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PubMed2002

Elements of transcription factor network design for T-lineage specification.

The complex spectrum of cell types produced in mammalian hematopoiesis can be understood as the output of highly combinatorial transcription factor action. The generation of multiple diverse combinations of transcription factors from the common starting state of the hematopoietic stem cell must be explained through the cross-regulatory interactions of these transcription factors at several levels. Here, the operation of such a network is addressed through a focus on murine T cell development, where we have recently established regulatory linkages between GATA-3 and PU.1 and multiple other factors essential to this differentiation pathway. The action of both essential/rate-limiting factors and factors with effects that shift qualitatively with dose and time of action can be traced through the regulatory interaction network. Hypothetical models are proposed to indicate the network nodes that are differentially activated in normal T cell lineage progression and in cells diverted to other potential fates.

Animals↗
PubMedDate not supplied

The Wilhelmine W. Key 2002 Invitational Lecture. Phylogeography, haplotype trees, and invasive plant species.

The distribution of genetic variants in plant populations is strongly affected both by current patterns of microevolutionary forces, such as gene flow and selection, and by the phylogenetic history of populations and species. Understanding the interplay of shared history and current evolutionary events is particularly confounding in plants due to the reticulating nature of gene exchange between diverging lineages. Certain gene sequences provide historically ordered neutral molecular variation that can be converted to gene genealogies which trace the evolutionary relationships among haplotypes (alleles). Gene genealogies can be used to understand the evolution of specific DNA sequences and relate sequence variation to plant phenotype. For example, in a study of the RPS2 gene in Arabidopsis thaliana, resistant phenotypes clustered in one portion of the gene tree. The field of phylogeography examines the distribution of allele genealogies in an explicit geographical context and, when coupled with a nested clade analysis, can provide insight into historical processes such as range expansion, gene flow, and genetic drift. A phylogeographical approach offers insight into practical issues as well. Here we show how haplotype trees can address the origins of invasive plants, one of the greatest global threats to biodiversity. A study of the geographical diversity of haplotypes in invasive Phragmites populations in the United States indicates that invasiveness is due to the colonization and spread of distinct genotypes from Europe ( Saltonstall 2002). Likewise, a phylogeographical analysis of Tamarix populations indicates that hybridization events between formerly isolated species of Eurasia have produced the most common genotype of the second-worst invasive plant species in the United States.

Biodiversity↗
PubMed2006

Tracing hematopoietic precursor migration to successive hematopoietic organs during zebrafish development.

Although the ontogeny of hematopoietic stem cells (HSCs) in vertebrates has been studied intensely, a lineage relationship between the HSCs found in the developmentally successive hematopoietic organs remains to be shown. By using an in situ photoactivatable cell tracer in the transparent zebrafish embryo, we demonstrated that definitive blood precursors appeared between the dorsal aorta and axial vein, validating the homology of this tissue with the AGM (aorta-gonad-mesonephros) of amniotes. These cells first migrated through the blood to a previously undescribed caudal hematopoietic tissue (CHT), where they differentiated, expanded, and further migrated to seed the definitive hematopoietic organs, the thymus and kidney. Immigrants on the way to the thymus expressed c-myb and ikaros but not rag1; they were probably no longer HSCs, however, because they lacked scl and runx1 expression, unlike immigrants to the kidney. The CHT thus has a hematopoietic function similar to that of the mammalian fetal liver.

Animals↗
PubMed2003

R5 retrotransposons insert into a family of infrequently transcribed 28S rRNA genes of planaria.

