Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “structural phylogenetics”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 397 records · Page 22Linked to original sources
PubMed1984

Ribosomal RNA structure in the diploid and phylogenetically polyploid amphibian species Hyla and Odontophrynus.

Ribosomal RNA of the diploid amphibian species Hyla chrysoscelis and Odontophrynus americanus is structurally modified by hidden breaks. Phylogenetically polyploid related species like the tetraploid Hyla versicolor, the tetraploid Odontophrynus americanus and the octoploid Ceratophrys ornata do not show hidden breaks in ribosomal RNA. Structural modifications of rRNA molecules in diploid amphibians has no detectable effect on the ribosomal activity in vitro.

Amphibians↗
PubMed1995

A concept of the development of the mammalian rhombencephalon based on physical rotational forces.

The premammalian forms do not show the metencephalic and myelencephalic divisions of the rhombencephalon. The seven longitudinal grey columns, in relation to the seven nerve components are direct cranial uninterrupted continuations from the spinal cord. The isthmus rhombencephali is a tubular structure. The phylogenetically ancient ependyma rich in tanycytes lines the fourth ventricle. The neural canal does not open into the subarachnoid space and the ependyma never becomes directly continuous with the pia mater. On the other hand, in mammals, the rhombencephalon is divided into the metencephalon and myelencephalon. The seven longitudinal grey columns get fragmented and their cell masses undergo migrations. The isthmus loses its tubular nature and undergoes modifications. The fourth ventricle opens into the subarachnoid space through three openings. The phylogenetically ancient ependyma is retained as a continuous structure only along the inferolateral angle of the fourth ventricle. At the openings of the lateral recesses, the ependyma becomes directly continuous with the pia, a neural crest derivative. The oval bundle, the corpus trapezoideum and the myelencephalic component of the nuclei pontis show extensive migrations. The above phenomena can be explained by physical rotation forces and not merely by migrations.

Animals↗
PubMed2026

The large mitochondrial genome of Syndiclis anlungensis (Lauraceae): Genome structure, comparative analysis, and phylogenetic relationships among Syndiclis species.

The complete mitochondrial genome (mitogenome) of Syndiclis anlungensis, a critically endangered tropical tree, was determined in this study. The mitogenome spans 2,368,454&#xa0;bp across four contigs and harbors 41 protein-coding genes, 22 tRNA genes, and three rRNA genes. Potential mutation regions, including 1317 repeat sequences and 698 simple sequence repeats (SSRs), were accurately located in the S. anlungensis mitogenome. Sixty-five transferred fragments of the repeats were found between its mitochondrial and chloroplast genomes. When compared to three other Laurales mitogenomes, extensive gene order shuffling is evident, leaving only five conserved gene clusters intact. Codon usage analysis reveals a pronounced A/T bias in both mitochondrial and chloroplast genes, and three mitochondrial genes (atp9, rps19, and sdh3) stand out for their high divergence across eleven Syndiclis taxa. Selection analyses indicate strong purifying pressure on rpl2, rpl16, and sdh3 (Ka/Ks&#xa0;<&#xa0;1), with no positive selection detected. Using 41 mitochondrial protein-coding gene sequences from sixteen and three individuals of Syndiclis and Beilschmiedia species, respectively, our phylogenetic tree recovers Syndiclis as monophyletic, with two well-supported clades: one includes S. anlungensis, S. chinensis, S. lotungensis, S. marlipoensis, and a putative new Syndiclis species from Yunnan; the other contains S. furfuracea, S. hongkongensis, S. kwangsiensis, and three putative new Syndiclis species from Guangdong and Vietnam.

Genome, Mitochondrial↗
PubMed1965

Phylogenetic origins of antibody structure. I. Multichain structure of immunoglobulins in the smooth dogfish (Mustelus canis).

The elasmobranch Mustelus canis has been shown to produce antibodies to Limulus hemocyanin. The serum of both normal and immunized M. canis contains immunoglobulins having sedimentation coefficients of approximately 7S and 17S. Antibody activity was found in the 17S immunoglobulin which may be dissociated to 7S components with concomitant loss of activity. Both 17S and 7S serum, immunoglobulins were antigenically identical. They consisted of light and heavy chains present in amounts comparable to those of higher vertebrates. Peptide maps indicated that the light chains had an entirely different primary structure than the heavy chains, but that the corresponding chains of 7S and 17S dogfish serum immunoglobulins were similar in primary structure. The heavy chains appeared to resemble the n chains of immunoglobulins of higher vertebrates in their starch gel electrophoretic behavior. It is suggested that the elasmobranch M. canis may have only one major class of immunoglobulins resembling that of macroglobulins (gammaM-immunoglobulins) seen in higher vertebrates. The results indicate that the multichain structure of antibodies is an ancient evolutionary development.

