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At least 109 records · Page 6Linked to original sources
PubMed1985

Transformed Xenopus embryos as a transient expression system to analyze gene expression at the midblastula transition.

The onset of transcriptional activity during embryogenesis in Xenopus laevis is at the 4000- to 8000-cell stage (stage 8-8.5) and is referred to as the midblastula transition (MBT). Most exogenous circular DNA that is microinjected into the fertilized egg also is expressed at the MBT. The transformed Xenopus embryo at these early stages was used as a transient expression system in order to determine the effects of (1) promoter strength, (2) physical conformation, (3) degree of replication, and (4) a regulatory molecule on the expression of an injected gene coding for chloramphenicol acetyl transferase. This gene linked to a relatively strong promoter (SV40 early promoter -pSV2CAT), a weak promoter (adenovirus early promoter -pE3CAT), or in circular or linear form is expressed at stage 8-8.5 following injection into fertilized eggs. pE3CAT coinjected with the E1a protein (enhances the transcription of the E3 promoter) is also expressed at stage 8.5, but expression is enhanced 2-7.6 fold. These data suggest that the inhibition of transcription prior to the MBT could not be perturbed by either the presence of different promoters or a positive regulatory molecule such as the E1a protein.

Acetyltransferases↗
PubMed1979

Mutational analysis of the simian virus 40 replicon: pseudorevertants of mutants with a defective replication origin.

The circular genome of simian virus 40 is a model mammalian replicon, containing a unique origin of replication (ori) and coding for a protein (SV40 T antigen) known to be involved in initiation of viral DNA replication and to bind in vitro to the origin region. Mutations within the ori sequence lead to defective viral DNA replication and the formation of small viral plaques after infection of a cell monolayer. Second-site revertants (pseudorevertants) of ori mutants were isolated by random local mutagenesis of mutant DNA followed by transfection of cultured cells and the selection of large plaques. In each case, reversion of the plaque phenotype was associated with an increased rate of viral DNA replication. The second-site mutations that suppressed the replication defects were localized by in vitro recombination or marker rescue experiments to the gene for T antigen. Their map positions differ from those of previously described T antigen mutants, possibly reflecting a specific ori-binding domain of T antigen. From these results we infer that T antigen interacts with the ori signal during virus development as it does in vitro and that this interaction regulates the rate of viral DNA replication.

Antigens, Neoplasm↗
PubMed2026

Mitogenome assembly and phylogenetic relationships of Phalaris arundinacea.

INTRODUCTION: As a perennial herb of Poaceae, Phalaris arundinacea plays key roles in grazing, production, and soil and water conservation because of its well-developed rhizomes and seed dispersal. We assembled and annotated the first mitogenome of P. arundinacea to support evolutionary and taxonomic research. METHODS: We assembled and annotated the first complete mitochondrial genome of P. arundinacea by integrating Illumina short reads with Nanopore long reads via a hybrid assembly strategy. The genome architecture was comprehensively characterized, encompassing codon usage bias, repetitive sequence organization, and inter-organellar genetic exchange with the chloroplast genome. RESULTS AND DISCUSSION: Assembly of the P. arundinacea mitogenome revealed two circular structures with a combined length of 526,717 bp. The genome comprised a set of 37 protein-coding genes (PCGs), 27 tRNAs, and 8 rRNAs, with the rRNA genes exhibiting full assembly (100% coverage). The mitochondrial genome contained 154 forward and 164 palindromic repeats, along with 25 tandem repeats and 124 simple sequence repeats (SSRs). Notably, 102 SSRs were distributed on contig1, predominantly in tetrameric form. Furthermore, 376 RNA editing sites were predicted. A total of 104 fragments were integrated into the mitochondrial genome from the chloroplast, amounting to 55,866 bp of transferred sequence. Finally, phylogenetic analysis of 28 plant mitogenomes placed P. arundinacea closest to species within the genus Poa (P. chaixii and P. pratensis). Comparative analysis of non-synonymous-to-synonymous substitution rate (Ka/Ks) ratios across divergent species revealed that the mitochondrial genome of P. arundinacea underwent stabilizing evolutionary dynamics, characterized by predominant purifying selection with several lineage-specific variations in selective pressure. Our findings support the close phylogenetic relationship between P. arundinacea and species of the genus Poa and provide a reference mitochondrial genome resource for future comparative studies within Phalaris that incorporate broader taxon sampling. These results support deeper phylogenetic investigations of P. arundinacea and facilitate future work on its germplasm characterization and applied use.

