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PubMed2006

Custom-built moments for edge location.

We present a general construction of functions whose moments serve to locate and parametrize step edges within an image. Previous use of moments to locate edges was limited to functions supported on a circular region, but our method allows the use of "custom-designed" functions supported on circles, rectangles, or any desired shape, and with graphs whose shape may be chosen with great freedom. We present analyses of the sensitivity of our method to pixelization errors or discrepancy between the image and an idealized edge model. The parametric edge description yielded by our method makes it especially suitable as a component of wedgelet image coding.

Algorithms↗

PubMed2002

Plasmid-borne genes code for an angular dioxygenase involved in dibenzofuran degradation by Terrabacter sp. strain YK3.

The genes responsible for angular dioxygenation of dibenzofuran in actinomycetes were cloned by using a degenerate set of PCR primers designed by using conserved sequences of the dioxygenase alpha subunit genes. One sequence of alpha subunit genes was commonly amplified from four dibenzofuran-utilizing actinomycetes: Terrabacter sp. strains YK1 and YK3, Rhodococcus sp. strain YK2, and Microbacterium sp. strain YK18. A 5.2-kb PstI fragment encoding the alpha and beta subunits of the terminal dioxygenase, ferredoxin, and ferredoxin reductase (designated dfdA1 to dfdA4, respectively) was cloned from the large circular plasmid pYK3 isolated from Terrabacter sp. strain YK3. We confirmed that transcription of the dfdA1 gene was induced by dibenzofuran in Terrabacter sp. strain YK3. Southern blot hybridization analysis revealed that this type of dioxygenase gene is distributed among diverse dibenzofuran-utilizing actinomycetes. However, genes homologous to dfdA1 were not detected in dibenzofuran utilization-deficient mutants of Terrabacter, Rhodococcus, and Microbacterium species. When the dfdA1 to dfdA4 genes were introduced into a non-dibenzofuran-degrading mutant of Rhodococcus sp. strain YK2, strain YK2-RD2, which had spontaneously lost the gene homologous to dfdA1, the ability to degrade dibenzofuran was restored. Analysis of the breakdown products indicated that DfdA has angular dioxygenase activity. This dfdA transformant degraded several aromatic compounds, indicating that the novel angular dioxygenase possesses broad substrate specificity.

Actinomycetales↗

PubMed1986

Expression, secretion and folding of human growth hormone in Escherichia coli. Purification and characterization.

An efficient secretion vector containing a gene coding for an E. coli signal peptide fused to human growth hormone (hGH) was cloned into E. coli. The recombinant fusion protein was expressed and correctly processed hGH was secreted into the periplasmic space at a yield of 10-15 micrograms hGH/A600. Purification of hGH from the periplasmic fraction by anion exchange and size exclusion gave hGH of greater than 90% purity. Characterization by SDS-PAGE, amino terminal analysis, trypsin mapping, and circular dichroism demonstrated that the fusion protein was correctly processed to authentic hGH and that the E. coli periplasm provided an appropriate environment for proper folding of hGH and disulfide bond formation.

Amino Acid Sequence↗

PubMed1995

Increased expression of LD1 genes transcribed by RNA polymerase I in Leishmania donovani as a result of duplication into the rRNA gene locus.

Eukaryotic protein-coding genes are generally transcribed by RNA polymerase II (Pol II), which has a lower transcription rate than that of Pol I. We report here the duplication of two LD1 genes into the rRNA locus and their resultant transcription by Pol I. The multigenic LD1 locus is present in a 2.2-Mb chromosome in all stocks of Leishmania spp. and is also present in multicopy 200- to 450-kb linear chromosomes or multicopy circular DNAs in over 15% of stocks examined. Genomic rearrangement in Leishmania donovani LSB-51.1 resulted in duplication of a 3.9-kb segment of LD1 containing two genes (orfF and orfG) and of a 1.3-kb segment from approximately 10 kb downstream into the rRNA gene repeat region of the 1.2-Mb chromosome. Short sequences (12 or 13 bp) common to the 2.2-Mb LD1 and 1.2-Mb rRNA loci suggest that this gene conversion occurred by homologous recombination. Transcription of the duplicated genes is alpha-amanitin resistant, indicating transcription by Pol I, in contrast to the alpha-amanitin-sensitive (Pol II) transcription of the genes in the 2.2-Mb LD1 locus. This results in higher transcript abundance than expected from the gene copy number in LSB-51.1 and in elevated expression of at least the orfF gene product.