Animals↗
PubMed1966

Phylogenetic origins of antibody structure. II. Immunoglobulins in the primary immune response of the bullfrog, Rana catesbiana.

The anuran amphibian, Rana catesbiana, has been found to possess at least two kinds of immunoglobulins corresponding to gammaG- and gammaM-classes. These classes have the same chain structures as those of their counterparts in higher animal species. Light chains of both immunoglobulins had molecular weights of 20,000. Heavy chains of the gammaM-class had molecular weights of 72,100; those of the gammaG-class had molecular weights of 53,600. The carbohydrate content of the gammaG-immunoglobulin was 2.1%, and that of the gammaM-protein was 10.8%. The amino acid compositions of the immunoglobulins were generally similar to those of mammalian immunoglobulins. After a single injection of phage antigen (f2), the order of appearance of phage-neutralizing activity in the frog immunoglobulin classes was (a) gammaM-antibodies, and (b) gammaG-antibodies. The results of this and previous studies suggest that the gammaG-immunoglobulins emerged at some point in evolution between the elasmobranchs and the anuran amphibians.

Animals↗
PubMed1968

Phylogenetic origins of antibody structure. 3. Antibodies in the primary immune response of the sea lamprey, Petromyzon marinus.

The sea lamprey, Petromyzon marinus, has been found to produce specific antibodies after immunization with bacteriophage f2. Antibody activity is localized in 6.6S and 14S fractions of lamprey serum. The 6.6S antibodies were purified by a combination of zone electrophoresis, ion exchange chromatography, and gel filtration. Antigenic analysis of the 6.6S antibodies showed them to be free of other serum proteins and antigenically similar or identical to the 14S fraction. Evidence has been obtained which suggests that the 6.6S immunoglobulins consist of light components (molecular weight 25,000) and heavy components (molecular weight 70,000). In the immunoglobulin, these polypeptides appear to be linked via weak interactions but not by interchain disulfide bonds. Molecular weight analyses support the view that the chains can undergo concentration-dependent dissociation in aqueous solutions. Amino acid analyses showed that the compositions of the light and heavy components were similar and that aspartic acid or asparagine was the predominant amino terminal residue. Starch gel electrophoresis indicated that the subunits of lamprey antibodies are diffusely heterogeneous. The heavy chain mobility corresponded to that of micro-chains and resembled that of heavy chains of shark and sting ray immunoglobulins. In the course of the fractionation a 46S natural hemagglutinin composed of lower molecular weight subunits was isolated. This hemagglutinin did not resemble the lamprey immunoglobulin although it had a similar zone electrophoretic mobility in the beta-region. These studies are consistent with the hypothesis that micro-chains were the earliest of the heavy chain classes to emerge and further support the view that the multichain structure of immunoglobulins is a fundamental feature of antibody molecules.

Animals↗
PubMed1989

Ferredoxin and rubredoxin from Butyribacterium methylotrophicum: complete primary structures and construction of phylogenetic trees.

Complete amino acid sequences of ferredoxin and rubredoxin from Butyribacterium methylotrophicum, a methylotrophic hetero-acetogen, were determined by combination of protease digestion, Edman degradation, carboxypeptidase digestion, and/or partial acid hydrolysis. The ferredoxin was composed of 55 amino acids with a molecular weight of 5,732 excluding iron and sulfur atoms and showed a typical 2[4Fe-4S]-type ferredoxin sequence with an internal repeat at the 14-23 and 42-51 positions. The rubredoxin was composed of 53 amino acids with a molecular weight of 5,672 excluding iron atom and showed a sequence similar to those of other anaerobic rubredoxins. The sequences were compared to those of corresponding proteins from six different bacteria to construct phylogenetic trees, which showed essentially the same topology. The relationships between the ferredoxin sequences from this bacterium and those of Clostridium thermoaceticum and Methanosarcina barkeri, both of which possess a carbonyl-dependent acetyl-CoA metabolic system, are also discussed.

Amino Acid Sequence↗
PubMed1985

A phylogenetic study of the structural and functional characteristics of corticosteroid binding globulin in primates.