A small (100 bp) region of the 28S rRNA gene has been shown to serve as the target site for the insertion of non-long terminal repeat (non-LTR) retrotransposons in both arthropods and nematodes. Here we characterize a lineage of non-LTR retrotransposons that inserts into this target site in the phylum Platyhelminthes. Dugesiid planaria contain elements, named R5, that insert 8 bp upstream of the target site used by arthropod R2 elements. The complete sequence of this element from Girardia tigrina revealed that it encoded two open reading frames (ORFs). The second ORF contained reverse transcriptase and restriction enzyme-like endonuclease domains similar to those found in R2 and R4, the elements that insert into the 28S genes of nematodes. The closest relative of R5, however, was the element NeSL-1, which inserts into the spliced leader 1 exons of nematodes. The rRNA genes of dugesiid planaria are unusual in that they comprise two types of rDNA units that differ by 8%-10% in nucleotide sequence of the 18S and 28S coding regions. Type II units are transcribed in adult tissues at levels that are less than 1% that of the type I units. R5 elements were only found inserted in the type II units, where presumably they cause less harm to the host. A second unusual aspect of the dugesiid rRNA genes is that the target site for the R5 insertion is duplicated 300 bp upstream of the original insertion site. R5 elements were identified at both sites. These findings expand the distribution of non-LTR elements that are specialized for insertion into the 28S gene and suggest that still more elements exist in other eukaryotic taxa. Attempts to trace the phylogeny of R5 did not offer sufficient resolution to determine whether R2, R4, and R5 represent the same lineage or whether they represent independent specializations for the 28S gene.

Animals↗
PubMed2003

Genomic reduction and evolution of novel genetic membranes and protein-targeting machinery in eukaryote-eukaryote chimaeras (meta-algae).

Chloroplasts originated just once, from cyanobacteria enslaved by a biciliate protozoan to form the plant kingdom (green plants, red and glaucophyte algae), but subsequently, were laterally transferred to other lineages to form eukaryote-eukaryote chimaeras or meta-algae. This process of secondary symbiogenesis (permanent merger of two phylogenetically distinct eukaryote cells) has left remarkable traces of its evolutionary role in the more complex topology of the membranes surrounding all non-plant (meta-algal) chloroplasts. It took place twice, soon after green and red algae diverged over 550 Myr ago to form two independent major branches of the eukaryotic tree (chromalveolates and cabozoa), comprising both meta-algae and numerous secondarily non-photosynthetic lineages. In both cases, enslavement probably began by evolving a novel targeting of endomembrane vesicles to the perialgal vacuole to implant host porter proteins for extracting photosynthate. Chromalveolates arose by such enslavement of a unicellular red alga and evolution of chlorophyll c to form the kingdom Chromista and protozoan infrakingdom Alveolata, which diverged from the ancestral chromalveolate chimaera. Cabozoa arose when the common ancestor of euglenoids and cercozoan chlorarachnean algae enslaved a tetraphyte green alga with chlorophyll a and b. I suggest that in cabozoa the endomembrane vesicles originally budded from the Golgi, whereas in chromalveolates they budded from the endoplasmic reticulum (ER) independently of Golgi-targeted vesicles, presenting a potentially novel target for drugs against alveolate Sporozoa such as malaria parasites and Toxoplasma. These hypothetical ER-derived vesicles mediated fusion of the perialgal vacuole and rough ER (RER) in the ancestral chromist, placing the former red alga within the RER lumen. Subsequently, this chimaera diverged to form cryptomonads, which retained the red algal nucleus as a nucleomorph (NM) with approximately 464 protein-coding genes (30 encoding plastid proteins) and a red or blue phycobiliprotein antenna pigment, and the chromobiotes (heterokonts and haptophytes), which lost phycobilins and evolved the brown carotenoid fucoxanthin that colours brown seaweeds, diatoms and haptophytes. Chromobiotes transferred the 30 genes to the nucleus and lost the NM genome and nuclear-pore complexes, but retained its membrane as the periplastid reticulum (PPR), putatively the phospholipid factory of the periplastid space (former algal cytoplasm), as did the ancestral alveolate independently. The chlorarachnean NM has three minute chromosomes bearing approximately 300 genes riddled with pygmy introns. I propose that the periplastid membrane (PPM, the former algal plasma membrane) of chromalveolates, and possibly chlorarachneans, grows by fusion of vesicles emanating from the NM envelope or PPR. Dinoflagellates and euglenoids independently lost the PPM and PPR (after diverging from Sporozoa and chlorarachneans, respectively) and evolved triple chloroplast envelopes comprising the original plant double envelope and an extra outermost membrane, the EM, derived from the perialgal vacuole. In all metaalgae most chloroplast proteins are coded by nuclear genes and enter the chloroplast by using bipartite targeting sequences--an upstream signal sequence for entering the ER and a downstream chloroplast transit sequence. I present a new theory for the four-fold diversification of the chloroplast OM protein translocon following its insertion into the PPM to facilitate protein translocation across it (of both periplastid and plastid proteins). I discuss evidence from genome sequencing and other sources on the contrasting modes of protein targeting, cellular integration, and evolution of these two major lineages of eukaryote "cells within cells". They also provide powerful evidence for natural selection's effectiveness in eliminating most functionless DNA and therefore of a universally useful non-genic function for nuclear non-coding DNA, i.e. most DNA in the biosphere, and dramatic examples of genomic reduction. I briefly argue that chloroplast replacement in dinoflagellates, which happened at least twice, may have been evolutionarily easier than secondary symbiogenesis because parts of the chromalveolate protein-targeting machinery could have helped enslave the foreign plastids.

