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PubMed2006

Phylogeny of Chaetanthera (Asteraceae: Mutisieae) reveals both ancient and recent origins of the high elevation lineages.

Penalized likelihood analysis of previously published chloroplast DNA (cpDNA) ndhF sequences suggests that the central-southern Andean genus Chaetanthera diverged ca. 16.5 million years (my) ago, well before the uplift of the Andes to their present heights. Penalized likelihood analysis based on new nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS) sequences indicates that the most relictual lineages occupy high elevation Andean habitats that did not exist until some 10my later. This result is contrary to the expectation that younger habitats should be occupied by phylogenetically younger lineages. The results are interpreted with respect to the development of aridity in lowland habitats during the Miocene and Pliocene, which presumably extinguished the lowland relatives of the high elevation taxa or, in effect, forced them upwards in search of adequate moisture. As the more northerly lineages were being displaced upward, others diversified in the mediterranean-type climate area of central Chile, giving rise to additional high elevation taxa again, at an early date, as well as lowland taxa. Some species of Chaetanthera from lowland central Chile appear as the phylogenetically youngest taxa, suggesting secondary adaptation to lowland aridity. At the same time, at least two high elevation species, Chaetanthera peruviana and Chaetanthera perpusilla, appear to have been derived recently from a lower elevation ancestor, while some middle to low elevation taxa seem to have evolved recently out of a high elevation complex. The results suggest that the younger high elevation habitats have served as both "cradle" and "museum" for Chaetanthera lineages.

Asteraceae↗
PubMed2006

A molecular assessment of phylogenetic relationships and lineage accumulation rates within the family Salamandridae (Amphibia, Caudata).

We examine phylogenetic relationships among salamanders of the family Salamandridae using approximately 2700 bases of new mtDNA sequence data (the tRNALeu, ND1, tRNAIle, tRNAGln, tRNAMet, ND2, tRNATrp, tRNAAla, tRNAAsn, tRNACys, tRNATyr, and COI genes and the origin for light-strand replication) collected from 96 individuals representing 61 of the 66 recognized salamandrid species and outgroups. Phylogenetic analyses using maximum parsimony and Bayesian analysis are performed on the new data alone and combined with previously reported sequences from other parts of the mitochondrial genome. The basal phylogenetic split is a polytomy of lineages ancestral to (1) the Italian newt Salamandrina terdigitata, (2) a strongly supported clade comprising the "true" salamanders (genera Chioglossa, Mertensiella, Lyciasalamandra, and Salamandra), and (3) a strongly supported clade comprising all newts except S. terdigitata. Strongly supported clades within the true salamanders include monophyly of each genus and grouping Chioglossa and Mertensiella as the sister taxon to a clade comprising Lyciasalamandra and Salamandra. Among newts, genera Echinotriton, Pleurodeles, and Tylototriton form a strongly supported clade whose sister taxon comprises the genera Calotriton, Cynops, Euproctus, Neurergus, Notophthalmus, Pachytriton, Paramesotriton, Taricha, and Triturus. Our results strongly support monophyly of all polytypic newt genera except Paramesotriton and Triturus, which appear paraphyletic, and Calotriton, for which only one of the two species is sampled. Other well-supported clades within newts include (1) Asian genera Cynops, Pachytriton, and Paramesotriton, (2) North American genera Notophthalmus and Taricha, (3) the Triturus vulgaris species group, and (4) the Triturus cristatus species group; some additional groupings appear strong in Bayesian but not parsimony analyses. Rates of lineage accumulation through time are evaluated using this nearly comprehensive sampling of salamandrid species-level lineages. Rate of lineage accumulation appears constant throughout salamandrid evolutionary history with no obvious fluctuations associated with origins of morphological or ecological novelties.

Animals↗
PubMed2003

Seven GC-rich microbial genomes adopt similar codon usage patterns regardless of their phylogenetic lineages.

