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At least 145 records · Page 8Linked to original sources
PubMed1981

Alcohol dehydrogenase gene of Drosophila melanogaster: relationship of intervening sequences to functional domains in the protein.

The gene that codes for Drosophila alcohol dehydrogenase (ADH; alcohol:NAD+ oxidoreductase EC 1.1.1.1) was identified in a bacteriophage lambda library of genomic Drosophila DNA by using ADH cDNA cloned DNA as a probe. The DNA sequence of the protein encoding region was shown to be in agreement with the amino acid sequence of the ADH. Two intervening DNA sequences (introns) were identified within the protein encoding region: one was 65 nucleotides and located between the codons for amino acid residues 32 and 33, and one was 70 nucleotides and located between the codons for amino acid residues 167 and 168. Both contained the 5' G-T and 3' A-G dinucleotides characteristic of intron boundaries of eukaryotic genes. On the basis of secondary structure predictions, the first 140 amino acid residues of Drosophila ADH are in an alternating beta-sheet/alpha-helix arrangement which is characteristic of the coenzyme binding domain of dehydrogenases. The smaller of the two introns interrupts the domain predicted to bind the adenine portion of the coenzyme.

Alcohol Dehydrogenase↗
PubMed1992

Identification of motor neurons to the longitudinal muscle of the guinea pig ileum.

Motor neurons that innervate the longitudinal muscle of the guinea pig ileum were identified by retrograde transport from the longitudinal muscle plexus in organotypic culture. Motor neurons had short projections, less than 3.5 mm long, and never had Dogiel type II morphology; most labeled neurons had morphological characteristics of Dogiel type I neurons. Immunoreactivity for choline acetyltransferase was present in 97% of retrogradely labeled nerve cell bodies, reflecting the dominant cholinergic input to the longitudinal muscle layer. Substance P immunoreactivity was present in 48% of motor neurons, indicating that it or a similar tachykinin that mediates noncholinergic excitatory transmission is likely to be released by a subset of cholinergic motor neurons. This strongly suggests that the difference in frequency dependence of substance P and acetylcholine release is attributable to different release mechanisms rather than to activation of separate populations of motor neurons. Immunoreactivity for the calcium-binding protein calretinin was present in 87% of longitudinal muscle motor neurons. The neurochemical coding of longitudinal muscle motor neurons indicated that they constitute about one quarter of all myenteric neurons and are distinct from circular muscle motor neurons.

Animals↗
PubMed2026

Complete mitochondrial genomes of eight cyclophyllidean tapeworms: genome pattern and phylogenetic analysis.

Cyclophyllidean tapeworms are widespread parasites of significant medical and veterinary importance. However, mitochondrial (mt) genomic resources for cyclophyllideans from China, particularly those recovered from wildlife hosts, remain comparatively limited. In this study, we sequenced and characterized the complete mt genomes of eight cyclophyllidean isolates collected from diverse wild and domestic hosts in China, including two Hymenolepis sp. isolates and two Raillietina sp. isolates from China, and four additional isolates of previously sequenced Taenia species. The circular mt genomes ranged from 13,387 to 14,021 bp in length, encoding 36 typical genes with variable non-coding regions. Comparative analysis revealed highly conserved gene composition and mostly conserved mt architecture, with localized rearrangement patterns detected among the cyclophyllidean lineages examined. In particular, all sampled Taeniidae exhibited a consistent trnL1-trnS2 arrangement, whereas the examined non-Taeniidae families showed the trnS2-trnL1 arrangement, confirming and extending, across additional wildlife-associated isolates, a previously proposed family-associated gene-order marker within Cyclophyllidea. Phylogenetic analyses based on concatenated amino acid sequences of the 12 protein-coding genes placed the eight isolates within their expected families, in topologies broadly consistent with previous mitogenomic studies. These data provide additional Chinese mitogenomic references, especially for underrepresented wildlife-associated isolates, and support family-associated gene-order patterns in Cyclophyllidea.

Animals↗
PubMed1977

Personality connotations of psychiatric diagnoses. Implications for a similarity model.

