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At least 649 records · Page 36Linked to original sources
PubMed1986

The RNA component of the Bacillus subtilis RNase P. Sequence, activity, and partial secondary structure.

The gene defining the catalytic RNA component of RNase P in Bacillus subtilis 168 was cloned into bacteriophage lambda and plasmid vectors. The nucleotide sequence of the gene and its surroundings was determined from the cloned DNA and by directly sequencing or reverse transcribing the RNase P RNA. The B. subtilis RNase P RNA sequence (400-401 nucleotides) is remarkably different from that of Escherichia coli (377 nucleotides) (Reed, R. E., Baer, M. F., Guerrier-Takada, C., Donis-Keller, H., and Altman, S. (1982) Cell 30, 627-636; Sakamoto, H., Kimura, N., Nagawa, F., and Shimura, Y. (1983) Nucleic Acids Res. 11, 8237-8251). At best the two are less than 50% similar in sequence. To verify that the RNase P RNA gene was analyzed, a modified, putative gene was cloned adjacent to a bacteriophage T7 promoter and various transcripts were tested for RNase P activity. The intact gene transcript, but not fragments, showed full activity. Full catalytic activity was restored upon mixing the fragments. The extensive differences between the B. subtilis and E. coli RNase P RNAs precluded full covariance analysis of secondary structure, but phylogenetically consistent foldings for portions of both molecules could be derived.

Bacillus subtilis↗
PubMed1986

Amino acid replacements in yeast iso-1-cytochrome c. Comparison with the phylogenetic series and the tertiary structure of related cytochromes c.

The structural and folding requirements of eukaryotic cytochromes c have been investigated by determining the appropriate DNA sequences of a collection of 46 independent cyc 1 missense mutations obtained in the yeast Saccharomyces cerevisiae and by deducing the corresponding amino acid replacements that abolish function of iso-1-cytochrome c. A total of 33 different replacements at 19 amino acid positions were uncovered in this and previous studies. Because all of these nonfunctional iso-1-cytochromes c are produced at far below the normal level and because a representative number are labile in vitro, most of the replacements appear to be affecting stability of the protein or heme attachment. By considering the tertiary structure of related cytochromes c, the loss of function of most of the mutant iso-1-cytochromes c could be attributed to either replacements of critical residues that directly interact with the heme group or to replacements that disrupt the proper folding of the protein. The replacements of residues interacting with the heme group include those required for covalent attachment (Cys-19 and Cys-22), ligand formation (His-23 and Met-85), and formation of the immediate heme environment (Leu-37, Tyr-53, Trp-64, and Leu-73). Proper folding of the protein is prevented by replacements of glycine residues at sites that cannot accommodate side chains (Gly-11 and Gly-34); by replacements of residues with proline, which limit the torsion angle (Leu-14 and His-38); and by replacements apparently unable to direct the local folding of the backbone into the proper conformation (Pro-35, Tyr-72, Asn-75, Pro-76, Lys-84, Leu-99, and Leu-103). Even though most of the missense mutations occurred at sites corresponding to evolutionarily invariant or conserved residues, a consideration of the replacements in functional revertants indicates that the requirement for residues evolutionarily preserved is less stringent than commonly assumed.

Alleles↗
PubMed1987

[Ultrastructure of the juxtaglomerular apparatus of the kidney and of the peripolar cells in the sand lizard (Lacerta agilis)].

In 9 sand lizards ultrastructure of the juxtaglomerular complex of the kidney has been studied. It is presented as juxtaglomerular cells, situating in the middle tunic of the afferent glomerular arteriole near the vascular pole of the renal corpuscle. Cytoplasm of these cells contains secretory granules at various stages of development: young, maturing and mature, as well as solid corpuscles and myofilaments. In some nephrons primitive forms of the macula densa and the juxtaglomerular island occur. Their presence demonstrates phylogenetically new structural organization of the juxtaglomerular complex in lizards. For the first time in reptilia peripolar cells are found, they are situated on the basal membrane of the external part of the glomerular capsule near the vascular pole of the renal corpuscle. A suggestion is made on their functional interconnection with the juxtaglomerular complex.

Animals↗
PubMed1983

[Cross-reactivity of 3M KCl extracts of fetal tissue from various species in the macrophage electrophoresis mobility (MEM) test. I. Extracts from fetuses of mammals and one species of fowl].

