Behavioral responses of seven species of asteroids to the asteroid predator,Solaster dawsoni (responses of asteroids to the predator Solaster dawsoni)

Summary Seven asteroid species common to the northern California coast were studied for their defensive responses to the predator Solaster dawsoni. The presence or absence of an escape response was used to predict whether or not these species were susceptible to predation from Solaster. Strong escape responses were displayed by Patiria miniata, Henricia leviuscula, Leptasterias hexactis, Pycnopodia helianthoides, and small Pisaster ochraceus. Subsequent capture and consumption of Patiria, Henricia, Leptasterias and small P. ochraceus were observed. Solaster attacked all Pisaster spp. tested, but Pisaster brevispinus and larger P. ochraceus protected themselves from predation by utilizing their pedicellariae against Solaster whenever contact occurred. Dermasterias imbricata appeared to be immune to predation by Solaster. Contact between these two asteroids failed to elicit a defensive response in the former or an attack by the latter asteroid.     

Capnocytophaga: New genus of gram-negative gliding bacteria. IV. DNA base composition and sequence homology

Isolates of Gram-negative fermentative gliding bacteria which are prominantly cultivated from the subgingival sulcus in association with periodontal lesions have been the subject of a collaborative taxonomic study. Thirty-five oral strains, isolated from various states of periodontal health and disease, were examined for DNA base composition and patterns of DNA sequence homology. The phentotypically similar organism, Bacteroides ochraceus ATCC 27872, as well as two representatives of gliding bacteria in the family Cytophagaceae, Myxococcus fulvus and Sporocytophaga myxococcoides, were included in these comparisons. Mol-percent guanine and cytosine (% G+C) was determined by thermal denaturation. Relatedness was also assessed by interspecific reassociation of DNA measured by the use of a single-strand specific S1 endonuclease. DNA purified from oral gliders, B. ochraceus ATCC27872 and S. myxococcoides contained 33–41% G+C as compared with 67% in DNA from M. fulvus. Three homology groups (designated as 25, 4 and 27) were delineated by DNA homology. Homology at the 77% level was demonstrated between B. ochraceus ATCC 27872 and the oral reference strain 25. Homology group 4 comprised four strains, all of which were isolated from cases of rapidly advancing periodontal disease. The relatively high degree of genetic divergence, observed as intergroup homology levels of less than 25%, supports the naming of three species of Capnocytophaga, C. ochracea, C. sputigena and C. gingivalis by Leadbetter et al. (1979) corresponding to DNA homology groups 25, 4 and 27, respectively.     

Evolution of sea urchin non-repetitive DNA

Summary New methods have been applied to the determination of single copy DNA sequence differences between the sea urchin speciesStrongylocentrotus purpuratus, S. franciscanus, S. drobachiensis, andLytechinus pictus. The thermal stability of interspecies DNA duplexes was measured in a solvent (2.4 M tetraethylammonium chloride) that suppresses the effect of base composition on melting temperature. The lengths of duplexes were measured after digestion with S1 nuclease and correction made for the effect of length on thermal stability. The degree of base substitution that has occurred in the single copy DNA during sea urchin evolution is significantly larger than indicated by earlier measurements. We estimate that 19% of the nucleotides of the single copy DNA are different in the genomes of the two sea urchin congeners,S. purpuratus, andS. franciscanus, which apparently diverged only 15 to 20 million years ago.     

Structural genes adjacent to interspersed repetitive DNA sequences

The observation that repetitive and single copy sequences are interspersed in animal DNAs has suggested that repetitive sequences are adjacent to single copy structural gene sequences. To test this concept, single copy DNA sequences contiguous to interspersed repetitive sequences were prepared from sea urchin DNA by hydroxyapatite fractionation (repeat-contiguous DNA fraction). These single copy sequences included about one third of the total nonrepetitive sequence in the genome as determined by the amounts recovered during the hydroxyapatite fractionation and by reassociation kinetics. ³H-labeled mRNA from sea urchin gastrula was prepared by puromycin release from polysomes and used in DNA-driven hybridization reactions. The kinetics of mRNA hybridization reactions with excess whole DNA were carefully measured, and the rate of hybridization was found to be 3–5 times slower than the corresponding single copy DNA driver reassociation rate. The mRNA hybridized with excess repeat-contiguous DNA with similar kinetics relative to the driver DNA. At completion 80% of that mRNA hybridizable with whole DNA (approximately 65%) had reacted with the repeat-contiguous DNA fraction (50%). This result shows that 80–100% of the mRNA molecules present in sea urchin embryos are transcribed from single copy DNA sequences adjacent to interspersed repetitive sequences in the genome.     

