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PubMed2026

Mitochondrial genome characteristics and phylogenetic analysis of Ramaria longispora.

This study, for the first time, assembled and annotated the complete mitochondrial genome of R. longispora using high-throughput sequencing technology. The genome is a circular molecule with a total length of 157,712 bp and a GC content of 31.55%. It encodes 71 genes, including 15 core protein-coding genes (PCGs), 25 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, 5 free-stranding open reading frames (ORFs), and 24 intronic ORFs. Among these, most free-stranding ORFs have unknown functions but include a DNA polymerase gene, while the intronic ORFs primarily encode LAGLIDADG and GIY-YIG endonucleases. The mitochondrial genome contains 39 introns. Phylogenetic analyses based on 15 core PCGs using Bayesian inference (BI) and maximum likelihood (ML) methods revealed that this R. longispora is most closely related to Ramaria flavescens and Ramaria ichnusensis. This study provides foundational data for mitochondrial genome research in the Ramaria genus and offers important references for taxonomic and evolutionary studies of this group.

Mitochondrial genome↗
PubMed1992

Mitochondrial encephalomyopathies: defects of nuclear DNA.

The term "mitochondrial diseases" encompasses a heterogeneous group of disorders in which a primary mitochondrial dysfunction is suspected or proven by morphologic, genetic, or biochemical criteria. Clinically, these progressive disorders usually affect muscle, either alone (mitochondrial myopathies) or in combination with other systems, most often brain (encephalomyopathies). Mitochondria are unique among intracellular organelles in that mitochondrial proteins are encoded by two genomes, nuclear DNA (nDNA) and mitochondrial DNA (mtDNA). The vast majority of mitochondrial proteins are encoded by the nuclear genome, whereas mtDNA (a circular, double stranded 16.5 kb molecule) encodes only 13 polypeptides, all of them subunits of respiratory chain complexes. In addition to structural genes, mtDNA also codes for 22 transfer RNAs and two ribosomal RNAs. Our understanding of mitochondrial diseases has grown at an impressive rate in the past few years, and most of the progress has been in the area of mtDNA genetics, where several mtDNA mutations have been associated with specific diseases (reviewed in this issue by Zeviani et al.). In comparison, our understanding of mitochondrial disorders due to nDNA lesions has lagged behind and, to date, molecular defects of nuclear genes have been documented in only a few patients. We will review which alterations in the nuclear genome can cause mitochondrial disorders and which criteria are useful in identifying such mutations. While several examples will be provided, this is not intended as a complete review of the subject.

Cell Nucleus↗
PubMed2026

The complete mitochondrial genome of Ramulus bifarius (Phasmida: Phasmatidae; Clitumninae).

We successfully acquired the complete mitochondrial genome information of Ramulus bifarius (S. C. Chen and Y. H. He, p. 476, Phasmatodea of China, 2008), which can be used for subsequent related molecular studies. The mitogenome of R. bifarius exhibits a circular duplex structure, with a total length of 16,915 bp and a high adenine and thymine bias of 76.7%. It contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a single control region.

China↗
PubMed2025

Complete genome sequence and genomic characterization of the probiotic Limosilactobacillus reuteri PSC102.

BACKGROUND: Gut microbiota are potential sources of probiotics and play an essential role in maintaining intestinal health. Limosilactobacillus reuteri PSC102 (L. reuteri PSC102), which was isolated from the feces of healthy pigs, exhibited health-beneficial properties. AIM: We aimed to conduct a whole-genome sequencing analysis of L. reuteri PSC102 to determine its molecular characteristics as a probiotic strain. METHODS: Limosilactobacillus reuteri PSC102 cells were cultured in De Man-Rogosa-Sharpe medium, followed by DNA extraction for genomic analysis using the PacBio-Illumina sequencing platform. The EzBioCloud software was used to perform gene assembly, and the genes were interpreted by the National Center for Biotechnology Information (NCBI) and the Glimmer program. Core and pan-genomic analyses were performed to assess the extent of functional conservation in the genomic sequence. Moreover, the NCBI database and the Basic Local Alignment Search Tool software were used to identify antimicrobial resistance genes and virulence factors. RESULTS: Limosilactobacillus reuteri PSC102 consists of a single circular chromosome with 2,048,626 bp, a guanine- cytosine of 38.9%, 18 rRNA genes, and 69 tRNA genes. Among the 1,846 protein-coding sequences, genes associated with probiotic characteristics were identified, including genes involved in host-microbe interactions, stress tolerance, biogenesis, and defense mechanisms. Furthermore, the genome of L. reuteri PSC102 comprises 2,446 pan-genome and 1,222 core-genome orthologous gene clusters. A total of 74 unique genes were identified in L. reuteri PSC102 genome. These genes mostly encode proteins potentially involved in the transport and metabolism of amino acids and carbohydrates. Moreover, antibacterial resistance genes and virulence factors were absent in L. reuteri PSC102. CONCLUSION: The results of the molecular insight into L. reuteri PSC102 corroborates its use as a probiotic in humans and other animals.