Extracts were prepared by the 3M KCl method from fetal tissues of human, mouse, cattle, pig, sheep, cat, guinea pig, and chicken origin. Lymphocytes of tumor bearing mice and tumor patients reacted specifically in the MEM-test with antigenic components of the extracts. The cellular sensitization of the tumor-bearer was not correlated with the localization and the histologic type of the tumor. The cross-reacting oncofetal antigens obviously represent phylogenetically conserved structures.

Animals↗
PubMed1983

[Cross-reactivity of 3M KCl-extracts of fetal tissue from various species in the macrophage electrophoresis mobility test. II. Tissue extracts from lower vertebrates in various phases of development].

Cellular sensitization was detected by the MEM-test using 3M KCl-extracts of fetuses from man and mouse and of different metamorphic stages of the water frog (tadpoles) and the carp (yolk sack-bearing stage). The sensitization demonstrated was independent on the type of tumor tested. The occurrence of active components in the extracts was correlated with certain stages of individual development of water frog and carp. The evidence of these components in species of several classes of vertebrates confirms the assumption of phylogenetically conserved structures.

Animals↗
PubMed1981

[Neuropathological and morphometrical investigations on the localization of the perinatal hypoxic brain damage (author's transl)].

The localization and extent of nerve cell damage caused by perinatal hypoxia has been examined in 83 cases. In 54% of the cases nerve cell damage was localized in the medulla oblongata, in 40% the thalamus and in one third the substantia grisea centralis was affected by nerve cell necroses. In contrast to the phylogenetically older structures of CNS, nerve cell lesions occurred in our material only in 30% in the cerebral cortex and in 18% of our observation the cerebellar cortex. The results show, that the brain stem is especially vulnerable to perinatal hypoxia, this is at variance with hitherto existing conceptions. In a fourth part of the material, nerve cell damage was found in the medulla spinalis, especially in the columna anterior, After prolonged hypoxia the neuron-glia index in the lamina tecti deviates by 0.0491 from that following peracute anoxia. This caused by loss of nerve cells in the brain stem due to perinatal continuous hypoxia.

Birth Injuries↗
PubMedDate not supplied

[The ultrastructure of the myelinated fibers of the rat endbrain in hypokinesia].

Myelin fibres structure in phylogenetically different regions of telencephalon--in hippocampus, cingular cortex and sensomotor cortex of cerebrum of rats, in hypokinesia lasting for 40 and 90 days was studied electron-microscopically. Changes in ultrastructure of myelin fibres in these formations were found which exposed unequally in different regions and depended on the experiment duration. In 40 days hypokinezia changes were noted only in hippocampus and cingular cortex, while in neocortex they were prominent only in 90-days hypokinisia. Moreover, in neocortex changes were different in large and fine fibres, being more prominent in the former.

Animals↗
PubMed1996

Phylogenetic analysis of tmRNA secondary structure.

The bacterial tmRNA acts with dual tRNA-like and mRNA-like character to tag incomplete translation products for degradation. Comparative analysis of 17 tmRNA genes (including eight new sequences) has allowed us to deduce conserved features of the tmRNA secondary structure. Except in a segment that includes the first codon of the tag reading frame, tmRNA is highly structured, with four pseudoknots and a total of 11 conserved base pairing regions. The previously identified tRNA minihelix structure is connected by a long base paired region to a large structured domain composed of a pseudoknot, followed by the tag reading frame and a string of three rather similar pseudoknots. The conservation of numerous structural elements among diverse eubacterial species indicates that these elements have important function beyond simply forming an endonuclease-resistant link between the reading frame and the tRNA-like domain.

Bacteria↗
PubMed1997

Highly polymorphic microsatellite loci in the colonial ascidian Botryllus schlosseri.

Five mircosatellite loci are characterized for the colonial ascidian Botryllus schlosseri. Within one population from Monterey, California, these loci have 3 to 17 alleles, observed heterozygosities from 0.40 to 0.63, expected heterozygosities from 0.52 to 0.84, and an overall paternity exclusion rate (QT) of 0.78. Three of the five loci demonstrated Mendelian patterns of inheritance in laboratory crosses. The size distribution of alleles suggests that most allelic diversity within these loci is generated by single-step and less frequently multistep mutations. However, several alleles may also have been generated by single based insertions or deletions. Mutation rates for the five microsatellite loci are less than 1 x 10(-2) per generation. Because or their highly polymorphic nature, these loci should prove useful for exploring issues of identity, kinship, population structure, and phylogenetics.

Alleles↗
PubMed1993

Secondary structure of RNase MRP RNA as predicted by phylogenetic comparison.

