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At least 1,207 records · Page 67Linked to original sources
PubMed1999

The phylogeny of land plants inferred from 18S rDNA sequences: pushing the limits of rDNA signal?

Previous studies of the phylogeny of land plants based on analysis of 18S ribosomal DNA (rDNA) sequences have generally found weak support for the relationships recovered and at least some obviously spurious relationships, resulting in equivocal inferences of land plant phylogeny. We hypothesized that greater sampling of both characters and taxa would improve inferences of land plant phylogeny based on 18S rDNA sequences. We therefore conducted a phylogenetic analysis of complete (or nearly complete) 18S rDNA sequences for 93 species of land plants and 7 green algal relatives. Parsimony analyses with equal weighting of characters and characters state changes and parsimony analyses weighting (1) stem bases half as much as loop bases and (2) transitions half as much as transversions did not produce substantially different topologies. Although the general structure of the shortest trees is consistent with most hypotheses of land plant phylogeny, several relationships, particularly among major groups of land plants, appear spurious. Increased character and taxon sampling did not substantially improve the performance of 18S rDNA in phylogenetic analyses of land plants, nor did analyses designed to accommodate variation in evolutionary rates among sites. The rate and pattern of 18S rDNA evolution across land plants may limit the usefulness of this gene for phylogeny reconstruction at deep levels of plant phylogeny. We conclude that the mosaic structure of 18S rDNA, consisting of highly conserved and highly variable regions, may contain historical signal at two levels. Rapidly evolving regions are informative for relatively recent divergences (e.g., within angiosperms, seed plants, and ferns), but homoplasy at these sites makes it difficult to resolve relationships among these groups. At deeper levels, changes in the highly conserved regions of small-subunit rDNAs provide signal across all of life. Because constraints imposed by the secondary structure of the rRNA may affect the phylogenetic information content of 18S rDNA, we suggest that 18S rDNA sequences be combined with other data and that methods of analysis be employed to accommodate these differences in evolutionary patterns, particularly across deep divergences in the tree of life.

DNA, Plant↗
PubMed1997

Flightlessness and phylogeny amongst endemic rails (Aves:Rallidae) of the New Zealand region.

The phylogenetic relationships of a number of flightless and volant rails have been investigated using mtDNA sequence data. The third domain of the small ribosomal subunit (12S) has been sequenced for 22 taxa, and part of the 5' end of the cytochrome-b gene has been sequenced for 12 taxa. Additional sequences were obtained from outgroup taxa, two species of jacana, sarus crane, spur-winged plover and kagu. Extinct rails were investigated using DNA extracted from subfossil bones, and in cases where fresh material could not be obtained from other extant taxa, feathers and museum skins were used as sources of DNA. Phylogenetic trees produced from these data have topologies that are, in general, consistent with data from DNA-DNA hybridization studies and recent interpretations based on morphology. Gallinula chloropus moorhen) groups basally with Fulica (coots), Amaurornis (= Megacrex) ineptus falls within the Gallirallus/Rallus group, and Gallinula (= Porphyrula) martinica is basal to Porphyrio (swamphens) and should probably be placed in that genus. Subspecies of Porphyrio porphyrio are paraphyletic with respect to Porphyrio mantelli (takahe). The Northern Hemisphere Rallus aquaticus is basal to the south-western Pacific Rallus (or Gallirallus) group. The flightless Rallus philippensis dieffenbachii is close to Rallus modestus and distinct from the volant Rallus philippensis, and is evidently a separate species. Porzana (crakes) appears to be more closely associated with Porphyrio than Rallus. Deep relationships among the rails remain poorly resolved. Rhynochetus jubatus (kagu) is closer to the cranes than the rails in this analysis. Genetic distances between flightless rails and their volant counterparts varied considerably with observed 12S sequence distances, ranging from 0.3% (Porphyrio porphyrio melanotus and P. mantelli mantelli) to 7.6% (Rallus modestus and Rallus philippensis). This may be taken as an indication of the rapidity with which flightlessness can evolve, and of the persistence of flightless taxa. Genetic data supported the notion that flightless taxa were independently derived, sometimes from similar colonizing ancestors. The morphology of flightless rails is apparently frequently dominated by evolutionary parallelism although similarity of external appearance is not an indication of the extent of genetic divergence. In some cases taxa that are genetically close are morphologically distinct from one another (e.g. Rallus (philippensis) dieffenbachii and R. modestus), whilst some morphologically similar taxa are evidently independently derived (e.g. Porphyio mantelli hochstetteri and P.m. mantelli).