Amanitins↗

PubMedDate not supplied

TTV, a new human virus with single stranded circular DNA genome.

TT virus (TTV) was found in 1997 from a hepatitis patient without virus markers. However, the real impact of TTV on liver diseases remains uncertain to date. Due to the lack of suitable cell systems to support the growth of TTV, the biology of TTV is still obscure. This review tries to summarise the current status of TTV on aspects other than the taxonomic diversity of TTV. TTV was the first human virus with a single stranded circular DNA genome. TTV was considered to be a member of Circoviridae, but others suggested it conformed to a new family. TTV is distinct from ambisense viruses in the genus Circovirus, since the former genome is negative stranded. The genome structure of TTV is more related to chicken anaemia virus in the genus Gyrovirus, however, the sequence similarity is minimal except for a short stretch at 3816-3851 of TA278. Currently the working group is proposing the full name for TTV as TorqueTenoVirus and the TTV-like mini virus as TorqueTenoMiniVirus (TTMV) in a new genus Anellovirus (ring). TTVs are prevalent in non-human primates and human TTV can cross-infect chimpanzees. Furthermore, TTV sequences have been detected in chickens, pigs, cows and sheep. TTV can be transmitted by mother-to-child infection. However, within a year after birth, the prevalence reaches the same level for children born to both TTV-positive and TTV-negative mothers even without breast-feeding. The non-coding region surrounding a short 113 nt GC-rich stretch and occupying approximately one-third of the genome is considered to contain the putative replication origin. Three mRNAs are expressed by TTV, 3.0 and 1.2 and 1.0 kb species. A protein translated from the 3.0 kb mRNA is considered to be the major capsid protein as well as replicase. The nature of the proteins translated by the other two mRNAs are still putative.

Animals↗

PubMed1970

Simian virus 40 deoxyribonucleic acid transcription in vitro: binding and transcription patterns with a mammalian ribonucleic acid polymerase.

The in vitro transcription pattern of simian virus 40 (SV40) deoxyribonucleic acid (DNA) by a mammalian ribonucleic acid (RNA) polymerase, was studied by electron microscopy and velocity sedimentation techniques. It was found that (i) the majority of supercoiled SV40 DNA molecules displayed a single binding site for the enzyme, (ii) the supercoiled structure of SV40 DNA was frequently retained during transcription, and (iii) the majority of RNA molecules synthesized from the supercoiled SV40 DNA template showed no self-complementarity and sedimented relatively homogeneously in the 15S to 16S region of a sucrose gradient (in contrast, the RNA product synthesized from the nicked-circular SV40 DNA template showed self-complementarity and sedimented heterogeneously). RNA polymerase preparations isolated from SV40-infected monkey cells were more active than those isolated from uninfected monkey cells.

Animals↗

PubMed1995

Complete sequence of the mitochondrial DNA of the rhodophyte Chondrus crispus (Gigartinales). Gene content and genome organization.