Chimera↗
PubMed1997

Multiple recruitment of class-I aldolase to chloroplasts and eubacterial origin of eukaryotic class-II aldolases revealed by cDNAs from Euglena gracilis.

The photosynthetic protist Euglena gracilis is one of few organisms known to possess both class-I and class-II fructose-1,6-bisphosphate aldolases (FBA). We have isolated cDNA clones encoding the precursor of chloroplast class-I FBA and cytosolic class-II FBA from Euglena. Chloroplast class-I FBA is encoded as a single subunit rather than as a polyprotein, its deduced transit peptide of 139 amino acids possesses structural motifs neccessary for precursor import across Euglena's three outer chloroplast membranes. Evolutionary analyses reveal that the class-I FBA of Euglena was recruited to the chloroplast independently from the chloroplast class-I FBA of chlorophytes and may derive from the cytosolic homologue of the secondary chlorophytic endosymbiont. Two distinct subfamilies of class-II FBA genes are shown to exist in eubacteria, which can be traced to an ancient gene duplication which occurred in the common ancestor of contemporary gram-positive and proteobacterial lineages. Subsequent duplications involving eubacterial class-II FBA genes resulted in functional specialization of the encoded products for substrates other than fructose-1,6-bisphosphate. Class-II FBA genes of Euglena and ascomycetes are shown to be of eubacterial origin, having been acquired via endosymbiotic gene transfer, probably from the antecedants of mitochondria. The data provide evidence for the chimaeric nature of eukaryotic genomes.

Amino Acid Sequence↗
PubMed1998

Multilocus phylogeny of cichlid fishes (Pisces: Perciformes): evolutionary comparison of microsatellite and single-copy nuclear loci.

Among vertebrates, cichlid fishes are the paradigmatic example of adaptive radiation and ecological specialization. In turn, molecular genetic studies of cichlids have focused primarily on more recently diverged groups. Here, we present an evolutionary hypothesis of the major lineages of cichlid fishes based on DNA sequence data from two nuclear loci. One marker, Tmo-4C4, is a single-copy locus containing a region of amino acid similarity to the muscle protein TITIN. Flanking sequence from a second, microsatellite, locus Tmo-M27, shows similarity to mammalian RAS guanine nucleotide-releasing factor. We compare and combine data from these loci to evaluate phylogenetic performance. In separate and combined analyses, the sequence data support and clarify previous morphological hypotheses of cichlid major-group relationships. Indian and Malagasy cichlids form a basal, paraphyletic group. Neotropical cichlids are the sister clade to an African assemblage composed of the paraphyletic west and Pan-African lineages and a group of east African rift lake taxa. We use a consensus phylogeny of the Cichlidae to trace evolutionary changes in the microsatellite repeat motif at Tmo-M27. Analysis reveals that the repeat region was nearly lost in the ancestor to cichlids and then amplified extensively in African taxa. Results demonstrate that the two new DNA markers could be widely applied in perciform systematics. Furthermore, the comparative approach can unveil mutational dynamics of simple-sequence repeat loci over long periods of fish evolution. Simple-sequence repeat regions are increasingly being found in introns of important regulatory genes. We address issues involving their function and suggest caution in making assumptions of strict neutrality.

Animals↗
PubMed1999

Tectal fiber connections in a non-teleost actinopterygian fish, the sturgeon Acipenser.