A monospecific antiserum against human corticosteroid binding globulin (hCBG) has been used to identify structural similarities between hCBG and CBG in the blood of other primates and representative species of different vertebrate classes. Double immunodiffusion analysis indicated that only CBG in Old World monkeys and apes cross-react with the hCBG antiserum. This was confirmed by a solid-phase radioimmunoassay for hCBG which also demonstrated that CBG in apes is immunologically identical to hCBG and that Old World monkey CBG comprises most, but not all, of the hCBG epitopes. The electrophoretic mobilities of human, gorilla and gibbon CBG were similar (RF 0.50-0.51), but differed from Old World monkey CBG (RF 0.44-0.49) and chimpanzee CBG (RF 0.47). Although serum/plasma cortisol binding capacities were similar in Old World primates, the dissociation half-times (t 1/2) of cortisol were higher from human and ape CBG (18-25 min) than from Old World monkey CBG (14-18 min). The steroid binding specificities of human and ape (CBG corticosterone greater than cortisol greater than progesterone greater than or equal to testosterone) were also different from those of Old World monkey CBG (corticosterone much greater than cortisol approximately equal to progesterone greater than testosterone). Lemur plasma cortisol binding capacity and CBG dissociation t 1/2 of cortisol were similar to hCBG, but its steroid binding specificity was different (cortisol greater than corticosterone greater than progesterone greater than or equal to testosterone) and it did not cross-react with the hCBG antiserum.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1986

[Characteristics of the structural organization of the phylogenetically new fields in the human neocortex].

The myeloarchitectonics of the specific human fields 40, 39, 37c, 37b of neocortex and also fields 17 and 19 which are the cortex end of visual analyzer has been studied with the help of neurohistological and quantitative methods. According to the character of the fibrous bundles, their diameter, the quantity of the fibrous in them and the diameter of the fibrous gradual changes from field 17 to field 19 and further to field 39 have been shown. It is an evidence of the succession between phylogenetically older and younger fields of the cortex. The peculiarities of the field quantitative myeloarchitectonics differing in the function and genesis are marked by heterochronous growth of these fields square in the process of evolution.

Adult↗
PubMed1985

Comparative sequence analysis as a tool for studying the secondary structure of mRNAs.

Analysis of phylogenetically conserved secondary structure has been important in the development of models for the secondary structure of structural RNAs. In this paper, we apply this type of analysis to several families of informational RNAs to evaluate its usefulness in developing secondary structure models for mRNAs and mRNA precursors. We observed many conserved helices in all mRNA groups analyzed. Three criteria were used to identify potential helices which were not conserved solely because of coding sequence constraints, and may therefore be important for the structure and function of the RNA. These results suggest that this approach will be useful in deriving secondary structure models for informational RNAs when used in conjunction with other complementary techniques, and in designing experiments to determine the functional significance of conserved base pairing interactions.

Actins↗
PubMed1997

A family of gram-negative bacterial outer membrane factors that function in the export of proteins, carbohydrates, drugs and heavy metals from gram-negative bacteria.

Gram-negative bacteria have evolved transport complexes that export macromolecules and toxic substances across the two membranes of the cell envelope in a single energy coupled step. The process requires (1) a cytoplasmic membrane export system, (2) a membrane fusion protein (MFP), and (3) an outer membrane factor (OMF). Families comprising the former two constituents have been described previously. We here present an analysis of the phylogenetic and structural characteristics of the OMF family. Twenty-one members of this family have been identified, and based on available evidence, they function in conjunction with ABC, RND, MFS and/or other types of cytoplasmic transport systems. OMFs exhibit fairly uniform sizes (398-495 residues with two exceptions), and based on computational analyses, they may form beta-barrel structures consisting of up to 16 beta-strands. Phylogenetic analyses reveal that while the MFPs cluster in accordance with the type of cytoplasmic membrane transport systems with which they function, OMFs do not. We conclude that OMFs probably comprise a family of outer membrane porin-type proteins of uniform structure which did not coevolve with their cognate cytoplasmic membrane transport systems.

Bacterial Outer Membrane Proteins↗
PubMed2026

Genome-wide characterization of heat shock protein genes reveals thermal stress-responsive candidates in Litopenaeus vannamei.