Animals↗
PubMed2002

A genomic schism in birds revealed by phylogenetic analysis of DNA strings.

The molecular systematics of vertebrates has been based entirely on alignments of primary structures of macromolecules; however, higher order features of DNA sequences not used in traditional studies also contain valuable phylogenetic information. Recent molecular data sets conflict over the phylogenetic placement of flightless birds (ratites - paleognaths), but placement of this clade critically influences interpretation of character change in birds. To help resolve this issue, we applied a new bioinformatics approach to the largest molecular data set currently available. We distilled nearly one megabase (1 million base pairs) of heterogeneous avian genomic DNA from 20 birds and an alligator into genomic signatures, defined as the complete set of frequencies of short sequence motifs (strings), thereby providing a way to directly compare higher order features of nonhomologous DNA sequences. Phylogenetic analysis and principal component analysis of the signatures strongly support the traditional hypothesis of basal ratites and monophyly of the nonratite birds (neognaths) and imply that ratite genomes are linguistically primitive within birds, despite their base compositional similarity to neognath genomes. Our analyses show further that the phylogenetic signal of genomic signatures are strongest among deep splits within vertebrates. Despite clear problems with phylogenetic analysis of genomic signatures, our study raises intriguing issues about the biological and genomic differences that fundamentally differentiate paleognaths and neognaths.

Animals↗
PubMed1992

Mutation of a cysteine in the first transmembrane segment of Na,K-ATPase alpha subunit confers ouabain resistance.

The cardiac glycoside ouabain inhibits Na,K-ATPase by binding to the alpha subunit. In a highly ouabain resistant clone from the MDCK cell line, we have found two alleles of the alpha subunit in which the cysteine, present in the wild-type first transmembrane segment, is replaced by a tyrosine (Y) or a phenylalanine (F). We have studied the kinetics of ouabain inhibition by measuring the current generated by the Na,K-pump in Xenopus oocytes injected with wild-type and mutated alpha 1 and wild-type beta 1 subunit cRNAs. When these mutations, alpha 1C113Y and alpha 1C113F [according to the published sequence [Verrey et al. (1989) Am. J. Physiol., 256, F1034] were introduced in the alpha 1 subunit of the Na,K-ATPase from Xenopus laevis, the inhibition constant (Ki) of ouabain increased greater than 1000-fold compared with wild-type. A more conservative mutation, serine alpha 1C113S did not change the Ki. We observed that the decreased affinity for ouabain was mainly due to a faster dissociation, but probably also to a slower association. Thus we propose that an amino acid residue of the first transmembrane segment located deep in the plasma membrane participates in the structure and the function of the ouabain binding site.

Amino Acid Sequence↗
PubMed2006

Oil biodegradation by Bacillus strains isolated from the rock of an oil reservoir located in a deep-water production basin in Brazil.

Sixteen spore forming Gram-positive bacteria were isolated from the rock of an oil reservoir located in a deep-water production basin in Brazil. These strains were identified as belonging to the genus Bacillus using classical biochemical techniques and API 50CH kits, and their identity was confirmed by sequencing of part of the 16S rRNA gene. All strains were tested for oil degradation ability in microplates using Arabian Light and Marlin oils and only seven strains showed positive results in both kinds of oils. They were also able to grow in the presence of carbazole, n-hexadecane and polyalphaolefin (PAO), but not in toluene, as the only carbon sources. The production of key enzymes involved with aromatic hydrocarbons biodegradation process by Bacillus strains (catechol 1,2-dioxygenase and catechol 2,3-dioxygenase) was verified spectrophotometrically by detection of cis,cis-muconic acid and 2-hydroxymuconic semialdehyde, and results indicated that the ortho ring cleavage pathway is preferential. Furthermore, polymerase chain reaction (PCR) products were obtained when the DNA of seven Bacillus strains were screened for the presence of catabolic genes encoding alkane monooxygenase, catechol 1,2-dioxygenase, and/or catechol 2,3-dioxygenase. This is the first study on Bacillus strains isolated from an oil reservoir in Brazil.

