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PubMed1991

Replication of avian influenza viruses in humans.

Volunteers inoculated with avian influenza viruses belonging to subtypes currently circulating in humans (H1N1 and H3N2) were largely refractory to infection. However 11 out of 40 volunteers inoculated with the avian subtypes, H4N8, H6N1, and H10N7, shed virus and had mild clinical symptoms: they did not produce a detectable antibody response. This was presumably because virus multiplication was limited and insufficient to stimulate a detectable primary immune response. Avian influenza viruses comprise hemagglutinin (HA) subtypes 1-14 and it is possible that HA genes not so far seen in humans could enter the human influenza virus gene pool through reassortment between avian and circulating human viruses.

Adult↗
PubMed1992

Diversity of aminoglycoside resistance in Enterobacter cloacae in Greece.

Ninety Enterobacter cloacae strains isolated from 12 Greek hospitals were examined in terms of epidemiological types and resistance mechanisms. Using O serotyping 69% of the strains were assigned to a specific serotype and overall 16 different serotypes were identified. The combination of serotyping, phagetyping and biotyping efficiently discriminated most of the strains, indicating that single epidemic strains were not prevalent, although serotypes 3, 7, and group II predominated. Eight representative strains, all resistant to gentamicin, tobramycin, amikacin and netilmicin, were further examined for transferability and mechanisms of resistance. Aminoglycoside resistance was found to be transferable in most strains, and 13 R plasmids of 40-120 MDa molecular weight were detected. The enzymes detected consisted of three enzymes active against gentamicin [ANT(2h'), AAC(3)-I and AAC(3)-V]; three active against tobramycin [ANT(2"), AAC(3)-V and AAC(6')-I]; two active against netilmicin [AAC(3)-V and AAC(6')-I]; and one active against amikacin [AAC(6')-I]. APH(3') and ANT (3"), which modify neomycin and streptomycin plus spectinomycin respectively, were also found. Overall up to five aminoglycoside modifying enzymes were detected on the same R plasmid, AAC(6')-I plus ANT(2") being the most prevalent. The high incidence of multiresistance in Enterobacter cloacae and the fact that resistance is due to enzymatic inactivation of the antibiotics, indicate that in Greece this species might act as a gene pool for the spread of resistance to other bacteria of clinical relevance.

Aminoglycosides↗
PubMed1993

Trimethoprim resistance in South African isolates of aerobic gram-negative faecal flora.

Aerobic gram-negative commensal faecal flora from 362 healthy volunteers was examined for resistance to trimethoprim. Three hundred fifty-seven trimethoprim-resistant organisms were isolated from 272 of the volunteers (297 Escherichia coli, 46 Klebsiella spp., 9 Enterobacter spp. and 7 other species). Trimethoprim resistance was associated with resistance to other antibiotics at the following frequencies: ampicillin 71.4%, tetracycline 88%, cephalosporins 14% and aminoglycosides 4%. High-level resistance to trimethoprim (MIC > or = 1024 mg/l) occurred in 98.6% of the isolates. Trimethoprim resistance was transferable in 51.2% of the isolates. An X+ factor was required to mobilize resistance in a further 3.4%. Resistance to other antibiotics cotransferred with trimethoprim at the following frequencies: ampicillin 55.4%, tetracycline 30%, cephalosporins 1.5% and aminoglycosides 2.6%. Restriction enzyme analysis of 148 plasmids revealed 79 different profiles. Two restriction profiles represented 10.1 and 8.8% of these plasmids, respectively. The large number of different antibiograms and restriction profiles indicates that there is a large gene pool of trimethoprim-resistant organisms in the faecal flora.

Bacteria, Aerobic↗
PubMed1990

P-related sequences in Drosophila bifasciata: a molecular clue to the understanding of P-element evolution in the genus Drosophila.

