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PubMed1994

Two new members in the Contracaecum osculatum complex (Nematoda, Ascaridoidea) from the Antarctic.

The genetic structure of adults and larvae of Contracaecum osculatum (sensu lato) from the Antarctic is analyzed on the basis of 24 enzyme loci. Significant deviations of genotype frequencies from the Hardy-Weinberg equilibrium were found, even in samples recovered from the same host. These data indicate that two distinct, reproductively isolated species coexist in C. osculatum (sensu lato) samples from the Antarctic. They were provisionally designated C. osculatum D and E, as they do not correspond to any of the three species previously detected in this complex from the Atlantic Arctic Boreal region (C. osculatum A, B and C). An allozyme diagnostic key for the identification of the five members of the C. osculatum complex, at the larval and adult stage and in both sexes, is given. Species D and E were found to be genetically quite variable: average P99 = 84.3, A = 3.3 and He = 0.23. Both showed high values of intraspecific gene flow: Nm = 4.6 and 6.1 respectively; similar values were found for the Arctic-Boreal C. osculatum A, B and C. The most related members of the complex are the Antarctic species E and the Arctic-Boreal species A (DNei = 0.21), while the most differentiated ones are the Arctic-Boreal species B and C (DNei = 0.76). The evolutionary divergence of C. osculatum C started more than 3 million years ago, in a Pliocene refugium (Baltic Sea). As to the other C. osculatum species, their evolutionary divergence took place during Pleistocene, when this complex achieved a bipolar distribution. This process involved two distinct colonizations of the marine Antarctic region by ancestors of the northern hemisphere, about 1.5 and 1 million years ago, giving origin to C. osculatum D and E respectively.

Animals↗
PubMed2003

Effective number of breeders and maintenance of genetic diversity in the captive bearded vulture population.

We combined pedigree data with data derived from 14 microsatellite loci to investigate genetic diversity and its maintenance in the captive source population for the reintroduction of the bearded vulture into the Alps. We found the captive population to be genetically more variable than the largest natural population in Europe, both in terms of mean number of alleles per locus and mean observed and expected heterozygosity. Allelic diversity of the captive population was higher than, and mean heterozygosity measurements were comparable with the ones found in two large, extinct populations from Sardinia and the Alps represented by museum specimens. The amount of genetic variability recruited with the founders was still present in the captive population of the year 2000, mainly because the carriers of rare alleles were still alive. However, the decline in expected heterozygosity and the loss of alleles over generations in captivity was significant. Point estimates of effective population size, N(e), based on pedigree data and estimates of effective number of breeders, N(b), based on allele frequency changes, ranged from 20 to 30 and were significantly smaller than the census size. The results demonstrate that the amount of genetic variability in the captive bearded vulture population is comparable or even larger than the amount present in natural populations. However, the population is in danger to lose genetic variability over time because of genetic drift. Management strategies should therefore aim at preserving genetic variability by minimising kinship, and at increasing N(e) by recruiting additional founders and enhancing gene flow between the released, the captive and natural populations.

Alleles↗
PubMed2003

Genetic variability at neutral markers, quantitative trait land trait in a subdivided population under selection.

Genetic variability in a subdivided population under stabilizing and diversifying selection was investigated at three levels: neutral markers, QTL coding for a trait, and the trait itself. A quantitative model with additive effects was used to link genotypes to phenotypes. No physical linkage was introduced. Using an analytical approach, we compared the diversity within deme (H(S)) and the differentiation (F(ST)) at the QTL with the genetic variance within deme (V(W)) and the differentiation (Q(ST)) for the trait. The difference between F(ST) and Q(ST) was shown to depend on the relative amounts of covariance between QTL within and between demes. Simulations were used to study the effect of selection intensity, variance of optima among demes, and migration rate for an allogamous and predominantly selfing species. Contrasting dynamics of the genetic variability at markers, QTL, and trait were observed as a function of the level of gene flow and diversifying selection. The highest discrepancy among the three levels occurred under highly diversifying selection and high gene flow. Furthermore, diversifying selection might cause substantial heterogeneity among QTL, only a few of them showing allelic differentiation, while the others behave as neutral markers.

Computer Simulation↗
PubMed2003

Temporal and geographic genetic variation in Culex pipiens quinquefasciatus (Diptera: Culicidae) from Florida.

