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PubMed1999

Ribosomal internal transcribed spacer 2 (ITS2) exhibits a common core of secondary structure in vertebrates and yeast.

Molecular mechanisms of ITS2 processing, a eukaryotic insertion between the 5.8S and LSU rRNA, remain largely elusive even in yeast. To delineate ITS2 structural and functional features which could be common to eukaryotes, we first produced phylo-genetically supported folding models in the vertebrate lineage, then tested them in deeper branchings and, more particularly, among yeasts. ITS2 comparisons between four Teleostei, a Chondrichthyes specimen and two jawless organisms have revealed a common folding architecture in four to five domains of secondary structure emerging from a preserved structural core. This folding, largely reminiscent of ITS2 architecture in mammals, is also preserved in amphibia and in chicken, despite dramatic sequence variations. Preferential conservation is located around a central loop and at the apex of a long stem in the ITS2 3'-half. Interestingly, these two independent structural features contain, respectively, the 3'-ends of the two transient rRNA precursors 8S and 12S RNA identified in mammals, suggesting a preservation of these intermediates of processing over the entire vertebrate group. Surprising similarities between the vertebrate ITS2 folding shape and that of invertebrates as well as protista have made intriguing the significant differences from the yeast model. A detailed comparative analysis including four relatively close species and Schizosaccharomyces pombe, a deep yeast branching, has revealed an alternative phylogenetically supported four-domain folding presenting strong similarities to the vertebrate model. Remarkably, the two best conserved regions of vertebrates have unambiguously preserved counterparts which are also sites for internal processing in yeast. Therefore, molecular mechanisms involved in ITS2 excision in vertebrates and yeast might be more closely related than currently believed and might require a very similar trans -acting machinery.

Animals↗
PubMed1980

Variable patterns of total DNA and rDNA methylation in animals.

Restriction endonucleases were used to determine the degree of methylation at the sequences CCGG and GCGC in a wide range of animal DNAs. Both total DNA methylation and ribosomal DNA methylation were studied. Whole DNA methylation was indetectable in arthropods, fractional in other invertebrate phyla, and high in the vertebrates. Ribosomal DNA was predominantly unmethylated in all animals except fish and amphibia, where it was heavily methylated. We discuss the evolutionary and functional implications of these results, and suggest that the large differences between genome types are the result of evolutionary changes in the relative size of heavily methylated and unmethylated compartments.

Animals↗
PubMed1991

The genetic control and germ cell kinetics of the female and male germ line in mammals including man.

The female germ line (germ cell lineage, Keimbahn) is provided with only one proliferation wave, the oogenic, whereas male gametogenesis involves two successive waves: prespermatogenic, which corresponds to the female proliferation wave, and spermatogenesis, which is responsible for the immense number of male gametes produced in mature testes. Both male proliferation systems are linked by the transitional or T prospermatogonia. Using the reverse percentage of labelled metaphases method, it has been shown that the first differences between female and male germ cells can be identified by the end of the first wave, when oogonia and multiplying or M prospermatogonia are proliferating. This prenatal first wave of proliferation of male germ cells was also demonstrated in man and ceases around the 22nd week of pregnancy. Spermatogenesis involves a stock of stem cells (stem spermatogonia), a flexibly reacting pool of undifferentiated spermatogonia and several generations of differentiating spermatogonia, which proliferate almost exponentially. Furthermore, it consists of spermatocytes and haploid spermatids transforming into spermatozoa. The oocytes pass through the preleptotene stage, synthesizing DNA, and thereafter traverse the meiotic prophase up to the diplotene stage. In mammals they act as 'pre-embryos' in a similar but to a lesser degree than oocytes of amphibia and insects. The maternal chromosomes are largely responsible for the development of the embryo, the paternal genome for the development of the extra-embryonic tissue. The synthesis of transgenic animals is a powerful weapon in the armoury of geneticists, as has recently been demonstrated: a 14 kb genomic DNA fragment (Sry) is sufficient to induce testis differentiation and subsequent male development when introduced into chromosomally female mouse embryos.

Animals↗
PubMed2001

The DIRS1 group of retrotransposons.

