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PubMed2004

Cotton leaf curl Gezira virus-satellite DNAs represent a divergent, geographically isolated Nile Basin lineage: predictive identification of a satDNA REP-binding motif.

Cotton leaf curl Gezira virus (CLCuGV), a species of the genus Begomovirus (family Geminiviridae), was recently cloned from cotton, okra, and Sida alba plants exhibiting leaf-curling and vein-thickening symptoms in Sudan. Here, we describe a previously unknown lineage of single-stranded DNA satellite (satDNA) molecules, which are associated with CLCuGV, and are required for development of characteristic disease symptoms. Co-inoculation of cotton and Nicotiana benthamiana plants with satDNAs cloned from cotton, okra, and S. alba, together with CLCuGV as the 'helper virus' resulted in the development of characteristic leaf-curling and vein-thickening symptoms in both hosts. An anatomical study of symptomatic, virus-infected cotton leaves revealed that spongy parenchyma cells had developed instead of collenchyma cells at the sites of vein thickening. Phylogenetically, the CLCuGV-associated satDNAs from Sudan, together with their closest relatives from Egypt, form a new satDNA lineage comprising only satDNAs from the Upper and Lower Nile Basins. Analysis of satellites and their helper virus sequences identified a predicted REP-binding site consisting of the directly repeated sequence, 'CGGTACTCA', and an inverted repeated sequence, 'TGAGTACCG', which occur in the context of a 17-nucleotide motif. The conserved REP-binding motif identified herein, together with strict geographic isolation, and apparent host-restriction, may be the collective hallmark of these new satDNA-begomovirus lineages, extant in the Nile Basin.

Binding Sites↗

PubMed2004

At most three ES cells contribute to the somatic lineages of chimeric mice and of mice produced by ES-tetraploid complementation.

Chimeric or entirely embryonic stem (ES) cell-derived mice ("ES mice") can be produced by injecting ES cells into diploid (2n) or tetraploid (4n) host blastocysts, respectively. Usually, between 10 and 15 ES cells are injected into the host blastocyst, but it is not clear how many of the injected cells contribute to the somatic lineages, thus serve as "founder cells" of the embryo proper. We have used genetically labeled ES cells to retrospectively determine the number of founder ES cells that generate the somatic lineages of chimeric and of ES mice. ES cell clones individually labeled with provirus were mixed in equal numbers and injected into 2n or 4n blastocysts to generate chimeric or ES mice. Southern analysis of DNA from the resulting animals indicated that the somatic lineages were most often derived from one or two and sometimes from up to three founder ES cells. The number of founder cells was independent of the total number of cells injected into the host blastocysts. Our results are consistent with the notion that constraints of the host embryo restrict the number of ES cells that can contribute to a chimeric or an ES mouse.

Animals↗

PubMed2004

Lineage-specific imprinting and evolution of the zinc-finger gene ZIM2.

We have carried out an in-depth comparative analysis of a 100-kb genomic interval containing two imprinted genes, PEG3 and ZIM2, using sequences derived from human, mouse, and cow. In all three mammals, ZIM2 is located at a similar genomic distance and in the same orientation relative to PEG3, indicating the basic structural conservation of this imprinted locus. However, several lineage-specific changes have occurred that affect the exon structure and imprinting status of ZIM2. Human ZIM2 and PEG3 share a set of 5' exons and a common promoter, and both genes are paternally expressed. In contrast, mouse and cow Zim2 genes do not share 5' exons with Peg3, and Zim2 employs a separate downstream promoter in both species. The imprinting status of Zim2 is also not conserved among mammals; mouse Zim2 is expressed biallelically in testis but predominantly from the maternal allele in brain, while cow Zim2 is expressed biallelically in testis. The separate transcription of Zim2 and Peg3 and the change in promoter usage and imprinting status appear to have resulted from independent insertional events that have placed unrelated genes, Zim1 and Ast1, respectively, between Zim2 and Peg3 in mouse and cow. Our results suggest that PEG3 and ZIM2 represent the two original genes at this locus and that rearrangements have occurred independently in different mammalian lineages in recent evolutionary times. Our data also suggest that exon-sharing of human PEG3 and ZIM2 was not ancestral, but may represent a fusion event joining the two neighboring genes and bringing ZIM2 under paternal expression control. These observations are striking in light of the structural and functional conservation that typifies other imprinted domains and suggest that the PEG3/ZIM2 imprinted domain may have evolved in an unusual lineage-specific pattern.

