A mathematical model of the mechanism of vertebrate somitic segmentation.

A mathematical model for the mechanism of periodic pattern formation in the process of somitogenesis is proposed. It is assumed that the metameric arrangement first appears before somite formation at the stage of transition of mesodermal cells into a polarized state. The model is based on the assumption that besides the mechanism of contact cell polarization there exists a mechanism of polarization suppression due to excretion of some chemical substance by polarized cells. Periodicity appears as a result of interaction of a kinematic wave of somitogenic cell determination with the cell cycles of mesodermal cells.     

Pair-rule gene expression in the somitic stage chick embryo: association with somite segmentation and border formation

Abstract. In vertebrates, metameric organization is highlighted by the formation of somites from mesenchymal cells of the segmental plate which then differentiate into dermamyotomal and sclerotomal tissues. The resegmentation of the sclerotome into rostral and caudal halves follows, coincident with the production of specific extracellular matrix molecules at the abutment of these two cell types. Ultimately, cells from the caudal sclerotome migrate ventrally and contribute to the chondrogenic prevertebrae. The objective of this work is to investigate the molecular steps regulating these events. Our study is focused on the paired-box containing genes, which have been implicated in delineating boundaries early in development. A chick embryo system, which is readily accessible to manipulation and observation during early development, is used in this study. We have identified the existence of the paired-box motif in the chicken genome by polymerase chain reaction and hybridization with the mouse Pax 1 paired-box sequence. Expression of paired-box genes occurs early in development as shown by Northern analysis, and is localized by in situ hybridization to the edge of each somite, a patch at the central core of each somite, and the periphery of the neural tube. This specific spatial pattern of expression is consistent with the hypothesis that the pair-rule genes function as effecters of border formation in the early embryo. Moreover, the patch of positive cells at the center of a resegmenting somite appear to migrate ventrally, and may contribute to structures of the prevertebrae. These findings are relevant to our understanding of the mechanism of somite resegmentation and implicate the involvement of pair-rule genes in the process.     

Pair-rule gene expression in the somitic stage chick embryo: association with somite segmentation and border formation

Abstract. In vertebrates, metameric organization is highlighted by the formation of somites from mesenchymal cells of the segmental plate which then differentiate into dermamyotomal and sclerotomal tissues. The resegmentation of the sclerotome into rostral and caudal halves follows, coincident with the production of specific extracellular matrix molecules at the abutment of these two cell types. Ultimately, cells from the caudal sclerotome migrate ventrally and contribute to the chondrogenic prevertebrae. The objective of this work is to investigate the molecular steps regulating these events. Our study is focused on the paired-box containing genes, which have been implicated in delineating boundaries early in development. A chick embryo system, which is readily accessible to manipulation and observation during early development, is used in this study. We have identified the existence of the paired-box motif in the chicken genome by polymerase chain reaction and hybridization with the mouse Pax 1 paired-box sequence. Expression of paired-box genes occurs early in development as shown by Northern analysis, and is localized by in situ hybridization to the edge of each somite, a patch at the central core of each somite, and the periphery of the neural tube. This specific spatial pattern of expression is consistent with the hypothesis that the pair-rule genes function as effecters of border formation in the early embryo. Moreover, the patch of positive cells at the center of a resegmenting somite appear to migrate ventrally, and may contribute to structures of the prevertebrae. These findings are relevant to our understanding of the mechanism of somite resegmentation and implicate the involvement of pair-rule genes in the process.     