Only three retrotransposons of the DIRS1 group have previously been described: DIRS1 from the slime mold Dictyostelium discoideum, PAT from the nematode Panagrellus redivivus, and Prt1 from the zygomycetous fungus Phycomyces blakesleeanus. Analyses of the reverse transcriptase sequences encoded by these elements suggest that they are related to the long terminal repeat (LTR) retroelements, such as the Ty3/gypsy retrotransposons and the vertebrate retroviruses. The DIRS1-group elements, however, have several unusual structural features which distinguish them from typical LTR elements: (1) they lack the capacity to encode DDE-type integrases or aspartic proteases; (2) they have open reading frames (ORFs) of unknown function; (3) they integrate without creating duplications of their target sites; and (4) although they are bordered by terminal repeats, these sequences differ from typical LTRs in that they are either inverted repeats or "split" direct repeats. Because of the small number of DIRS1-like elements described, and the unusual structures of these elements, little is known about their evolution, distribution, and replication mechanisms. Here, we report the identification of several new DIRS1-like retrotransposons, including elements from nematodes, sea urchins, fish, and amphibia. We also present evidence for the existence of DIRS1-like sequences in the human genome. In addition, we show that the lack of DDE-type integrase genes from elements of the DIRS1 group is explained by the finding that the previously uncharacterized ORFs of these elements encode proteins related to the site-specific recombinase of bacteriophage lambda. The presence of lambda-recombinase-like genes in DIRS1 elements also accounts for the lack of target-site duplications for these elements and may be related to the unusual structures of their terminal repeats.

Amino Acid Sequence↗
PubMed1995

Phylogenetic relationships of amphibian families inferred from DNA sequences of mitochondrial 12S and 16S ribosomal RNA genes.

Nucleotide sequence comparisons were used to investigate ordinal and familial relationships within the class Amphibia. Approximately 850 base pairs of the mitochondrial 16S ribosomal RNA (rRNA) gene from representatives of 28 of the 40 families of extant amphibians were sequenced. Phylogenetic analyses of these data together with published data of the 12S rRNA gene for the same families and both genes for three more taxa (approximately 1,300 base pairs total for 35 taxa) support the monophyly of each of the three amphibian orders: Anura (confidence value with the interior-branch test: P(c) = 99%), Caudata (P(c) = 100%), and Gymnophiona (P(c) = 99%). An analysis using the four-cluster method cannot discriminate significantly between all three possible unrooted trees involving the three orders of amphibians and an outgroup. Within the Anura, there is support for the monophyly of the two suborders: Neobatrachia (P(c) = 100%) and Archaeobatrachia (P(c) = 97%); the latter was believed to be paraphyletic on the basis of morphology. Within the Archaeobatrachia, the following pairs of taxa cluster: Pelobatidae + Pelodytidae (P(c) = 99%), Pipidae + Rhinophrynidae (P(c) = 99%), Ascaphus + Leiopelmatidae (P(c) = 89%), and Bombina + Discoglossidae (P(c) = 99%). The latter six taxa cluster (P(c) = 94%) such that Pelobatidae + Pelodytidae forms a basal lineage within the Archaeobatrachia. Three major lineages are distinguished within the Neobatrachia: the superfamily Bufonoidea sensu Duellman (P(c) = 86%), the superfamily Ranoidea sensu Lynch (P(c) = 99%), and the Sooglossidae. Basal within the Bufonoidea, Myobatrachidae + Heleophrynidae cluster at P(c) = 96%. The enigmatic Dendrobatidae clusters with the bufonoid families (P(c) = 92%) and is excluded from the ranoid families (P(c) = 99%). (ABSTRACT TRUNCATED AT 250 WORDS)

Amphibians↗
PubMed2002

Estrogen regulates development of the somatic cell phenotype in the eutherian ovary.