Culex (Culex) pipiens quinquefasciatus Say field population from Vero Beach, FL, sampled monthly over a period of 8 mo, a colony sample, and six geographic samples were analyzed for genetic variation at 12 enzymes (10 "neutral" gene enzymes with 11 putative loci and two "complex" gene enzymes) by using polyacrylamide gel electrophoresis. The analysis of the 11 putative loci in both temporal and geographic samples showed that the four loci (Gpi, Hk, Mdhp-2, and Pgm) diagnostic of Cx. p. quinquefasciatus in the southern United States are present in similar frequencies in Florida samples. The Cx. p. quinquefasciatus colony sample showed significantly lower genetic variation than the temporal field samples, measured by mean number of alleles per locus (colony 1.2 +/- 0.1 versus field 1.44 +/- 0.03), percentage of polymorphic loci (colony 18.2% versus field 28.4%), mean observed heterozygosity (H(o) = colony 0.027 +/- 0.02 versus field 0.09 +/- 0.01), and mean Hardy-Weinberg expected heterozygosity (H(e) = colony 0.025 +/- 0.02 versus field 0.085 +/- 0.01). Three of the 11 loci (Acoh, Pgd, and Pgm) from the Vero Beach field samples showed bimodal patterns in their frequencies of the most common allele during peak density of the population. The low value of F(st) of 0.058 indicated minimum population substructuring among the temporal samples. Genetic variability values between geographic samples from the Florida panhandle and south Florida were not significant. Gene flow estimates based on F(ST), = 0.05, indicating low levels of gene flow among the geographic samples of Cx. p. quinquefasciatus. The average Nei's and modified Rogers' genetic distances among the six populations were 0.005 +/- 0.001 and 0.077 +/- 0.007, respectively. The cluster analysis did not suggest geographic clustering. The analysis of the "complex" gene enzymes in both temporal and geographic samples of Cx. p. quinquefasciatus from Florida showed the presence of two highly amplified esterases (Estbeta1 and Estalpha2\Estbeta2), indicating resistance to organophosphate insecticides and highly amplified Aldox enzyme (an enzyme that indicates resistance to at least one insecticide and a herbicide). Comparison of our results with previous studies on Cx. p. quinquefasciatus populations in the United States indicates that the genetic characteristics of the Florida populations of Cx. p. quinquefasciatus are very similar to populations from areas where ecological conditions are very different.

Alleles↗
PubMed1990

A novel fluorescence-based system for assaying and separating live cells according to VDJ recombinase activity.

We describe two retroviral vector-based recombination substrate systems designed to assay for lymphoid VDJ recombinase activity in cultured cells. Both substrates incorporate a constitutive dominant marker gene (the simian virus promoter-driven neo gene) to allow selection of cells that stably integrate the substrate. Both substrates also include a second marker gene that becomes transcriptionally active only when inverted by a site-specific recombination event between flanking immunoglobulin variable-region gene segments. The first vector, similar in structure to previous retrovirus-based recombination substrates, utilizes the bacterial guanine-xanthine phosphoribosyltransferase gene (gpt) as its activatable marker; detection of inversion (VDJ recombinase activity) involves drug selection and Southern blotting analyses. We have used this vector to make a more extensive and quantitative survey of VDJ recombinase activity in B-lineage cell lines than has previously been performed with stable substrates, and we have compared our results with those of other studies that use transient recombination substrates. In the second vector, the activatable gene is the bacterial beta-galactosidase gene (lacZ). Detection for inversional activation of this gene is achieved by a fluorogenic assay, termed FACS-Gal, that detects beta-galactosidase activity in viable cells. The latter assay has the unique advantage of rapidly detecting cells that undergo recombination and also allows viable sorting of cells on the basis of the presence or absence of VDJ recombinase activity. We have used the lacZ vector to rapidly quantitate VDJ recombinase activity in B-lineage cell lines and compared the results with those obtained with the gpt vector. We have also used the lacZ vector to isolate variant pre-B-cell lines with low and high levels of VDJ recombinase activity.

Animals↗
PubMed2000

A B cell superantigen-induced persistent "Hole" in the B-1 repertoire.