Gene duplication,genome duplication,and the functional diversification of vertebrate globins

The functional diversification of the vertebrate globin gene superfamily provides an especially vivid illustration of the role of gene duplication and whole-genome duplication in promoting evolutionary innovation. For example, key globin proteins that evolved specialized functions in various aspects of oxidative metabolism and oxygen signaling pathways (hemoglobin [Hb], myoglobin [Mb], and cytoglobin [Cygb]) trace their origins to two whole-genome duplication events in the stem lineage of vertebrates. The retention of the proto-Hb and Mb genes in the ancestor of jawed vertebrates permitted a physiological division of labor between the oxygen-carrier function of Hb and the oxygen-storage function of Mb. In the Hb gene lineage, a subsequent tandem gene duplication gave rise to the proto α- and β-globin genes, which permitted the formation of multimeric Hbs composed of unlike subunits (α₂β₂). The evolution of this heteromeric quaternary structure was central to the emergence of Hb as a specialized oxygen-transport protein because it provided a mechanism for cooperative oxygen-binding and allosteric regulatory control. Subsequent rounds of duplication and divergence have produced diverse repertoires of α- and β-like globin genes that are ontogenetically regulated such that functionally distinct Hb isoforms are expressed during different stages of prenatal development and postnatal life. In the ancestor of jawless fishes, the proto Mb and Hb genes appear to have been secondarily lost, and the Cygb homolog evolved a specialized respiratory function in blood-oxygen transport. Phylogenetic and comparative genomic analyses of the vertebrate globin gene superfamily have revealed numerous instances in which paralogous globins have convergently evolved similar expression patterns and/or similar functional specializations in different organismal lineages.     

A multi-cell, multi-scale model of vertebrate segmentation and somite formation

Somitogenesis, the formation of the body's primary segmental structure common to all vertebrate development, requires coordination between biological mechanisms at several scales. Explaining how these mechanisms interact across scales and how events are coordinated in space and time is necessary for a complete understanding of somitogenesis and its evolutionary flexibility. So far, mechanisms of somitogenesis have been studied independently. To test the consistency, integrability and combined explanatory power of current prevailing hypotheses, we built an integrated clock-and-wavefront model including submodels of the intracellular segmentation clock, intercellular segmentation-clock coupling via Delta/Notch signaling, an FGF8 determination front, delayed differentiation, clock-wavefront readout, and differential-cell-cell-adhesion-driven cell sorting. We identify inconsistencies between existing submodels and gaps in the current understanding of somitogenesis mechanisms, and propose novel submodels and extensions of existing submodels where necessary. For reasonable initial conditions, 2D simulations of our model robustly generate spatially and temporally regular somites, realistic dynamic morphologies and spontaneous emergence of anterior-traveling stripes of Lfng. We show that these traveling stripes are pseudo-waves rather than true propagating waves. Our model is flexible enough to generate interspecies-like variation in somite size in response to changes in the PSM growth rate and segmentation-clock period, and in the number and width of Lfng stripes in response to changes in the PSM growth rate, segmentation-clock period and PSM length.     

Malformed, a mutation of Drosophila melanogaster producing mirror-image duplication of a portion of the orbit.

Clonal analysis using mitotic recombination in Drosophila melanogaster shows that the region of the orbit duplicated within the compound eye of the mutant Malformed often originates from a cell population different from that giving rise to the normal orbital region, although, occasionally, both regions may arise from the same progenitor cell. We prefer an interpretation of the action of this mutation based on the misreading of the positional information at the time late in development when imaginal cells are specified to differentiate into particular cuticular structures, rather than an interpretation based on early localized cell death followed by mirror-image duplication.     

Genetics of rye phosphatases: evidence of a duplication

Summary Genetic analyses were conducted on alkaline phosphatases of the endosperm of dry kernels and leaf acid phosphatases in four open pollinated and one inbred line of cultivated rye (Secale cereale L.). A total of seven alkaline phosphatase isozymes were observed occurring at variable frequencies in the different cultivars analyzed. We propose that at least five loci control the alkaline phosphatases of rye endosperm — Alph-1, Alph-2, Alph-3, Alph-4 and Alph-5 — all of which have monomeric behaviour. The leaf acid phosphatases are controlled by one locus and have a dimeric quaternary structure. All loci coding for alkaline phosphatase isozymes showed one active, dominant allele and one null, recessive allele, except for the locus Alph-3 which showed two active, dominant alleles and one null, recessive one. The linkage analyses suggest the existence of two linkage groups for alkaline phosphatases: one of them would contain Alph-2, Alph-4, Alph-5 and the locus/loci coding isozymes 6 and 7. This linkage group is located in the 7RS chromosome arm. The other group would include Alph-1 and Alph-3 loci, being located in the 1RL chromosome arm. Leaf acid phosphatases have been previously located in the 7RL chromosome arm. Our data also support an independent relationship between loci controlling the endosperm alkaline phosphatases and leaf acid phosphatases.     

