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At least 163 records · Page 9Linked to original sources
PubMed1978

RNA from the insect trypanosome Crithidia luciliae contains transcripts of the maxi-circle and not of the mini-circle component of kinetoplast DNA.

We have hybridized total cellular RNA of Crithidia luciliae with the kinetoplast DNA of this organism. To allow the discrimination of DNA from mini-circles (2300 base pairs) and maxi-circles (33 000 base pairs), kinetoplast DNA was digested with restriction endonucleases and the fragments were separated by electrophoresis through an agarose gel and transferred to nitrocellulose filters by blotting. No mini-cricle transcripts were found under conditions where maxi-circle fragments showed extensive and specific hybridization. Since maxi-circle sequences are present at less than 1% of the concentration of mini-circle sequences, we conclude that mini-circles may not be transcribed at all. Predominant hybridization with the maxi-circle fragments is obtained with a segment of only 2300--2500 base pairs. The possibility that this segment codes for unusually small mitochondrial ribosomal RNAs is discussed.

Animals↗
PubMed1991

Identification and immunohistochemistry of cholinergic and non-cholinergic circular muscle motor neurons in the guinea-pig small intestine.

Motor neurons which innervate the circular muscle layer of the guinea-pig small intestine were retrogradely labelled, in vitro, with the carbocyanine dye, DiI, applied to the deep muscular plexus. By combining retrograde tracing and immunohistochemistry, the chemical coding of motor neurons was investigated. Five classes of neuron could be distinguished on the basis of the co-localization of immunoreactivity for the different antigens; the five classes were also characterized by different lengths and polarities of their axonal projections and by their cell body shapes. Two classes with local or orally directed axons were immunoreactive for choline acetyltransferase and substance P and are likely to be cholinergic excitatory motor neurons. Two other classes had anally directed axons; they were immunoreactive for vasoactive intestinal polypeptide and are likely to be inhibitory motor neurons. A small proportion of neurons with short projections to the circular muscle were immunoreactive for neither substance P nor for vasoactive intestinal polypeptide, but are likely to be cholinergic. The morphological and histochemical identification of excitatory and inhibitory motor neurons provides a neuroanatomical basis for the final motor pathways involved in the polarized reflex motor activity of the gut.

Animals↗
PubMed1978

Free ribosomal RNA genes in Paramecium are tandemly repeated.

The genes coding for 17S and 25S rRNA in Paramecium tetraurealia were isolated. The macronuclear ribosomal DNA (rDNA) exists as relatively small, extrachromosomal molecules with both linear and circular forms. Electron microscopy and restriction endonuclease analysis revealed that the rDNA is arranged as tandem repeats with an average repeat size of 5.5 X 10(6) daltons. Some heterogeneity of repeat lengths was found both by electron microscopy and by restriction enzyme analysis. The rDNA does not snap back after denaturation. This study provides additional evidence that extrachromosomal rDNA may be a common feature among lower eukaryotes. However, in contrast to several other cases, the rDNA of Paramecium is not palindromic, but occurs as tandem repeats as in higher eukaryotes.

Animals↗
PubMed1991

Three envelope proteins of hepatitis B virus: large S, middle S, and major S proteins needed for the formation of Dane particles.

The infectious particles of hepatitis B virus are called Dane particles and consist of viral nucleic acid encapsulated within a core particle that is enveloped by virus-coded surface proteins. The major S protein constitutes a significant fraction of these surface proteins. In addition, there are two other related proteins (large S and middle S), but their role in envelope formation has not yet been elucidated. We modified the translation initiation codon ATG of each of the envelope proteins by site-directed mutagenesis and found that mutant genomes that did not produce one or two of these proteins were unable to form Dane particles. The particles released into the culture medium by such mutants did not carry DNA. Synthesis of virus-coded RNA still occurred normally, and core particles carrying DNA accumulated intracellularly. The DNA in such core particles was mostly in the double-stranded open circular form, in contrast to the normal situation in which the particles contain mostly RNA and its complementary single-stranded DNA or else contain linear DNA that is partially single stranded and otherwise duplex. The role of the large S and middle S proteins in the formation of Dane particles is discussed.

Blotting, Northern↗
PubMed1995

The spatial coding strategies of one-year-old infants in a locomotor search task.