The bacterial toxin protein A from Staphylococcus aureus (SpA) interacts with B cell antigen receptors encoded by variable region heavy chain (V(H)) clan III genes via a V region framework surface that has been highly conserved during the evolution of the adaptive immune system. We have investigated the consequences of exposure to this prototypic B cell superantigen, and found that treatment of neonates or adults induces a T cell-independent deletion of a large supraclonal set of susceptible B cells that includes clan III/V(H) S107 family-expressing lymphocytes. In studies of different SpA forms, the magnitude of the induced deletion directly correlated with the V(H)-specific binding affinity/avidity. Upon cessation of SpA exposure, the representation of conventional splenic (B-2 subset) lymphocytes normalized; however, we found that the V(H) family-restricted deficit of peritoneal B-1 cells persisted. SpA treatment also induced a persistent loss of splenic S107-mu transcripts, with a loss of certain natural antibodies and specific tolerance to phosphorylcholine immunogens that normally recruit protective antimicrobial responses dominated by the S107-expressing B-1 clone, T15. These studies illustrate how a B cell superantigen can exploit a primordial Achilles heel in the immune system, for which B-1 cells, an important source of natural antibodies and host immune responses, have special susceptibility.

Adult↗
PubMed2001

Production and validation of the pharmacokinetics of a single-chain Fv fragment of the MGR6 antibody for targeting of tumors expressing HER-2.

The HER-2 antigen, which is overexpressed in many breast carcinomas, is an ideal target for monoclonal antibodies due to its low expression in normal tissue and its homogeneous distribution in the tumor mass. We have developed and characterized the murine MAb MGR6 against HER-2, which is able to inhibit proliferation of tumor cells overexpressing HER-2. On the basis of these preclinical results, phase I studies in breast carcinoma patients were conducted and radiolocalization data indicated an antibody half life which directly paralleled that of other whole antibodies and thus resulting in a limited in vivo diagnostic capacity. To obtain a smaller reagent with possibly improved in vivo properties, a single chain variable fragment (scFv) of the original MGR6-producing hybridoma was generated by phage display technology. Biologically active MGR6 scFv was purified rapidly and at high yield by metal affinity chromatography. Competition FACS and ELISA analyses identified an epitope on the HER-2 extracellular domain that was shared by the scFv and the parental MAb. BlAcore analysis indicated a Koff of 9.3 x 10(-4) s(-1), similar to that of the intact MGR6 MAb. Distribution and elimination half-lives of MGR6 scFv, calculated from in vivo preclinical evaluations, were much faster (13 min and 6.2 h, respectively) than previously published results for the intact MAb (mean t1/2beta of 46 h). This represents a theoretical improvement in pharmacokinetics with respect to the parental murine MAb and points to the potential for utilizing this fragment in redirecting therapeutic agents, such as radioisotopes, to different human carcinomas overexpressing HER-2.

Amino Acid Sequence↗
PubMed2004

Discerning between recurrent gene flow and recent divergence under a finite-site mutation model applied to North Atlantic and Mediterranean Sea fin whale (Balaenoptera physalus) populations.

Genetic divergence among conspecific subpopulations can be due to either low recurrent gene flow or recent divergence and no gene flow. Here we present a modification of an earlier method developed by Nielsen and Wakeley (2001), which accommodates a finite-site mutation model, to assess which of the two models of divergence is most likely given the observed data. We apply the method to nucleotide sequence data collected from the variable part of the mitochondrial control region in fin whales (Balaenoptera physalus) from the Atlantic coast off Spain and the Mediterranean Sea. Our estimations strongly favor a model of recurrent gene flow over a model of recent divergence and zero gene flow. We estimated the migration rate at two females per generation. While the estimated rate is high by evolutionary standards, exchange rates of this order of magnitude is low from an ecological and conservation perspective and entirely consistent with the current paucity of fin whale sightings in the Strait of Gibraltar today. Intensive commercial shore-based whaling during the 1920s removed substantial numbers of fin whales in the Strait of Gibraltar and this local population has seemingly since failed to recover.

Animals↗
PubMed2002

[Genetic differentiation of pedunculate oak Quercus robur L. in the European part of Russia based on RAPD markers].