Amino Acid Sequence↗

PubMed2006

Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup.

Comparative genetic analysis between human and chimpanzee may detect genetic divergences responsible for human-specific characteristics. Previous studies have identified a series of genes that potentially underwent Darwinian positive selection during human evolution. However, without a closely related species as outgroup, it is difficult to identify human-lineage-specific changes, which is critical in delineating the biological uniqueness of humans. In this study, we conducted phylogeny-based analyses of 2633 human brain-expressed genes using rhesus macaque as the outgroup. We identified 47 candidate genes showing strong evidence of positive selection in the human lineage. Genes with maximal expression in the brain showed a higher evolutionary rate in human than in chimpanzee. We observed that many immune-defense-related genes were under strong positive selection, and this trend was more prominent in chimpanzee than in human. We also demonstrated that rhesus macaque performed much better than mouse as an outgroup in identifying lineage-specific selection in humans.

Adaptation, Biological↗

PubMed2004

Phylogeny of muroid rodents: relationships within and among major lineages as determined by IRBP gene sequences.

The rodent family Muridae is the single most diverse family of mammals with over 1300 recognized species. We used DNA sequences from the first exon ( approximately 1200bp) of the IRBP gene to infer phylogenetic relationships within and among the major lineages of muroid rodents. We included sequences from every recognized muroid subfamily except Platacanthomyinae and from all genera within the endemic Malagasy subfamily Nesomyinae, all recognized tribes of Sigmodontinae, and a broad sample of genera in Murinae. Phylogenetic analysis of the IRBP data suggest that muroid rodents can be sorted into five major lineages: (1) a basal clade containing the fossorial rodents in the subfamilies Spalacinae, Myospalacinae, and Rhizomyinae, (2) a clade of African and Malagasy genera comprising the subfamilies Petromyscinae, Mystromyinae, Cricetomyinae, Nesomyinae, and core dendromurines, (3) a clade of Old World taxa belonging to Murinae, Otomyinae, Gerbillinae, Acomyinae, and Lophiomyinae, (4) a clade uniting the subfamilies Sigmodontinae, Arvicolinae, and Cricetinae, and (5) a unique lineage containing the monotypic Calomyscinae. Although relationships among the latter four clades cannot be resolved, several well-supported supergeneric groupings within each are identified. A preliminary examination of molar tooth morphology on the resulting phylogeny suggests the triserial murid molar pattern as conceived by evolved at least three times during the course of muroid evolution.

Animals↗

PubMed2004

Evidence for two independent lineages of Griffithsia (Ceramiaceae, Rhodophyta) based on plastid protein-coding psaA, psbA, and rbcL gene sequences.

The ceramiaceous red algal genus Griffithsia has characteristic large vegetative cells visible to the unaided eye and thousands of nuclei in a single cell at maturity. Its members often occur intertidally along temperate to tropical coasts. Although previous morphological studies indicated that Griffithsia is subdivided into four groups, there is no molecular phylogeny for the genus. We present the multigene phylogeny of the genus based on plastid protein-coding psaA, psbA, and rbcL genes from ten samples of eight Griffithsia species, eight samples of five putative relatives, such as Anotrichium and Halurus, and three outgroup taxa. Saturation plots for each of the three datasets showed no evidence of saturation at any codon position. The partition homogeneity test indicated that none of the individual datasets resulted in significantly incongruent trees. All the analyses of individual and concatenated datasets separated Griffithsia into two well-defined lineages: Lineage 1 was composed of Griffithsia corallinoides, Griffithsia pacifica, and Griffithsia tomo-yamadae, while lineage 2 encompassed Griffithsia antarctica, Griffithsia japonica, Griffithsia teges, Griffithsia traversii, and Griffithsia sp. Our results support the monophyly of the four Anotrichium species and cast a question on the autonomy of Halurus. The monophyly of the tribe Griffithsieae is well resolved, although interrelationships among Griffithsia, Anotrichium, and Halurus were unclear. Our study indicates that the psaA and psbA genes are powerful new tools for the genus-level phylogeny of red algal groups, such as Griffithsia. This is the first report on the multigene phylogeny of the Ceramiales algae based on three protein-coding plastid genes.