Characterization of a new BAC library for rainbow trout: evidence for multi-locus duplication

A 10X rainbow trout bacterial artificial chromosome (BAC) library was constructed to aid in the physical and genetic mapping efforts of the rainbow trout genome. The library was derived from the Swanson clonal line (YY male) and consists of 184,704 clones with an average insert size of 137,500 bp (PFGE) or 118,700 bp (DNA fingerprinting). The clones were gridded onto 10 large nylon membranes to produce high-density arrays for screening the library by hybridization. The library was probed with 11 cDNAs from the NCCCWA EST project chosen because of interest in their homology to known gene sequences, seven known genes, and a Y-specific sex marker. Putative positive clones identified by hybridization were re-arrayed and gridded for secondary confirmation. FPC analysis of HindIII and EcoRV DNA fingerprinting was used to estimate the level of redundancy in the library, to construct BAC contigs and to detect duplicated loci in the semi-duplicated rainbow trout genome. A good correlation (R2 = 0.7) was found between the number of hits per probe and the number of contigs that were assembled from the positive BACs. The average number of BACs per contig was 9.6, which is in good agreement with 10X genome coverage of the library. Two-thirds of the loci screened were predicted to be duplicated as the positive BACs for those genes were assembled into two or three different contigs, which suggests that most of the rainbow trout genome is duplicated.     

The pericentromeric region of human chromosome 11: evidence for a chromosome-specific duplication

We have identified a chromosome duplication in the pericentromeric region of human chromosome 11 located in 11p11 and 11q14. A detailed physical map of each duplicated region was generated to describe the nature of the duplication, the involvement at the centromere and to resolve the correct maps. All clones were evaluated to ensure they were representative of their genetic origin. The order of clones, based on their marker content, as well as the distance covered was determined by SEGMAP. Each duplication encompasses more than 1 Mb of DNA and appears to be chromosome 11 specific. Ten STS markers were mapped within each duplication. Comparative sequence analysis along the duplication identified 35 nucleotide changes in 2,036 bp between the two copies, suggesting the duplication occurred over 14 million years ago. A suggested organization of the pericentromeric region, including the duplications and alpha-related repetitive sequences, is presented.     

Drosophila asterless and vertebrate Cep152 Are orthologs essential for centriole duplication

The centriole is the core structure of centrosome and cilium. Failure to restrict centriole duplication to once per cell cycle has serious consequences and is commonly observed in cancer. Despite its medical importance, the mechanism of centriole formation is poorly understood. Asl was previously reported to be a centrosomal protein essential for centrosome function. Here we identify mecD, a severe loss-of-function allele of the asl gene, and demonstrate that it is required for centriole and cilia formation. Similarly, Cep152, the Asl ortholog in vertebrates, is essential for cilia formation and its function can be partially rescued by the Drosophila Asl. The study of Asl localization suggests that it is closely associated with the centriole wall, but is not part of the centriole structure. By analyzing the biogenesis of centrosomes in cells depleted of Asl, we found that, while pericentriolar material (PCM) function is mildly affected, Asl is essential for daughter centriole formation. The clear absence of several centriolar markers in mecD mutants suggests that Asl is critical early in centriole duplication.     