Alkanes↗
PubMed2006

Phylogeography and demographic history of the deep-sea fish Aphanopus carbo (Lowe, 1839) in the NE Atlantic: Vicariance followed by secondary contact or speciation?

Comparative phylogeography for the commercially valuable deep-sea fish Aphanopus carbo from a large area of the NE Atlantic revealed remarkable patterns of concordance using two mtDNA markers. Two strongly supported phylogroups were identified from complete sequences of the control region (731-733 bp) and partial sequences of cytochrome b (414 bp) In one of these groups, all sequences from the Mid-Atlantic Ridge (Faraday seamount), mainland Portugal and Madeira were clustered together. The other group constituted all the sequences from the southern coast of Pico island (Azores, central group). The remaining sampling localities had sequences represented in both phylogroups. Although the two clades were strongly differentiated (Phi(ST) = 0.8281 for the CR and Phi(ST) = 0.9083 for the cytb) no evidence for any geographical pattern in this structure, was found. Historical demography of the mitochondrial control region was analysed to clarify the phylogenetic signals embedded in each phylogroup. Mismatch distributions for both clades suggested that both phylogroups were in agreement with sudden expansion models, and both with similar time estimates of expansion (tau = 4.30 and tau = 3.45 for phylogroup one and two, respectively). A molecular clock based on cytb sequences was enforced and dating of divergence for the two phylogroup was 412.5 KY, a time that coincides with geological events that might have caused a split in the original population of black scabbardfish. Once climatic conditions and sea level were restored, the two separate populations came into contact again, leaving traces of the historical events in the non-recombinant mtDNA genes. An alternative hypothesis suggested is that two species of scabbardfish are present. The outcome from the comparison of the same mtDNA regions of the closely related Aphanopus intermedius from Angola clustered with the ones from phylogroup two (from the southern coast of Pico island, Azores). Therefore, these two species may have overlapping distribution ranges and are found sympatrically in the Azores.

Animals↗
PubMedDate not supplied

Binding of polyamine-containing toxins in the vestibule of the nicotinic acetylcholine receptor ion channel.

Several wasp venoms contain philanthotoxins (PhTXs) that act as noncompetitive inhibitors (NCIs) on cation-selective ion channels including the nicotinic acetylcholine receptor (nAChR). In the search for a ligand with high affinity and specificity for the nAChR we tested a series of newly developed PhTX analogues. Modulation of the structural elements of PhTXs can significantly influence their binding affinities. This approach resulted in the development of the photolabile compound MR44. In photoaffinity labelling studies 125I-MR44 was used to map the ligand-binding site at the Torpedo californica nAChR. Upon UV irradiation of the receptor-ligand complex, 125I-MR44 was mainly incorporated into the receptor alpha-subunit. Proteolytic mapping and microsequencing identified the site of 125I-MR44 cross-linking within the sequence alphaHis-186 to alphaLeu-199 that in its C-terminal region partially overlaps with the agonist-binding site. Since bound agonists had only minor influence on 125I-MR44 photocrosslinking, the site where the hydrophobic head group of 125I-MR44 binds must be located outside the zone that is sterically influenced by agonists bound at the nAChR. A possible site of interaction of 125I-MR44 would be the N-terminal region of the labelled sequence, in which aromatic amino-acid residues are accumulated. We suggest that the polyamine moiety of 125I-MR44 interacts with the high affinity non-competitive inhibitor site deep in the ion channel, while the aromatic ring of this compound binds in the vestibule of the nAChR to a hydrophobic region on the alpha-subunit that is located close to the agonist binding site.

Animals↗
PubMed1994

Refined 1.89-A structure of the histidine-binding protein complexed with histidine and its relationship with many other active transport/chemosensory proteins.