Algal Proteins↗

PubMed2005

The mammalian alphaD-globin gene lineage and a new model for the molecular evolution of alpha-globin gene clusters at the stem of the mammalian radiation.

We have explored the evolution of the alpha-globin gene family by comparative sequence and phylogenetic analyses of mammalian alpha-globin genes. Our analyses reveal the existence of a new alpha-globin gene lineage in mammals that is related to the alpha(D)-globin genes of birds, squamates and turtles. The gene is located in the middle of the alpha-globin gene cluster of a marsupial, Sminthopsis macroura and of humans. It exists in a wide variety of additional mammals, including pigs, cows, cats, and dogs, but is a pseudogene in American marsupials. Evolutionary analyses suggest that the gene has generally evolved under purifying selection, indicative of a functional gene. The presence of mRNA products in humans, pigs, and cows also suggest that the gene is expressed and likely to be functional. The analyses support the hypothesis that the alpha(D)-globin gene lineage has an ancient evolutionary origin that predates the divergence of amniotes. The structural similarity of alpha-globin gene clusters of marsupials and humans suggest that an eight gene cluster (5'-zeta2-zeta1-alpha(D)-alpha3-alpha2-alpha1-theta-omega-3'), including seven alpha-like genes and one beta-like globin gene (omega-globin) existed in the common ancestor of all marsupial and eutherian mammals. This basic structure has remained relatively stable in marsupials and in the lineage leading to humans, although omega-globin has been lost from the alpha-globin gene cluster of humans.

Animals↗

PubMed2006

Nuclear and mitochondrial sequence data reveal the major lineages of starlings, mynas and related taxa.

We investigated the phylogenetic relationships among the major lineages of the avian family Sturnidae and their placement within the Muscicapoidea clade using two nuclear (RAG-1 and myoglobin) and one mitochondrial gene (ND2). Among Muscicapoidea, we recovered three clades corresponding to the families Cinclidae, Muscicapidae and Sturnidae (sensu [Sibley, C.G., Monroe Jr., B.L., 1990. Distribution and Taxonomy of Birds of the World. Yale University Press, New Haven, CT]). Within the sturnoid lineage Mimini and Sturnini are sister groups, with Buphagus basal to them. We identified three major lineages of starlings: the Philippine endemic genus Rhabdornis, an Oriental-Australasian clade (genera Scissirostrum, Gracula, Mino, Ampeliceps, Sarcops, Aplonis), and an Afrotropical-Palaearctic clade (all African taxa, Sturnus and Acridotheres). We discuss the biogeographic implications of our findings and suggest an Asiatic origin for this family. The congruence between the age of major clades, estimated by NPRS, and palaeoclimatic data present evidence for the role of climatic changes in shaping present day distribution of the group.

Animals↗

PubMed2006

Toothed whale monophyly reassessed by SINE insertion analysis: the absence of lineage sorting effects suggests a small population of a common ancestral species.

Morphological data have indicated that toothed whales form a monophyletic group. However, research published in the last several years has made the issue of the monophyly or paraphyly of toothed whales a subject of debate. Our group previously characterized three independent loci in which SINE insertions were shared among dolphins and sperm whales, thus supporting the traditional, morphologically based hypothesis of toothed whale monophyly. Although in recent years a few additional molecular works proposed this topology, there is still skepticism over this monophyly from the view point of molecular systematics. When the phylogeny of rapidly radiated taxa is examined using the SINE method, it is important to consider the ascertainment bias that arises when choosing a particular taxon for SINE loci screening. To overcome this methodological problem specific to the SINE method, we examined all possible topologies among sperm whales, dolphins and baleen whales by extensively screening SINE loci from species of all three lineages. We characterized nine independent SINE loci from the genomes of sperm whales and dolphins, all of which cluster sperm whales and dolphins but exclude baleen whales. Furthermore, we characterized ten independent loci from baleen whales, all of which were amplified in a common ancestor of these whales. From these observations, we conclude that toothed whales form a monophyletic group and that no ancestral SINE polymorphisms hinder their phylogenetic assignment despite the short divergence times of the major lineages of extant whales during evolution. These results suggest that a small population of common ancestors of all toothed whales ultimately diverged into the lineages of sperm whales and dolphins.