The complete nucleotide sequence of the circular mitochondrial (mt) DNA from the red alga Chondrus crispus was determined (25,836 nucleotides, A+T content 72.1%). Fifty one genes were identified. They include genes encoding three subunits of the cytochrome oxidase (cox1 to 3), apocytochrome b (cob), seven subunits of the NADH dehydrogenase complex (nad1 to 6, nad4L), two ATPase subunits (atp6 and atp9), three ribosomal RNAs (rrn5, srn and lrn), 23 tRNAs and four ribosomal proteins (rps3, rps11, rps12 and rpl16). Two subunits of the succinate dehydrogenase complex (sdhB and sdhC), usually found on nuclear genomes, are also located on the mtDNA of C. crispus. One group IIb intron is inserted in the tRNAIle gene. Six potentially functional open reading frames were identified, four of them having counterparts among green plant mtDNAs. The use of a modified genetic code and the absence of RNA editing, previously reported for the cox3 gene, appears as a general characteristic of this molecule. Mitochondrial genes are encoded on both DNA strands, in two opposite major transcriptional directions, suggesting the existence of two main transcriptional units. Two long and stable stem-loops were identified in intergenic regions, which are believed to be involved with transcription and replication. The main structural features of this genome are compared with the overall organization of mtDNAs and are discussed in view of the evolution of mitochondria.

Amino Acid Sequence↗

PubMed1993

Self-limiting infection by int/nef-double mutants of simian immunodeficiency virus.

Simian immunodeficiency virus (SIVmac) infectious for rhesus monkeys was altered by site-directed mutagenesis of genes influencing in vivo replication and persistence with the long-term goal to develop attenuated lentiviruses with limited replication capacity in vivo. Double mutants of SIVmac (termed delta-int 1 to 3) were generated by introducing frameshift and deletion mutations into the nef gene and into the pol gene region coding for the integrase protein. Delta-int/delta-nef viruses formed after transfection of CD(4+)-lymphocyte cell lines were unable to establish sustained replication. In contrast, both wild-type SIVmac and mutant SIVmac delta-nef (coding for a truncated NEF protein and a wild-type INT protein) replicated continuously and at a comparable rate. However, a transient and self-limiting infection of the C8166 T-cell line was observed subsequent to transfection of double mutant proviruses into HeLa-tat-III cells. Viruses attenuated by int/nef-double mutation were able to enter the T-cells, initiate synthesis of viral DNA as shown by PCR amplification of closed circular episomes, and express viral antigens in infected cells as demonstrated by immunocytochemical staining. Integration of the int mutant viruses into the chromosome was completely inhibited. Episomal viral DNA was detectable in the infected cells for up to 2 weeks, after which it disappeared. Thus, SIVmac attenuated by int and nef mutation established a transient infection of permissive cells resulting in the expression of viral antigen from episomal viral DNA over a limited period of time.

Antigens, Viral↗

PubMed1986

Analysis of the mitochondrial and nuclear genomes of two basidiomycetes, Coprinus cinereus and Coprinus stercorarius.

The mitochondrial and nuclear genomes of Coprinus stercorarius and C. cinereus were compared to assess their evolutionary relatedness and to characterize at the molecular level changes that have occurred since they diverged from a common ancestor. The mitochondrial genome of C. stercorarius (91.1 kb) is approximately twice as large as that of C. cinereus (43.3 kb). The pattern of restriction enzyme recognition sites shows both genomes to be circular, but reveals no clear homologies; furthermore, the order of structural genes is different in each species. The C. stercorarius mitochondrial genome contains a region homologous to a probe derived from the yeast mitochondrial var1 gene, whereas its nuclear genome does not. By contrast, the C. cinereus nuclear, but not mitochondrial, genome contains a region homologous to the var1 probe. Only a small fraction of either the nuclear or mitochondrial genomes, perhaps corresponding to the coding sequences, is capable of forming duplexes in interspecies solution reassociations, as measured by binding to hydroxylapatite. Those sequences capable of reassociating were found to have approximately 15% divergence for the mitochondrial genomes and 7%-15% divergence for the nuclear genomes, depending on the conditions of reassociation.

Basidiomycota↗

PubMed1990

The MURF3 gene of T. brucei contains multiple domains of extensive editing and is homologous to a subunit of NADH dehydrogenase.

