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PubMed2003

Stem cell plasticity, cell fusion, and transdifferentiation.

One of the most contentious issues in biology today concerns the existence of stem cell plasticity. The term "plasticity" refers to the capacity of tissue-derived stem cells to exhibit a phenotypic potential that extends beyond the differentiated cell phenotypes of their resident tissue. Although evidence of stem cell plasticity has been reported by multiple laboratories, other scientists have not found the data persuasive and have remained skeptical about these new findings. This review will provide an overview of the stem cell plasticity controversy. We will examine many of the major objections that have been made to challenge the stem cell plasticity data. This controversy will be placed in the context of the traditional view of stem cell potential and cell phenotypic diversification. What the implications of cell plasticity are, and how its existence may modulate our present understanding of stem cell biology, will be explored. In addition, we will examine a topic that is usually not included within a discussion of stem cell biology--the direct conversion of one differentiated cell type into another. We believe that these observations on the transdifferentiation of differentiated cells have direct bearing on the issue of stem cell plasticity, and may provide insights into how cell phenotypic diversification is realized in the adult and into the origin of cell phenotypes during evolution.

Animals↗
PubMed2001

Divergence pattern of animal gene families and relationship with the Cambrian explosion.

There are many gene families that are specific to multicellular animals. These have either diverged from ancestral genes that are shared with fungi and/or plants or evolved from an ancestral gene unique to animals. The evolution of gene families involved in cell-cell communication and developmental control has been studied to establish whether the number of member genes increased dramatically immediately prior to or in concert with the Cambrian explosion. A molecular phylogeny-based analysis of several animal-specific gene families has revealed that gene diversification by duplication occurred during two active periods interrupted by a long intervening quiescent period. Intriguingly, the Cambrian explosion is situated in the silent period, indicating that there is no direct link between the first burst of gene diversification and the Cambrian explosion itself. The importance of gene recruitment as a possible molecular mechanism for morphological diversity, and its possible role for the Cambrian explosion, are discussed.

Animals↗
PubMed2006

Synthesis of small tripeptide molecules through a catalysis sequence comprising metathesis and aminohydroxylation.

Tripeptidic structures were synthesized by using a combination of two independent consecutive catalytic procedures. Cross-metathesis of N-acroyl amino acid esters yields fumaric amide compounds with exclusive E double-bond geometry. This represents an unprecedented example of complete double-bond selectivity in this kind of reaction. A subsequent asymmetric aminohydroxylation of the chiral fumaric amides was carried out without the need of any further ligand and gave high yields and no side products. This reaction transforms the central fumaric amide unit into a hydroxy aspartic acid moiety and relies on the inherent stereochemistry of the starting fumaric diamides. An additional feature of our sequence is the ease of generating stereochemical diversification within the aminohydroxylation reaction. As a consequence, rapid conformational and configurational diversification can be achieved from the overall two-step catalytic sequence. The versatility of this approach is demonstrated by starting from two different N-acroyl amino esters, which led to the synthesis of eight structurally and stereochemically different tripeptides that could all be identified individually. As such, the present two-step catalytic approach should serve to efficiently synthesize large families of tripeptidic molecular probes.

Amides↗
PubMed1991

The chicken D locus and its contribution to the immunoglobulin heavy chain repertoire.

Sixteen D elements were characterized from the chicken genome, 15 of which are extremely homologous. Early expression of this D repertoire was studied for both DJ and VDJ alleles. No N diversification occurs at either DJ or VD junctions. Only P additions were observed, the length of which does not appear restricted to a dinucleotide. A selection for the almost exclusive usage of the first reading frame of the D elements takes place during B cell expansion in the bursa, in parallel with the selection of productive rearrangements. All three reading frames were observed for the DJ allele at each developmental stage, although some bias for the first reading frame occurs already at the junctional stage. The high incidence of D-D junctions observed (25% among DJ sequences) might represent the major functional contribution of this multigene cluster in a system in which diversity will be generated later on by successive superimposed gene conversions. Other possible functions are discussed. The onset of D diversification through gene conversion between day 15 and day 18 of embryonic development is further documented.

Age Factors↗
PubMed2003

Extensive proliferation of T cell lineage-restricted progenitors in the thymus: an essential process for clonal expression of diverse T cell receptor beta chains.