The ability of 1-year-old infants to remember the location of a nonvisible target was investigated in 3 experiments. Infants searched for a toy hidden in one of many possible locations within a circular bounded space. The presence, number, and spatial arrangement of local cues or "landmarks" within this space were varied. The results of Experiment 1 showed that search performance was highly successful when a landmark was coincident with the location of the toy ("direct"), but less successful when a landmark was adjacent to the target location ("indirect"). The results of Experiment 2 suggested that search with an indirect landmark may be more fragile than search with no landmarks at all. In Experiments 3a and 3b, 2 different configurations of indirect landmarks were employed; search performance was equally poor with both of these and was inferior to search with no landmarks. It is concluded that infants of this age are able to associate a nonvisible target with a direct landmark and are able to code the distance and direction of a target with respect to themselves or with respect to the larger framework. However, there was no evidence that they can code the distance and direction of a target relative to another object. The difficulty of coding with indirect landmarks is interpreted in terms of cognitive complexity and conflict between spatial strategies.

Child Development↗
PubMed1995

Exonucleolytic processing of small nucleolar RNAs from pre-mRNA introns.

Many small nucleolar RNAs (snoRNAs) in vertebrates are encoded within introns of protein genes. We have reported previously that two isoforms of human U17 snoRNA are encoded in introns of the cell-cycle regulatory gene, RCC1. We have now investigated the mechanism of processing of U17 RNAs and of another intron-encoded snoRNA, U19. Experiments in which the processing of intronic RNA substrates was tested in HeLa cell extracts suggest that exonucleases rather than endonucleases are involved in the excision of U17 and U19 RNAs: (1) Cutoff products that would be expected from endonucleolytic cleavages were not detected; (2) capping or circularization of substrates inhibited formation of snoRNAs; and (3) U17 RNA was faithfully processed from a substrate carrying unrelated flanking sequences. To study in vivo processing the coding regions of snoRNAs were inserted into intron 2 of the human beta-globin gene. Expression of resulting pre-mRNAs in simian COS cells resulted in formation of correctly processed snoRNAs and of the spliced globin mRNA, demonstrating that snoRNAs can be excised from a nonhost intron and that their sequences contain all the signals essential for accurate processing. When the U17 sequence was placed in a beta-globin exon, no formation of U17 RNA took place, and when two U17 RNA-coding regions were placed in a single intron, doublet U17 RNA molecules accumulated. The results support a model according to which 5'-->3' and 3'-->5' exonucleases are involved in maturation of U17 and U19 RNAs and that excised and debranched introns are the substrates of the processing reaction.

Base Sequence↗
PubMed1984

Monkey B-lymphotropic papovavirus DNA: nucleotide sequence of the region around the origin of replication.

We have determined the nucleotide sequence of the HindIII-B DNA segment of African green monkey B-lymphotropic papovavirus (LPV), which shows a highly restricted host range and whose genome is a 5.1-kilobase-long circular DNA. The segment, consisting of 1,123 base pairs, contained the origin of DNA replication, the putative control region for early transcription, and the region probably coding for the amino-terminal portion of T antigens. The symmetrical region at the center of replication origin, 5'-GAGGC CA GGGGCCCC TA GCCTC-3' (on the L strand), has diverged in the central portion from the corresponding regions of primate polyomaviruses simian virus 40, BK virus, and JC virus, but resembles that of mouse polyomavirus. The structure of the control region upstream of the replication origin was unique to LPV and contained several repeated sequences, the longest of which were two 60-base-pair tandem repeats. The amino-terminal region common to LPV small T and large T antigens showed some homology (41%) in the deduced amino acid sequence to that of both simian virus 40 and the mouse polyomavirus. Like other polyomaviruses, the probable carboxyl-terminal region unique to LPV small T antigen contained two sets of the Cys-x-Cys-x-x-Cys structure. These data show that, despite the unique structures in the control region, LPV is evolutionally related to the mouse polyomavirus and to simian virus 40.

Amino Acid Sequence↗
PubMed1978

Circular dichroism studies of the interaction of a limited hydrolysate of T4 gene 32 protein with T4 DNA and poly[d(A-T)].poly[d(A-T)].

gp32 I is a protein with a molecular weight of 27 000. It is obtained by limited hydrolysis of T4 gene 32 coded protein, which is one of the DNA melting proteins. gp32 I itself appears to be also a melting protein. It denatures poly[d(A-T)].poly[d(A-T)] and T4 DNA at temperatures far (50-60 degrees C) below their regular melting temperatures. Under similar conditions gp32 I will denature poly[d(A-T).poly[d(A-T)] at temperatures approximately 12 degrees C lower than those measured for the intact gp32 denaturation. For T4 DNA gp32 shows no melting behavior while gp32 I shows considerable denaturation (i.e., hyperchromicity) even at 1 degree C. In this paper the denaturation of poly[d(A-T)].poly[d(A-T)] and T4 DNA by gp32 I is studied by means of circular dichroism. It appears that gp32 I forms a complex with poly[d(A-T)]. The conformation of the polynucleotide in the complex is equal to that of one strand of the double-stranded polymer in 6 M LiCl. In the gp32 I DNA complex formed upon denaturation of T4 DNA, the single-stranded DNA molecule has the same conformation as one strand of the double-strand T4 DNA molecule in the C-DNA conformation.