The major concern of this study was to identify the personality traits connotated by a number of diagnostic labels such as paranoid, schizoid, hysterical, and cyclothymic. Twenty psychiatrists were given a list of nonpsychotic personality disorders and were asked to indicate what personality traits were typically associated with them. Results showed good agreement among psychiatrists on the personality traits they believed to be implied by the diagnostic terms. A factor analysis of the ratings showed a circular configuration of relative similarity among the different diagnoses. The results are interpreted as indicating that diagnostic labels are types of codes for various sectors of an implicit space of traits, signs, and symptoms.

Antisocial Personality Disorder↗
PubMed1996

HIV-1 protein expression from synthetic circles of DNA mimicking the extrachromosomal forms of viral DNA.

We have constructed circular forms of human immunodeficiency virus type 1 viral DNA in vitro that closely resemble the single and double long terminal repeat circular forms of unintegrated viral DNA formed in the nuclei of infected cells. We have analyzed viral protein expression after transient transfection of these circular DNAs into HeLa cells and compared it with expression from a transfected linearized plasmid containing an integrated provirus. Both circular forms are expressed, as judged by the appearance of extracellular p24, and expression is trans-activated by human immunodeficiency virus type 1 Tat. Viral p24 production, however, is approximately an order of magnitude lower than that obtained with transfected integrated viral DNA. Similar data were obtained when a luciferase reporter gene was substituted for the coding regions of the viral DNA. Positional effects of the transcriptional initiation and termination signals in the long terminal repeat appear to account for some of the low expression levels. These data suggest that unintegrated circular viral DNAs are transcriptionally active, although at low levels, and may contribute to overall viral replication in infected people under some conditions.

Base Sequence↗
PubMed1984

A transcription enhancer acts in vitro over distances of hundreds of base-pairs on both circular and linear templates but not on chromatin-reconstituted DNA.

We have analyzed the effect of nucleosome formation and of the simian virus (SV40) enhancer on the efficiency of in vitro transcription. In a whole cell extract made from HeLa cells, nucleosome assembly on DNA results in the formation of chromatin-like complexes. However, transcription was detectable only when the DNA templates were partially or totally depleted of nucleosomes. On nucleosome-free templates, when the SV40 enhancer was present upstream from the complete SV40 early or rabbit beta-globin promoters, there was a five- to tenfold stimulation of specific transcription. When present upstream from its homologous promoter, the SV40 enhancer activated SV40 early transcription independently of its orientation with respect to the coding sequence. Point mutations known to impair the SV40 enhancer function in vivo had a similar effect in vitro. The extent of the enhancing effect was the same with linear or circular templates. When the SV40 enhancer was inserted upstream from the rabbit beta-globin gene, the activation of transcription was reduced with increasing distance between the enhancer and beta-globin upstream promoter elements, but was still significant over a distance of more than 400 base-pairs.

Chromatin↗
PubMed1975

Physiochemical properties of DNA binding proteins: gene 32 protein of T4 and Escherichia coli unwinding protein.

The single-stranded DNA binding protein coded for by gene 32 of bacteriophage T4 and a similar protein isolated from uninfected Escherichia coli both induce characteristic changes in the circular dichroism (CD) of single-stranded nucleic acids. These CD changes have been adapted as an assay of protein-DNA complex formation. Far-ultraviolet CD spectra show the secondary structure of the two proteins to be similar with approximately 20% alpha helix, approximately 20% beta structure, and 60% random coil. Both proteins show prominent Cotton effects arising from their aromatic chromophores. Nitration of five of the nine tyrosyl residues of gene 32 protein prevents DNA binding, while prior formation of the DNA complex protects all tyrosyl residues from nitration. The tyrosyl residues may participate in gene 32 protein-DNA binding by intercalation between bases of the single strand. In contrast, no tyrosyl residues can be nitrated in the E. coli protein suggesting that surface tyrosyls do not play a part in binding of E. coli protein to DNA. Approximately 50 amino acids can be cleaved from the gene 32 protein with trypsin. This cleavage also occurs spontaneously in infected cell extracts. The remaining protein of mol wt 30000 has the same CD spectra and DNA binding properties as the native protein. The physicochemical properties can be correlated with previous work on the structures and functions of the group of DNA "unwinding proteins".

Amino Acids↗
PubMed1990

Intermolecular homologous recombination in plants.