Tectal fiber connections were studied in members of an early branch of the actinopterygian lineage, the sturgeons Acipenser transmontanus and A. schrenkii, by means of biocytin, HRP, biotinylated dextran amine, and DiI tract tracing methods. The aim of this study is to elucidate the visual pathway via the optic tectum to the thalamus as a part of a series of studies on the visual pathways in sturgeons. After biocytin or biotinylated dextran amine injections to the optic tectum terminals are found bilaterally in the medial and lateral portions of both the dorsal thalamus and ventral thalamus. Ipsilateral projections are much more abundant. Tectal recipient areas in the thalamus overlap in part with the retinal recipient areas. After HRP or DiI injections to the dorsal or ventral thalamus, tectal neurons projecting to the thalamus were labeled in the ipsilateral or bilateral stratum periventriculare. Dendritic morphology of tectothalamic neurons suggests that they receive direct retinal input. These results suggest that visual information passes through the tectum to the thalamic areas which also receive direct retinal projections. In this regard, the visual system of Acipenser resembles that of chondrichthyans (sharks). Other fiber connections of the tectum are also described, which have not previously been studied by tracer methods in a sturgeon.

Animals↗
PubMed1993

Development of segment specificity in identified lineages of the grasshopper CNS.

The purpose of this study was to determine the factors underlying differences in population size and composition between segmentally homologous neuronal lineages. The segmental median neuroblasts (MNBs) of grasshoppers are identified stem cells that each produce a midline group of neurons. We traced the embryonic development of the group in two disparate segments, counting MNB progeny and profiles of dying cells in fixed and stained preparations of staged embryos. In the metathoracic segment (T3), about 95 MNB progeny survive embryonic development, whereas in the next posterior segment, the first abdominal (A1), only about 60 survive. In T3, the MNB arises at 29% of embryogenesis and dies at 78%, whereas in A1 the MNB arises at 30% and dies at 73%. In T3, the number of MNB progeny initially increases at a steady rate, 10 cells being added per 5% of embryogenesis. Between 70% and 78% growth tapers off; although the T3 MNB continues to divide, cells die at the same time, specifically removing last-born progeny. By contrast, in A1 the MNB progeny increase in two phases, one from 30% to 45% and the other from 60% to 73%, again at the rate of 10 cells per 5%. Between the two phases, the number of A1 progeny is stable. The A1 MNB continues to divide, but cells die at the same time, specifically removing earlier-born progeny. The episodes of cell death in A1 and T3 coincide with embryonic molts, and thus may be hormonally triggered. Cell death is greater in A1 than T3, accounting for most of the difference in population size. The difference in MNB longevity makes a lesser contribution. The present data, together with corollary anatomical data (Thompson and Siegler, 1991), support the hypothesis that progeny fated to become certain neuronal types are selectively removed from the two MNB lineages: intersegmental interneurons from T3 and efferent neurons and local interneurons from A1.

Abdomen↗
PubMed1991

Glial cell lineages in the neural crest.

We have been studying how and when the different peripheral glial cell lineages individualize during avian embryonic development. Three different and complementary experimental approaches were used for this purpose: 1) the quail/chick chimera system allowed the tracing in vivo of the origin of the various types of peripheral glial cells (Schwann cells of nerves, satellite glial cells of sensory and autonomic ganglia, and enteric glial cells), and the analysis of the non-neuronal cell population of ganglia; 2) characterisation of early cell-type specific markers that discriminate between the different glial cell subpopulations; and 3) analysis of the progeny of neural crest cells in clonal cultures. As a result of these approaches, two novel glial-specific markers, expressed earlier than any previously described myelin components, have been identified and partly characterised. The divergence of glial and neuronal cell lineages is a process that is not completely terminated during the phase of neural crest migration. Whereas some cells are apparently already totally committed to a glial fate at this stage, others retain dual neuronal/glial potentialities.

Animals↗
PubMed1987

Cell lineage analysis in ascidian embryos by intracellular injection of a tracer enzyme. III. Up to the tissue restricted stage.