Steroids play a critical role in gonadal differentiation in birds, reptiles, and amphibia whereas gonadal differentiation in mammals is thought to be determined by genetic mechanisms. The gonads of female mice incapable of synthesizing estrogens due to disruption of the aromatase gene (ArKO) provide a unique model to test the role of estrogen in regulating the gonadal phenotype. We have shown that in the absence of estrogen, genetically female mice develop testicular tissue within their ovaries. The ovaries develop cells that possess structural and functional characteristics of testicular interstitial cells and of seminiferous tubule-like structures lined with Sertoli cells. Moreover, the ovaries express mRNA for the testis-specific Sertoli cell transcription factor Sox 9 and espin protein, which is specific for inter-Sertoli cell junctions. The development of the testicular tissue in this model can be reverted/postponed by replacing estrogen. When ArKO female mice were fed a diet containing phytoestrogens, the appearance of Leydig and Sertoli cells was postponed and reduced. Furthermore, administration of estradiol-17beta decreased the number of Sertoli and Leydig cells in the ovaries. These findings constitute definitive evidence that estrogen plays a critical role in maintaining female somatic interstitial and granulosa cells in the eutherian ovary.

Animals↗
PubMed1985

Evidence for a dual mechanism in the anesthetic action of an opioid peptide.

Loss of righting reflex (LRR) produced by various concentrations of the leucine-enkephalin analog BW831c (TYR.D-ALA.GLY.PHE.D-LEU.NHEt.HCI) was determined in amphibia at 1 atm and 120 atm of helium. EC50 for LRR was 22.1 +/- 1.6 microM and 44 +/- 6.9 microM, respectively. The octanol/water partition coefficient (P) was 26 +/- 3.6, suggesting that this peptide is sufficiently lipid soluble for a classic Meyer-Overton type of anesthetic action. The ratio (EC50 at 120 atm)/(EC50 at 1 atm) for the peptide (2.0 +/- 0.31) was essentially the same as that for the long-chain alcohol, octanol (1.8 +/- 0.08), and similar to those reported for phenobarbital and the gaseous anesthetics. Thus, peptide-induced LRR was reversible by pressure. Peptide-induced LRR also was completely reversible by naloxone, whereas octanol-induced LRR was unaffected by up to 100 microM naloxone. These findings are consistent with a dual mechanism of anesthetic action for this peptide: one, an opiate receptor-specific mechanism, reversible with the specific opiate antagonist, naloxone; the other, a nonspecific mechanism, related to lipid solubility and reversible with the application of the physical agent, pressure.

1-Octanol↗
PubMed1989

Epithelial action potentials in embryos of the Australian lungfish.

The epithelial cells of the skin of embryonic Australian lungfish (Neoceratodus forsteri) between stages 30 and 39, are mechanosensitive and excitable, showing overshooting action potentials 400-800 ms long with a rapid rise followed by a slower repolarization (usually with a shoulder on the repolarizing phase), which propagate at around 10 mm s-1. This skin impulse system is very similar to that found in embryonic and larval Amphibia; the significance of this similarity is discussed.

Action Potentials↗
PubMed2005

Energetics of the smallest: Do bacteria breathe at the same rate as whales?

Power laws describing the dependence of metabolic rate on body mass have been established for many taxa, but not for prokaryotes, despite the ecological dominance of the smallest living beings. Our analysis of 80 prokaryote species with cell volumes ranging more than 1,000,000-fold revealed no significant relationship between mass-specific metabolic rate q and cell mass. By absolute values, mean endogenous mass-specific metabolic rates of non-growing bacteria are similar to basal rates of eukaryote unicells, terrestrial arthropods and mammals. Maximum mass-specific metabolic rates displayed by growing bacteria are close to the record tissue-specific metabolic rates of insects, amphibia, birds and mammals. Minimum mass-specific metabolic rates of prokaryotes coincide with those of larger organisms in various energy-saving regimes: sit-and-wait strategists in arthropods, poikilotherms surviving anoxia, hibernating mammals. These observations suggest a size-independent value around which the mass-specific metabolic rates vary bounded by universal upper and lower limits in all body size intervals.

Animals↗
PubMed1985

The evolution of the terrestrial vertebrates: environmental and physiological considerations.