Non-repetitive DNA sequence divergence in phylogenetically diploid and tetraploid teleostean species of the family cyprinidae and the order isospondyli

Non-repetitive DNA of anciently tetraploid teleostean species was analysed for the presence of duplicated sequences. Closely related diploid species were investigated in comparison. From the reassociation kinetics of total nuclear DNA, rate constants and fraction sizes of classes of repetitive and non-repetitive sequences were determined. DNA fractions enriched in the slowest renaturing sequence class were prepared and subjected to reassociation. The rate constants of these reactions were compared with the values expected for single-copy DNA from analytical genome size determinations. From reassociated DNA enriched in non-repetitive sequences also the melting temperatures were determined as a measure of internal base sequence heterogeneity. It has been shown that the two ancient tetraploids Cyprinus carpio and Thymallus thymallus are, with regard to the thermal stability of reassociated non-repetitive DNA, and with regard to the correspondence of reaction rates with the values expected for single copy DNA, indistinguishable from diploid controls (Rutilus rutilus, Clupea harengus and Sprattus sprattus). The tetraploid species Salmo irideus, Salvelinus fontinalis and Coregonus lavaretus appear as very recent tetraploids with regard to these criteria. The significance of the results for estimating the time of occurence of polyploidisation events in these taxa is discussed.     

Satellite DNA properties of the germ line limited DNA and the organization of the somatic genomes in the nematodesAscaris suum andParascaris equorum

During the early cleavage divisions in some Ascarids, parts of the chromosomes are eliminated from the somatic blastomeres (chromatin diminution, Boveri, 1887) while the chromosomes in the germ line cells maintain their integrity. To characterize the germ line and soma genome, DNA was isolated from gametes and embryonic somatic cells of two Ascarid species,Parascaris equorum var. univalens andAscaris suum. It was shown that the germ line limited DNAs of these species have the same density and almost identical reassociation kinetics: in CsCl the predominant component of the germ line limited DNA ofP. equorum andA. suum has the buoyant density of 1.697g/cm³, while soma DNA of both species bands at 1.700 g/cm³. InP. equorum there is a small additional germ line limited satellite DNA component with the density of 1.690 g/cm³, identical to that of mitochondrial DNA of both organisms. Comparison of the reassociation kinetics of germ line and soma DNA demonstrates for both species that the eliminated DNA sequences are highly repetitive. In contrast to these similarities between the germ line limited DNAs ofP. equorum andA. suum the analysis of their base composition revealed differences (40% guanine plus cytosine inP. equorum and 36% inA. suum). The only very fast reassociating DNA sequences which we could isolate from soma DNA was demonstrated to be foldback DNA. The reassociation kinetics of totalA. suum soma DNA was investigated by hydroxylapatite chromatography. Least squares analysis of the data revealed about 10% of intermediate repetitive DNA sequences. Their interspersion between single copy DNA sequences was analyzed by comparing the reassociation kinetics of DNA fragments 0.35 and 7.2 kilobases long. Thus the DNA sequence arrangement ofAscaris does not follow the short period interspersion pattern observed in most organism.     