Cell lineages during embryogenesis of the ascidian Halocynthia roretzi were analyzed up until the stage where each blastomere was fated to be only a single tissue type (i.e., the tissue restricted stage) by intracellular injection of horseradish peroxidase using the iontophoretic injection method. Initially, the developmental fates of all blastomeres of the 64-cell stage embryo were examined, and thereafter, only the fates of daughter blastomeres of those blastomeres that were not tissue restricted at the 64-cell stage were traced. The developmental fates of blastomeres were highly invariant except for two candidates for "equivalence groups" (J. Kimble, J. Sulston, and J. White (1979). In "Cell Lineage, Stem Cells and Cell Determination," pp. 59-68. Elsevier, Amsterdam/New York), in which cellular interaction is suggested to be involved in the specification of the fates. The right and left a8.25 cells gave rise to the otolith and ocellus, and the right and left b8.17 cells gave rise to the spinal cord and endodermal strand in a complementary manner. No fixed relationship existed between the position of the blastomere and its derivative. Most restrictions of cell fates occurred early in cleavage. The numbers of blastomeres which generated a single type of tissue were 44 at the 64-cell stage and 94 at the 110-cell stage. Eight pairs of blastomeres had not yet become tissue restricted by the 110-cell stage. Almost complete lineages of epidermis, nervous system, muscle, mesenchyme, notochord, and endodermal tissues were described, and a fate map was constructed for the blastula. For certain tissues, the primordial cells occupied two different regions. Supplementary investigations of the lineage of muscle cells were also performed on embryos of another species, Ciona intestinalis.

Animals↗
PubMed1985

Effects of cytoplasmic inheritance on production traits of dairy cattle.

Pedigrees of 4461 cows were traced to the original female in a maternal line. Cytoplasmic origin was defined as the first female in the maternal lineage. There were 102 cytoplasmic lines. Most cows were at least 10 generations removed from the origin. After adjustment for sire, herd, calving year, calving month, and age, cytoplasmic effects accounted for 2.0, 1.8, 1.8, and 3.5% of total variation of milk yield, milk fat yield, 3.7% fat-corrected milk yield, and milk fat percentage in first lactation. Cytoplasmic effects were also in models that included adjustments for sires, maternal grand-sires, and dam's production. Correlations among independent subsets agreed with expectations. Cytoplasmic origin was a significant source of variation of production traits of dairy cattle.

Animals↗
PubMed2004

Cladogenesis, coalescence and the evolution of the three domains of life.

In this article, we explore the large-scale structure of the tree of life by using a simple model with a constant number of species and rates of speciation that equal the rates of extinction. In addition, we discuss the consequences of horizontal gene transfer for the concept of a most recent common ancestor of all living organisms (cenancestor). A simple null hypothesis based on coalescence theory explains some features of the observed topologies of the tree of life. Simulations of genes and organismal lineages suggest that there was no single common ancestor that contained all the genes ancestral to those shared among the three domains of life. Each contemporary molecule has its own history that traces back to an individual molecular cenancestor. However, these molecular ancestors were likely to be present in different organisms and at different times.

Alleles↗
PubMed1998

Trans-splicing group II introns in plant mitochondria: the complete set of cis-arranged homologs in ferns, fern allies, and a hornwort.

The fragmentation of group II introns without concomitant loss of splicing competence is illustrated by extraordinary gene arrangements in plant mitochondrial genomes. The mitochondrial genes nad1, nad2, and nad5, all encoding subunits of the NADH dehydrogenase, require trans-splicing for functional assembly of their mRNAs in flowering plants. Tracing the origins of trans-splicing group II introns shows that they have evolved from formerly cis-arranged homologs whose descendants can still be identified in lineages of early branching land plants. In this contribution we present the full set of ancestor introns for all five conserved mitochondrial trans-splicing positions. These introns are strikingly small in the quillwort Isoetes lacustris, the continuous nad2 gene intron in this species representing the smallest (389 nt) land plant group II intron yet identified. cDNA analysis shows correct splicing of the introns in vivo and also identifies frequent RNA editing events in the flanking nad gene exons. Other representatives of the ancestral cis-arranged introns are identified in the fern Osmunda regalis, the horsetail Equisetum telmateia, and the hornwort Anthoceros crispulus. Only the now identified intron in Osmunda carries significant traces of a former maturase reading frame. The identification of a continuous homolog in Anthoceros demonstrates that intron invasion into the affected genes in some cases predated the split of vascular and nonvascular plants more than 400 million years ago. As an alternative to disruption after size increase, the respective introns can get secondarily lost in certain lineages.