Physiological evidence has long been used to suggest that the gnathostomous vertebrates (those possessing jaws) were primitively fresh water. The same was also the case for the Osteichthyes (bony fish) and the Tetrapoda (Amphibia, Reptilia, Aves, Mammalia). However, the geological evidence favours a marine origin for the vertebrates as a whole, and, for the gnathostomes and the osteichthyans in particular. Some of the earliest amphibian remains may be associated with tidally influenced sediments. Furthermore, during the early part of the Devonian, fresh water chemistry may well have been different from that of today, lessening the divide between marine and non-marine environments. Urea formation via the ornithine cycle, and urea retention in the body fluids, are useful adaptations for terrestrial life. They prevent excessive water loss associated with the elimination of nitrogenous waste. These abilities may have been primitive for the gnathostomes, and were developed in the marine environment to reduce osmotic dehydration. In the aqueous medium, gaseous exchange is effected by the gills. These organs are, on the whole, useless in air. For vertebrates, air-breathing is effected by an inflatable sac, with moist linings, and an internal location. Some form of air-breathing sac was primitive for the osteichthyans, and may have been primitive for the gnathostomes. Again, this adaptation for terrestrial life developed in response to conditions experienced in the marine, aquatic environment. A new model of tetrapod evolution is proposed in the light of the basic marine origin and character of the ancestors of the tetrapods.

Adaptation, Physiological↗
PubMed1986

Mechanisms of DNA sequence amplification and their evolutionary consequences.

DNA sequence amplification is a phenomenon that occurs predictably at defined stages during normal development in some organisms and has been shown to occur spontaneously, but sporadically, in a variety of cells, including mammalian cells, selected for overproduction of a gene product. Developmentally programmed gene amplification includes rDNA amplification during oögenesis in amphibia, chorion protein gene amplification in Drosophila and the chromosomal changes accompanying macronuclear formation in ciliates. Selected gene amplification is illustrated by mutant mammalian cells which have been selected in vitro or in vivo for the overproduction of a gene product. In these cells the unit of DNA that is amplified is much larger than the gene under selection, and appears to be formed by multiple recombination events, which bring together sequences not normally adjacent to each other. Often the product of amplification can be seen microscopically as aberrant chromosome forms. The vast majority of DNA amplification events occur in somatic nuclei, and thus would not have any direct effect on the evolution of a genome. However, the ability to amplify DNA in somatic cells does have consequences for the composition of the genomes of the organisms in which it can occur, and should DNA amplification occur, even sporadically, in germ-line cells the potential effect on evolution would be great.

Amphibians↗
PubMed2000

The corneal surface of aquatic vertebrates: microstructures with optical and nutritional function?

The anterior surface of the mammalian cornea plays an important role in maintaining a smooth optical interface and consequently a sharp retinal image. The smooth surface is produced by a tear film, which adheres to a variety of microprojections, which increase the cell surface area, improve the absorbance of oxygen and nutrients and aid in the movement of metabolic products across the outer cell membrane. However, little is known of the structural adaptations and tear film support provided in other vertebrates from different environments. Using field emission scanning electron microscopy; this study examines the density and surface structure of corneal epithelial cells in representative species of the classes Cephalaspidomorphi, Chondrichthyes, Osteichthyes, Amphibia, Reptilia, Aves and Mammalia, including some Marsupialia. Variations in cell density and the structure and occurrence of microholes, microridges, microplicae and microvilli are described with respect to the demands placed upon the cornea in different aquatic environments such as marine and freshwater. A progressive decrease in epithelial cell density occurs from marine (e.g. 29348 cells mm(-2) in the Dover sole Microstomius pacficus) to estuarine or freshwater (e.g. 5999 cells mm(-2) in the black bream Acanthopagrus butcheri) to terrestrial (e.g. 2126 cells mm(-2) in the Australian koala Phascolarctos cinereus) vertebrates, indicating the reduction in osmotic stress across the corneal surface. The microholes found in the Southern Hemisphere lampreys, namely the pouched lamprey (Geotria australis) and the shorthead lamprey (Mordacia mordax) represent openings for the release of mucus, which may protect the cornea from abrasion during their burrowing phase. Characteristic of marine teleosts, fingerprint-like patterns of corneal microridges are a ubiquitous feature, covering many types of sensory epithelia (including the olfactory epithelium and the oral mucosa). Like microplicae and microvilli, microridges stabilize the tear film to maintain a smooth optical surface and increase the surface area of the epithelium, assisting in diffusion and active transport. The clear interspecific differences in corneal surface structure suggest an adaptive plasticity in the composition and stabilization of the corneal tear film in various aquatic environments.