Circular Dichroism↗
PubMed1991

Isolation, physical map and gene map of mitochondrial DNA from the cryptomonad Pyrenomonas salina.

Mitochondrial DNA (mtDNA) from the cryptomonad Pyrenomonas salina was isolated by CsCl-buoyant density centrifugation of whole-cell DNA in the presence of Hoechst dye 33258. mtDNA consists of circular molecules about 47 kb in size as estimated from restriction enzyme analysis. A physical map for six restriction enzymes (Bam HI, Bge I, Eco RI, Pst I, Sac I and Sal I) has been constructed. Genes coding for the small subunit of rRNA, cytochrome oxidase subunits I and II, and apocytochrome b were localized on this map using Southern blot hybridization with heterologous gene probes from Oenothera. Genes for 5S rRNA and NADH dehydrogenase subunit 5 are absent from P. salina mtDNA. The mitochondrial genome, being the first analysed to this extent in chromophytic algae, should be valuable for taxonomic and phylogenetic studies.

Centrifugation, Density Gradient↗
PubMed1995

Plasmodium falciparum: alterations in organelle transcript abundance during the erythrocytic cycle.

The malaria parasite Plasmodium falciparum has two extrachromosomal DNAs, a 6 kb reiterated element which appears to be the mitochondrial DNA and a 35 kb circular DNA of unknown function. Examination of relative steady-state transcript abundance during parasite development in the erythrocyte shows that transcripts of 6 kb element protein-coding genes are least abundant in the ring and early trophozoite stages and most abundant in late trophozoites and schizonts, while transcripts from the RNA polymerase subunits of the 35 kb DNA, also least abundant in ring stage, are relatively similar in abundance in succeeding stages. The fragmented rRNAs of the 6 kb element appear to be constitutively abundant except for an increase in the schizont stage, while rRNAs from the 35 kb DNA are least abundant in early trophozoites and most abundant in schizonts. Thus the relative abundance of organelle transcripts alters during the erythrocytic portion of the P. falciparum developmental cycle. These alterations may reflect the relative importance of the roles played by organelle gene products in different life cycle stages.

Animals↗
PubMed1981

One and two codon insertion mutants of bacteriophage f1.

Simple methods for introducing one or two extra codons of genetic information into the f1 genome in vitro have been devised. The methods use various combinations of enzymes to insert three or six base-pairs into the RF1 DNA of the bacteriophage. Since such insertions do not cause frameshifts in coding regions, a number of these mutants are viable. Several such mutants were mapped and characterized. The methods described and variations of them can be applied to other circular DNA genomes.

Codon↗
PubMed1993

Structure/function studies of HIV-1(1) reverse transcriptase: dimerization-defective mutant L289K.

Virion-derived HIV-1 reverse transcriptase (RT) has subunits of molecular mass 66 and 51 kDa (p66 and p51, respectively) in an approximately 1:1 ratio. Since enzyme activity appears to depend on dimerization of these subunits, identification of critical regions of primary sequence required for proper dimerization could lead to potential targets for antiviral therapy. A central region of primary sequence contains a leucine hepta-repeat motif from leucine 282 to leucine 310 that has been suggested to be involved in dimerization [Baillon, J. G., Nashed, N. T., Kumar, A., Wilson, S. H., & Jerina, D. M. (1991) New Biol. 3, 1015-1019]. A region including this hepta-repeat was recently shown to be involved in protein-protein interactions required for dimerization [Becerra, S. P., Kumar, A., Lewis, M. S., Widen, S. G., Abbotts, J., Karawya, E. M., Hughes, S. H., Shiloach, J., & Wilson, S. H. (1991) Biochemistry 30, 11708-11719]. To investigate the role of this repeat motif in dimerization, we performed site-directed mutagenesis of these leucine residues from position 282 to position 310. Mutations were introduced into p66 and p51 RT coding sequences, and the individually purified RT subunit polypeptides were compared with wild-type polypeptides for dimerization. Physical characterization of the purified mutant peptides was conducted by circular dichroism analysis. Binding between p66 and p51 was studied by gel filtration, ultracentrifugation, and CD analysis. L289K-p66 was unable to dimerize with itself and wild-type or L289K-p51. The leucine repeat motif in the p66 subunit appears to be critical in formation of the heterodimer.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1992

Morphogenesis of recombinant HIV-2 gag core particles.

