.9987 and discriminatory power (DP) of 92.30%. The data on the seven of the 10 polymorphisms (DYS19; DYS389I; DYS389II; DYS390; DYS391; DYS392 and DYS393) that have been most studied in worldwide populations were compared with similar data from neighboring Mediterranean populations in order to address the question of shared ancestry, gene flow and population affinities. Overall, results indicate Sicily is closest genetically to the mainland Italian population but also with evidence of a significant African component in the male gene pool. These findings are consistent with those obtained from other genetic markers (autosomal and mitochondrial DNA as well as the classical blood groups) and also with the recorded settlement history (either peaceful or due to invasion) of the island.

Chromosomes, Human, Y↗

exl, an exchangeable genetic island in Neisseria meningitidis.

The genetic structure and evolution of a novel exchangeable meningococcal genomic island was defined for the important human pathogen Neisseria meningitidis. In 125 meningococcal strains tested, one of three unrelated nucleotide sequences, designated exl (exchangeable locus), was found between a gene required for heme utilization, hemO, and col, encoding a putative Escherichia coli collagenase homologue. The 5' boundary of each exl cassette was the stop codon of hemO, whereas the 3' boundary was delineated by a 33-bp repeat containing neisserial uptake sequences located downstream of col. One of the three alternative exl cassettes contained the meningococcal hemoglobin receptor gene, hmbR (exl3). In other meningococcal strains, hmbR was absent from the genome and was replaced by either a nucleotide sequence containing a novel open reading frame, exl2, or a cassette containing exl3. The proteins encoded by exl2 and exl3 had no significant amino acid homology to HmbR but contained six motifs that are also present in the lipoprotein components of the lactoferrin (LbpB), transferrin (TbpB), and hemoglobin-haptoglobin (HpuA) uptake systems. To determine the evolutionary relationships among meningococci carrying hmbR, exl2, or exl3, isolates representing 92 electrophoretic types were examined. hmbR was found throughout the population structure of N. meningitidis (genetic distance, >0.425), whereas exl2 and exl3 were found in clonal groups at genetic distances of <0.2. The commensal neisserial species were identified as reservoirs for all of the exl cassettes found in meningococci. The structure of these cassettes and their correlation with clonal groups emphasize the extensive gene pool and frequent horizontal DNA transfer events that contribute to the evolution and virulence of N. meningitidis.

Amino Acid Sequence↗

Ancestral proportions and admixture dynamics in geographically defined African Americans living in South Carolina.

We analyzed admixture in samples of six different African-American populations from South Carolina: Gullah-speaking Sea Islanders in coastal South Carolina, residents of four counties in the "Low Country" (Berkeley, Charleston, Colleton, and Dorchester), and persons living in the city of Columbia, located in central South Carolina. We used a battery of highly informative autosomal, mtDNA, and Y-chromosome markers. Two of the autosomal markers (FY and AT3) are linked and lie 22 cM apart on chromosome 1. The results of this study indicate, in accordance with previous historical, cultural, and anthropological evidence, a very low level of European admixture in the Gullah Sea Islanders (m = 3.5 +/- 0.9%). The proportion of European admixture is higher in the Low Country (m ranging between 9. 9 +/- 1.8% and 14.0 +/- 1.9%), and is highest in Columbia (m = 17.7 +/- 3.1%). A sex-biased European gene flow and a small Native American contribution to the African-American gene pool are also evident in these data. We studied the pattern of pairwise allelic associations between the FY locus and the nine other autosomal markers in our samples. In the combined sample from the Low Country (N = 548), a high level of linkage disequilibrium was observed between the linked markers, FY and AT3. Additionally, significant associations were also detected between FY and 4 of the 8 unlinked markers, suggesting the existence of significant genetic structure in this population. A continuous gene flow model of admixture could explain the observed pattern of genetic structure. A test conditioning on the overall admixture of each individual showed association of ancestry between the two linked markers (FY and AT3), but not between any of the unlinked markers, as theory predicts. Thus, even in the presence of genetic structure due to continuous gene flow or some other factor, it is possible to differentiate associations due to linkage from spurious associations due to genetic structure.

Africa↗

Salmonella plasmids of the pre-antibiotic era.

In order to provide a profile of the plasmid gene pool in Salmonella prior to the clinical use of antibiotics, a molecular genetic analysis was made of plasmids in strains collected by E.D.G. Murray between 1917 and 1954. These pre-antibiotic era (PAE) salmonellae contain conjugative plasmids of the same incompatibility groups as contemporary enterobacterial plasmids. Upon analysis of total plasmid content, 42 plasmids, sized between 23 and 72 MDa, were found. We defined and investigated six groups of these PAE Salmonella plasmids in terms of three groups of genes; those involved in plasmid maintenance and incompatibility, DNA repair and virulence. Of the five groups, three were replicon-typed to groups IncI1, IncX and IncFII; one group exhibited no homology to contemporary Inc/Rep probes, and one group represented virulence plasmids containing a common plasmid-partitioning locus. The results indicated that most of the PAE groups were progenitors of contemporary R-plasmids, except for the virulence plasmids, which have generally not evolved as vectors of antibiotic resistance.

Bacteriophage Typing↗

Origins of hyperphenylalaninemia in Israel.

Mutations and polymorphisms at the phenylalanine hydroxylase (PAH) gene were used to study the genetic diversity of the Jewish and Palestinian Arab populations in Israel. PAH mutations are responsible for a large variety of hyperphenylalaninemias (HPAs), ranging from the autosomal recessive disease phenylketonuria to various degrees of nonclinical HPA. Seventy-two Jewish and 36 Palestinian Arab families with various HPAs, containing 115 affected genotypes, were studied by haplotype analysis, screening for previously known PAH lesions and a search for novel mutations. Forty-one PAH haplotypes were observed in this sample. Four mutations previously identified in Europe (IVS10nt546, R261Q, R408W and R158Q) were found, and were associated with the same haplotypes as in Europe, indicating possible gene flow from European populations into the Jewish and Palestinian gene pools. Of particular interest is a PAH allele with the IVS10nt546 mutation and haplotype 6, that might have originated in Italy more than 3,000 years ago and spread during the expansion of the Roman Empire. These results, together with previous identification of three PAH mutations unique to Palestinian Arabs [IVSnt2, Edel(197-205) and R270S], indicate that the relatively high genetic diversity of the Jewish and Palestinian populations reflects, in addition to genetic events unique to these communities, some gene flow from neighboring and conquering populations.

Amino Acid Metabolism, Inborn Errors↗