Two P-elements (bif1 and bif2) were isolated from a genomic library of Drosophila bifasciata. Both elements are internally deleted and have lost the coding capacity for a functional transposase. One of the elements (bif2) contains an insert consisting of a repetitive sequence. The terminal inverted repeats and the segments necessary for passive mobility are well conserved. Element bif2 has retained rudiments of the coding sequence of exon 0 and exon 3, but the reading frame is destroyed by insertions and deletions. The comparison of the D. bifasciata P-elements with P-elements of Drosophila melanogaster and Drosophila nebulosa reveals that the two latter sequences are more similar to each other than either of them is to the D. bifasciata elements. This finding contradicts the phylogenetic relationship of the species and can be taken as an indirect but unequivocal evidence for recent horizontal gene transfer from a relative of D. nebulosa to the gene pool of D. melanogaster. The P-elements of D. bifasciata are phylogenetically ancient and have evolved independently for about 50 million years. A higher substitution rate at the third codon position as well as a predominance of conservative replacements at the amino acid level indicates that the P-elements of D. bifasciata have been under selective constraint over a long period and that immunobilization has occurred only recently.

Amino Acid Sequence↗
PubMed1996

Geographic distribution and origin of CFTR mutations in Germany.

The geographic distribution and origin of CFTR mutations in Germany was evaluated in 658 three-generation families with cystic fibrosis (CF). Fifty different mutations were detected on 1305 parental CF chromosomes from 22 European countries and overseas. The major mutation. delta F508 was identified on 71.5% of all CF chromosomes, followed by R553X (1.8%), N1303K (1.3%), G542X (1.1%), G551D (0.8%) and R347P (0.8%). According to the grandparents' birthplace, 74% of CF chromosomes had their origin in Germany; the delta F508 percentage was 77%, 75%, 70% and 62% in northern, southern, western and eastern Germany, respectively. Ten or more mutant alleles in the investigated CF gene pool originated from Austria, the Czech Republic, Poland, Russia, Turkey and the Ukraine. This widespread geographic origin of CFTR mutations in today's Germany reflects the many demographic changes and migrations in Central Europe during the 20th century.

Cystic Fibrosis↗
PubMed2003

Hybridization, transgressive segregation and evolution of new genetic systems in Drosophila.

Introgressive hybridization facilitates incorporation of genes from one species into the gene pool of another. Studies on long-term effects of introgressive hybridization in animal systems are sparse. Drosophila nasuta (2n = 8) and D. albomicans (2n = 6)-a pair of allopatric, morphologically almost identical, cross-fertile members of the nasuta subgroup of the immigrans species group-constitute an excellent system to analyse the impact of hybridization followed by transgressive segregation of parental characters in the hybrid progeny. Hybrid populations of D. nasuta and D. albomicans maintained for over 500 generations in the laboratory constitute new recombinant hybrid genomes, here termed cytoraces. The impact of hybridization, followed by introgression and transgressive segregation, on chromosomal constitution and karyotypes, some fitness parameters, isozymes, components of mating behaviour and mating preference reveals a complex pattern of interracial divergence among parental species and cytoraces. This assemblage of characters in different combinations in a laboratory hybrid zone allows us to study the emergence of new genetic systems. Here, we summarize results from our ongoing studies comparing these hybrid cytoraces with the parental species, and discuss the implications of these findings for our understanding of the evolution of new genetic systems.

Animals↗
PubMed2006

Lack of carriers of citrullinaemia and DUMPS in Indian Holstein cattle.

The present study investigated the occurrence of 2 autosomal recessive genetic diseases, bovine citrullinaemia and deficiency of uridine monophosphate synthase (DUMPS), in Indian Holstein cattle. The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis was performed on a group of 642 animals, mainly HF and HF crossbred cattle, to identify carriers of these diseases. None of the animals were carriers of citrullinaemia or DUMPS. It is possible that with the mounting selection pressure, the international gene pool may diminish, and consequently the risk of dissemination of inherited defects will increase. It is therefore recommended to screen breeding bulls for their breed-specific genetic diseases before they are inducted in artificial insemination programmes, to minimize the risk.