For clonal diversification of TCR, a large number of T cell progenitors are required in which highly diverse TCRbeta chains are accommodated individually. In the present study, we examined the proliferative potential of thymic progenitors that have been defined to be T cell lineage restricted. We show that the earliest fetal thymus (FT) cells from Rag2(-/-) mice, when cultured individually in a thymic organ culture system, produced 150-1,800 CD25(+) cells. Since differentiation and proliferation of Rag2(-/-) thymocytes are arrested at the stage of TCRbeta chain gene rearrangement, the observed proliferation was considered to represent the proliferative potential of progenitors prior to the TCRbeta rearrangement. A comparable level of proliferation was revealed to occur by analyzing the Dbeta-Jbeta rearrangement profiles of T cells generated from single progenitors in the earliest population of FT from normal mice. The proliferative potential of progenitors declined along with the progression of developmental stages. Such an extensive proliferation of progenitors after the restriction to the T cell lineage may be an essential process ensuring the clonal diversification of TCRbeta chains.

Animals↗
PubMed2005

Olfactory morphology of carcharhinid and sphyrnid sharks: does the cephalofoil confer a sensory advantage?

Many hypotheses have been advanced to explain the adaptive significance of the sphyrnid cephalofoil, including potential advantages of spacing the olfactory organs at the distal tips of the broad surface. We employed comparative morphology to test whether the sphyrnid cephalofoil provides better stereo-olfaction, increases olfactory acuity, and samples a greater volume of the medium compared to the situation in carcharhiniform sharks. The broadly spaced nares provide sphyrnid species with a significantly greater separation between the olfactory rosettes, which could lead to an enhanced ability to resolve odor gradients. In addition, most sphyrnid species possess prenarial grooves that greatly increase the volume of water sampled by the nares and thus increase the probability of odorant encounter. However, despite a much greater head width, and a significantly greater number of olfactory lamellae, scalloped hammerhead sharks do not possess a greater amount of olfactory epithelial surface area than the carcharhiniform sandbar sharks. Therefore, sphyrnid sharks might not possess any greater olfactory acuity than carcharhinids. Despite this, there are clear olfactory advantages to the cephalofoil head morphology that could have led to its evolution, persistence, and diversification. persistence, and diversification.

Animals↗
PubMed2006

HIV global surveillance: foundation for retroviral discovery and assay development.

The high level of HIV genetic diversity has important implications for screening, diagnostic testing and patient monitoring. Continued diversification and global redistribution of HIV groups, subtypes and recombinants make it imperative that serological and molecular assays be designed and evaluated to ensure reliable performance on all HIV infections. Recognizing the importance of this issue, we initiated a comprehensive program to monitor global diversification of HIV, search for newly emerging variants, assemble large-volume panels of genetically and geographically diverse strains, and develop strategies to determine the impact of HIV diversity on assays used for detecting and monitoring HIV infection. Efforts to identify and characterize rare and emerging HIV strains have lead to the identification of HIV-1 group O, group N, and dual infections of groups M and O. A panel of plasma specimens was established that includes specimens collected from 12 countries in Africa, Asia, Europe, and South America; the panel comprises infections due to HIV-1 group M subtypes A, B, C, D, F, and G, as well as CRF01, CRF02, and unique recombinant forms, group N, and group O. Serological and molecular characterization of this unique panel has provided vital sequence data to support assay development and an invaluable source of well-defined specimens to evaluate and compare assay performance. The ability to address the challenge posed by ongoing evolution of HIV and the emergence of new variants requires continued surveillance of global HIV strain diversity, a sound scientific foundation for assay development, and suitable panels to evaluate and validate assay performance.

Africa↗
PubMed2004

Evolutionary trace analysis of scorpion toxins specific for K-channels.

Scorpion alpha-K(+) channel toxins are a large family of polypeptides with a similar structure but diverse pharmacological activities. Despite many structural and functional data available at present, little progress has been made in understanding the toxin's molecular basis responsible for the functional diversification. In this paper, we report the first complete cDNA sequences of toxins belonging to subfamily 6 and identify five new members, called alpha-KTx 6.6-6.10. By analyzing the rates of mutations that occurred in the corresponding cDNAs, we suggest that accelerated evolution in toxin-coding regions may be associated with the functional diversification of this subfamily. To pinpoint sites probably involved in the functional diversity of alpha-KTx family, we analyzed this family of sequences using the evolutionary trace method. This analysis highlighted one channel-binding surface common for all the members. This surface is composed of one conserved lysine residue at position 29 assisted by other residues at positions 10, 26, 27, 32, 34, and 36. Of them, the positions 29, 32, and 34 have been reported to be the most major determinants of channel specificity. Interestingly, another contrary surface was also observed at a higher evolutionary time cut-off value, which may be involved in the binding of ERG (ether-a-go-go-related gene) channel-specific toxins. The good match between the trace residues and the functional epitopes of the toxins suggested that the evolutionary trace results reported here can be applied to predict channel-binding sites of the toxins. Because, the side-chain variation in the trace positions is strongly linked with the functional alteration and channel-binding surface transfer of alpha-KTx family, we conclude that our findings should also be important for the rational design of new toxins targeting a given potassium channel with high selectivity.