RNase MRP is a ribonucleoprotein endoribonuclease that has been shown to cleave mitochondrial primer RNA sequences from a variety of sources. The bulk of RNase MRP activity is found in the nucleus where its function remains unknown. Two different approaches have resulted in predictions of distinct secondary structures for RNase MRP RNA. In order to analyze more definitively the higher-order structure of RNase MRP RNA, we have conducted a phylogenetic comparison of the available RNase MRP RNA sequences from human, mouse, rat, cow, toad, and yeast. The resulting secondary structure shares features in common with previously described structures for prokaryotic and eukaryotic RNase P RNAs (1) and RNase MRP RNAs (2, 3). In addition, the phylogenetic structure is consistent with available chemical modification data on RNase MRP RNA and with the detailed analysis of the To antigen binding domain located near the 5' end of the RNase MRP RNA. The structure is not limited to RNase MRP RNAs, but can be expanded to cover both eukaryotic RNase P RNAs and RNase P/MRP RNAs from plants.

Animals↗
PubMed2003

Phylogenetic classification of protozoa based on the structure of the linker domain in the bifunctional enzyme, dihydrofolate reductase-thymidylate synthase.

We have determined the crystal structure of dihydrofolate reductase-thymidylate synthase (DHFR-TS) from Cryptosporidium hominis, revealing a unique linker domain containing an 11-residue alpha-helix that has extensive interactions with the opposite DHFR-TS monomer of the homodimeric enzyme. Analysis of the structure of DHFR-TS from C. hominis and of previously solved structures of DHFR-TS from Plasmodium falciparum and Leishmania major reveals that the linker domain primarily controls the relative orientation of the DHFR and TS domains. Using the tertiary structure of the linker domains, we have been able to place a number of protozoa in two distinct and dissimilar structural families corresponding to two evolutionary families and provide the first structural evidence validating the use of DHFR-TS as a tool of phylogenetic classification. Furthermore, the structure of C. hominis DHFR-TS calls into question surface electrostatic channeling as the universal means of dihydrofolate transport between TS and DHFR in the bifunctional enzyme.

Amino Acid Sequence↗
PubMed2004

Convergence, divergence, and homogenization in the ecological structure of emydid turtle communities: the effects of phylogeny and dispersal.

Studies that have explored the origins of patterns of community structure from a phylogenetic perspective have generally found either convergence (similarity) in community structure between regions through adaptive evolution or lack of convergence (dissimilarity) due to phylogenetic conservatism in the divergent ecological characteristics of lineages inhabiting different regions. We used a phylogenetic approach to document a third pattern in the structure of emydid turtle communities. Emydid communities in southeastern North America tend to have a higher proportion of aquatic species than those in the northeast. This pattern reflects phylogenetic conservatism in the ecology and biogeography of two basal emydid clades, limiting convergence in community structure between these regions. However, differences in community structure between northeastern and southeastern North America have also been homogenized considerably by the dispersal of species with phylogenetically conserved ecological characteristics between regions. This pattern of ecologically conservative dispersal may be important in many continental and oceanic systems.

Animals↗
PubMed1997

Evolutionary relationship of the ligand-gated ion channels and the avermectin-sensitive, glutamate-gated chloride channels.

Two cDNAs, GluClalpha and GluClbeta, encoding glutamate-gated chloride channel subunits that represent targets of the avermectin class of antiparasitic compounds, have recently been cloned from Caenorhabditis elegans (Cully et al., Nature, 371, 707-711, 1994). Expression studies in Xenopus oocytes showed that GluClalpha and GluClbeta have pharmacological profiles distinct from the glutamate-gated cation channels as well as the gamma-aminobutyric acid (GABA)- and glycine-gated chloride channels. Establishing the evolutionary relationship of related proteins can clarify properties and lead to predictions about their structure and function. We have cloned and determined the nucleotide sequence of the GluClalpha and GluClbeta genes. In an attempt to understand the evolutionary relationship of these channels with the members of the ligand-gated ion channel superfamily, we have performed gene structure comparisons and phylogenetic analyses of their nucleotide and predicted amino acid sequences. Gene structure comparisons reveal the presence of several intron positions that are not found in the ligand-gated ion channel superfamily, outlining their distinct evolutionary position. Phylogenetic analyses indicate that GluClalpha and GluClbeta form a monophyletic subbranch in the ligand-gated ion channel superfamily and are related to vertebrate glycine channels/receptors. Glutamate-gated chloride channels, with electrophysiological properties similar to GluClalpha and GluClbeta, have been described in insects and crustaceans, suggesting that the glutamate-gated chloride channel family may be conserved in other invertebrate species. The gene structure and phylogenetic analyses in combination with the distinct pharmacological properties demonstrate that GluClalpha and GluClbeta belong to a discrete ligand-gated ion channel family that may represent genes orthologous to the vertebrate glycine channels.