Contrasting patterns of DNA sequence arrangement in Apis mellifera (Honeybee) and Musca domestica (housefly)

We have examined the organization of the repeated and single copy DNA sequences in the genomes of two insects, the honeybee (Apis mellifera) and the housefly (Musca domestica). Analysis of the reassociation kinetics of honeybee DNA fragments 330 and 2,200 nucleotides long shows that approximately 90% of both size fragments is composed entirely of non-repeated sequences. Thus honeybee DNA contains few or no repeated sequences interspersed with nonrepeated sequences at a distance of less than a few thousand nucleotides. On the other hand, the reassociation kinetics of housefly DNA fragments 250 and 2,000 nucleotides long indicates that less than 15% of the longer fragments are composed entirely of single copy sequences. A large fraction of the housefly DNA therefore contains repeated sequences spaced less than a few thousand nucleotides apart. Reassociated repetitive DNA from the housefly was treated with S1 nuclease and sized on agarose A-50. The S1 resistant sequences have a bimodal distribution of lengths. Thirty-three percent is greater than 1,500 nucleotide pairs, and 67% has an average size about 300 nucleotide pairs. The genome of the housefly appears to have at least 70% of its DNA arranged as short repeats interspersed with single copy sequences in a pattern qualitatively similar to that of most eukaryotic genomes.     

Genetic relatedness of the genomes of equine herpesvirus types 1, 2, and 3.

Genomic DNAs of equine herpesvirus type 1 (EHV-1), EHV-2 (equine cytomegalovirus), and EHV-3 were examined by reassociation kinetic and thermal denaturation analyses to determine the extent and degree of homology among the three viral DNAs. Results of reassociation analyses indicated a limited homology among the three EHV genomes. Homologous DNA sequences equivalent to 1.8 to 3.7 megadaltons between EHV-1 and equine cytomegalovirus, 7.6 to 8.2 megadaltons between EHV-1 and EHV-3, and 1.3 to 1.9 megadaltons between equine cytomegalovirus and EHV-3 were detected. Examination by thermal denaturation of the DNA homoduplexes and heteroduplexes formed during reassociation revealed a high degree of base pairing within the duplexes, suggesting that closely related sequences may be conserved among the genomes of EHV.     

Relationships between species ofLeymus,Psathyrostachys, andHordeum (Poaceae,Triticeae) inferred from Southern hybridization of genomic and cloned DNA probes

We have used total genomic DNA as a probe to size-fractionated restriction enzyme digests of genomic DNA from a range ofTriticeae species from the generaLeymus Hochst.,Psathyrostachys Nevski, andHordeum L., and hybrids betweenHordeum andLeymus to investigate their taxonomic relationships. Genomic Southern hybridization was found to be an effective and simple way to assess the distribution and diversity of essentially species-specific and common, repetitive DNA sequences, and is hence especially useful in evolutionary studies. The DNA sequences ofH. vulgare seem to diverge substantially from those ofH. brachyantherum, H. lechleri, H. procerum, andH. depressum. The genome ofThinopyron bessarabicum shows little homology to those of theLeymus species investigated, confirming thatT. bessarabicum is not an ancestral genome inLeymus. Although the genomes ofLeymus andPsathyrostachys share substantial proportions of DNA sequences, they include divergent repeated sequences as well. Hybridization with a ribosomal DNA probe (pTa 71) showed that the coding regions containing structural genes encoding the 18 S, 5.8 S, and 26 S ribosomal RNA were conserved among the species investigated, whereas the intergenic spacer region was more variable, presenting different sizes of restriction fragments and enabling a classification of the species. The rye heterochromatin probe pSc 119.2 hybridized to DNA fromH. lechleri andT. bessarabicum, but not to DNA from the other species investigated.     

Studies on DNA sequences in the Osmundaceae

Summary Phylogenetic relationships ofOsmunda cinnamomea, O. claytoniana, andO. regalis were explored by means of DNA sequence comparisons. Hydroxyapatite thermal elution profiles of self-reassociated repetitive DNA fragments were very similar, indicating the absence of gross differences in the amount of recent amplification or addition of repetitive DNA in any of these three genomes. Interspecific DNA sequence comparisons showed, in contrast to our earlier interpretation, that repeated DNA sequences ofO. claytoniana are nearly equally diverged from those ofO. cinnamomea andO. regalis. Differences between repetitive sequences of the three species can be interpreted as reflecting amplification events which occurred subsequent to speciation. The data obtained suggest that the threeOsmunda species most likely arose more or less simultaneously from a common ancestor. These findings were verified in experiments with tracer DNA preparations enriched for single copy sequences. On the basis of the hybridization data presented here and of the fossil record, the rate of single copy sequence divergence in the ferns is comparable to that in the primates, although slower than that observed in other animal taxa. From this first evaluation of rates of DNA evolution in plants it would seem that the rates for plants and animals are roughly comparable. The evidence suggests that species divergence is accompanied by further reiteration of preexisting repeat sequences. The rate of addition of repetitive sequences probably is slower in ferns than in angiosperms. This difference might be attributable to the much larger effective generation time in ferns.     