Limosilactobacillus reuteri↗
PubMed1977

Role of DNA gyrase in phiX replicative-form replication in vitro.

Preparations containing DNA gyrase activity Gellert, M., Mizuchi, K., O'Dea, M.H. & Nash, H.A. (1976) Proc. Natl. Acad. Sci. USA 73, 3872-3876] have been extensively purified from Escherichia coli. Such fractions, in the presence of ATP and Mg2+, catalyze supertwisting of relaxed circular double-stranded DNA replicative forms of a number of DNAs that results in the formation of superhelical replicative forms. Relaxed phiX174 replicative form (phiX RFIV) is not attacked by the A protein endonuclease coded for by the phiX DNA genome. After exposure to preparations of DNA gyrase, the relaxed phiX174 replicative form is converted to phiX RFI which can then be attacked by the phiX gene A protein and participate in replication of duplex phiX DNA.

Adenosine Triphosphate↗
PubMed1995

Isolation, characterization and transformation, by autonomous replication, of Mucor circinelloides OMPdecase-deficient mutants.

Pyrimidine auxotrophs of Mucor circinelloides were isolated after mutagenesis with nitrosoguanidine and selected for resistance to 5-fluoroorotate. These mutants were genetically and biochemically characterized and found to be deficient either in orotidine-5'-monophosphate decarboxylase (OMPdecase) activity or in orotate phosphoribosyl transferase (OPRTase) activity. Different circular DNA molecules containing the homologous pyrG gene were used to transform a representative OMPdecase-deficient strain to uracil prototrophy. Southern analysis, as well as mitotic stability analysis of the transformants, showed that the transforming DNA is always maintained extrachromosomally. The smallest fragment tested that retained both the capacity to complement the pyrG4 mutation and the ability to be maintained extrachromosomally when cloned in a suitable vector is a 1.85 kb M. circinelloides genomic DNA fragment. This fragment consists of the pyrG coding region flanked by 606 nucleotides at the 5' and 330 nucleotides at the 3' ends, respectively. Sequence analysis reveals that it does not share any element in common with another M. circinelloides genomic DNA fragment which also promotes autonomous replication in this organism, except those related to transcription. Furthermore, it differs from elements which have been shown to be involved in autonomous replication in other fungal systems. An equivalent plasmid harbouring the heterologous Phycomyces blakesleeanus pyrG gene yielded lower transformation rates, but the transforming DNA was also maintained extrachromosomally. Our results suggest that autonomous replication in M. circinelloides may be driven by elements normally present in nuclear coding genes.

Base Sequence↗
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↗
PubMed1993

Integrons: novel DNA elements which capture genes by site-specific recombination.

Integrons are unusual DNA elements which include a gene encoding a site-specific DNA recombinase, a DNA integrase, and an adjacent site at which a wide variety of antibiotic resistance and other genes are found as inserts. One or more genes can be found in the insert region, but each gene is part of an independent gene cassette. The inserted genes are expressed from a promoter in the conserved sequences located 5' to the genes, and integrons are thus natural expression vectors. A model for gene insertion in which circular gene cassettes are inserted individually via a single site-specific recombination event has been proposed and verified experimentally. The gene cassettes include a gene coding region and, at the 3' end of the gene an imperfect inverted repeat, a 59-base element. The 59-base elements are a diverse family of elements which function as sites recognized by the DNA integrase. Site-specific insertion of individual genes thus represents a further mechanism which contributes to the evolution of the genomes of Gram-negative bacteria and their plasmids and transposons. Members of the most studied class of integrons, which include the sulI gene in the conserved sequences, are believed to be mobile DNA elements on the basis that they are found in many independent locations, and a discrete boundary is found at the outer end of the 5'-conserved segment. However, the length of the 3'-conserved segment is variable in the integrons examined to date, and it is likely that this variability has arisen as the result of insertion and deletion events. Though the true extent of the 3'-conserved segment remains to be determined, it seems likely that these integrons are mobile DNA elements. The second known class of integrons comprises members of the Tn7 transposon family.

Base Sequence↗
PubMed1998

Pulsed-field gel electrophoresis analysis of the genome of Rhodococcus fascians: genome size and linear and circular replicon composition in virulent and avirulent strains.