Using randomly amplified polymorphic DNA markers (RAPD), genetic variation and differentiation in four populations of pedunculate oak Quercus robur L. were examined. The populations occupy a large part of the Quercus robur range in the European Russia (Voronezh and Novgorod oblasts; Republics of Mordovia and Bashkortostan). With each of six random primers (A02, A09, A17, B01, B08, B11), 96 DNA samples were analyzed by PCR. In all, 48 putative polymorphic RAPD loci were detected. We failed to reveal population-specific DNA fragments for any primer although the frequencies of 14 fragments were significantly different among populations. The oak populations studied exhibited high variability: 73-90% of genes were polymorphic and the effective allele number was about 1.4. The total genetic variation varied from 0.202 (Vor) to 0.245 (Nov), which corresponded to the estimates for populations of this species from Central and Western Europe. The populations examined showed low among-population differentiation (GST = 0.098); gene flow Nem was 4.61. The proportion of among-population variation of the RAPD loci studied accounted for 7% of the total variability; more than 93% of the total variability was explained by individual and within--population variation.

Genetic Variation↗
PubMed2002

V(H) mutation status, CD38 expression level, genomic aberrations, and survival in chronic lymphocytic leukemia.

In chronic lymphocytic leukemia (CLL), biologic risk factors such as immunoglobulin variable heavy chain gene (V(H)) mutation status, CD38 expression level, and genomic aberrations have recently been identified, but the relative prognostic impact of the individual parameters is unknown. In the current study, we analyzed V(H) mutation status by polymerase chain reaction and sequencing (n = 300), genomic aberrations by fluorescence in situ hybridization (+3q, 6q-, +8q, 11q-, +12q, 13q-, t(14q), 17p-) (n = 300), and CD38 expression by triple-color FACS (CD5, CD19, CD38) (n = 157) in a unicentric CLL cohort. The prognostic influence of V(H) mutation rate and CD38 expression level was tested by maximally selected log-rank statistics. A corrected P value (P(cor)) for a cutoff level allowing the best separation of 2 subgroups with different survival probabilities was identified at 97% V(H) homology (95% confidence interval [CI], 96%-98% homology, P(cor) <.001) and at 7% CD38 expression (95% CI, 20%-71% expression, P(cor) =.02). In univariate analyses, unmutated V(H) genes and high CD38 expression levels predicted for shorter survival times. The overall incidence of genomic aberrations was similar in the V(H) unmutated and V(H) mutated subgroups. High-risk genomic aberrations such as 17p- and 11q- occurred almost exclusively in the V(H) unmutated subgroup, whereas favorable aberrations such as 13q- and 13q- as single abnormalities were overrepresented in the V(H) mutated subgroup. In multivariate analysis, unmutated V(H), 17p deletion, 11q deletion, age, WBC, and LDH were identified as independent prognostic factors, indicating a complementary role of V(H) mutation status and genomic aberrations to predict outcome in CLL.

ADP-ribosyl Cyclase↗
PubMed1991

A major fraction of human intraepithelial lymphocytes simultaneously expresses the gamma/delta T cell receptor, the CD8 accessory molecule and preferentially uses the V delta 1 gene segment.

The frequency of T cell receptor (TcR) type and the variable gene segment expression in human intraepithelial lymphocytes (IEL) from the large intestinal mucosa were studied by flow cytometry and immunohistochemistry, and compared to those in peripheral blood lymphocytes (PBL) - or lamina propria lymphocytes (LPL). Employing anti-gamma/delta TcR and anti-alpha/beta TcR monoclonal antibodies (mAb), flow cytometric analysis revealed that a large fraction of IEL (37%) are gamma/delta T cells, whereas within LPL and PBL gamma/delta T cells comprise a minor population (4.6% and 3.8% respectively). At these sites the number of gamma/delta T cells labeled with anti-CD8 mAb were 58.3% (IEL), 43.3% (LPL) and 24.4% (PBL). In situ staining of serial sections of large intestine confirmed these results. Hence, these data suggest a selective accumulation of CD8+ gamma/delta T cells in the human epithelium of the large intestine. Furthermore, analysis of gamma/delta TcR bearing IEL+ disclosed a marked preponderance of cells using the V delta 1 gene segment, whereas gamma/delta TcR+ PBL preferentially express V delta 2. Strikingly, the majority of these V delta 1+ IEL bear the CD8 molecule on their surface. These results are taken as evidence for a selective localization of V delta 1+ CD8+ gamma/delta T cells in the epithelium of the large intestine.