To study DNA topological requirements for homologous recombination in plants, we have constructed pairs of plasmids that contain nonoverlapping deletions in the neomycin phosphotransferase gene [APH(3')II], which, when intact, confers kanamycin resistance to plant cells. Protoplasts isolated from Nicotiana tabacum were cotransformed with complementary pairs of plasmids containing these truncated gene constructs. Homologous recombination or gene conversion within the homologous sequences (6 to 405 base pairs) of the protein-coding region of the truncated genes led to the restoration of the functional APH(3')II gene, rendering these cells resistant to kanamycin. Circular plasmid DNAs recombined very inefficiently, independent of the length of the homologous region. A double-strand break in one molecule only slightly increased the recombination frequency. The most favorable substrates for recombination were linear molecules. In this case, the recombination frequency was positively correlated with the length of the homologous regions. The recombination frequency of plasmids linearized at sites proximal to the deletion-homology junction was significantly higher than when linearization was distal to the homologous region. Vector homology within cotransformed plasmid sequences also increased the recombination frequency.

Blotting, Southern↗
PubMed2026

Assembly and comparative analysis of the mitochondrial genome of Pleione yunnanensis: genome structure and evolutionary insights.

BACKGROUND: Pleione yunnanensis a terrestrial or semi-epiphytic herbaceous plant belonging to the Orchidaceae family, is valued for both its medicinal uses and ornamental appeal. Although its chloroplast genomes have been sequenced, its complete mt genome had not previously been resolved, limiting genetic and evolutionary studies of the species. RESULTS: In this work, we assembled and characterized the first complete mt genome of P. yunnanensis, revealing a structurally complex, multibranched system composed of 14 circular-mapping molecules totaling 468,176 bp with a GC content of 44.32%. The genome encodes 44 annotated genes, including 28 protein-coding genes (PCGs), 15 tRNAs, and one rRNA. The multibranched architecture provides new evidence supporting the dynamic and recombinational nature of plant mt genomes. Repeat analysis uncovered 29 simple sequence repeats (SSRs), 19 tandem repeats, and 118 dispersed repeats, indicating a comparatively lower repeat abundance than that found in closely related orchids with similar mt genome sizes. Codon-usage profiling of PCGs showed a marked bias toward A/T-ending codons. Prediction of RNA editing sites identified 4,708 putative edits across mitochondrial PCGs. Most mitochondrial genes displayed Ka/Ks ratios close to 1.0, suggesting relaxed selective constraints or lineage-specific evolutionary patterns rather than strong positive selection. Moreover, we detected 69 chloroplast-derived homologous fragments, including 15 intact genes, suggesting ongoing plastid-mitochondrial DNA transfer. Phylogenetic reconstruction and collinearity comparisons demonstrated that P. yunnanensis clustered closely with Dendrobium species, including D. amplum and D. hancockii, within the Orchidaceae clade. CONCLUSIONS: This study provides the first complete mt genome of P. yunnanensis, providing a foundational genomic resource for the genus Pleione. The results not only improve our understanding of mt genome structure and evolution in Orchidaceae, but also offer valuable molecular evidence for phylogenetic inference, germplasm identification, and conservation of this endangered medicinal species.

Orchidaceae↗
PubMed1978

Aspects of the regulation of histone genes.

Sequencing of cloned histone DNA of the sea urchin Psammechinus miliaris has confirmed the map of the histone genes obtained earlier by rather less refined techniques. Sequencing of spacer has revealed that it is unlikely to code for protein. Some interesting sequences in the prelude regions to the structural genes have been found. The technique of injecting DNA into the germinal vesicle of the Xenopus oocyte has been greatly simplified, so that now many of the parameters governing the transcription of the injected genes can be investigated. Some mRNA-like molecules appear when circular histone DNA is inserted into the oocyte nucleus. We are cautiously optimistic that the technique can be further developed and will provide a useful tool for the study of the molecular mechanisms governing the expression of structural genes coding for proteins.

Animals↗
PubMed1980

Some yeast mitochondrial RNAs are circular.