Animals↗
PubMed1991

Primary structure and oxygen-binding properties of the hemoglobin from the lesser hedgehog tenrec (Echinops telfairi, Zalambdodonta). Evidence for phylogenetic isolation.

The primary structures of the alpha- and beta-hemoglobin chains of the lesser hedgehog tenrec (Echinops telfairi, Zalambdodonta) are presented. Chain separation was performed by carboxymethyl-cellulose chromatography. The peptides, obtained by tryptic digestion of the oxidized chains, were prefractionated by gel chromatography and isolated by reversed-phase HPLC. For sequence analysis gas and liquid phase sequencers were employed. The tenrec hemoglobin consists of one alpha- and two beta-chains the latter occurring in a 1:1 ratio and differing in beta 16 Gly/Cys and beta 118 Phe/Leu. Two external cysteine residues at beta 16 and beta 52 cause reversible polymerization to octamers and most likely irreversible formation of higher polymers. A comparison of the whole chains and certain positions of tenrec hemoglobin with those of Insectivora sensu strictu, Scandentia and Proto- and Metatheria corroborates a long and independent evolution of tenrec and its phylogenetic isolation from the Insectivora s.str. (hedgehog, musk shrew and mole). Replacements at positions involved in heme and subunit interface contacts are discussed. Compared to human hemoglobin the tenrec pigment shows a low intrinsic oxygen affinity as well as lower chloride and temperature sensitivities, a reduced Bohr effect and a strong response to 2,3-DPG. The possible adaptive significance of these properties is discussed in relation to the large diurnal body temperature variations seen in tenrecs.

Amino Acid Sequence↗
PubMedDate not supplied

[Neuronal reactions of the olfactory centers of the forebrain during stimulation of the hypothalamic structures in rabbits].

During stimulation of phylogenetically ancient parts of the hypothalamus (the anterior and lateral), neuronal reactions have been recorded in the prepyriform lobe and tuberculum olfactorium. These reactions are characterized by a short latent period (6-25 msec) and high stability to rhythmic stimulation. Neuronal reactions in the same olfactory centers during stimulation of phylogenetically more recent hypothalamic structures (the posterior and medial) exhibit a long latent period (30-120 msec) and are readily exhausted by rhythmic stimulation.

Animals↗
PubMed2005

Phylogenetic analysis of ecomorphological divergence, community structure, and diversification rates in dusky salamanders (Plethodontidae: Desmognathus).

An important dimension of adaptive radiation is the degree to which diversification rates fluctuate or remain constant through time. Focusing on plethodontid salamanders of the genus Desmognathus, we present a novel synthetic analysis of phylogeographic history, rates of ecomorphological evolution and species accumulation, and community assembly in an adaptive radiation. Dusky salamanders are highly variable in life history, body size, and ecology, with many endemic lineages in the southern Appalachian Highlands of eastern North America. Our results show that life-history evolution had important consequences for the buildup of plethodontid-salamander species richness and phenotypic disparity in eastern North America, a global hot spot of salamander biodiversity. The origin of Desmognathus species with aquatic larvae was followed by a high rate of lineage accumulation, which then gradually decreased toward the present time. The peak period of lineage accumulation in the group coincides with evolutionary partitioning of lineages with aquatic larvae into seepage, stream-edge, and stream microhabitats. Phylogenetic simulations demonstrate a strong correlation between morphology and microhabitat ecology independent of phylogenetic effects and suggest that ecomorphological changes are concentrated early in the radiation of Desmognathus. Deep phylogeographic fragmentation within many codistributed ecomorph clades suggests long-term persistence of ecomorphological features and stability of endemic lineages and communities through multiple climatic cycles. Phylogenetic analyses of community structure show that ecomorphological divergence promotes the coexistence of lineages and that repeated, independent evolution of microhabitat-associated ecomorphs has a limited role in the evolutionary assembly of Desmognathus communities. Comparing and contrasting our results to other adaptive radiations having different biogeographic histories, our results suggest that rates of diversification during adaptive radiation are intimately linked to the degree to which community structure persists over evolutionary time.

Adaptation, Biological↗