Animals↗
PubMed2000

Sterol 14-demethylase P450 (CYP51) provides a breakthrough for the discussion on the evolution of cytochrome P450 gene superfamily.

Biodiversity is the most characteristic feature of cytochrome P450. Finding of CYP51 distributing widely in biological kingdoms provided breakthroughs for the discussion on the evolution and diversification of P450. Molecular phylogenetic analysis demonstrated that CYP51 appeared in the prokaryotic era and distributed into most kingdoms concomitant with phylogenetic divergence. This is the first evolutionary evidence indicating the prokaryotic origin of P450. Modification of substrate specificity of eukaryotic CYP51s occurred independently to adapt to the different sterol precursors existing in each kingdom. Formation of CYP51 variants through the mutation of active site and the selection of the advantageous ones from them were demonstrated by the emergence of azole-resistant CYP51s in Candida albicans under the environments rich in azole antifungal agents. These findings illustrate the most probable core process of P450 diversification consisting of modification of active site and selection of the resulting variants through interaction with endogenous and exogenous chemicals.

Amino Acid Sequence↗
PubMed1996

Developmental evolution of metazoan bodyplans: the fossil evidence.

Evidence from the fossil record, developmental biology and metazoan phylogeny demonstrates that the rapid origination of major metazoan bodyplans during the late Neoproterozoic and earliest Cambrian was intimately associated with a series of innovations in developmental control mechanisms that included the Hox gene cluster. The interval between about 565 Ma (million years ago) and 530 Ma evidently includes the protostome-deuterostome branching, diversification of independent higher metazoan clades, diversification of important developmental control systems, and formation of higher metazoan bodyplans. Comparative paleontological and developmental studies will allow further tests of alternative models for the sequence of these events, illuminating the association between developmental and bodyplan evolution.

Animals↗
PubMed1996

Antibody expression from the core region of the human IgH locus reconstructed in transgenic mice using bacteriophage P1 clones.

Mice carrying transgenic human immunoglobulin gene miniloci can be used for the production of human monoclonal antibodies. The human variable region (V) gene segments in these miniloci undergo productive rearrangement in mouse lymphoid tissue to yield a population of B lymphocytes expressing a repertoire of antibodies. Many of the miniloci studied to date have included only a small number of germline gene segments in an artificially compact configuration. Here we describe the use of the bacteriophage P1 cloning system to create mice carrying the core region of the human immunoglobulin heavy chain (IgH) locus. Three P1 clones carrying overlapping regions of the human IgH locus (spanning the five JH-proximal VH segments, the entire DH and JH clusters, and the C mu and C delta constant regions) were injected into mouse eggs and appear to have reconstituted the core region of the locus (> 180 kb) following homologous recombination with each other. While this translocus yielded a titer of serum immunoglobulin similar to that obtained with a smaller plasmid-based minilocus, the P1-based locus gave rise to substantially greater diversification by somatic hypermutation. Such diversification is important for obtaining high-affinity antibodies. The results show the usefulness of the P1 system in facilitating the manipulation and recreation of large transgenes.

Amino Acid Sequence↗
PubMed1997

Phylogeny of the grassland leafhopper genus Flexamia (Homoptera: Cicadellidae) based on mitochondrial DNA sequences.