11S and 18S fractions of yeast mitochondrial RNAs, isolated by electrophoresis through agarose gels, have been found by electron microscopy to contain approximately 50% circular molecules. Circles in the 11S fraction have a contour length of 0.36 +/- 0.02 micron, which is approximately equal to the length of the majority of linear molecules also present. Circles in the 18S fraction have an average length of 0.78 +/- 0.11 micron. The size distribution is broader than for the 11S fraction, and we cannot exclude the possibility that more than one size class may be present. The 11S circular RNA forms circular R loops and RNA-DNA hybrids with DNA fragments of the oxi 3 region of mtDNA, which contains the structural gene for subunit 1 of cytochrome oxidase. As judged from the electron micrographs, the complete RNA participates in hybrid formation and the sequences coding for it appear to be continuous. Both 11S and 18S circles withstand treatment with DNAase and pronase. They are not eliminated by treatment with 1 M glyoxal in 50% formamide for 1 hr at 50 degrees C. We conclude that they are covalently closed. The function of the circular RNAs is unknown. They may be active as mRNAs, storage forms, or arise in a cut-and-splice process which generates mRNAs from longer transcripts.

Mitochondria↗
PubMed1981

Nucleotide sequence of cloned unintegrated avian sarcoma virus DNA: viral DNA contains direct and inverted repeats similar to those in transposable elements.

We have determined the nucleotide sequence of portions of two circular avian sarcoma virus (ASV) DNA molecules cloned in a prokaryotic host--vector system. The region whose sequence was determined represents the circle junction site--i.e., the site at which the ends of the unintegrated linear DNA are fused to form circular DNA. The sequence from one cloned molecule, SRA-2, shows that the circle junction site is the center of a 330-base-pair (bp) tandem direct repeat, presumably representing the fusion of the long terminal repeat (LTR) units known to be present at the ends of the linear DNA. The circle junction site is also the center of a 15-bp imperfect inverted repeat, which thus appears at the boundaries of the LTR. The structure of ASV DNA--unique coding region flanked by a direct repeat that is, in turn, terminated with a short inverted repeat--is very similar to the structure of certain transposable elements. Several features of the sequence imply that circularization to form the SRA-2 molecule occurred without loss of information from the linear DNA precursor. Circularization of another cloned viral DNA molecule, SRA-1, probably occurred by a different mechanism. The circle junction site of the SRA-1 molecule has a 63-bp deletion, which may have arisen by a mechanism that is analogous to the integration of viral DNA into the host genome. Flanking one side of the tandem direct repeat is the binding site for tRNATrp, the previously described primer for synthesis of the first strand of viral DNA. The other side of the direct repeat is flanked by a polypurine tract, A-G-G-G-A-G-G-G-G-G-A, which may represent the position of the primer for synthesis of the second strand of viral DNA. An A+T-rich region, upstream from the RNA capping site, and the sequence A-A-T-A-A-A are present within the direct repeat sequence. These sequences may serve as a promoter site and poly(A) addition signal, respectively, as proposed for other eukaryotic transcription units.

Avian Sarcoma Viruses↗
PubMed1984

SV40 immortalization of adult human mesenchymal cells from neuroretina. Biological, functional and molecular characterization.

Human adult mesenchymal cells from neuroretina (human choroid cells, HC) have acquired an infinite lifespan, following phenotypic transformation with a wild-type SV40. Immortalized cells (HC/SV40) contain high numbers of free circular viral DNA, and integrated molecules in a head-to-tail array in the cellular DNA. HC/SV40 cells express both the virus-coded "T" antigens and the cell-coded p53 transformation-associated protein. The transformed phenotype was further characterized by loss of contact inhibition of cell division, inability to induce the retraction of a fibrin clot and to spread within fibrin, and the existence of an altered distribution of actin cables. For the first time we also describe a coupling of the immunofluorescence and the quantitative cytofluorometric analyses, a new transformation parameter, since we show that SV40 transformation causes reorganization of the cell membrane by inducing the unmasking of the antigen recognized by the 4F2 monoclonal antibody, which is present in a "cryptic" form in the untransformed cells. Though the HC/SV40 cells have been continuously passaged over a 3-year period, they have not yet achieved a fully malignant phenotype, since they retain serum-dependency and the presence of a well developed fibronectin pericellular network, and they are not tumorigenic in nude mice. Thus this human immortal cell line constitutes a very useful tool for studying the progression toward full malignancy and the relationships between evolution of transformation parameters and changes in the viral and cellular genome interplay.