Total DNA of virulent and avirulent strains of Rhodococcus fascians was resolved by pulsed-field gel electrophoresis (PFGE) into a discrete number of fragments by digestion with the endonucleases AseI and DraI. Restriction endonucleases PacI, PmeI, and SwaI yielded no fragments upon digestion of R. fascians genome, and all the other tested endonucleases recognizing 6 bp released too many fragments. The genome size was 5.6 megabases for the type strain R. fascians DSM 20669, and 5.8 megabases for the virulent R. fascians D188 strain. However the genome size of R. fascians CECT 3001 (NRRL B15096) was 8.0 megabases. No linear chromosome in the megabase range was observed under pulse conditions in which Saccharomyces cerevisiae and Schizosaccharomyces pombe chromosomes were perfectly resolved, suggesting that the R. fascians chromosome is circular. A new linear plasmid pIRN640 of 640 kb was found in the avirulent R. fascians CECT 3001 that did not hybridize with a probe internal to the fas region of pFiD188 known to be involved in plant pathogenicity in the virulent strain R. fascians D188. Virulence was correlated in all strains tested with the presence of the fas region. The AseI and DraI bands corresponding to the extrachromosomal elements were identified providing the basis for a physical map of this organism.

DNA, Circular↗
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↗
PubMed1996

Cloning and characterization of the major histone H2A genes completes the cloning and sequencing of known histone genes of Tetrahymena thermophila.

A truncated cDNA clone encoding Tetrahymena thermophila histone H2A2 was isolated using synthetic degenerate oligonucleotide probes derived from H2A protein sequences of Tetrahymena pyriformis. The cDNA clone was used as a homologous probe to isolate a truncated genomic clone encoding H2A1. The remaining regions of the genes for H2A1 (HTA1) and H2A2 (HTA2) were then isolated using inverse PCR on circularized genomic DNA fragments. These partial clones were assembled into intact HTA1 and HTA2 clones. Nucleotide sequences of the two genes were highly homologous within the coding region but not in the noncoding regions. Comparison of the deduced amino acid sequences with protein sequences of T. pyriformis H2As showed only two and three differences respectively, in a total of 137 amino acids for H2A1, and 132 amino acids for H2A2, indicating the two genes arose before the divergence of these two species. The HTA2 gene contains a TAA triplet within the coding region, encoding a glutamine residue. In contrast with the T. thermophila HHO and HTA3 genes, no introns were identified within the two genes. The 5'- and 3'-ends of the histone H2A mRNAs; were determined by RNase protection and by PCR mapping using RACE and RLM-RACE methods. Both genes encode polyadenylated mRNAs and are highly expressed in vegetatively growing cells but only weakly expressed in starved cultures. With the inclusion of these two genes, T. thermophila is the first organism whose entire complement of known core and linker histones, including replication-dependent and basal variants, has been cloned and sequenced.

Amino Acid Sequence↗
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↗
PubMedDate not supplied

Selecting and using a videokeratoscope for mapping of corneal topography (continuing education credit).

1. Modern videokeratography (VK) projects circular Placido rings onto the specular cornea where they are captured by a single or dual camera. The computer within the system employs electronic edge detection to analyze the reflected image(s), and a reconstruction algorithm transforms the two-dimensional circular pattern into a representation of the three-dimensional shape of the cornea. 2. The most familiar product of a videokeratoscope is a color-coded contour map of corneal surface power, in which cool colors represent low corneal powers and warm colors suggest high corneal powers. These maps provide both an accurate and highly intuitive method of determining the shape of the cornea. 3. The primary applications of VK are in determination of corneal curvature and astigmatism prior to and following refractive surgery, both photorefractive keratectomy (PRK) and radial keratotomy (RK), and in the diagnosis of keratoconus. Corneal mapping also is useful in the determination of other disease states. It is likely that within 5 years corneal topographical mapping will be mandatory measurement for all pre- and post-refractive surgery. 4. Consequently, every hospital and surgeon's office will soon have access to one or more videokeratoscopes. As systems become less expensive and more application-specific, the instruments will most likely become standard equipment for clinicians in the fitting of contact lenses. At that point, interaction with these systems will fall into the job description of virtually every nurse/technician. Many technicians will be called on to give quick selection criteria and advice to surgeons and physicians regarding videokeratography.

Cornea↗
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↗
PubMed1994

Physical map and gene organization of the mitochondrial genome of Chondrus crispus (Rhodophyta, Gigartinales).

Organellar DNA, i.e. a mixture of plastid and mitochondrial DNAs, was purified from the rhodophyte Chondrus crispus and analysed with restriction endonucleases. Mitochondrial DNA fragments were identified by heterologous hybridization, cloned, mapped and partially sequenced. The mitochondrial genome of C. crispus consists of a 25.9 kb circular molecule on which twenty genes were localized. Compared with other plant mitochondrial genomes, C. crispus mitochondrial DNA appears as a relatively small molecule with a high coding capacity and a specific gene organization. The use of a modified genetic code and the absence of RNA editing, previously reported for the cox3 gene, is a general characteristic of the sequenced genes of this molecule. This is the first detailed description of a red algal mitochondrial genome.

Base Sequence↗