Animals↗

PubMed2006

Unravelling the phylogeny of Lejeuneaceae (Jungermanniopsida): evidence for four main lineages.

With about 1000 species in approximately 90 genera, Lejeuneaceae are the largest family of liverworts and make up a large and important part of cryptogamic diversity in the humid tropics. Maximum parsimony, Maximum likelihood and Bayesian analyses of a dataset including four markers (rbcL, psbA, trnL-trnF region of cp DNA, nrITS region) of 134 accessions resulted in similar topologies that support the presence of four main lineages within Lejeuneaceae. Model-based analyses support a division of Lejeuneaceae into two lineages corresponding to the subfamilies Ptychanthoideae and Lejeuneoideae. The latter lineage splits into the tribes Lejeuneeae, Brachiolejeuneeae and the genus Symbiezidium. In contrast, the Maximum parsimony analysis resolves Brachiolejeuneeae and Symbiezidium in serial sister relationships to the remainder of Lejeuneaceae. Sporophyte characters support a split into two subfamilies as seen in the model-based analyses. Some deep nodes remain unresolved, possibly indicating a series of initial diversifications which occurred over a short time period.

Base Sequence↗

PubMed2004

The myoseptal system in Chimaera monstrosa: collagenous fiber architecture and its evolution in the gnathostome stem lineage.

Recent studies have revealed the 3D morphology and collagen fiber architecture of myosepta in teleostome fishes. Here we present the first data set on the myoseptal structure of a representative of the chondrichthyan clade. We investigate the series of myosepta in the ratfish Chimaera monstrosa (Holocephali) from the anterior to the posterior body using microdissections of cleared and stained specimens, polarized light microscopy of excised myosepta, and histology. The features of the myoseptal system of Chimaera are compared to data from closely related vertebrate groups and are mapped onto a phylogenetic tree to further clarify the characteristics of the myoseptal series in the gnathostome ancestor. The 3D morphology and collagen fiber architecture of the myoseptal series in C. monstrosa resembles that of Teleostomi (Actinopterygii+Sarcopterygii) with regard to several features. Our comparative analysis reveals that some of them have evolved in the gnathostome stem lineage. (1) A series of epineural and epaxial lateral tendons (LTs) along the whole body, and a series of epipleural and hypaxial LTs in the postanal region evolved in the gnathostome stem lineage. (2) The LTs increase in length towards the posterior body (three-fold in Chimaera). Data on Chimaera and some comparative data on actinopterygian fishes indicate that LTs also increase in thickness towards the posterior body, but further data are necessary to test whether this holds true generally. (3) Another conspicuous apomorphic gnathostome feature is represented by multi-layer structures of myosepta. These are formed along the vertebral column by converging medial regions of successive sloping parts of myosepta. (4) The dorsalmost and ventralmost flanking parts of myosepta bear a set of mediolaterally oriented collagen fibers that are present in all gnathostomes but are lacking in outgroups. Preanal hypaxial myosepta are clearly different from epaxial myosepta and postanal hypaxial myosepta in terms of their collagen fiber architecture. In Chimaera, preanal hypaxial myosepta consist of an array of mediolaterally oriented collagen fibers closely resembling the condition in other gnathostome groups and in petromyzontids. Only one series of tendons, the myorhabdoid tendons of the flanking parts of myosepta, have evolved in the stem lineage of Myopterygii (Gnathostomata+Petromyzontida). Similar to LTs, the tendons of this series also increase in length towards the posterior body. In combination with other studies, the present study provides a framework for the design of morphologically based experiments and modeling to further address the function of myosepta and myoseptal tendons in gnathostomes.

Journal Article↗

PubMed2001

Induction of megakaryocytic differentiation in primary human erythroblasts: a physiological basis for leukemic lineage plasticity.