Animals↗
PubMed1998

Transcription and splicing patterns of M- and O-type P elements in drosophila bifasciata, D. helvetica, and scaptomyza pallida

RT-PCR was applied to analyze the splicing patterns of P-element-derived mRNAs in Drosophila bifasciata, D. helvetica, and Scaptomyza pallida. D. melanogaster was used as a control. The experiments revealed that P elements are transcribed in all species investigated. However, there are differences in the splicing patterns of IVS3, which has to be removed in order to produce transposase mRNA instead of repressor mRNA. These differences are observed among species as well as between the P element subfamilies, the M and the O type, which coexist in the genomes of D. bifasciata and S. pallida. In D. helvetica M-type transposase mRNA was found in the germline and repressor mRNA in the soma, as has been previously described for the canonical (M-type-related) P element of D. melanogaster. In contrast, in S. pallida only repressor mRNA of M-type elements was detected in all tissues. In D. bifasciata, M-type IVS3, although activated both in the soma and the germline, is never completely excised. Instead, two alternative double-spliced variants occur in which two small introns are removed within the IVS3 region. One of these variants codes for a protein 12 aa longer than the regular transposase. Taking these findings together, transposase production and transpositional activity of M-type elements seem to be limited to D. helvetica and D. melanogaster, whereas M-type elements have become immobile in D. bifasciata and S. pallida. Unlike the M type, the splicing of O-type transcripts in D. bifasciata and S. pallida follows the classical rules of tissue-specific P element regulation: transposase mRNA is produced exclusively in the germline whereas repressor mRNA is formed in somatic cells. Thus O-type elements are thought to be still transpositionally active in both species. This finding is in accordance with the postulated recent transfer of O-type elements between the gene pools of D. bifasciata and S. pallida. In addition, we were able to show that the IVS3 double-spliced variants of both P element types are produced regularily in all species of the genus Drosophila investigated so far, but not in S. pallida.

Journal Article↗
PubMed1997

Evolution of the freshwater eels.

The freshwater anguillid eels have an unusual life history and world-wide distribution. Questions about the phylogenetic relationships of this group and how their long spawning migrations and larval phase may contribute to their global distribution have not been addressed. This paper is first presentation of molecular phylogeny of Anguilla species, and based on this phylogenetic tree we suggest new aspect of the evolution of this group. Namely, ancestral eels originated during the Eocene or earlier, in the western Pacific Ocean near present-day Indonesia. A group derived from this ancestor dispersed westward, probably by larval transport in the global circum-equatorial current through the northern edge of the Tethys Sea. This group split into the ancestor of the European and American eels, which entered into the Atlantic Ocean, and a second group, which dispersed southward and split into the east African species and Australian species. Thus the world-wide distribution of the eel family can be understood from knowledge of continental drift, ocean currents, a specialized larva and evolutionary forces favoring dispersal and speciation of segregated gene pool.

Anguilla↗
PubMed2002

A high degree of genetic diversity is revealed in Isatis spp. (dyer's woad) by amplified fragment length polymorphism (AFLP).

Genetic diversity in 38 genotypes, representing 28 individual genotypes from five landraces of Isatis tinctoria (three German: Tubingen, Potsdam and Erfurt, one Swiss and one English), five genotypes of Isatis indigotica (Chinese woad) and five genotypes of Isatis glauca, were investigated using AFLP analysis. Five primer combinations detected a total of 502 fragments of which 436 (86.9%) were polymorphic. The level of polymorphism recorded within each species was 29.8, 86.9 and 35.8% for I. indigotica, I. tinctoria and I. glauca, respectively. Clearly, genetic diversity within I. tinctoria was greater than that observed in I. indigotica or I. glauca. Cluster analyses of the AFLP data using UPGMA and PCO revealed the complete separation of the genotypes of each species into distinct groups. I. indigotica separated as an entirely independent group, whereas I. glauca formed a separate cluster within the I. tinctoria group. Indeed, I. tinctoria and I. glauca are more closely related to each other than either is to I. indigotica. In addition, the genotypes of each landrace, apart from one from the English group, were clearly discriminated. However, the anomalous genotype did associate with the rest of its group when it was linked with the Erfurt group. These results provide new and useful information about the make-up of the Isatis genome, which has not previously been evaluated. They will be useful in the selection of plant material for variety development and conservation of the gene-pool.