Leafhoppers (Cicadellidae) are a highly diverse group of sap-sucking insects, many species of which specialize on grasses. Past attempts to examine the roles of host transfer or host plant coevolution in the diversification of leafhopper species using cladistic methods have been hindered by a paucity of discrete, phylogenetically informative morphological characters. To demonstrate the utility of DNA sequence data for species-level phylogenetic studies of Cicadellidae, we estimated phylogenetic relationships among species in the North American grassland leafhopper genus Flexamia DeLong using partial nucleotide sequences of mitochondrial 16S rDNA and NADH dehydrogenase 1, totaling 1496 base pairs and 810 potentially informative characters. Analyses of the partitioned and combined sequence data using maximum parsimony, neighbor-joining, and maximum likelihood criteria yielded similar estimates of relationships in which most nodes were well-supported by bootstrap and decay indices. These estimates largely agreed with a previously published, intuitive, morphology-based phylogeny for the genus. A parsimony reconstruction of host associations based on these results suggests that the origins of various Flexamia clades coincided with host transfers among grass subfamilies or genera. Nevertheless, associations with certain subfamilies, genera, or species of grasses appear to have been largely conserved in the evolutionary diversification of Flexamia.

Animals↗
PubMed2001

Evolution of Lycopodiaceae (Lycopsida): estimating divergence times from rbcL gene sequences by use of nonparametric rate smoothing.

By use of nonparametric rate smoothing and nucleotide sequences of the rbcL gene, divergence times in Lycopodiaceae are estimated. The results show that much extant species diversity in Lycopodiaceae stems from relatively recent cladogenic events. These results corroborate previous ideas based on paleobotanical and biogeographical data. Previous molecular phylogenetic analyses recognized a split into neotropical and paleotropical clades in Huperzia, which contains 85-90% of all living species. Connecting this biogeographical pattern with continent movements, the diversification of this epiphytic group was suggested to coincide with that of angiosperms in the mid to Late Cretaceous. Results presented here are consistent with this idea, and the diversification of the two clades is resolved as Late Cretacous (78 and 95 Myr). In the related genera Lycopodium and Lycopodiella, the patterns are somewhat different. Here species diversity is scattered among different subgeneric groups. Most of the high-diversity subgeneric groups seem to have diversified very recently (Late Tertiary), whereas the cladogenic events leading to these groups are much older (Early to Late Cretaceous). Our analysis shows that, although much living species diversity stems from relatively recent cladogenesis, the origins of the family (Early Carboniferous) and generic crown groups (Early Permian to Early Jurassic) are much more ancient events.

Evolution, Molecular↗
PubMed2002

Speciation in the globeflower fly Chiastocheta spp. (Diptera: Anthomyiidae) in relation to host plant species, biogeography, and morphology.

Phylogenetic relationships among the Chiastocheta species (Diptera, Anthomyiidae) were investigated using a 1320-bp mitochondrial DNA fragment including parts of cytochrome oxidase subunits I and II. Larvae of the Chiastocheta genus feed exclusively on Trollius (Ranunculaceae) seeds. Six Chiastocheta species (and two vicariant taxa) coexist on Trollius europaeus in Europe, where they were shown to be the sole pollinator of their host plant. In Asia, several Trollius species are parasitized by Chiastocheta spp., and several other Trollius species are free of Chiastocheta. The plant-insect association is thus obligate in Europe but facultative in Asia. This system therefore provides a unique opportunity to study the evolution of an obligate mutualism between a plant and its seed parasite pollinators and its consequences on insect diversification. Most parsimonious, distance, and maximum likelihood analyses of 16 haplotypes from Europe and 14 from Asia show that European species do not form a monophyletic group. The species relationship indicated by egg morphology is only partly supported by molecular data. Moreover, a strong discrepancy between nucleotide variation and male genitalia morphology variation was found, particularly within and among European species coexisting on a single host plant. Molecular divergence across species ranges from 0 to 4.6%, suggesting a recent origin of the genus and several events of diversification, involving both host shifts and within-host-plant radiation. We discuss alternative evolutionary scenarios that are consistent with molecular data.

Animals↗
PubMed2002

Gene transfer in bacteria: speciation without species?

Although Bacteria and Archaea reproduce by binary fission, exchange of genes among lineages has shaped the diversity of their populations and the diversification of their lineages. Gene exchange can occur by two distinct routes, each differentially impacting the recipient genome. First, homologous recombination mediates the exchange of DNA between closely related individuals (those whose sequences are sufficient similarly to allow efficient integration). As a result, homologous recombination mediates the dispersal of advantageous alleles that may rise to high frequency among genetically related individuals via periodic selection events. Second, lateral gene transfer can introduce novel DNA into a genome from completely unrelated lineages via illegitimate recombination. Gene exchange by this route serves to distribute genes throughout distantly related clades and therefore may confer complex abilities--not otherwise found among closely related lineages--onto the recipient organisms. These two mechanisms of gene exchange play complementary roles in the diversification of microbial populations into independent, ecologically distinct lineages. Although the delineation of microbial "species" then becomes difficult--if not impossible--to achieve, a cogent process of speciation can be predicted.

