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Results for “structural phylogenetics”

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At least 775 records · Page 43Linked to original sources
PubMed2002

The phylogeny of Goussia and Choleoeimeria (Apicomplexa; Eimeriorina) and the evolution of excystation structures in coccidia.

The phylogenetic relationships of Goussia janae and Choleoeimeria sp. were analyzed using the small subunit ribosomal RNA gene (SSU rDNA). This is a first attempt to study the molecular phylogeny of coccidian genera parasitizing strictly poikilotherm hosts. The biliary Eimeria-like coccidia of reptiles classified into the genus Choleoeimeria form a sister clade to the family Eimeriidae, which confirms the separate generic status of the genus Choleoeimeria. The position of Goussia is less robustly resolved, since it forms a trichotomy with the Eimeriidae and Sarcocystidae, or alternatively constitutes the earliest branch of the coccidian lineage. Morphological similarities, namely the extracytoplasmic location of the endogenous stages, and the presence of sutures in the sporocyst wall are discussed in the context of the traditional classification of eimeriids. In contrast to the morphology-based systematics, the monophyly of Goussia and Choleoeimeria is not supported by the SSU rDNA data.

Animals↗
PubMed1998

Automatic detection of conserved RNA structure elements in complete RNA virus genomes.

We propose a new method for detecting conserved RNA secondary structures in a family of related RNA sequences. Our method is based on a combination of thermodynamic structure prediction and phylogenetic comparison. In contrast to purely phylogenetic methods, our algorithm can be used for small data sets of approximately 10 sequences, efficiently exploiting the information contained in the sequence variability. The procedure constructs a prediction only for those parts of sequences that are consistent with a single conserved structure. Our implementation produces reasonable consensus structures without user interference. As an example we have analysed the complete HIV-1 and hepatitis C virus (HCV) genomes as well as the small segment of hantavirus. Our method confirms the known structures in HIV-1 and predicts previously unknown conserved RNA secondary structures in HCV.

Algorithms↗
PubMed2000

Biofilm community structure in polluted rivers: abundance of dominant phylogenetic groups over a complete annual cycle.

The seasonal dynamics of river biofilm communities in two German rivers, the Elbe and one of its tributaries, the Spittelwasser, were investigated for the first time by using fluorescence in situ hybridization and a standardized biofilm sampling procedure. We show the importance of members of the beta subclass of the class Proteobacteria, which formed the largest single group in the massively polluted Spittelwasser at all times. Clear seasonal peaks of abundance were observed for the planctomycetes and the Cytophaga-Flavobacterium cluster.

Animals↗
PubMed1990

bicoid mRNA localization signal: phylogenetic conservation of function and RNA secondary structure.

Transcripts of the bicoid (bcd) gene are localized to the anterior pole of the Drosophila oocyte, thereby allowing formation in the embryo of an anteroposterior gradient of the bcd protein morphogen. We previously showed that a 630 nucleotide portion of the 3' noncoding region of the bcd mRNA is necessary for this localization, and is sufficient to confer anterior localization on a heterologous transcript. Here I have used a comparative analysis to begin to more precisely define the cis-acting mRNA localization signal. The bcd genes from six additional Drosophila species were cloned, and DNA of the 3' noncoding regions sequenced. Three of these regions were tested interspecifically for mRNA localization in D. melanogaster and each functioned correctly; these regions must therefore contain the cis-acting signal. The primary sequences, which are up to 50% divergent from the D. melanogaster gene, show patchy homology throughout most of the region. Interestingly, all seven species can potentially form a large stereotypic secondary structure. This structure is a likely candidate for the localization signal and can be used for the rational design of mutations to test that possibility.

Animals↗
PubMed2001

[Characterization and phylogenetics of a new species of genus Methanobacterium].

A strain of methanogenic bacterium Px1 was isolated from an anaerobic digester in the department of environmental sciences, TsingHua University, which treated the wastewater from Beijing Beer Factory. The isolate is curved rod, light-yellow colony, uses only H2 + CO2 as the substrate for CH4 formation. On the basis of physiology, morphology, structural characteristics and phylogenetic analysis, it is turned out that strain Px1 is a new species of the genus Methanobacterium, the name Methanobacterium curvum sp. nov. is proposed.

DNA, Bacterial↗
PubMed2003

Cysteine proteases and cell differentiation: excystment of the ciliated protist Sterkiella histriomuscorum.