The structure of the histidine-binding protein (HBP, M(r) = 26,100), involved solely in active transport, has been determined by the molecular replacement technique and refined to 1.89-A resolution and to an R-factor of 0.199. The structure is that of two protein molecules, each with a bound L-histidine, in the asymmetric unit. Replacement solution was achieved by using a model of the crystal structure of the ligand-free, open-cleft form of the lysine/arginine/ornithine-binding protein which was modified so that the two domains are close to each other by bending the hinge connecting the two domains. The bound histidine is held in place by 10 hydrogen bonds, 2 salt links, and about 60 van der Waals contacts. Elucidation of the HBP structure brings a total of eight different binding proteins structures determined in our laboratory, including those with specificities for monosaccharides, maltodextrins (linear and cyclic), aliphatic amino acids, and inorganic oxyanions. These structures comprise about a third of the entire family of periplasmic binding proteins which act as initial primary high-affinity receptors of active transport in Gram-negative bacteria. Two of the binding proteins with specificities for glucose/galactose and maltodextrins also serve in a similar capacity in chemotaxis. Though these proteins have different molecular weights (ranging from 26,000 to 40,000), amino acid sequences, and ligand specificities, their three-dimensional structures are similar overall. They are elongated (axial ratios of 2:1) and composed of two similar globular domains separated by a deep cleft wherein the ligand-binding site is located. These structures provide understanding of molecular recognition of a variety of ligands at the atomic level and functional roles of the binding proteins.

Bacterial Proteins↗
PubMed1999

Regions of variant histone His2AvD required for Drosophila development.

One way in which a distinct chromosomal domain could be established to carry out a specialized function is by the localized incorporation of specific histone variants into nucleosomes. H2AZ, one such variant of the histone protein H2A, is required for the survival of Drosophila melanogaster, Tetrahymena thermophila and mice (R. Faast et al., in preparation). To search for the unique features of Drosophila H2AZ (His2AvD, also referred to as H2AvD) that are required for its essential function, we have performed amino-acid swap experiments in which residues unique to Drosophila His2AvD were replaced with equivalently positioned Drosophila H2A.1 residues. Mutated His2AvD genes encoding modified versions of this histone were transformed into Drosophila and tested for their ability to rescue null-mutant lethality. We show that the unique feature of His2AvD does not reside in its histone fold but in its carboxy-terminal domain. This C-terminal region maps to a short alpha-helix in H2A that is buried deep inside the nucleosome core.

Amino Acid Sequence↗
PubMed1995

Differential expression of GABAA/benzodiazepine receptor subunit mRNAs and ligand binding sites in mouse cerebellar neurons following in vivo ethanol administration: an autoradiographic analysis.

The gamma-aminobutyric acidA (GABAA)/benzodiazepine (BZ) receptor is a pentamer composed of subunits belonging to several classes (alpha 1-6, beta 1-4, gamma 1-4, delta, and rho 1 and rho 2). In situ hybridization, radioligand autoradiography, and immunocytochemistry were used to examine GABAA/BZ receptor alpha 1, alpha 6, beta 2, beta 3, and gamma 2 subunit expression in murine Purkinje, granule, and deep cerebellar neurons after in vivo ethanol exposure. Chronic ethanol treatment resulted in decreased alpha 1 subunit mRNA expression in each cell type, whereas the expression of alpha 6 and gamma 2 subunit mRNA levels increased; no changes were observed in the expression of beta 2 and beta 3 subunit mRNA. GABA and BZ agonist binding and antibody staining paralleled the changes in mRNA levels. Acute ethanol injection resulted in increased expression of alpha 1 and beta 3 mRNAs, whereas levels of alpha 6, beta 2, and gamma 2 mRNAs remained stable. Our results indicate that, in cerebellar neurons, the expression of specific GABAA/BZ receptor subunit mRNAs, polypeptides, and binding sites is independently regulated by in vivo administration of alcohol. The observed changes were not restricted to any one cerebellar cell type, because subunit expression in Purkinje, granule, and deep cerebellar cells was similarly affected.

Animals↗
PubMedDate not supplied

Prenatal development of calbindin D-28K in human visual cortex.