Journal Article↗
PubMed2002

Diversity of chloroplast DNA SSRs in wild and cultivated soybeans: evidence for multiple origins of cultivated soybean.

Soybean [ Glycine max (L.) Merr.] is one of the major crops in the world and was domesticated from a wild progenitor, Glycine soja Sieb. & Zucc., in East Asia. In order to address the questions concerning the evolution and maternal lineage of soybean, we surveyed the variation in chloroplast DNA simple sequence repeats (cpSSR) of 326 wild and cultivated soybean accessions that were collected from various Asian countries. Twenty-three variants were detected at six cpSSRs in the accessions tested. All of the variants were found in wild soybean, whereas only 14 variants existed in the cultigen. Combining the variants at the six cpSSRs gave 52 haplotypes in the former and eight haplotypes in the latter. Both analyses indicated a considerably higher genetic diversity in the wild soybean. Around 75% of the cultivated accessions tested possessed a common haplotype (no. 49), which was detected in only seven wild accessions, six from southern Japan and one from southern China. The predominant haplotype in the cultigen may therefore have originated from a rare haplotype of the wild soybean that is presently distributed in the southern areas of Japan and China. The remaining seven haplotypes in the cultigen were distributed regionally, and except for three rare haplotypes, largely overlapped with the distributions of wild accessions with the same respective haplotypes. Our results strongly suggest that the cultivated soybeans with different cpDNA haplotypes originated independently in different regions from different wild gene pools and/or hybrid swarms between cultivated and wild forms.

Journal Article↗
PubMed2002

Considerations of correlated fertility between genders on genetic diversity: the Pinus densiflora seed orchard as a model.

The correlation between 99 clone female and male fertilities in a first generation seed orchard of Pinus densiflora was studied over 6 years. The effective number of the parent ( N(p)) and the variance effective population number [ N(e)((v))] were used to assess the impact of total (Psi(T)), female (psi(f)) and male (psi(m)) fertility variation. A theoretical framework was developed to account for female and male fertility correlations as well as the impact of possible pollen contamination. Total fertility variation was described by the sibling coefficient (Psi(T): the probability that two genes randomly chosen from the gamete gene pool originate from the same parent), which was further subdivided into psi(f) and psi(m). These parameters were compared under various conditions including the total seed harvest, imposing on equal seed harvest among the orchard's clones and two contamination scenarios ( M = 0 and 20%). Fertility variations among females, males and clones were observed within and among years. Sibling coefficients (Psi(T)) were lower, but the effective number of parent ( N(p)) and variance effective population number ( N(e)((v))) were higher in years with moderate female and good male strobilus production. N(p) for female and male reproductive outputs varied from 49 to 82 and from 57 to 93, respectively. N(p) was higher for males than females. When the crop of the 6 years was pooled, N(p) for female, male and the clone were 73, 87 and 85, respectively. The impact of female-male fertility correlation for conditions with no-, positive- and negative-correlations were assessed and their impact on Psi(T), N(p) and N(e)((v)) was also evaluated. It was demonstrated that the practice of equal seed harvesting from every clone, or the mixing of seeds from several years, would substantially improve the genetic diversity and the genetic representation of the seed orchard population when a positive correlation between gender fertilities was observed. The relevance of these results to supplemental-mass-pollination was discussed under two cases where equal- and un-equal amounts of pollen from clones were included in the pollen mixes.

Journal Article↗
PubMed2002

Assessment of genetic relationships in Cucurbita pepo (Cucurbitaceae) using DNA markers.