Seven GC-rich (group I) and three AT-rich (group II) microbial genomes are analyzed in this paper. The seven microbes in group I belong to different phylogenetic lineages, even different domains of life. The common feature is that they are highly GC-rich organisms, with more than 60% genomic GC content. Group II includes three bacteria, which belong to the same subdivision as Pseudomonas aeruginosa in group I. The genomic GC content of the three bacteria is in the range of 26-50%. It is shown that although the phylogenetic lineages of the organisms in group I are remote, the common feature of highly genomic GC content forces them to adopt similar codon usage patterns, which constitutes the basis of an algorithm using a set of universal parameters to recognize known genes in the seven genomes. The common codon usage pattern of function known genes in the seven genomes is GGS type, where G, G, and S are the bases of G, non-G, and G/C, respectively. On the contrary, although the phylogenetic lineages of the three bacteria in group II are quite close, the codon usage patterns of function known genes in these genomes are obviously distinct. There are no universal parameters to identify known genes in the three genomes in group II. It can be deduced that the genomic GC content is more important than phylogenetic lineage in gene recognition programs. We hope that the work might be useful for understanding the common characteristics in the organization of microbial genomes.

Algorithms↗
PubMed1990

Patterns of cell lineage in the cerebral cortex reveal evidence for developmental boundaries.

Experimental aggregation chimeric mice offer a perspective on cell lineage relationships that is complementary to that of prospective tracing methods such as dye injections or recombinant retroviruses. To create a lineage map of cerebral cortex, the position and genotype of cortical neurons in three-dimensional space were reconstructed with the aid of a computer-assisted mapping system. Chi-square statistical analyses indicate that the spatial distribution of cell lineages in the cerebral cortex is highly nonrandom. When individual dimensions are analyzed separately, a high degree of order is found in the spatial distribution of neuronal genotype ratios in the anterior-posterior dimension but not in the medial-lateral dimension. This suggests an arrangement of lineage-related neurons into "slabs" or "stripes" of cells that are organized in the plane perpendicular to the neuraxis. Additionally, a highly significant variation in genotype ratios was found in the radial dimension (i.e., among cortical cell layers). These data suggest the hypothesis that separate sets of progenitor cells give rise to the superficial and deep layers of cortex. Taken together, our data are consistent with a picture of the developing nervous system in which early developmental restrictions to cell mixing set up boundaries that may be of considerable developmental genetic importance.

Animals↗
PubMed2003

Molecular evolution of avian reovirus: evidence for genetic diversity and reassortment of the S-class genome segments and multiple cocirculating lineages.

Nucleotide sequences of the S-class genome segments of 17 field-isolates and vaccine strains of avian reovirus (ARV) isolated over a 23-year period from different hosts, pathotypes, and geographic locations were examined and analyzed to define phylogenetic profiles and evolutionary mechanism. The S1 genome segment showed noticeably higher divergence than the other S-class genes. The sigma C-encoding gene has evolved into six distinct lineages. In contrast, the other S-class genes showed less divergence than that of the sigma C-encoding gene and have evolved into two to three major distinct lineages, respectively. Comparative sequence analysis provided evidence indicating extensive sequence divergence between ARV and other orthoreoviruses. The evolutionary trees of each gene were distinct, suggesting that these genes evolve in an independent manner. Furthermore, variable topologies were the result of frequent genetic reassortment among multiple cocirculating lineages. Results showed genetic diversity correlated more closely with date of isolation and geographic sites than with host species and pathotypes. This is the first evidence demonstrating genetic variability among circulating ARVs through a combination of evolutionary mechanisms involving multiple cocirculating lineages and genetic reassortment. The evolutionary rates and patterns of base substitutions were examined. The evolutionary rate for the sigma C-encoding gene and sigma C protein was higher than for the other S-class genes and other family of viruses. With the exception of the sigma C-encoding gene, which nonsynonymous substitutions predominate over synonymous, the evolutionary process of the other S-class genes can be explained by the neutral theory of molecular evolution. Results revealed that synonymous substitutions predominate over nonsynonymous in the S-class genes, even though genetic diversity and substitution rates vary among the viruses.

Amino Acid Sequence↗
PubMed1988

Large-cell hematolymphoid neoplasms of uncertain lineage.