Bacteria↗
PubMed1994

The appendix functions as a mammalian bursal equivalent in the developing rabbit.

In this paper we present genomic DNA sequence and histological evidence that the appendix is a site of diversification of the rabbit's primary antibody repertoire. By 6 weeks after birth, the B cell follicular regions of the rabbit appendix and the distribution of the resident lymphoid cells bear a strong morphological resemblance to similar regions within two primary lymphoid tissues, the chicken bursa and the sheep ileal Peyer's patch. However, similarities between the rabbit appendix, chicken bursa and sheep ileal Peyer's patch end as these animals reach adulthood. The rabbit appendix undergoes morphological and cellular distribution changes as it matures taking on the appearance of a secondary lymphoid tissue, while the sheep ileal Peyer's patch and the chicken bursa both involute. We determined DNA sequences of PCR amplified rearranged variable region genes from germinal center B cells of 6 week old rabbits isolated from several different appendix dark zones and light zones. There was a trend toward a higher degree of diversification from the germ-line VH gene DNA sequence in dark zones than light zones. It is likely that both gene conversion and somatic hypermutation are responsible for the nucleotide changes we observed. Our findings suggest that the rabbit appendix functions as a mammalian bursal equivalent early in development. As the rabbit matures, the appendix appears to evolve into a secondary lymphoid tissue resembling secondary GALT in appearance and possibly in function.

Amino Acid Sequence↗
PubMed1993

Bioamine receptors: evolutionary and functional variations of a structural leitmotiv.

Bioamines act as neurohormonal messengers through their binding to receptors which belong to the largest membrane protein family known so far: the seven spanning membrane receptors. This class of receptors transmits the effect of agonist binding to intracellular effectors by interacting with an intermediary G-protein. The diversity of receptor subtypes inside the protein family, observed in many animal species, is the result of a long evolutionary process. The tendency to protein diversification depends upon gene duplications and upon the continuous accumulation of mutations. The maintenance of vital functions in organisms, however, strictly requires enough structural conservation to ensure the functionality of the corresponding proteins. Both forces cooperate to ensure the adaptation of organisms to a changing environment. We have reviewed here the main conformational and functional constraints exerted on the structure of the bioamine receptors. They are mainly the transmembrane conformation of the receptors, their ability to bind ligands, to interact with G-proteins and to desensitize. The molecular basis of the biochemical and pharmacological differences used to classify the members of the receptor family have also been examined. Interestingly, this classification is very close to that obtained by the molecular phylogeny methods, used to elucidate the evolutionary relationships between bioamine receptors. However, this latter classification allows to accurately distinguish between different receptor subtypes (paralogous genes) and species homologous (orthologous genes). In addition, the calculation of phylogenetical distances reveals two main periods of diversification: the first one occurred before the separation of arthropods from vertebrates, in the Precambrian, and corresponds to the appearance of the main subtypes of the bioamine receptors. The second one, which occurred about 400 million years ago, might accompany the cephalization of the CNS in vertebrates.

Animals↗
PubMed1994

Andean tapaculos of the genus Scytalopus (Aves, Rhinocryptidae): a study of speciation using DNA sequence data.

Tapaculos of the genus Scytalopus are secretive birds which tunnel like mice through dense understory of humid forest in the Andes, Central America, and south-eastern Brazil. Their agoraphobic habits make Scytalopus species highly sensitive to habitat discontinuities, so they are well suited for analyzing diversification patterns in montane forest biota. This study uses DNA sequence data to test hypotheses about past speciation events. The DNA data support that allopatric and parapatric populations with different songs represent different species. The high degree of phylogenetic resolution obtained by DNA-data permits a better description of geographical patterns of endemism. The data suggests that the commonly observed biogeographic pattern, where related species have long linear distributions along the Andes in different altitudinal zones, arose by divergence in disjunct isolates rather than by parapatric divergence. The approach seems well suited for identifying areas that have a special role for the diversification process. The paper finally discusses how detailed phylogenetic studies can be used to test interpretations of biogeographic patterns of high relevance for pinpointing top priority areas for conservation.

Animals↗