Adult↗
PubMed1991

Biased VH gene expression in murine CD5 B cells results from age-dependent cellular selection.

Flow cytometry-purified, peritoneal and splenic CD5+ and CD5- B cells from neonatal and adult C57BL/6 mice were studied for expression of VH and Vx gene families in RNA colony blot assays, and for frequencies of clones secreting antibodies to bromelain-treated mouse red blood cells (BrMRBC), single-stranded DNA, trimethyl ammonium and bovine gamma-globulin, by limiting dilution. The results show few overall differences between the two B cell subsets, which both manifest ontogenic D-proximal VH preferences that are lost with age. Biased VH11 expression in CD5 B cells is high in adult peritoneum and spleen but absent in newborns. It only partly correlates with the selection of anti-BrMRBC reactivity, which is considerably higher in peritoneum than in spleen. No particular Vx bias was observed in any of the populations studied with the possible exception of Vx22 in peritoneal CD5+ B cells. We conclude that the antibody repertoire expressed by peritoneal CD5+ B cells of adult mice is not the result of a genetic program, but rather the consequence of local, age-dependent cellular selection mechanisms.

Aging↗
PubMed1994

Regulation of VH-gene expression is a lineage-specific developmental marker.

We have previously shown that in IgH congenic mice VH-gene family usage in neonatal spleen B cells and adult Ig-secreting cells is entirely determined by the IgH locus, while in adult resting B cells it is regulated by genetic element(s) located outside the IgH locus. Two observations reported here demonstrate that the differential expression of VH genes is an intrinsic property of the respective cell populations, determined by both the IgH locus and by a cis element(s) operating independently in the same animal. First, the study of F1 hybrids between the IgH congenic B6a and CB.20 strains demonstrates that cis elements control VH-gene family expression. Second, studies in irradiation chimeras showed that the environment in which cell differentiation proceeds is unable to overcome those controls. In chimeras of IgH congenic donors, VH-gene expression in fetal liver-derived splenic B cells and Ig-secreting cells is dictated by the IgH haplotype, while in bone marrow-derived B cells is entirely determined by the cis element(s). These results show a developmental and cell lineage-related restriction in VH-gene expression, and suggest that most adult splenic Ig-secreting cells may originate from precursors originally present in fetal liver, but which are rare among adult bone marrow precursors and CD5+ B cells.

Aging↗
PubMed2003

Patch quality and connectivity influence spatial dynamics in a dune wolfspider.

The spatial population dynamics of the wolfspider Pardosa monticola, inhabiting patchily distributed grasslands in the Flemish coastal dunes of Belgium and Northern France were investigated with incidence function models using field survey data from 1998 and 2000. Vegetation height and patch size were related to habitat quality. Mark-recapture experiments revealed maximum cursorial dispersal distances of 280 m for moss dunes and 185 m for higher dune grassland. Higher shrub vegetation appeared to be dispersal barriers. These habitat-dependant cursorial distances and the theoretically estimated ballooning distance were included with patch distances into a connectivity index for both dispersal modes. Forward multiple regression indicated that patch occurrence was influenced by habitat quality and ballooning connectivity. Habitat quality and cursorial connectivity explained patterns in short-term colonisation. Extinction appeared to be stochastic and not related to habitat quality and connectivity. Genetic differentiation and variability was low. The discrepancy between the estimated low dispersal capacity and the indirect estimate of gene flow ( F(ST)) indicates that historical population dynamics and/or historical ballooning dispersal influence the genetic structure in this species.

Animals↗
PubMed2004

Microsatellite DNA suggests regional structure in the fusiform rust fungus Cronartium quercuum f. sp fusiforme.

This paper reports results obtained from microsatellite DNA analysis of genetic structure for populations of the native fungus Cronartium quercuum f. sp fusiforme infecting loblolly pine (Pinus taeda L.) over much of this host's natural range. Mostly all fusiform rust galls formed under field conditions are produced as a result of infection and colonization by haploid mycelium originating from a single basidiospore of C. quercuum fusiforme. If multiple infections do occur, then only a single haplotype must ultimately dominate and be responsible for gall formation. High levels of microsatellite variability exist in C. quercuum fusiforme and most of this variation occurs within local populations (average 88.4%). A statistically significant proportion, however, is found among populations, and the magnitude of this differentiation is closely associated with geographic distance between populations. Unweighted pair-group mean analysis and principal components analysis both indicate that at least four genetically distinct regional groups of C. quercuum fusiforme exist in the south Atlantic and Gulf coastal plains. In summary, the distribution of genetic variability in C. quercuum fusiforme is consistent with a hypothesis of at least four metapopulations with gene flow occurring less among regions than among populations within regions, and where overall levels of gene migration are related to geographic distance between populations.