Phalaris arundinacea↗
PubMed1972

Enzymatic oligomerization of bacteriophage P22 DNA and of linear Simian virus 40 DNA.

Linear double-stranded molecules of the circularly permuted and terminally redundant DNA of Salmonella bacteriophage P22 have been converted to oligomeric products in the presence of polynucleotide ligase coded for by the coliphage T4. The reaction has been monitored by sucrose density-gradient centrifugation and electron microscopy. It goes slowly and gives yields of 30-40%. The products are mainly dimers and trimers, but higher oligomers are also present.DNA ligase extracted from uninfected Escherichia coli seems unable to perform a similar reaction, which is concluded to involve the fully base-paired termini. Linear double-stranded molecules of simian virus(SV) 40 DNA, produced by the action of the bacterial restriction endonuclease R(1), are oligomerized by either ligase; therefore, this reaction seems to involve single-stranded cohesive ends. No mixed products could be found when P22 DNA and linear SV 40 DNA were exposed together to the T4 ligase.

Carbon Isotopes↗
PubMed1990

Somatic diversification of the chicken immunoglobulin light-chain gene.

The bursa of Fabricius provides a unique organ for the study of lineage-specific development in a multicellular organism. Unlike mammalian B cells, B cells in the chicken develop in a single wave of differentiation, beginning with the commitment of progenitor cells to the B cell lineage between days 10 and 15 of embryogenesis. By day 18 of embryogenesis, all lymphoid progenitor cells capable of differentiation along the B cell lineage have migrated to the bursa of Fabricius. Following migration to the bursa, these lymphoid progenitors enter exponential growth and begin to populate each of the 10(4) bursal follicles. Between day 18 of embryogenesis and 2-4 weeks of age, B cells undergo a stage of bursal-dependent differentiation. By the end of this period, chickens are able to mount primary immune responses against virtually all antigens. In addition, by this time sufficient numbers of B cells have migrated from the bursa to peripheral lymphoid organs so that the B cell immune system can be maintained even if the bird is bursectomized. Bursectomy of chicks after 4 weeks of age has no long-term effects on the development and maintenance of the B cell immune system in adult birds. Because of the central nature of the surface Ig molecule to B cell development in mammals, the chicken IgL gene locus has been intensively studied during avian B cell development. The chicken IgL locus is a particular interest because it has only one V region capable of rearrangement. Rearrangement of the IgL gene is not dependent on the bursal environment. B cell progenitors rearrange their IgL gene between days 10-15 of embryogenesis, prior to migration to the bursa. IgL gene rearrangement occurs by a deletional mechanism in which a precise joining of the IgL recombination signal sequences leads to a circular episomal element. During this deletion it appears that single nonrandom bases are added to both the V and J coding segments. Subsequent V-J joining occurs at random. Most progenitor B cells appear to rearrange only a single IgL allele. The high frequency of in-frame alleles observed in avian B cell lines appears to result from the selective amplification of cells with productive IgL rearrangements during bursal development between days 12 and 18 of embryogenesis. To create an immunological repertoire, chickens must diversify the coding sequence of this single functional V gene segment during development.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1988

Genetic analysis of the tomato golden mosaic virus. II. The product of the AL1 coding sequence is required for replication.

Tomato golden mosaic virus (TGMV) belongs to the geminivirus subgroup that is characterized by a split genome consisting of two single-stranded circular DNAs. The TGMV A genome component encodes the virus coat protein as well as all of the functions necessary for viral DNA replication. Analysis of the nucleotide sequence indicates that the TGMV A component has, in addition to the coat protein encoding ORF, four overlapping open reading frames (ORFs) with the potential to encode proteins of greater than 10 kD. We have investigated the functions of these putative proteins in both symptom formation and DNA replication by creating mutations in each of the ORFs. Our results show that the AL4 ORF, which is encoded within the N-terminal region of ORF AL1, is not essential for normal virus infection. In contrast, we find that disruption of the AL3 ORF results in delay and attenuation of symptom formation. We also report that the products of the AL1 and AL2 ORFs are absolutely required for symptom formation. Studies of DNA replication show that only the AL1 open reading frame is essential for viral DNA synthesis. The significance of these results for the development of vectors from the geminiviruses is discussed.

DNA Mutational Analysis↗
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↗
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↗