In almost every large study attempting to characterize non-Hodgkin's lymphomas, there is a small subset of tumors for which the lineage remains poorly defined. The investigators studied a series of 20 hematolymphoid neoplasms that could not be clearly assigned to the B or T cell lineage by phenotypic criteria. Histologically, 12 cases had an appearance suggesting a histiocytic origin, seven cases resembled a pleomorphic immunoblastic lymphoma, and one had a sarcomatoid appearance. By immunologic studies, a variety of B cell, T cell, and monocyte/macrophage markers were expressed on the neoplasms, often with coexpression of markers for different lineages. Twelve cases expressed the Ki-1 antigen. In immunogenotyping studies of T cell receptor (TCR) and immunoglobulin genes, 13 cases showed clonal rearrangements of the beta or gamma TCR gene; one of these cases also had clonal rearrangements of a light chain immunoglobulin gene. Seven cases showed a germline configuration with all combinations of probes and enzymes used. We conclude that a small subset of hematolymphoid neoplasms shows a pattern of diverse immunologic marker expression that does not appear to reflect normal differentiation. However, a majority of these cases contain clonal TCR gene rearrangements, suggesting a frequent relationship to the T lineage.

Adolescent↗
PubMed2004

Cloning of IgE from the echidna (Tachyglossus aculeatus) and a comparative analysis of epsilon chains from all three extant mammalian lineages.

In continuation of our evolutionary studies of immunoglobulin (Ig) expression, we present here the cloning of IgE from a monotreme, the short-beaked echidna (Tachyglossus aculeatus). Including echidna IgE, 15 epsilon chain sequences have been isolated and each of the three mammalian lineages (placentals, marsupials and monotremes) is now represented by at least two sequences. Phylogenetic analyses based on all available epsilon chains and a selection of other mammalian Ig isotypes (IgM, IgA and IgG) were generated using three different algorithms. The resulting trees strongly support the Theria hypothesis, which states that the monotreme lineage was the first of the three extant mammalian lineages to appear in evolution. Furthermore, to increase our understanding of IgE we have done a detailed comparative analysis, with focus on primary structure, potential N-glycosylation, charge distribution and conservation of residues in the putative receptor-binding site. The overall structure of IgE, i.e. four constant domains and the positions of putative disulfide-bridge formations, are conserved, as is an N-glycosylation site in the third constant domain. An increased homology was observed in the putative receptor-binding site, which suggests an important function for the IgE/Fc epsilon RI interaction. IgE has been found exclusively in mammals, but it is present in all extant mammalian lineages. This, together with the overall conservation of structure, indicates that IgE appeared as a separate isotype early in mammalian evolution and that structural maintenance may have a selective advantage.

Amino Acid Sequence↗
PubMed2001

Genetic characterization of Puumala hantavirus strains from Belgium: evidence for a distinct phylogenetic lineage.

Puumala hantavirus (PUUV) sequences were recovered from red bank voles (Clethrionomys glareolus) trapped between 1996 and 1998 in four localities of southern Belgium: Thuin, Montbliart, Momignies and Couvin. In addition, three PUUV isolates originating from bank voles trapped in the 1980s in southern (Montbliart) and northern (Turnhout) Belgium were genetically characterized. Analysis of the complete S and partial M segment sequences showed that the Belgian PUUV strains constitute a genetic lineage, distinct from other known PUUV lineages from Europe and Japan. This lineage also includes a wild strain (Cg-Erft) originating from a neighbouring area of Germany. Within the Belgian lineage, geographical clustering of genetic variants was observed. In the Montbliart site, the range of diversity between the most temporally distant strains (from 1986 and 1996-1998) was higher than between those from 1996 and 1998, suggesting slight genetic drift via accumulation of neutral or quasi-neutral substitutions with time.

Animals↗
PubMed1990

The splenic pool of mouse stem cells: in vitro differentiation and expression of the BP-1 alloantigen on cells of the lymphoid and myeloid lineages.