Cucurbita pepo (pumpkin, squash, gourd), an economically important species of the Cucurbitaceae, is extremely variable in fruit characteristics. The objective of the present study was to clarify genetic relationships across a broad spectrum of the C. pepo gene pool, with emphasis on domesticates, using AFLP, ISSR and SSR markers. Forty-five accessions were compared for presence or absence of 448 AFLP, 147 ISSR, and 20 SSR bands, their genetic distances (GDs) were estimated and UPGMA cluster analysis was conducted. The results obtained from these three marker systems were highly correlated (P << 0.001). Clustering was in accordance with the division of C. pepo into three subspecies, fraterna, texana and pepo, with the first two less distant to one another than to the last one. Within the clusters, sub-clustering occurred in accordance with fruit shape and size. The subsp. texana cluster consisted of six sub-clusters, one each for the representatives of its five cultivar-groups (Acorn, Crookneck, Scallop, Straightneck and Ovifera Gourd) and wild gourds. Within the subsp. pepo cluster, the representatives of two cultivar-groups (Zucchini and Orange Gourd) formed distinct sub-clusters and the representatives of two other groups (Cocozelle and Vegetable Marrow) tended to sub-cluster separately from one another but formed an assemblage with the representatives of the remaining group (Pumpkin). Within-group GDs were less than corresponding between-group GDs in nearly all comparisons. The smallest-fruited accession, 'Miniature Ball', appears to occupy a genetically central position within C. pepo.

Cucurbita↗
PubMed2003

Mapping of Rym14Hb, a gene introgressed from Hordeum bulbosum and conferring resistance to BaMMV and BaYMV in barley.

Hordeum bulbosum represents the secondary gene pool of barley and constitutes a potential source of various disease resistances in barley breeding. Interspecific crosses of H. vulgare x H. bulbosum resulted in recombinant diploid-barley progeny with immunity to BaMMV after mechanical inoculation. Tests on fields contaminated with different viruses demonstrated that resistance was effective against all European viruses of the soil-borne virus complex (BaMMV, BaYMV-1, -2). Genetic analysis revealed that resistance was dominantly inherited. Marker analysis in a F5 mapping family was performed to map the introgression in the barley genome and to estimate its size after several rounds of recombination. RFLP anchor-marker alleles indicative of an H. bulbosum introgression were found to cover an interval 2.9 cM in length on chromosome 6HS. The soil-borne virus resistance locus harboured by this introgressed segment was designated Rym14(Hb). For marker-assisted selection of Rym14(Hb) carriers, a diagnostic codominant STS marker was derived from an AFLP fragment amplified from leaf cDNA of homozygous-resistant genotypes inoculated with BaMMV.

Chromosome Mapping↗
PubMed2003

Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon.

A BC(2)F(2) population developed from an interspecific cross between Oryza sativa (cv IR64) and O. rufipogon (IRGC 105491) was used in an advanced backcross QTL analysis to identify and introduce agronomically useful genes from this wild relative into the cultivated gene pool. The objectives of this study were: (1) to identify putative yield and yield component QTLs that can be useful to improve the elite cultivar IR64; (2) to compare the QTLs within this study with previously reported QTLs in rice as the basis for identifying QTLs that are stable across different environments and genetic backgrounds; and (3) to compare the identified QTLs with previously reported QTLs from maize to examine the degree of QTL conservation across the grass family. Two hundred eighty-five families were evaluated in two field environments in Indonesia, with two replications each, for 12 agronomic traits. A total of 165 markers consisting of 131 SSRs and 34 RFLPs were used to construct the genetic linkage map. By employing interval mapping and composite interval mapping, 42 QTLs were identified. Despite its inferior performance, 33% of the QTL alleles originating from O. rufipogon had a beneficial effect for yield and yield components in the IR64 background. Twenty-two QTLs (53.4%) were located in similar regions as previously reported rice QTLs, suggesting the existence of stable QTLs across genetic backgrounds and environments. Twenty QTLs (47.6%) were exclusively detected in this study, uncovering potentially novel alleles from the wild, some of which might improve the performance of the tropical indica variety IR64. Additionally, several QTLs for plant height, grain weight, and flowering time detected in this study corresponded to homeologous regions in maize containing previously detected maize QTLs for these traits.

Base Sequence↗
PubMed2003

Molecular diversity and multilocus organization of the parental lines used in the International Rice Molecular Breeding Program.