Experimental evidence for kin-biased helping in a cooperatively breeding vertebrate

The widespread belief that kin selection is necessary for the evolution of cooperative breeding in vertebrates has recently been questioned. These doubts have primarily arisen because of the paucity of unequivocal evidence for kin preferences in cooperative behaviour. Using the cooperative breeding system of long-tailed tits (Aegithalos caudatus) in which kin and non-kin breed within each social unit and helpers are failed breeders, we investigated whether helpers preferentially direct their care towards kin following breeding failure. First, using observational data, we show that not all failed breeders actually become helpers, but that those that do help usually do so at the nest of a close relative. Second, we confirm the importance of kinship for helping in this species by conducting a choice experiment. We show that potential helpers do not become helpers in the absence of close kin and, when given a choice between helping equidistant broods belonging to kin and non-kin within the same social unit, virtually all helped at the nest of kin. This study provides strong evidence that kinship plays an essential role in the maintenance of cooperative breeding in this species.     

Gene duplication and the uniqueness of vertebrate genomes circa 1970-1999

In this article I review research undertaken over the past 30 years into the role that gene duplication played in shaping vertebrate genomes. I discuss early karyotype studies that pointed to a relative stability of mammalian and avian genomes, the discovery and possible evolutionary significance of enormous genomes in urodele amphibians and lungfish, genome compaction in certain specialised bony fish, evidence for two rounds of total genome doubling in early vertebrate evolution and the fate of duplicated genes in polyploid fish.     

Timed interactions between the Hox expressing non-organiser mesoderm and the Spemann organiser generate positional information during vertebrate gastrulation

We report a novel developmental mechanism. Anterior-posterior positional information for the vertebrate trunk is generated by sequential interactions between a timer in the early non-organiser mesoderm and the organiser. The timer is characterised by temporally colinear activation of a series of Hox genes in the early ventral and lateral mesoderm (i.e., the non-organiser mesoderm) of the Xenopus gastrula. This early Hox gene expression is transient, unless it is stabilised by signals from the Spemann organiser. The non-organiser mesoderm and the Spemann organiser undergo timed interactions during gastrulation which lead to the formation of an anterior-posterior axis and stable Hox gene expression. When separated from each other, neither non-organiser mesoderm nor the Spemann organiser is able to induce anterior-posterior pattern formation of the trunk. We present a model describing that convergence and extension continually bring new cells from the non-organiser mesoderm within the range of organiser signals and thereby create patterned axial structures. In doing so, the age of the non-organiser mesoderm, but not the age of the organiser, defines positional values along the anterior-posterior axis. We postulate that the temporal information from the non-organiser mesoderm is linked to mesodermal Hox expression.     

Homologous catalytic domains in a rumen fungal xylanase: evidence for gene duplication and prokaryotic origin

A cDNA (xynA), encoding xylanase A (XYLA), was isolated from a cDNA library, derived from mRNA extracted from the rumen anaerobic fungus, Neocallimastix patriciarum. Recombinant XYLA, purified from Escherichia coli harbouring xynA, had a M(r) of 53,000 and hydrolysed oat-spelt xylan to xylobiose and xylose. The enzyme did not hydrolyse any cellulosic substrates. The nucleotide sequence of xynA revealed a single open reading frame of 1821 bp coding for a protein of M(r) 66,192. The predicted primary structure of XYLA comprised an N-terminal signal peptide followed by a 225-amino-acid repeated sequence, which was separated from a tandem 40-residue C-terminal repeat by a threonine/proline linker sequence. The large N-terminal reiterated regions consisted of distinct catalytic domains which displayed similar substrate specificities to the full-length enzyme. The reiterated structure of XYLA suggests that the enzyme was derived from an ancestral gene which underwent two discrete duplications. Sequence comparison analysis revealed significant homology between XYLA and bacterial xylanases belonging to cellulase/xylanase family G. One of these homologous enzymes is derived from the rumen bacterium Ruminococcus flavefaciens. The homology observed between XYLA and a rumen prokaryote xylanase could be a consequence of the horizontal transfer of genes between rumen prokaryotes and lower eukaryotes, either when the organisms were resident in the rumen, or prior to their colonization of the ruminant. It should also be noted that Neocallimastix XYLA is the first example of a xylanase which consists of reiterated sequences. It remains to be established whether this is a common phenomenon in other rumen fungal plant cell wall hydrolases.     