The relative paucity of data about the development of the stem cell pool present in the spleen prompted this study. During in vitro cultures of B-enriched lymphocytes from mouse spleens and in the presence of a culture supernatant of WEHI-3 cells (WEHI-SUP), a population of cells expressing the BP-1 antigen appears progressively, reaches an optimal size 8 days after initiation of the culture, and disappears on day 28. In 8-day-old cultures, a minor population of cells bearing both BP-1 and B220 can be detected. The growth of this cell population, with characteristics of the B lymphoid lineage (pro-B), is strictly dependent on the presence of WEHI-SUP in the medium. After 2 weeks of culture, the BP-1 antigen is expressed on a cell population, which is essentially constituted of B220-, polynuclear cells. The BP-1 antigen, which is considered as characteristic of early cells of the B lymphoid lineage, can therefore also be expressed on cells of the myeloid lineage. The injection of BP-1+ or B220+ cells in irradiated mice can hardly reconstitute their B cell pool, whereas BP-1- and B220- cells are much more efficient in vivo progenitors of this cell lineage.

Animals↗
PubMed2003

Antimutagenic effect of Lentinula edodes (BERK.) Pegler mushroom and possible variation among lineages.

This study was performed to evaluate the efficiency of four different lineages (95/01, L1, 96/22 and JABK) of Lentinula edodes (BERK.) Pegler mushroom (shiitake) for inhibiting the N-ethyl-N-nitrosourea (ENU) clastogenicity in vivo. Male Swiss mice (10 animals/group) were treated during 15 consecutive days with dried mushroom added to basal diet under three different concentrations (1, 5 and 10%). At day 15, mice were intraperitoneally injected with ENU (50 mg/kg body weight) and sacrificed 24 h later for evaluation of micronucleated bone marrow polychromatic erythrocytes (MNPCE). Negative and positive controls (10 animals each), receiving basal diet and saline or ENU ip injection, respectively, were also evaluated. Results showed that pretreatments with diets containing the lineages 95/01, L1 and 96/22 reduce the frequencies of MNPCE induced by ENU. The absence of an antimutagenic activity for the lineage JABK might be related to intrinsic differences among the lineages such as biochemical composition. Taken together, our data show that the differences in protective activities of the mushrooms need to be clarified in further studies and the mechanisms for such activities need to be investigated.

Animals↗
PubMed2000

Interleukin-6 and other gp130-dependent cytokines selectively inhibit proliferation of macrophage-lineage hemopoietic progenitor cells.

OBJECTIVE: Hemopoiesis is regulated by cytokines with positive or negative effects on proliferation of lineage-committed or multipotent hemopoietic stem cells. We have investigated the roles of interleukin-6 and other gp130-dependent ligands on the proliferation of macrophage-lineage hemopoietic progenitor cells. METHODS: The responses of human and murine hemopoietic cells to combinations of cytokines involving interleukin-6 or related factors were assessed in short-term culture by clonogenic assay. RESULTS: Interleukin-6, leukemia inhibitory factor, and ciliary neurotrophic factor inhibited formation of colonies stimulated by macrophage colony-stimulating factor. These effects were dose dependent and selective for macrophage-lineage precursors. Progenitors from murine peripheral blood were inhibited by 37-93% in cultures containing interleukin-6 (11 experiments; median, 68%). Macrophage progenitors from murine bone marrow were also inhibited by interleukin-6 but were less sensitive (seven experiments; median, 48%). In cultures costimulated with leukemia inhibitory factor, peripheral blood and bone marrow progenitors were inhibited by 82% and 58%, respectively. Ciliary neurotrophic factor inhibited macrophage colonies by 66%. Multilineage bone marrow colony formation was not affected. In cultures of human bone marrow cells stimulated with macrophage colony stimulating factor and stem cell factor, interleukin-6 inhibited colony formation by 51-74%. Bone marrow colonies stimulated by granulocyte-macrophage colony stimulating factor were not inhibited by costimulation with interleukin-6. CONCLUSIONS: These results suggest a novel mechanism for the negative regulation of macrophage-lineage hemopoietic cells. They also demonstrate new properties of interleukin-6 and certain other gp 130-dependent ligands.