One hundred and ninety three parental lines obtained from 26 countries for an international rice molecular breeding program were evaluated using 101 well-distributed simple sequence repeat (SSR) markers. An overall genetic diversity of 0.68 and an average of 6.3 alleles per locus were revealed, indicating a high level of genetic variation in these lines. Cluster analysis of the 193 accessions showed three major groups and nine subgroups. Group I corresponded to the classical indica subspecies, whereas groups II and III belong to the japonica subspecies. Indica and japonica differentiation accounted for only 6.5% of the total variation in the entire sample and 93.5% was due to within-subspecies diversity. Differentiation among eco-geographic regions accounted for 24% of the diversity within the subspecies. Larger amounts of the eco-geographical differentiation were resolved within japonica than within indica. The largest indica-japonica differentiation based on the single locus level was detected by markers on chromosomes 9 and 12, while the smallest differentiation was detected by markers on chromosomes 4 and 8. Furthermore, genetic differences at the single-locus and two-locus levels, as well as components due to allelic and gametic differentiation, were revealed between indica and japonica and among the main geographic regions. The multilocus analysis in genetic diversity showed a higher proportion of variation caused by predominant non-random associations of different loci within and among the classified subspecies and geographic subdivisions. The results suggest that selection for eco-geographical adaptation on multilocus associations was largely responsible for the maintenance of the extensive variation in the primary gene pool of rice.

Alleles↗
PubMed2003

Analysis of eggplant ( Solanum melongena)-related germplasm: morphological and AFLP data contribute to phylogenetic interpretations and germplasm utilization.

A total of 94 Solanum accessions, including eggplants and related species, were morphologically characterized based on greenhouse observations, and molecularly analysed by the AFLP technique. Morphological parameters were helpful in assessing similarities or differences among accessions, and molecular data were used to support morphological conclusions. A dendrogram was computed based on the Dice genetic distances using the neighbour-joining method. The analysis was efficient in the assignment of a species name for eight out of nine accessions that were not previously classified, and revealed that 14 further accessions were misnamed in the collection originally received. The results indicate that the taxonomy of Solanum sections and subgenera including several species should be reconsidered. The AFLP technique was revealed as an efficient tool in determining genetic relationships among species. In general, morphological observations were consistent with molecular data, indicating that both approaches complemented to define the phylogenetic status of a large genus like Solanum. In terms of eggplant breeding, the molecular analysis of the Melongena complex, and of the other sections of the subgenus Leptostemonum, establishes useful germplasm relationships in the gene pool available for the genetic improvement of the cultivated species. The results we have provided highlight an urgent necessity to include molecular parameters in handling and characterizing the genebank-deposited germplasm related to cultivated crops.

Breeding↗
PubMed2003

Genetic relationships of tetraploid Elymus species and their genomic donor species inferred from polymerase chain reaction-restriction length polymorphism analysis of chloroplast gene regions.

The genetic relationships of 38 individuals from 13 Elymus tetraploid species, two Pseudoroegneria species and one Hordeum species were examined using polymerase chain reaction-restriction length polymorphism analysis of chloroplast gene regions. The 13 Elymus species contain SH and SY genomes with either a single spikelet or multiple spikelets per rachis node. The Pseudoroegneria and Hordeum species contain an S genome with single spikelet per rachis node and an H genome with multiple spikelets per rachis node, respectively. Four chloroplast gene regions, trnD-trnT intron, trnK [tRNA-Lys (UUU) exon1]- trnK [tRNA-Lys (UUU) exon2], trnC-trnD, and rbcL were amplified with specific primers and subsequently digested with up to 16 different restriction enzymes. Interspecific variation was detected in the four regions. A dendrogram based on similarity matrices using the unweighted pair group method with arithmetic average algorithm separated the 38 individuals into two distinct groups: the Elymus and Pseudoroegneria species as one group and Horduem as a second group. This result corresponded well with previous findings, and strongly suggested that a Pseudoroegneria species is the maternal donor to tetraploid Elymus species. Unlike previous studies using nuclear genes, the chloroplast DNA used in this study could not clearly separate the SY-genome species from SH-genome species. No clear separation between the species with a single spikelet per rachis node and the species with multiple spikelets per rachis node was found. Intra-specific variation was detected for the species studied. These observations provide molecular evidence for the highly diverse nature of the Elymus gene pool based on morphological characteristics.

Cluster Analysis↗