DNA sequence organization in the genome of Nicotiana tabacum

The genome of Nicotiana tabacum was investigated by DNA/DNA reassociation for its spectrum of DNA repetition components and pattern of DNA sequence organization. The reassociation of 300 nucleotide DNA fragments analyzed by hydroxyapatite chromatography reveals the presence of three major classes of DNA differing in reiteration frequency. Each class of DNA was isolated and characterized with respect to kinetic homogeneity and thermal properties on melting. These measurements demonstrate that the genome of N. tabacum has a 1C DNA content of 1.65 pg and that DNA sequences are represented an average of 12,400, 252, and 1 times each. — The organization of the DNA sequences in the N. tabacum genome was determined from the reassociation kinetics of long DNA fragments as well as S1 nuclease resistance and hyperchromicity measurements on DNA fragments after annealing to C₀t values at which only repetitive DNA sequences will reassociate. At least 55% of the total DNA sequences are organized in a short period interspersion pattern consisting of an alternation of single copy sequences, averaging 1400 nucleotides, with short repetitive elements approximately 300 nucleotides in length. Another 25% of the genome contains long repetitive DNA sequences having a minimal genomic length of 1500 nucleotides. These repetitive DNA sequences are much less divergent than the short interspersed DNA sequence elements. These results indicate that the pattern of DNA sequence organization in the tobacco genome bears remarkable similarity to that found in the genomes of most animal species investigated to date.     

DNA homologies among homothallic, pseudo-homothallic and heterothallic species of Neurospora.

Summary Highly purified DNAs from three homothallic speciesNeurospora africana, N. dodgei andN. lineolata; three reference strains representing authentic heterothallic species,N. crassa, N. intermedia andN. sitophila; and two strains of pseudo-homothallic speciesN. tetrasperma were characterized by spectrophotometry and DNA reassociation using hydroxyapatite chromatography. All of these known species are closely related on the basis of DNA characteristics such as base composition and thermal denaturation profiles of major DNA components. Minor components of ascospore DNA was, however, only 5–7% of total DNA instead of 15–20% minor component DNA shown by mycelial DNA. Species belonging to same group were not distinguishable morphologically, but all of these species were distinguishable by DNA:DNA homology studies. Greater DNA homology was noticed between DNAs of heterothallic species and DNAs of pseudohomothallic species than DNA of true homothallic species. Difference on DNA-nucleiotide sequences among homothallic species was very little. Pseudo-homothallic speciesN. tetrasperma was found to be distinctly different from homothallic species but closer to heterothallic species based on such studies.Supported in part by a contract No. E(40-1)4182 with the U.S. Energy Research and Development Administration. We are grateful to Departments of Oncology and Radiotherapy, College of Medicine, Howard University, Washington, D.C. for providing us with material assistance     

Single copy DNA and structural gene sequence relationships among four sea urchin species

Measurements of the divergence of single copy DNA sequences among four sea urchin species are presented. At a standard criterion for reassociation (0.12 M phosphate buffer, 60° C, hydroxyapatite binding) we observe the following extents of reaction and reductions in thermal stability for single copy DNA reassociation between Strongylocentrotus purpuratus tracer and heterologous driver DNA: S. dröbachiensis 68% and 2.5°C; S. franciscanus 51% and 3.5° C; Lytechinus pictus 12% and 7.5° C. The implied extents of sequence relatedness are consistent with the phylogenetic relationships of these species. The rate of single copy sequence divergence in the evolutionary lines leading to the Strongylocentrotus species is estimated to be 0.06–0.35% per million years. The rate of divergence of total single copy sequence has been compared to that of structural gene sequences represented in S. purpuratus gastrula polysomal messenger RNA. When closely related species, S. purpuratus and S. franciscanus, are compared, these polysomal sequences are found to diverge at a lower rate than does the total single copy sequence. For two very distantly related species, S. purpuratus and L. pictus, a small fraction of the single copy DNA sequence is probably conserved. These conserved sequences are not enriched in their content of structural gene sequences.Also staff member, Carnegie Institution of Washington, Washington, D.C. 20015     