Heat shock proteins (HSPs) are conserved molecular chaperones involved in protein folding, refolding, aggregation prevention, and degradation of damaged proteins. However, the genomic organization and thermal responsiveness of HSP genes in the Pacific white shrimp (Litopenaeus vannamei) remain incompletely understood. Here, we performed a genome-wide analysis of the HSP gene family and examined its phylogenetic relationships, structural features, duplication patterns, sequence variation, interaction networks, and transcriptional responses to acute heat stress. A total of 34 HSP genes were identified and classified into the HSP90, HSP70, HSP40/DNAJ, HSP60, and small HSP families. Phylogenetic, motif, gene structure, synteny, and subcellular localization analyses revealed evolutionary conservation and structural diversification among family members. Three duplicated gene pairs were identified, comprising two segmental duplications and one tandem duplication. All pairs exhibited Ka/Ks ratios below 1, consistent with purifying selection of varying strength. Sequence analysis identified 295 nonsynonymous single-nucleotide polymorphisms, of which 12 were consistently predicted to be deleterious by multiple algorithms. Protein-protein interaction analysis indicated enrichment of protein-folding and cellular stress-response functions. RT-qPCR analysis showed significant induction of HSPA4, HSP90AA1, TRAP1, BiP, and DNAJA1 after 6, 12, and 24&#xa0;h of exposure to 34&#xa0;&#xb0;C, whereas DNAJC3 was significantly induced only at 12&#xa0;h. All six genes reached their highest transcript abundance at 12&#xa0;h. These findings may provide a genomic framework for HSP genes in L. vannamei and identify candidate genes and variants associated with thermal stress responses.

Animals↗
PubMed2000

Neuroimaging evidence implicating cerebellum in support of sensory/cognitive processes associated with thirst.

Recent studies implicate the cerebellum, long considered strictly a motor control structure, in cognitive, sensory, and affective phenomenon. The cerebellum, a phylogenetically ancient structure, has reciprocal ancient connections to the hypothalamus, a structure important in vegetative functions. The present study investigated whether the cerebellum was involved in vegetative functions and the primal emotions engendered by them. Using positron emission tomography, we examined the effects on the cerebellum of the rise of plasma sodium concentration and the emergence of thirst in 10 healthy adults. The correlation of regional cerebral blood flow with subjects' ratings of thirst showed major activation in the vermal central lobule. During the development of thirst, the anterior and posterior quadrangular lobule, lingula, and the vermis were activated. At maximum thirst and then during irrigation of the mouth with water to alleviate dryness, the cerebellum was less activated. However, 3 min after drinking to satiation, the anterior quadrangular lobule and posterior cerebellum were highly activated. The increased cerebellar activity was not related to motor behavior as this did not occur. Instead, responses in ancient cerebellar regions (vermis, fastigal nucleus, archicerebellum) may be more directly related to vegetative and affective aspects of thirst experiences, whereas activity in neocerebellar (posterior) regions may be related to sensory and cognitive aspects. Moreover, the cerebellum is apparently not involved in the computation of thirst per se but rather is activated during changes in thirst/satiation state when the brain is "vigilant" and is monitoring its sensory systems. Some neocerebellar activity may also reflect an intentionality for gratification by drinking inherent in the consciousness of thirst.

Adult↗
PubMed1994

A comparative database of group I intron structures.

We have created a database of comparatively derived group I intron secondary structure diagrams. This collection currently contains a broad sampling of phylogenetically and structurally similar and diverse structures from over 200 publicly available intron sequences. As more group I introns are sequenced and added to the database, we anticipate minor refinements in these secondary structure diagrams. These diagrams are directly accessible by computer as well as from the authors.

Base Sequence↗
PubMed1979

Purification and primary structure of cytochrome c-552 from the cyanobacterium, Synechococcus PCC 6312.

Cytochrome c-552 (soluble 'cytochrome f') from the unicellular cyanobacterium Synechococcus PCC 6312 (ATCC 27167) was purified and the primary structure determined. The proposed sequence consists of one polypeptide chain of 87 residues. The sequence was determined by a combination of chemical and enzymatic cleavage, manual and automatic sequencing and mass spectroscopy. This is the first amino acid sequence of this cytochrome from a unicellular cyanobacterium to be determined in a study of the variation in primary structure between phylogenetically distant cyanobacteria. The sequence is compared to the primary structures of the cytochrome from filamentous cyanobacteria and from eukaryotic algae. The significance of these sequence comparisons to the current hypotheses concerning the origin of eukaryotic cells and their chloroplasts is discussed.

Amino Acid Sequence↗