The gag-pol coding region of the HIV-2BEN genome was expressed in CV-1 cells infected with four recombinant vaccinia viruses (VV). These recombinant VV encoded either the whole gag-pol region or the gag gene including the protease-coding region of the pol gene or the gag gene truncated at its 3'-end or only the pol gene. The HIV-2BEN gag precursor p55, its mature cleavage products p24 and p17 as well as the pol reverse transcriptase (RT) p66 were detected in VV-infected CV-1 cells. The p55 and two intermediate cleavage products p40 and p35 were myristilated. Comparison to lysates of permanently HIV-2BEN-infected Molt 4 clone 8 cells revealed that several additional gag and pol proteins were present in the VV-infected CV-1 cells. Deletion of the gag and pol overlapping region coding for the viral protease prevented cleavage of the recombinant gag precursor. Electron microscopy of VV-infected CV-1 cells revealed budding structures and immature as well as mature retroviral particles formed by the recombinant gag proteins. Striking differences in the ability to form complete particles were observed between the different recombinant VV. Expression of the truncated gag gene led to the formation of budding structures, but completely budded circular particles were not detectable. Such particles were produced by expression of the whole gag gene and the protease. Mature virions with an internal core structure were only detected in VVgagpol-infected cells. From these findings we conclude that the 3'-end of the gag gene coding for the p16 protein is essential for the formation of complete HIV-2 particles and that the pol proteins support the assembly of the viral core.

Base Sequence↗
PubMed1981

Endodeoxyribonuclease activity associated with Rauscher murine leukemia virus.

Preparations of purified Rauscher murine leukemia virus were found to contain an endodeoxyribonuclease after disruption of the virus with nonionic detergents. The enzyme makes single-strand breaks in linear or covalently closed circular phage double-stranded DNA molecules. The enzyme was partially purified by ion-exchange chromatography on DEAE- and carboxymethyl-Sepharose columns followed by electrophoresis in DNA-containing polyacrylamide gels. The enzyme was separated from reverse transcriptase (p80pol), and the final endonuclease preparation contained no detectable reverse transcriptase activity. The DEAE-Sepharose column-purified endonuclease activity contained a polypeptide of about 40,000 Mr that we term p40. Peptide mapping experiments demonstrated that p40 shares methionine-labeled tryptic peptides with Pr200gag-pol and Pr135pol. Six major methionine-labeled tryptic peptides derived from p40 were found in Pr200gag-pol, but only five of these were detected in Pr135pol. The four core proteins (p30, p15, pp12, and p10) and p80pol plus p40 account for most, but not all, of the peptide sequences of Pr200gag-pol. The endonuclease-associated p40 is similar in size and precursor origin to the avian retrovirus-coded endonuclease (p32). In view of these similarities to the avian p32 endonuclease and its association with partially purified Rauscher murine leukemia virus-associated endonuclease preparations, we propose that p40 is the Rauscher murine leukemia virus-coded endonuclease.

Chromatography, Ion Exchange↗
PubMed2026

Cancer-associated fusion transcripts: mechanisms, functional roles, and clinical implications.

Fusion transcripts are hybrid RNA molecules generated through genomic rearrangements or RNA-level fusion mechanisms. They represent important molecular features of many cancers and can function as oncogenic drivers, diagnostic biomarkers, prognostic indicators, and therapeutic targets. Since the discovery of the BCR::ABL1 fusion in chronic myeloid leukemia, numerous cancer-associated fusion transcripts have been identified across hematologic malignancies and solid tumors. These fusion events encompass diverse biological mechanisms, including constitutively active kinases, aberrant transcription factors, epigenetic regulators, and non-coding fusion RNAs. This review summarizes current knowledge of the mechanisms underlying fusion transcript formation, including genomic rearrangement-dependent and rearrangement-independent processes, as well as fusion circular RNAs. The functional roles of fusion transcripts in cancer biology and their clinical relevance as diagnostic, prognostic, and predictive biomarkers are discussed. In addition, recent advances in fusion transcript detection and characterization are reviewed, including next-generation sequencing, long-read sequencing, single-cell approaches, artificial intelligence-assisted computational methods, and CRISPR/Cas9-mediated strategies for functional modeling and functional validation of fusion transcripts. Despite the rapid expansion of fusion transcript catalogs, the biological and clinical significance of most identified fusion events remains incompletely understood. Future progress will depend on integrating advanced sequencing technologies, artificial intelligence-assisted computational prioritization, and systematic functional validation to distinguish clinically actionable fusion transcripts from biologically neutral events. Such multidisciplinary approaches will be essential for translating fusion transcript research into precision oncology and improving cancer diagnosis, patient stratification, and targeted therapy.

Humans↗