Animals↗
PubMed1997

TEL/AML1 fusion gene resulting from a cryptic t(12;21) is uncommon in adult patients with B-cell lineage ALL and CML lymphoblastic transformation.

TEL is a new member of the ETS-like family on chromosome 12 and forms fusion genes with several partners in leukemia. Among these fusion genes, the TEL/AML1 translocation resulting from t(12;21) is found in approximately one quarter of the childhood B-cell lineage acute lymphoblastic leukemia (ALL) cases and its prognosis is excellent. We examined 42 adult patients with B-cell lineage ALL and 13 adult patients with lymphoblastic transformation of chronic myeloid leukemia (CML) to detect TEL/AML1 fusion genes using the reverse transcriptase-polymerase chain reaction (RT-PCR) and Southern blotting, but no translocation was detected. These findings indicate that absence of the TEL/AML1 fusion transcript partly correlates with the poorer outcome of adult B-cell lineage ALL as compared with childhood ALL and the TEL/AML1 fusion transcript is specific for pediatric B-cell lineage ALL.

Adolescent↗
PubMed1995

Activation of cAMP-dependent protein kinase triggers a glial-to-neuronal cell-fate switch in an insect neuroblast lineage.

BACKGROUND: The grasshopper median neuroblast (MNB) is a multipotent progenitor cell that produces neurons and midline glia in distinct temporal phases. The MNB generates pioneer neurons during its first few divisions, and then switches to production of midline glial precursors. After the glia have been produced, the MNB reverts to generating neurons. We have investigated the molecular mechanism underlying the transition from glia production back to neuron production in the MNB lineage. RESULTS: We report evidence that this second transition in the MNB lineage is triggered by the activation of cAMP-dependent protein kinase (PKA). PKA is a heterodimer of a catalytic (PKA-C) and a cAMP-binding regulatory (R) subunit. The R subunit dissociates from PKA-C on binding cAMP, and free PKA-C than translocates into the nucleus. Nuclear localization of PKA-C can thus be used as an indicator of PKA activation within a cell. We have found that PKA-C is translocated into the nucleus at the time of the second switch in the MNB lineage. When PKA is prematurely activated in the MNB by microinjection of purified PKA-C, or by pharmacological agents that elevate intracellular cAMP levels, the glial-to-neuronal cell-fate switch takes place prematurely. Inhibition of PKA activity by microinjection of a peptide inhibitor, or by a non-hydrolyzable cAMP analog, blocks the glial-to-neuronal switch. CONCLUSIONS: Our results imply that elevation of cAMP in the MNB, and the resultant activation of PKA, is likely to be a trigger for the glial-to-neuronal cell-fate transition within the MNB lineage.

1-Methyl-3-isobutylxanthine↗
PubMed2002

Cryptic lineages in a small frog: the post-glacial history of the spring peeper, Pseudacris crucifer (Anura: Hylidae).

The spring peeper (Pseudacris crucifer) is believed to have been a primary herpetological invader of eastern North America following the most recent period of glacial retreat. We examined the phylogeographic pattern and population structure of P. crucifer to determine whether the distribution of haplotypic variants reflect post-Pleistocene recolonization dynamics. A number of geographically isolated evolutionary lineages were supported by both maximum parsimony and neighbor-joining analyses, and by coalescence approaches applied to mtDNA. South-western Ontario represents a high level of genotypic diversity (pi) due to the presence of two divergent lineages. The geographic distribution of these lineages are interpreted as reflecting post-glacial recolonization dynamics from separate, isolated refugia during the late Pleistocene that have come into secondary contact in SW Ontario. The phylogenetic placement of haplotypes from the range of P. crucifer bartramiana (Florida and South Carolina) does not allow for monophyly of P. crucifer crucifer, and therefore the bartramiana subspecies designation does not reflect a separate evolutionary lineage.

Animals↗
PubMed2003

Molecular phylogenetics of Houstonia (Rubiaceae): descending aneuploidy and breeding system evolution in the radiation of the lineage across North America.