The distribution of the calcium-binding protein calbindin D-28K (CB) was investigated in human fetal primary visual cortex. CB is present in Cajal-Retzius cells of layer I, in sparse neurons of the ventricular and intermediate zones (VZ, IZ), and in tangential fibres in IZ by 15 weeks (W) of gestation. Cajal-Retzius cells lose their staining by 30W. CB appears in layers II-VI mainly from 26W, following an inside-outside sequence. Until 34W, CB labelling is in somata and neuropil located primarily in layers IVA, IVC and V. Then reactive perikarya and puncta increase in layers II-IVA and deep IVB and C, but are reduced in infragranular layers from 34W to term. From 30W positive somata form clusters in the cell-rich bands in layers IV and V and labelled neuropil in layers III and IV has a periodic pattern from 34W. Also from 34W, numerous lightly reactive pyramidal cells are present in layers II to IVA in primary, but not secondary, visual cortex. Our results show precocious expression of CB before full laminar differentiation of the cortex and that some of this expression is transient.

Calbindins↗
PubMed1989

Flexibility plot of proteins.

The flexibility plot of a protein lies on the observation that amino acid residues with the highest turn potential, i.e. located in highly mobile regions of protein surface, also possess the smallest volumes as well as the lowest hydrophobicities. The plot is generated by shifting a five residue window along the protein sequence and calculating the value of the hydrophobicity-volume product for consecutive quintuplets of amino acid residues. The concomitant occurrence of small volumes and low hydrophobicities results in very deep minima. A threshold value has also been introduced in order to discriminate significant minima. To substantiate the interpretation that the selected minima actually indicate very flexible segments of a protein (loops, turns, etc.), we have compared plots obtained for model proteins (lysozyme, myoglobin, ribonuclease, trypsin, thermolysin and T4 lysozyme) with X-ray thermal factors profiles available for the same proteins. When compared to thermal profiles, the majority of flexible segments evidenced by our plots have been found to be in agreement with regions characterized by high thermal factors. Results have also been discussed in the light of local organization possessed by examined proteins.

Amino Acids↗
PubMed1999

A phylogenetic analysis of microbial communities associated with methane hydrate containing marine fluids and sediments in the Cascadia margin (ODP site 892B).

Methane hydrates represent an enormous carbon and energy source in many low temperature deep marine sediments. However, little information is available concerning the nature of the microbial communities associated with these structures. Here, we describe a phylogenetic analysis based on ribosomal DNA (rDNA) sequences obtained from sediment and fluid samples present in a region of gas hydrate formation in shallow sediments within the Cascadia margin in and around Ocean Drilling Program (ODP) Site 892B. Our studies detected diverse sulfur-utilizing microbes, methanogens, methanotrophs, and non-thermophilic members of the kingdom Crenarchaeota. This is the first culture-independent phylogenetic analysis of a gas hydrate habitat.

Archaea↗
PubMed2007

Physiological proteomics of the uncultured endosymbiont of Riftia pachyptila.

The bacterial endosymbiont of the deep-sea tube worm Riftia pachyptila has never been successfully cultivated outside its host. In the absence of cultivation data, we have taken a proteomic approach based on the metagenome sequence to study the metabolism of this peculiar microorganism in detail. As one result, we found that three major sulfide oxidation proteins constitute approximately 12% of the total cytosolic proteome, which highlights the essential role of these enzymes for the symbiont's energy metabolism. Unexpectedly, the symbiont uses the reductive tricarboxylic acid cycle in addition to the previously identified Calvin cycle for CO2 fixation.

Animals↗
PubMed2003

Absence of local sign withdrawal in chronic human spinal cord injury.

Local sign withdrawal, a reflex to direct the limb away from noxious cutaneous stimuli, is thought to be indicative of a modular organization of the spinal cord. To assess the integrity of such an organization of the spinal cord in chronic human spinal cord injury (SCI), we tested the electromyogram (EMG) and joint torque responses to cutaneous stimuli applied to 6 locations of the leg in 10 SCI volunteers and 3 spinal-intact controls. The 6 locations included the medial arch of the foot, the second metatarsal, the dorsum, the region over the sural nerve at the lateral malleolus, and the anterior and posterior aspects of the lower leg. Although spinal-intact subjects demonstrated local sign withdrawal, the data from SCI subjects indicated that an invariant flexion response pattern was produced regardless of stimulus location. Ankle dorsiflexion and hip flexion were produced in all subjects at all locations and no difference in the ratio of hip:ankle torques could be detected for the 6 test locations. A windup-crossover test, employing a sequence of 6 stimuli at 1-s intervals was used to assess whether common neuronal pathways were responsible for the loss of modular organization. An additional 10 SCI volunteers were tested using stimuli in which the stimulus location was switched between the 2nd and 3rd stimulus of the test sequence. The response to the crossover stimulus more closely resembled the response to the 3rd stimulus of a windup sequence than a response without conditioning stimuli. These results indicate that increased excitability produced by windup at one stimulus site is maintained at the 2nd site. This observation suggests that deep dorsal horn neurons, typically associated with musculotopic mapping, may be reorganized in chronic spinal cord injury.