Animals↗
PubMed2000

Light-adaptive role of nitric oxide in the outer retina of lower vertebrates: a brief review.

The role of nitric oxide (NO) as a novel neurochemical mechanism controlling light adaptation of the outer retina is discussed by considering mainly published results. The emphasis is on the retinae of fishes and amphibia, but some data from the mammalian (rabbit) retinae have also been included for completeness. In the fish retina, application of NO donors in the dark caused light-adaptive photomechanical movements of cones. The normal effect of light adaptation in inducing cone contractions was suppressed by pretreatment of retinae with an NO scavenger. NO donors modulated horizontal cell activity by uncoupling the cells' lateral gap junctional interconnections and enhancing negative feedback to cones, again consistent with a light-adaptive role of NO. Direct evidence for light adaptation-induced release of NO has been obtained in fish (carp) and rabbit retinae. The results strongly suggest that control of retinal light adaptation is, under multiple neurochemical control, with NO and dopamine having an interactive role.

Adaptation, Physiological↗
PubMed1996

Genetic analysis of dorsoventral pattern formation in the zebrafish: requirement of a BMP-like ventralizing activity and its dorsal repressor.

According to a model based on embryological studies in amphibia, dorsoventral patterning is regulated by the antagonizing function of ventralizing bone morphogenetic proteins (BMPs) and dorsalizing signals generated by Spemann's organizer. Large-scale mutant screens in the zebrafish, Danio rerio, have led to the isolation of two classes of recessive lethal mutations affecting early dorsoventral pattern formation. dino mutant embryos are ventralized, whereas swirl mutants are dorsalized. We show that at early gastrula stages, dino and swirl mutants display an expanded or reduced Bmp4 expression, respectively. The dino and swirl mutant phenotypes both can be phenocopied and rescued by the modulation of BMP signaling in wild-type and mutant embryos. By suppressing BMP signaling in dino mutants, adult fertile dino -/- fish were generated. These findings, together with results from the analysis of dino-swirl double mutants, indicate that dino fulfills its dorsalizing activity via a suppression of swirl-dependent, BMP-like ventralizing activities. Finally, cell transplantation experiments show that dino is required on the dorsal side of early gastrula embryos and acts in a non-cell-autonomous fashion. Together, these results provide genetic evidence in support of a mechanism of early dorsoventral patterning that is conserved among vertebrate and invertebrate embryos.

Animals↗
PubMed2004

The C terminus of the nuclear protein NuMA: phylogenetic distribution and structure.

The C terminus of the nuclear protein NuMA, NuMA-CT, has a well-known function in mitosis via its proximal segment, but it seems also involved in the control of differentiation. To further investigate the structure and function of NuMA, we exploited established computational techniques and tools to collate and characterize proteins with regions similar to the distal portion of NuMA-CT (NuMA-CTDP). The phylogenetic distribution of NuMA-CTDP was examined by PSI-BLAST- and TBLASTN-based analysis of genome and protein sequence databases. Proteins and open reading frames with a NuMA-CTDP-like region were found in a diverse set of vertebrate species including mammals, birds, amphibia, and early teleost fish. The potential structure of NuMA-CTDP was investigated by searching a database of protein sequences of known three-dimensional structure with a hidden Markov model (HMM) estimated using representative (human, frog, chicken, and pufferfish) sequences. The two highest scoring sequences that aligned to the HMM were the extracellular domains of beta3-integrin and Her2, suggesting that NuMA-CTDP may have a primarily beta fold structure. These data indicate that NuMA-CTDP may represent an important functional sequence conserved in vertebrates, where it may act as a receptor to coordinate cellular events.

Amino Acid Sequence↗
PubMed2003

Outline of the evolution of behavioral and nonbehavioral patterns of parental care among the vertebrates: critical characteristics of mammalian and avian parental behavior.