DNA sequence analysis of the recA genes from Proteus vulgaris, Erwinia carotovora, Shigella flexneri and Escherichia coli B/r

Summary The complete nucleotide sequences of therecA genes fromEscherichia coli B/r,Shigella flexneri, Erwinia carotovora andProteus vulgaris were determined. The DNA sequence of the coding region of theE. coli B/r gene contained a single nucleotide change compared with theE. coli K12 gene sequence whereas theS. flexneri gene differed at 7 residues. In both cases, the predicted proteins were identical in primary structure to theE. coli K12 RecA protein. The DNA sequences of the recA genes fromE. carotovora andP. vulgaris were 80% and 74% homologous, respectively, to theE. coli K12 gene. The predicted amino acid sequences of theE. carotovora andP. vulgaris RecA proteins were 91% and 85% identical respectively, to that ofE. coli K12. The RecA proteins from bothP. vulgaris andE. carotovora diverged significantly in sequence in the last 50 residues whereas they showed striking conservation throughout the first 300 amino acids which include an ATP-binding region and a subunit interaction domain. A putative LexA repressor binding site was localized upstream of each of the heterologous genes.     

Reassociation Kinetics and Cytophotometric Characterization of Peanut (Arachis hypogaea L.) DNA

The base composition of peanut (var. NC-17) DNA determined from thermal denaturation profiles showed an average guanine plus cystosine content of 34% which was in close approximation to 36% guanine plus cytosine calculated from the buoyant density. Buoyant density also indicated the absence of satellite DNA. The genome size, 2.0 × 10⁹ base pairs, as determined by reassociation kinetics of the single copy DNA was close to the genome size determined by cytophotometry, 2.1 × 10⁹ base pairs. Peanut DNA averaging 450 to 600 base pairs long, reassociated in phosphate buffer and fractionated by hydroxylapatite, indicated a DNA genome composition of 36% nonrepetitive or single copy DNA; reassociation in formamide and followed by optical methods indicated the repetitive DNA possesses highly repeated, intermediately repeated and rarely repeated components of DNA with DNA sequences repeated on the average about 38,000, 6,700, and 200 times each. Different criteria of reassociation in formamide revealed further subdivisions of these four separate components of DNA. The DNA of above mentioned NC-17 variety compared to Florigiant variety showed no differences in thermal denaturation profiles, buoyant density, or in genome size.     

Characterization of the nuclear genome of pearl millet.

The nuclear genome of pearl millet has been characterized with respect to its size, buoyant density in CsCl equilibrium density gradients, melting temperature, reassociation kinetics and sequence organization. The genome size is 0.22 pg. The mol percent G + C of the DNA is calculated from the buoyant density and the melting temperature to be 44.9 and 49.7%, respectively. The reassociation kinetics of fragments of DNA 300 nucleotides long reveals three components: a rapidly renaturing fraction composed of highly repeated and/or foldback DNA, middle repetitive DNA and single copy DNA. The single copy DNA consists of 17% of the genome. 80% of the repetitive sequences are at least 5000 nucleotide pairs in length. Thermal denaturation profiles of the repetitive DNA sequences show high Tm values implying a high degree of sequence homogeneity. About half of the single copy DNA is short (750--1400 nucleotide paris) and interspersed with long repetitive DNA sequences. The remainder of the single copy sequences vary in size from 1400 to 8600 nucleotide pairs.     

Absence of short period interspersion of repetitive and non-repetitive sequences in the DNA of Drosophila melanogaster

A sensitive search has been made in Drosophila melanogaster DNA for short repetitive sequences interspersed with single copy sequences. Five kinds of measurements all yield the conclusion that there are few short repetitive sequences in this genome: 1) Comparison of the kinetics of reassociation of short (360 nucleotide) and long (1,830 nucleotide) fragments of DNA; 2) reassociation kinetics of long fragments (2,200 nucleotide) with an excess of short (390 short nucleotide) fragments; 3) measurement of the size of S1 nuclease resistant reassociated repeated sequences; 4) measurement of the hyperchromicity of reassociated repetitive fragments as a function of length; 5) direct assay by kinetics of reassociation of the amount of single copy sequence present on 1,200 nucleotide long fragments which also contain repetitive sequences.     