Adult↗
PubMed1994

Expression of transforming growth factor-beta 2 in malignant melanoma correlates with the depth of tumor invasion. Implications for tumor progression.

Transforming growth factor-beta 2 (TGF-beta 2) is a potent regulatory of proliferation and differentiation of both normal and malignant cells. In addition, TGF-beta 2 can exert a variety of immunosuppressive effects, suggesting that the production of this molecule contributes to impaired immunological surveillance of tumor development. In vitro, TGF-beta 2 expression has been demonstrated in cell lines derived from metastatic malignant melanocytes. but not in those derived from normal melanocytes. We sought to evaluate a potential role of TGF-beta 2 in the initiation or progression of malignant melanoma in vivo. We examined by nucleic acid in situ hybridization the expression of TGF-beta 2 mRNA transcripts in 124 melanocytic lesions including metastatic and primary invasive melanomas, melanomas in situ, nevi with architectural disorder and cytologic atypia, ordinary benign melanocytic nevi, and Spitz nevi. All metastatic melanomas and a majority (94%) of primary melanomas invasive to Clark's level III, IV, or V expressed TGF-beta 2 mRNA. A minority (41%) of Clark's level II primary invasive melanomas expressed this factor. All definitive melanomas in situ and nevi were negative. The results suggest that TGF-beta 2 expression in malignant melanoma may be a critical event in the development of deep invasion and metastases in malignant melanoma.

Base Sequence↗
PubMed2025

Phylogenetic Methods Meet Deep Learning.

Deep learning (DL) has been widely used in various scientific fields, but its integration into phylogenetics has been slower, primarily due to the complex nature of phylogenetic data. The studies that apply DL to sequencing data often limit analyses to four-taxon trees. Many of these studies serve as "proof of principle" and perform similarly to traditional phylogeny reconstruction methods. New ways of using training data, such as encoding with compact bijective ladderized vectors or transformers, enable the handling of much larger trees and genomic data sets. This short perspective focuses on the application of DL in phylogenetics, introducing prevalent DL architectures. We highlight potential problems in the field by discussing the risks of using simulation-based training data and emphasize the importance of reproducibility and robustness in computational estimates. Finally, we explore promising research areas, including the combination of phylogenetics and population genetics in DL, the analysis of neighbor dependencies, and the potential to significantly reduce computational cost compared to traditional methods. This perspective illustrates the potential of DL in complementing traditional phylogeny reconstruction methods and aiding the advancement of phylogenetic analysis, especially in performing computationally demanding tasks such as model selection or estimating branch support values.

Humans↗
PubMed1986

Inhibitory potentials in neurons of the deep layers of the in vitro neocortical slice.

Neocortical neurons in slices of the rat sensorimotor region maintained in vitro generate postsynaptic potentials (PSPs) in response to focal extracellular stimulation. These PSPs are mainly depolarizing at the resting membrane potential (Vm) but a sequence of depolarizing-hyperpolarizing potentials is often disclosed by depolarizing the Vm. The stimulus-induced hyperpolarization can last up to 1000 ms and show two components: the early one (peak latency 10-20 ms), is inverted by diffusion of Cl- into the cell; the late one is diminished by augmenting [K+]o. The membrane conductance is increased throughout the stimulus-induced hyperpolarization, mainly during the first 10-60 ms. A decrease in excitability results from both the hyperpolarizing trend and the conductance increase. The latter is more effective in decreasing depolarizing than hyperpolarizing pulses of current injected intracellularly.

Animals↗