In myelodysplasias and acute myeloid leukemias, abnormalities in erythroid development often parallel abnormalities in megakaryocytic development. Erythroleukemic cells in particular have been shown to possess the potential to undergo megakaryocytic differentiation in response to a variety of stimuli. Whether or not such lineage plasticity occurs as a consequence of the leukemic phenotype has not previously been addressed. In this study, highly purified primary human erythroid progenitors were subjected to stimuli known to induce megakaryocytic differentiation in erythroleukemic cells. Remarkably, the primary erythroid progenitors rapidly responded with morphological and immunophenotypic evidence of megakaryocytic differentiation, equivalent to that seen in erythroleukemic cells. Even erythroblasts expressing high levels of hemoglobin manifested partial megakaryocytic differentiation. These results indicate that the lineage plasticity observed in erythroleukemic cells reflects an intrinsic property of cells in the erythroid lineage rather than an epiphenomenon of leukemic transformation.

Cell Differentiation↗

PubMed1992

Lineage and stage specific expression of HOX 1 genes in the human hematopoietic system.

Recent observations have demonstrated the expression of several members of the homeobox-containing (HOX) gene complexes within the hematopoietic compartment. We have analyzed the expression pattern of the entire HOX 1 locus in a panel of leukemia-derived human cell lines representing various blood phenotypes. The expression of the eleven HOX 1 genes is lineage-restricted and these genes are predominantly detected within cells of myelomonocytic origin. This is in strong contrast with the erythro-megakaryocytic specific expression of HOX 2 genes. Furthermore, we have observed that the expression of three HOX 1 genes within B lymphoid lineages is stage-related and that the expression of several of them is switched off during TPA-induced differentiation of Kg1 and U937. These observations suggest that HOX 1 homeoproteins could be regulators of lineage determination during hematopoiesis.

B-Lymphocytes↗

PubMed1999

Rat liver myofibroblasts and hepatic stellate cells: different cell populations of the fibroblast lineage with fibrogenic potential.

BACKGROUND & AIMS: Hepatic stellate cells (HSCs) are considered the principal matrix-producing cells of the damaged liver. However, other cell types of the fibroblast lineage that have not yet been characterized are also involved in liver tissue repair and fibrogenesis. METHODS: We established cultures of cells of the fibroblast lineage, termed rat liver myofibroblasts, and analyzed their phenotypical and functional properties in comparison with HSCs. RESULTS: HSCs and rat liver myofibroblasts were discernible by morphological criteria and growth behavior. Prolonged subcultivation of rat liver myofibroblasts was achieved, but HSCs were maintained in culture at maximum until second passage. HSCs were characterized by expression of glial fibrillary acidic protein, desmin, and vascular cell adhesion molecule 1, which were almost completely absent in rat liver myofibroblasts. For synthetic properties, HSCs and rat liver myofibroblasts displayed mostly overlapping properties with 4 striking differences. The complement-activating protease P100 and the protease inhibitor alpha(2)-macroglobulin were preferentially expressed by HSCs, whereas interleukin 6-coding messenger RNAs and the extracellular matrix protein fibulin 2 were almost exclusively detectable in rat liver myofibroblasts. CONCLUSIONS: The data show that morphologically and functionally different fibroblastic populations, HSCs and rat liver myofibroblasts, can be derived from liver tissue. HSCs may not represent the single matrix-producing cell type of the fibroblast lineage in the liver.

Animals↗

PubMed2003

Comparative analysis of bacterial viruses Bam35, infecting a gram-positive host, and PRD1, infecting gram-negative hosts, demonstrates a viral lineage.

Extra- and intracellular viruses in the biosphere outnumber their cellular hosts by at least one order of magnitude. How is this enormous domain of viruses organized? Sampling of the virosphere has been scarce and focused on viruses infecting humans, cultivated plants, and animals as well as those infecting well-studied bacteria. It has been relatively easy to cluster closely related viruses based on their genome sequences. However, it has been impossible to establish long-range evolutionary relationships as sequence homology diminishes. Recent advances in the evaluation of virus architecture by high-resolution structural analysis and elucidation of viral functions have allowed new opportunities for establishment of possible long-range phylogenic relationships-virus lineages. Here, we use a genomic approach to investigate a proposed virus lineage formed by bacteriophage PRD1, infecting gram-negative bacteria, and human adenovirus. The new member of this proposed lineage, bacteriophage Bam35, is morphologically indistinguishable from PRD1. It infects gram-positive hosts that evolutionarily separated from gram-negative bacteria more than one billion years ago. For example, it can be inferred from structural analysis of the coat protein sequence that the fold is very similar to that of PRD1. This and other observations made here support the idea that a common early ancestor for Bam35, PRD1, and adenoviruses existed.