The process of excystment of Sterkiella histriomuscorum (Ciliophora, Oxytrichidae) leads in a few hours, through a massive influx of water and the resorption of the cyst wall, from an undifferentiated resting cyst to a highly differentiated and dividing vegetative cell. While studying the nature of the genes involved in this process, we isolated three different cysteine proteases genes, namely, a cathepsin B gene, a cathepsin L-like gene, and a calpain-like gene. Excystation was selectively inhibited at a precise differentiating stage by cysteine proteases inhibitors, suggesting that these proteins are specifically required during the excystment process. Reverse transcription-PCR experiments showed that both genes display differential expression between the cyst and the vegetative cells. A phylogenetic analysis showed for the first time that the cathepsin B tree is paraphyletic and that the diverging S. histriomuscorum cathepsin B is closely related to its Giardia homologues, which take part in the cyst wall breakdown process. The deduced cathepsin L-like protein sequence displays the structural signatures and phylogenetic relationships of cathepsin H, a protein that is known only in plants and animals and that is involved in the degradation of extracellular matrix components in cancer diseases. The deduced calpain-like protein sequence does not display the calcium-binding domain of conventional calpains; it belongs to a diverging phylogenetic cluster that includes Aspergillus palB, a protein which is involved in a signal transduction pathway that is sensitive to ambient pH.

Amino Acid Sequence↗
PubMed1984

Cholinergic systems in the rat brain: I. projections to the limbic telencephalon.

The cholinergic projections to the limbic telecephalon in the rat were investigated by use of fluorescent tracer histology in combination with choline-O-acetyltransferase (ChAT) immunohistochemistry and acetylcholinesterase (AChE) histochemistry (pharmacohistochemical regimen). Propidium iodide or Evans Blue was infused into the olfactory bulb, hippocampus, dorsal retrohippocampal region, amygdala, and the entorhinal, perirhinal, pyriform, insular, and cingular cortices. Retrogradely transported fluorescent labels and ChAT and/or AChE were microscopically analyzed on the same brain section. Virtually all of the cholinergic projections to the limbic telencephalon derived from the basal forebrain cholinergic system composed of neurons associated with the medial septal nucleus, nuclei of the vertical and horizontal limbs of the diagonal band, the magnocellular preoptic area, the subpallidal substantia innominata and its rostral extension into the regions of the ventral pallidum laterally and the lateral preoptic area medially, and the nucleus basalis. The cingulate cortex received a small cholinergic projection from the dorsolateral tegmental nucleus in the brainstem. All of the presumed cholinergic innervation of the olfactory bulb, hippocampus, and dorsal retrohippocampal area and the majority of cholinergic afferents to posterior cingulate and entorhinal cortices derived from the medial septal nucleus, vertical and horizontal limbs of the diagonal band, magnocellular preoptic area, and rostral substantia innominata. Putative cholinergic afferents to the amygdala and to pyriform, insular, perirhinal, and anterior cingulate cortices orginated from ChAT-positive cells concentrated more caudally in the basal forebrain cholinergic system. Within the basal forebrain, no simple topographic pattern emerged to explain the cholinergic innervation of the limbic telencephalon, although an essentially reverse rostrocaudal organization was observed for afferents to the cingular region. It was noted, however, that most regions of the limbic telencephalon received cholinergic input from rostral portions of the basal forebrain cholinergic system, an observation inviting speculation that anterior aspects of the basal forebrain provide cholinergic afferents primarily to limbic structures in the telencephalon whereas more caudal portions are the source of cholinergic fibers preferentially innervating non-limbic regions. Of the total number of projection neurons innervating a given region of the limbic telencephalon, a greater proportion was ChAT-positive if phylogenetically newer target structures were innervated.(ABSTRACT TRUNCATED AT 400 WORDS)

Acetylcholinesterase↗
PubMed2004

Sequence analysis of L RNA of Lassa virus.

The L RNA of three Lassa virus strains originating from Nigeria, Ghana/Ivory Coast, and Sierra Leone was sequenced and the data subjected to structure predictions and phylogenetic analyses. The L gene products had 2218-2221 residues, diverged by 18% at the amino acid level, and contained several conserved regions. Only one region of 504 residues (positions 1043-1546) could be assigned a function, namely that of an RNA polymerase. Secondary structure predictions suggest that this domain is very similar to RNA-dependent RNA polymerases of known structure encoded by plus-strand RNA viruses, permitting a model to be built. Outside the polymerase region, there is little structural data, except for regions of strong alpha-helical content and probably a coiled-coil domain at the N terminus. No evidence for reassortment or recombination during Lassa virus evolution was found. The secondary structure-assisted alignment of the RNA polymerase region permitted a reliable reconstruction of the phylogeny of all negative-strand RNA viruses, indicating that Arenaviridae are most closely related to Nairoviruses. In conclusion, the data provide a basis for structural and functional characterization of the Lassa virus L protein and reveal new insights into the phylogeny of negative-strand RNA viruses.

Amino Acid Sequence↗
PubMed2004

Phylogenetic analysis of multiple loci reveal the population structure within Letharia in the Caucasus and Morocco.