An outline of the evolution of parental care among the vertebrates is presented, leading to a characterization of critical features of parental care among the mammals and birds. Among the lower vertebrates (fishes, amphibia) and reptiles there are a variety of patterns of parental care. These can be divided into those that involve parental behavior and those that are nonbehavioral. Among extant species, parental behavior is not the predominant form of parental care, although it is present in many species of fish, frog and reptile. Nonbehavioral patterns of parental care predominate and are equally effective as parental behavior. Parental behavior is based on reciprocal stimulus interaction (trophallaxis) between the parent and the offspring and includes behavior directed at the nest, eggs, and developing young. Among lower vertebrates and reptiles there are increases in the complexity and completeness of parental behaviors but only among the mammals and birds has parental behavior been elaborated as the only form of parental care. Critical characteristics of mammalian parental behavior are: simultaneous onset of birth, lactation, and maternal care, rapid formation of an attachment of the mother to her offspring, synchrony in the behavioral interaction between mother and young during their development until weaning, and the significance of the mother-offspring unit as the basis of social organization. Among birds there is the period of egg incubation in the nest preceding hatching of the young, in addition to the above characteristics of mammals, but the mother-offspring unit is not the basis for social organization.

Animals↗
PubMed1991

Southern analysis of the 230-kD bullous pemphigoid antigen gene in normal humans, animals, and patients with junctional epidermolysis bullosa.

To begin to characterize the 230-kD bullous pemphigoid antigen (BPA) gene, we performed Southern analysis on genomic DNA with probes derived from 7 kb of cDNA that spans most of the coding region of this hemidesmosomal plaque protein. When hybridized to a 1-kb fragment of this BPA cDNA, normal human genomic DNA digested with EcoRI, BamHI, PstI, HindIII, or EcoRV showed only a single band, which was unique for each enzyme, indicating a single human gene for BPA. To determine if a related gene exists in animals, we used probes covering the full 7 kb of cDNA for Southern analysis of genomic DNA from various vertebrates. A related gene was detected in other mammals (monkey, cow, dog, rabbit, mouse, and rat) but not in chicken, frog, or fish. Under these same hybridization conditions a probe for human beta-actin could detect an actin gene in all these species. Furthermore, immunofluorescence showed that an antibody raised against portions of the 230-kD BPA bound to the epidermal basement membrane of mammals but not that of a bird or amphibian. Finally, because most patients with junctional epidermolysis bullosa (JEB) have defective hemidesmosomes in ultrastructure, and probably function, we analyzed genomic DNA from these patients. No restriction fragment length polymorphisms (RFLP) were detected when the DNA from 11 normals and 8 JEB patients (representing 16 possible defective genes) was digested with BamHI, EcoRI, or PstI and hybridized to any part of the cDNA. These findings indicate that 1) there is a single BPA gene in humans; 2) a closely related gene exists in other mammals but not birds, amphibia, or fish; and 3) gross abnormalities of the BPA gene are not characteristic of JEB patients.

Animals↗
PubMed1976

The abundance of ferritin in yolk-sac derived red blood cells of the embryonic mouse.

Circulating red blood cells formed early in development have several distinctive properties which include retention of the nucleus (mammals), large size and characteristic haemoglobin type (mammals, birds, amphibia). The primitive or embryonic red cells of early development are replaced by the definitive red cells which contain fetal or adult haemoglobin; a second developmental change occurs in the haemoglobin of some mammals (man, cattle, sheep) but does not involve a cell replacement. Circulating yolk-sac derived red cells from embryonic mice are siderocytes; elevated ferritin levels are associated with the circulating red cells of bullfrog tadpoles, but not with those of the adult frog, again indicating that red cell iron metabolism can change during development. In order to extend the observations made on an amphibian to a mammal, the ferritin content of circulating red cells from embryonic mice was determined and found to be 0.65 mg/100 mg of soluble protein; no ferritin (less than or equal to 0.007 mg/100 mg of soluble protein) was detected in adult mouse red cells. Elevated ferritin levels appeared to be specifically associated with the yolk-sac derived population of red cells since a decline in red-cell ferritin content coincided with the replacement of yolk-sac derived red cells by definitive red cells derived from the liver. Fractionation of mixtures of yolk-sac derived and liver derived red cells showed that fractions rich in the definitive red cells contained less ferritin than the mixture. The results suggest that elevated ferritin levels may be a general characteristic of the circulating, haemoglobinized red cells formed early in development.

Aging↗