Bacillus Phages↗

PubMed1986

T-cell receptor beta chain gene rearrangements: genetic markers of T-cell lineage and clonality.

We have performed a series of investigations involving T-cell receptor beta chain (T beta) gene rearrangements in benign and malignant nonhematopoietic, B-cell, and T-cell proliferations. These studies provide the conceptual basis and the operational approach for the use of T beta gene rearrangements as markers of T-cell lineage, clonality, and differentiation, analogous to immunoglobulin gene rearrangements in B cells. Southern blot hybridization analysis for T beta gene rearrangements can now be utilized to identify and distinguish between non-T cells, polyclonal T cells, and monoclonal T cells. Determination of T beta gene rearrangements will play an important role in the further investigation and classification of T-cell neoplasia. However, the identification of a genetic marker of clonality for T cells has significant diagnostic and prognostic value as well. For example, determination of the T beta gene rearrangement unique to a particular malignant T-cell clone provides a specific genetic marker for that clonal T-cell proliferation. This genetic marker of the T-cell clone may provide a useful tool for monitoring the patient's therapeutic response and clinical course for early signs of relapse. Nonetheless, our studies demonstrate that the lineage specificity of immunoglobulin and T beta gene rearrangements is not absolute. It appears that only a multiparametric approach combining extensive monoclonal antibody immunophenotypic analysis, in vitro testing for functional help and suppression, and Southern blot hybridization analysis for immunoglobulin and T beta gene rearrangements allows the conclusive and unequivocal demonstration of the B- or T-cell derivation of all lymphoid neoplasms. Lymphoid malignancies that cannot be assigned to the B- or T-cell lineage following this extensive multiparametric analysis are exceedingly uncommon.

Cell Line↗

PubMed1998

Autoantibodies to T-lineage cells in aged mice.

Aging is accompanied by a marked decline in protective immune function. This loss of effective immunity is largely due to alterations in the T-cell compartment. There are major impairments in both the production of new T-cells within the thymus and in the functions of mature T-cells in peripheral lymphoid organs. The mechanism(s) underlying this age-related decline in T-lineage cells is not clear. Here, we demonstrate that aging is accompanied by the appearance of appreciable titers of anti-T-lineage autoantibodies. The autoantibodies, which are exclusively of the IgM class, begin to appear at 1 year of life and are universally found in the sera of 2-year-old mice. Among thymocytes, all CD4/CD8 subsets reacted with the autoantibodies, with the CD4+8+ subset showing the greatest reactivity. The autoantibodies also bound to resting peripheral CD4+ and CD8+ cells. Following activation with either anti-CD3 or with TCR-independent stimulators, reactivity to peripheral T-cells was diminished, suggesting that the determinants recognized by the autoantibodies are downregulated in response to activation signals. Lastly, thymocytes freshly isolated from old, but not young, mice have IgM antibodies bound to their surfaces. Thus, circulating autoantibodies in old mice have access to the thymus and bind to thymocytes in situ. These results lead to the proposal that the presence of anti-T-lineage autoantibodies in vivo interferes with normal T-cell development and/or function in aged animals.

Aging↗

PubMed1988

Hemopoietic lineage switch: v-raf oncogene converts Emu-myc transgenic B cells into macrophages.

Hemopoietic lineage commitment can be breached by concomitant expression of the c-myc and v-raf oncogenes. Switching to the myeloid lineage occurred frequently when B lineage cells, from either lymphomas or preleukemia bone marrow cells of Emu-myc transgenic mice, were infected with a retrovirus bearing v-raf. Cloned pre-B and B cell lines changed into either mature or immature macrophages as assessed by morphology, adherence, phagocytic activity, surface markers, and lysozyme production, but retained clonotypic immunoglobulin gene rearrangements. Although expression of the Emu-myc transgene was reduced or abolished in the more differentiated lines, the lines remained tumorigenic. The converted lines produced the myeloid growth factor GM-CSF, and most had karyotypic alterations. These results suggest that constitutive myc plus raf expression can provoke genetic reprogramming in lymphocytes.

Animals↗