Analysis of the chicken TBP-like protein(tlp) gene: evidence for a striking conservation of vertebrate TLPs and for a close relationship between vertebrate tbp and tlp genes.

TLP (TBP-like protein), which is a new protein dis-covered by us, has a structure similar to that of the C-terminal conserved domain (CCD) of TBP, although its function has not yet been elucidated. We isolated cDNA and genomic DNA that encode chicken TLP (cTLP) and determined their structures. The predicted amino acid sequence of cTLP was 98 and 91% identical to that of its mammalian and Xenopus counterparts, respectively, and its translation product was ubiquitously observed in chicken tissues. FISH detection showed that chicken tlp and tbp genes were mapped at 3q2.6-2.8 and 3q2.4-2.6 of the same chromosome, respectively. Genome analysis revealed that the chicken tlp gene was spliced with five introns. Interestingly, the vertebrate tbp genes were also found to be split by five introns when we focused on the CCDs, and their splicing points were similar to those of tlp. On the contrary, another TBP-resembling gene of Drosophila, trf1, is split by only one intron, as is the Drosophila 's tbp gene. These results support our earlier assumption that vertebrate TLPs did not directly descend from Drosophila TRF1. On the basis of these results together with phylogenetical exam-ination, we speculate that tlp diverged from an ancestral tbp gene through a process of gene duplication and point mutations.     

Structure of the monomeric isocitrate dehydrogenase: evidence of a protein monomerization by a domain duplication

NADP(+)-dependent isocitrate dehydrogenase is a member of the beta-decarboxylating dehydrogenase family and catalyzes the oxidative decarboxylation reaction from 2R,3S-isocitrate to yield 2-oxoglutarate and CO(2) in the Krebs cycle. Although most prokaryotic NADP(+)-dependent isocitrate dehydrogenases (IDHs) are homodimeric enzymes, the monomeric IDH with a molecular weight of 80-100 kDa has been found in a few species of bacteria. The 1.95 A crystal structure of the monomeric IDH revealed that it consists of two distinct domains, and its folding topology is related to the dimeric IDH. The structure of the large domain repeats a motif observed in the dimeric IDH. Such a fusional structure by domain duplication enables a single polypeptide chain to form a structure at the catalytic site that is homologous to the dimeric IDH, the catalytic site of which is located at the interface of two identical subunits.     

Dorsoventral axis determination in the somite: a re-examination

We have repeated classic dorsoventral somite rotation experiments (Aoyama and Asamoto, 1988, Development 104, 15-28) and included dorsal and ventral gene expression markers for the somitogenic tissue types, myotome and sclerotome, respectively. While the histological results are consistent with those previously published, gene expression analysis indicates that cells previously thought to be 'sclerotome' no longer express Pax1 mRNA, a sclerotome marker. These results, together with recent quail-chick transplantation experiments indicating that even very late sclerotome tissue fragments are multipotential (Dockter and Ordahl, 1998, Development 125, 2113-2124), lead to the conclusion that sclerotome tissue remains phenotypically and morphogenetically plastic during early embryonic somitogenesis. Myotome precursor cells, by contrast, appear to be determined within hours after somite epithelization; a finding consistent with recent reports (Williams and Ordahl, 1997, Development 124, 4983-4997). Therefore, while these findings support a central conclusion of Aoyama and Asamoto, that axis determination begins to occur within hours after somite epithelialization, the identity of the responding tissues, myotome versus sclerotome, differs. A simple model proposed to reconcile these observations supports the general hypothesis that determinative aspects of early paraxial mesoderm growth and morphogenesis occur in early and late phases that are governed principally by the myotome and sclerotome, respectively.