Base Sequence↗
PubMed1992

Differential expression of the msp130 gene among skeletal lineage cells in the sea urchin embryo: a three dimensional in situ hybridization analysis.

In order to examine the ontogeny of tissue-specific expression of the msp130 gene during early embryogenesis of the sea urchin, we have developed a whole-mount, non-radioactive in situ hybridization protocol suitable for these embryos. This protocol is adapted from the existing technology of immunohistochemical localization of digoxygenin-labelled hybridization probes in tissue sections. Transcript distribution patterns in the whole embryo are seen in three dimensions, and at much higher resolution and sensitivity than can be achieved using radioactive probes and sectioned material. We have traced the ontogeny of expression of the skeleton-specific gene, msp130, during the development of Strongylocentrotus purpuratus. Transcripts are first detected at the blastula stage, in micromere-lineage cells just prior to ingression. Appearance of msp130 transcripts remains strictly limited to this lineage through the pluteus stage. Estimated from the relative intensity of staining of the PMCs of an embryo, the relative abundance of msp130 transcripts is uniform among the 32 cells of this lineage in secondary mesenchyme blastulae and in gastrulae, indicating that expression is homogeneous among these cells up to the early prism stage. However, the relative intensity of stain, and therefore abundance of transcripts, changes dramatically and in a consistent pattern among the PMCs of an embryo during prism and pluteus stages, suggesting that these cells switch from an autonomous mode of regulation of the msp130 gene, to an inductive mode. In the pluteus larva, the highest levels of expression occur in those cells associated with the rapidly growing tips of the spicular skeleton.

Animals↗
PubMed1999

Phylogenetic evidence for Ty1-copia-like endogenous retroviruses in plant genomes.

SIRE-1 is a multi-copy, Ty1-copia-like retroelement family found in the genome of Glycine max. A sequenced SIRE-1 genomic copy has an uninterrupted ORF that can be translated into a gag-pol polyprotein, followed by an unprecedented second ORF whose conceptual translation yielded a theoretical protein predicted to possess many of the same secondary structural elements found in mammalian retroviral envelope proteins. Similar, but clearly pseudogenic, envelope-like sequences were recovered from conceptual translations of 10 Arabidopsis GenBank accessions. All were associated with identifiable Ty1-copia-like retroelements. Phylogenetic analysis of the adjacent ribonuclease H regions from these sequences and three similarly endowed elements, two from maize and one from tomato, indicate that the 14 elements constitute a monophyletic group distinct from several closely related plant Ty1-copia-like elements in which pol is immediately followed by a downstream LTR. The conservation of identifiable env-like gene features suggests that these plant elements are endogenous retroviruses whose ancestors were acquired from animal vectors. The finding that the env and env-less retroelements identified in this study form distinct lineages does not support the hypothesis that horizontal transmission of retrotransposons is sponsored by ancestral infectious retroviruses that subsequently lost all traces of env genes.

Endogenous Retroviruses↗
PubMed2005

Lineage restriction maintains a stable organizer cell population at the zebrafish midbrain-hindbrain boundary.

The vertebrate hindbrain is subdivided into segments, termed neuromeres, that are units of gene expression, cell differentiation and behavior. A key property of such segments is that cells show a restricted ability to mix across segment borders -- termed lineage restriction. In order to address segmentation in the midbrain-hindbrain boundary (mhb) region, we have analyzed single cell behavior in the living embryo by acquiring time-lapse movies of the developing mhb region in a transgenic zebrafish line. We traced the movement of hundreds of nuclei, and by matching their position with the expression of a midbrain marker, we demonstrate that midbrain and hindbrain cells arise from two distinct cell populations. Single cell labeling and analysis of the distribution of their progeny shows that lineage restriction is probably established during late gastrulation stages. Our findings suggest that segmentation as an organizing principle in early brain development can be extended to the mhb region. We argue that lineage restriction serves to constrain the position of the mhb organizer cell population.

Animals↗