A high amount of satellite DNA in the genome of Lupinus angustifolius L.

Embryo DNA, isolated from ungerminated seeds of Lupinus angustifolius L., contains an exceptionally high amount of guanine-cytosine-rich satellite DNA. The thermal denaturation curve of total embryo DNA is biphasic with an inflexion point at 62% denaturation, indicating the presence of satellite DNA. The satellite fraction could be separated from the mainband DNA by three successive preparative CsCl-gradient centrifugations. The densities of the DNA fractions are 1.7045 g cm^-3 and 1.6925 g cm^-3, respectively. The percentages of guanine-cytosine calculated from these densities are comparable to the percentages of GC calculated from the melting temperatures. Finally, ressociation studies prove that foldback DNA and highly repeated sequences are much more frequent in the satellite DNA fraction than in the mainband DNA.Abbreviation C _o t the product of the DNA concentration (mol nucleotides l^-1) and the time (s) of incubation in a DNA reassociation reaction - GC guanine-cytosine - np nucleotide parirs - T temperature interval between 16 and 84% denaturation     

The organization of the main component DNA of a crustacean genome with a paucity of middle repetitive sequences

The frequency classes and organization of the main component (mc) DNA of a crustacean, the land crab, Gecarcinus lateralis, have been characterized. The reassociation kinetics of 380 nucleotide long mcDNA fragments show that approximately 50% contain sequences repeated more than 800 times. Present in few, if any, copies are sequences repeated from 2 to 800 times. The remainder of the DNA reassociates as single copy sequences with a rate constant consistent with the organism's genome size. The reassociation kinetics of highly sheared DNA fragments of every true crab studied (Vaughn, 1975; Christie et al., 1976) are similar to each other and different from those of other invertebrate DNAs (Goldberg et al., 1975). Each of these genomes has a paucity of sequences repeated from 10 to 800 times and an abundance of highly repeated sequences. To determine if sequences repeated more than 800 times are interspersed with single copy sequences, we examined the arrangement of repetitive and non-repetitive sequences in mcDNA. The reassociation and melting properties of partially duplex mcDNA fragments of increasing lengths show that at least 75% of the DNA is organized in an interspersed pattern. In this pattern, single copy sequences with an average length of 800–900 nucleotides are interspersed with repetitive sequences. S1 nuclease digestion of reassociated 3100 nucleotide fragments indicates that 44% of the mcDNA is repetitive and that one-third of the repetitive sequences (average length=285 nucleotides) are interspersed with single copy sequences. We conclude that repetitive sequencies are interspersed with most of the single copy sequences in an interspersion pattern similar to that of Xenopus rahter than to that of another arthropod, Drosophila.Operated by Union Carbide Corporation for the Energy Research and Development Administration     

Homology of Balbiani rings among chironomid species and localization of a new mobile element on the polytene chromosomes

The results ofin situ cross-hybridization of the cloned DNA fragments of BRa, BRb and BRc fromChironomus thummi to the polytene chromosomes of 14Chironomus species andCamptochironomus tentans are presented. BRs of the species studied were demonstrated to contain the homologus DNA sequences. The cloned fragment from the BRa ofC. thummi hybridized with the BRa ofC. piger and with a region on the arm G ofC. tentans andC. plumosus, the latter species had no extra BR. The clone 16 from the BRb ofC. thummi hybridized only with the developed BR on the arm G of all species studied. The sequence from the BRc ofC. thummi was located in the BRc ofC. piger and in the developed BR ofC. plumosus andC. nuditarsis, which were located at the most distal end of arm G. These clones can be used as markers of homologous BRs. The new mobile elements C6.10 fromC. thummi genome were localized on the polytene chromosomes of 10Chironomus species andCamptochironomus tentans. The species of the generaLipiniella, Cryptochironomus andGlyptotendipes did not contain the sequences homologous to ME C6.10.