Adult↗
PubMed1985

A new member of the polyomavirus family: the hamster papovavirus. Complete nucleotide sequence and transformation properties.

The hamster papovavirus (HapV) is associated with multiple skin epitheliomas of the Syrian hamster. We have sequenced its genome. It is a double-stranded circular DNA of 5366 bp. The hypothetical genomic organization deduced from this nucleotide sequence is clearly of the polyoma type with the two strands coding in the opposite directions from a noncoding region that shows some of the features of a replication origin and a transcription control region. The amino acid sequences predicted from the open reading frames show an average of 50% homology with polyoma-coded polypeptides. The HapV is, after polyoma, the second example of a papovavirus coding for a middle T antigen. The cloned DNA can immortalize primary rat embryo cells and transform an established rat cell line. The viral DNA is stably integrated into the host genome.

Animals↗
PubMed2026

Treemble: a graphical tool to generate Newick strings from phylogenetic tree images.

SUMMARY: Phylogenetic trees are ubiquitous and central to biology, but most published trees are available only as visual diagrams and not in the machine-readable Newick format. There are, thus, thousands of published trees in the scientific literature that are unavailable for follow-up analyses, comparisons, and supertree construction. Experts can easily read such diagrams, but the manual construction of a Newick string from a diagram is laborious, error-prone, and time-consuming. Previous attempts to semi-automate the reading of tree images relied on image processing techniques. These often encounter difficulties as typical published tree diagrams contain various graphical elements and annotations that overlap the branches, such as error bars on internal nodes. Here we introduce Treemble, a user-friendly desktop application for generating Newick strings from tree images. The user simply clicks to mark node locations, assisted by a deep learning-based node detection tool, and Treemble algorithmically assembles the tree from the node coordinates alone. Treemble also facilitates the automatic reading of tip name labels and can be used for both rectangular and circular trees. AVAILABILITY AND IMPLEMENTATION: Treemble is a native desktop application for macOS and Windows and is freely available, with documentation, at treemble.org. Source code is available at github.com/John-Allard/Treemble. The trained node detection model is available at huggingface.co/John-Allard/treemble-1.

Phylogeny↗
PubMed1991

Conversion of a single-stranded simian virus 40 (SV40)-based shuttle vector to its double-stranded form does not require the SV40 T antigen in monkey cells.

We have transfected the single-stranded DNA form of the simian virus 40 (SV40)-based shuttle vector pZ189 into CV1P simian cells. Although the strand used did not code for the T antigen, we observed its conversion to a double-stranded DNA form. We deduced that the replication step converting a circular single-stranded DNA to a double-stranded one is independent of the SV40 T antigen in simian cells.

Animals↗
PubMed1988

Observations on integrative transformation in Schizosaccharomyces pombe.

Three different Schizosaccharomyces pombe strains have been transformed with a circular or linearized non-ars plasmid carrying the ura4+ gene as a selectable marker. The first strain shows full homology between the genomic ura4-294 gene (point mutation) and the marker gene on the plasmid. The second strain carries a 600 bp deletion (ura4-D6) that decreases homology between plasmid and chromosome. No homology remains in the third strain which has a complete deletion of the ura4 gene on the chromosome (ura4-D18). When sequence homology exists between transforming DNA and the chromosomal ura4 region, gene conversion is strongly preferred over integration of the circular plasmid. Reduction of the length of homology leads to a decrease of transformation frequencies, and homology dependent as well as a minority of homology independent integrations are observed. In the complete absence of homology two rare types of transformants are encountered: either the circular plasmid replicates autonomously, although it is devoid of an ars sequence, or alternatively the plasmid integrates into the genome at various positions. Transformation with plasmid cut within the coding region of ura4 can lead to tandemly arranged multiple integrations, when no homology exists between the free ends and the chromosome. The integrations occur at the ura4 locus, when homology is retained between plasmid and chromosome, and at various sites in the genome of the strain with a complete deletion of the ura4 gene. The results suggest that homology dependent events (conversion, integration) are strongly preferred in transformation of S. pombe with non-ars plasmids. In addition low frequency integration by illegitimate recombination is observed.(ABSTRACT TRUNCATED AT 250 WORDS)

Chromosome Deletion↗