The sequence variation within the genus Letharia in the Caucasus and Morocco was investigated. Twelve thalli from each area were sequenced at eight different loci. Phylogenetic analysis of the multiple loci data revealed the cryptic species Letharia 'lupina' in Morocco, previously known only from western North America. The two cryptic species L. vulpina and L. 'lupina' locally share the same ecology but are genetically isolated from each other. In the Caucasus, five different haplotypes of L. vulpina were detected, and in Morocco four L. vulpina haplotypes and six L. 'lupina' haplotypes were found. For L. vulpina, allelic differences were detected at five of the eight loci in the Caucasus and Morocco. The populations of L. vulpina in both the Caucasus and Morocco contain more genetic variation than those previously investigated in Europe, which indicates that the Caucasus and Morocco acted as refugia during quaternary glaciations, and that central and northern Europe may have been recolonised from one or both of these areas.

Alleles↗
PubMed2001

Signature of quaternary structure in the sequences of legume lectins.

Legume lectins exhibit a wide variety of oligomerization and sugar specificity while retaining the characteristic jelly-roll tertiary fold. An attempt has been made here to find whether this diversity is reflected in their primary structures by constructing phylogenetic trees. Dendrograms based on sequence alignment showed clustering related to the oligomeric nature of legume lectins. Though the clustering primarily follows the oligomeric states, it also appears to correlate with different sugar specificities indicating an interdependence of these two properties. Analysis of the structure-based alignment and the alignment of the sequences of the carbohydrate-binding loops alone also revealed the same features. By a close examination of the interfaces of the various oligomers it was also possible, in some cases, to pinpoint a few key residues responsible for the stabilization of the interfaces.

Amino Acid Sequence↗
PubMed2025

Genetic and phenotypic diversity of wine-associated Hanseniaspora species.

The genus Hanseniaspora includes apiculate yeasts commonly found in fruit- and fermentation-associated environments. Their genetic diversity and evolutionary adaptations remain largely unexplored despite their ecological and oenological significance. This study investigated the phylogenetic relationships, genome structure, selection patterns, and phenotypic diversity of Hanseniaspora species isolated primarily from Australian wine environments, focusing on Hanseniaspora uvarum, the most abundant non-Saccharomyces yeast in wine fermentation. A total of 151 isolates were sequenced, including long-read genomes for representatives of the main phylogenetic clades. Comparative genomics revealed ancestral chromosomal rearrangements between the slow-evolving lineage (SEL) and fast-evolving lineage (FEL) that could have contributed to their evolutionary split, as well as significant loss of genes associated with mRNA splicing, chromatid segregation and signal recognition particle protein targeting in the FEL. Pangenome analysis within H. uvarum identified extensive copy number variation, particularly in genes related to xenobiotic tolerance and nutrient transport. Investigation into the selective landscape following the FEL/SEL divergence identified diversifying selection in 229 genes in the FEL, with significant enrichment in genes within the lysine biosynthetic pathway. Furthermore, phenotypic screening of 116 isolates revealed substantial intraspecific diversity, with specific species exhibiting enhanced ethanol, osmotic, copper, SO₂, and cold tolerance.

Wine↗
PubMed2003

Techniques for dissecting adult aleocharine beetles (Coleoptera: Staphylinidae).

Methodology for detailed dissections of the phylogenetically most informative structures from adult aleocharine staphylinid beetles is provided. These methods include specimen preparation, relaxation, clearing, bleaching, dehydration and full dissection. A detailed summary of mouthpart and male and female genitalic dissections is provided. Recently described character systems, including those of the mouthparts and the thoracic regions, have been successfully used in phylogenetic studies of aleocharine staphylinids. This paper provides the first thorough description of the techniques necessary to reveal these character systems.

Animals↗
PubMed2004

The structure, expression and function prediction of DAZAP2, a down-regulated gene in multiple myeloma.

In our previous studies, DAZAP2 gene expression was down-regulated in untreated patients of multiple myeloma (MM). For better studying the structure and function of DAZAP2, a full-length cDNA was isolated from mononuclear cells of a normal human bone marrow, sequenced and deposited to Genbank (AY430097). This sequence has an identical ORF (open reading frame) as the NM_014764 from human testis and the D31767 from human cell line KG-1. Phylogenetic analysis and structure prediction reveal that DAZAP2 homologues are highly conserved throughout evolution and share a polyproline region and several potential SH2/SH3 binding sites. DAZAP2 occurs as a single-copy gene with a four-exon organization. We further noticed that the functional DAZAP2 gene is located on Chromosome 12 and its pseudogene gene is on Chromosome 2 with electronic location of human chromosome in Genbank, though no genetic abnormalities of MM have been reported on Chromosome 12. The ORF of human DAZAP2 encodes a 17-kDa protein, which is highly similar to mouse Prtb. The DAZAP2 protein is mainly localized in cytoplasm with a discrete pattern of punctuated distribution. DAZAP2 may associate with carcinogenesis of MM and participate in yet-to-be identified signaling pathways to regulate proliferation and differentiation of plasma cells.

Amino Acid Sequence↗