Basidiomycota↗
PubMed2003

Fine-scale phylogeographical analysis of Mediterranean Anacamptis palustris (Orchidaceae) populations based on chloroplast minisatellite and microsatellite variation.

The phylogeographical history of the rare marsh orchid Anacamptis palustris (Orchidaceae) was reconstructed using highly polymorphic chloroplast minisatellite and microsatellite loci. Allelic variation at chloroplast microsatellite loci was due to length variation in poly(A/T) repeats and was informative on a regional scale, but was not sufficient to unravel relationships among populations on a local geographical scale. The minisatellite locus, however, was found to be highly variable. Nine distinct repeat types were found and variation in repeat number occurred in five repeat types. The distribution of chloroplast haplotypes, combining microsatellite and minisatellite repeat type variation, provided a clear phylogeographical picture on a large geographical scale, whereas length variation in one highly polymorphic minisatellite repeat type provided fine-scale phylogeographical information. Mediterranean populations could be divided into four main lineages, a western European lineage, a northern and central Italian lineage, a well-isolated southern Italian (Apulian) lineage, and an eastern European lineage. Variation at the most variable minisatellite repeat type N revealed 19 alleles and allowed the study of seed-mediated gene flow and an estimation of the ratio of pollen to seed flow among neighbouring populations.

Base Sequence↗
PubMed1997

Isolation of anti-T cell receptor scFv mutants by yeast surface display.

Yeast surface display and sorting by flow cytometry have been used to isolate mutants of an scFv that is specific for the Vbeta8 region of the T cell receptor. Selection was based on equilibrium binding by two fluorescently labeled probes, a soluble Vbeta8 domain and an antibody to the c-myc epitope tag present at the carboxy-terminus of the scFv. The mutants that were selected in this screen included a scFv with threefold increased affinity for the Vbeta8 and scFv clones that were bound with reduced affinities by the anti-c-myc antibody. The latter finding indicates that the yeast display system may be used to map conformational epitopes, which cannot be revealed by standard peptide screens. Equilibrium antigen binding constants were estimated within the surface display format, allowing screening of isolated mutants without necessitating subcloning and soluble expression. Only a relatively small library of yeast cells (3 x 10[5]) displaying randomly mutagenized scFv was screened to identify these mutants, indicating that this system will provide a powerful tool for engineering the binding properties of eucaryotic secreted and cell surface proteins.

Antibodies, Monoclonal↗
PubMed1999

Development of an optimized expression system for the screening of antibody libraries displayed on the Escherichia coli surface.

Polypeptide library screening technologies are critically dependent upon the characteristics of the expression system employed. A comparative analysis of the lpp-lac, tet and araBAD promoters was performed to determine the importance of tight regulation and expression level in library screening applications. The surface display of single-chain antibody (scFv) in Escherichia coli as an Lpp-OmpA' fusion was monitored using a fluorescently tagged antigen in conjunction with flow cytometry. In contrast to the lpp-lac promoter, both tet and araBAD promoters could be tightly repressed. Tight regulation was found to be essential for preventing rapid depletion of library clones expressing functional scFv and thus for maintaining the initial library diversity. Induction with subsaturating inducer concentrations yielded mixed populations of uninduced and fully induced cells for both the tet and araBAD expression systems. In contrast, homogeneous expression levels were obtained throughout the population using saturating inducer concentrations and could be adjusted by varying the induction time and plasmid copy number. Under optimal induction conditions for the araBAD system, protein expression did not compromise either cell viability or library diversity. This expression system was used to screen a library of random scFv mutants specific for digoxigenin for clones exhibiting improved hapten dissociation kinetics. Thus, an expression system has been developed which allows library diversity to be preserved and is generally applicable to the screening of E. coli surface displayed libraries.

Antibodies↗