Nuclear and chloroplast DNA sequence variation was used to infer evolutionary relationships within and among members of Houstonia (Rubiaceae) and other closely related genera in North America. Sequences from the internal transcribed spacer (ITS) of the nrDNA and a cpDNA intron in the trnL gene were used to reconstruct phylogenetic relationships of 30 species of Houstonia and closely related genera. The data suggest that the North American species of Houstonia are not monophyletic, but belong to the same lineage as Stenaria. The radiation of this lineage has been accompanied by changes in the basic chromosome number of the major clades through descending aneuploidy. This loss of chromosomes was also associated with northward colonization of North America. However, other characters, such as an annual versus perennial habit, heterostylous and homostylous breeding systems, and the evolution of self fertilization, seem to be labile throughout the lineage, originating multiple times throughout the evolutionary history of the lineage.

Aneuploidy↗
PubMed1997

CD8 lineage commitment in the absence of CD8.

The absence of cytotoxic T lymphocyte activity and the failure of MHC class I-restricted T cell receptor (TCR) transgenic thymocytes to mature in CD8alpha-deficient mice suggest that CD8 may be essential for CD8 lineage commitment. We report that variants of the antigenic peptide that delete TCR transgenic thymocytes from CD8 wild-type but not CD8alpha-deficient mice can restore positive selection of CD8 lineage cells in the absence of CD8. The positively selected cells down-regulate CD4, up-regulate TCR, respond to the antigenic peptide, and express CD8beta mRNA. Interestingly, there was no enhanced selection of CD4+ T cells, implying that the TCR-MHC interaction, even in the absence of CD8, provided instructive signaling for commitment to the CD8 lineage. Our results are discussed in terms of recent models of T cell lineage commitment.

Animals↗
PubMed1997

The influence of the MAPK pathway on T cell lineage commitment.

During development, progenitor thymocytes differentiate into either CD4 or CD8 T cells, and this fate decision depends on the specificity of the T cell antigen receptor (TCR) for MHC class II or class I molecules. Based on the mechanisms of fate specification known for simple metazoan organisms, we sought to determine whether the extracellular signal-related kinases (ERKs) play a role in T cell differentiation and lineage commitment. Using a dominant gain-of-function mutant of the erk2 gene, we show that differentiation into the CD4 lineage is favored. We also show that, conversely, the addition of a pharmacological inhibitor of the ERK pathway favors differentiation into the CD8 lineage. We present a quantitative selection model that incorporates these results as well as those of recent reports on the role of Notch in T cell lineage specification.

Animals↗
PubMed2002

Cuticular hydrocarbons suggest three lineages in Reticulitermes (Isoptera: Rhinotermitidae) from North America.

Cuticular hydrocarbon mixtures can be used to discriminate insect taxa. They have utility for determining phylogenetic relationships where they are independent characters with discrete states and represent a hierarchical distribution of shared, derived characters. We report inferred degrees of relatedness among the chemical phenotypes of Reticulitermes from PAUP (phylogenetic analysis using parsimony) analyses of cuticular hydrocarbon characters. One hundred and forty-one Reticulitermes colonies collected from California, Georgia, New Mexico, Arizona and Nevada were used. Initial maximum parsimony analyses sorted the 141 colonies into 26 chemical phenotypes. Subsequent analyses, using the ancestral species Coptotermes formosanus and Heterotermes sp. as outgroups, sorted Reticulitermes taxa into three major lineages, each characterized by a different set of dominant methyl-branched or unsaturated hydrocarbon components. Reticulitermes in lineage I have cuticular hydrocarbon mixtures with a preponderance of internally branched monomethylalkanes and 11,15-dimethylalkanes. Those in lineage II are defined by a preponderance of 5-methylalkanes and 5,17-dimethylalkanes. Taxa in lineage III are characterized by the predominance of olefins and a relative paucity of n-alkanes and methyl-branched alkanes. Bootstrap analyses and decay indices provided statistical support and robustness for these chemical-based relationships.

Animals↗