Mitochondrial MURF3 transcripts of T. brucei are extensively edited by the addition and deletion of uridines. The editing creates potential initiation and termination codons and a continuous open reading frame. The predicted amino acid sequence has homology to a subunit of NADH dehydrogenase (ND7). ND7 is independently edited in two distinct domains, suggesting two editing initiation sites. Editing in the two domains is differentially regulated: the 5' domain is edited in both bloodstream and procyclic forms but the 3' domain is completely edited only in the bloodstream form. Two potential guide RNA (gRNA) coding sequences were identified in the same minicircle. One is complementary to edited sequence in the 5' domain, the other to edited sequence in the 3' domain.

Amino Acid Sequence↗

PubMed1995

Transcription of the Y chromosomal gene, Sry, in adult mouse brain.

The Y chromosomal gene Sry encodes a putative transcription factor which appears to serve as a master switch initiating testicular development. Here we show that this gene is transcribed in hypothalamus, midbrain, and testis of adult male but not adult female mice. In contrast to its circular transcripts in adult testis, those in brain are linear and may be translated. We propose that Sry exerts a role in the regulation of sex differentiation of the mammalian nervous system.

Animals↗

PubMed1997

Identification of the cholinergic neurons in guinea-pig sphincter of Oddi ganglia.

The muscular tone of the sphincter of Oddi (SO) can be up- or down-regulated by neurons that lie within ganglia in the wall of the tissue. Previous studies have demonstrated that neurons in the ganglia of the guinea-pig SO can be classified into two major populations, one of which expresses tachykinins and enkephalin and another which expresses nitric oxide synthase. Although results of previous pharmacological studies indicate that acetylcholine is released in the SO, the neurons that express this neurotransmitter have not previously been identified. This study was conducted to establish which neurons in the ganglia of the guinea-pig SO are cholinergic by examining the distribution of choline acetyltransferase (ChAT) immunoreactivity, since the enzyme, ChAT is necessary for acetylcholine synthesis. Choline acetyltransferase immunoreactivity was intense and widespread in the ganglionated plexus of the SO. ChAT-immunoreactive nerve fibers were present in ganglia, interganglionic fiber bundles and in the circular muscle layer. Neurons that were immunoreactive for ChAT comprised about 69% of the population and most of these neurons were also tachykinin-immunoreactive. Co-expression of ChAT and nitric oxide synthase was not observed in nerve cell bodies or nerve fibers. Data from this study support the concept that SO ganglia are largely made up of two populations of neurons, one excitatory and the other inhibitory, on the basis of their chemical coding. The excitatory neurons are cholinergic and co-express tachykinin and opiate peptides and the inhibitory neurons are ChAT-negative and express nitric oxide synthase.

Animals↗

PubMed2001

A novel mitochondrial gene order in the crinoid echinoderm Florometra serratissima.

The complete nucleotide sequence of the mitochondrial genome of the crinoid Florometra serratissima has been determined. It is a circular DNA molecule, 16,005 bp in length, containing the genes for 13 proteins, small and large ribosomal RNAs, and 22 transfer RNAs (tRNAs). Three regions of unassigned sequence (UAS) greater than 73 bp have been located. The largest, UAS I, is 432 bp long and exhibits sequence similarity to the putative mitochondrial control regions seen in other animals. UAS II (77 bp) and UAS III (73 bp) are located between the 5' ends of coding sequences and may play roles as bidirectional promoters. Analyses of nucleotide composition revealed that the major peptide-encoding strand is high in T and low in C. This bias is reflected in a specific pattern of codon usage. Molecular phylogenetic analyses based on cytochrome c oxidase (COI, COII, and COIII) amino acid and nucleotide sequences did not resolve all the relationships between echinoderm classes. The overall animal mitochondrial gene content has been maintained in the crinoid, but there is extensive rearrangement with respect to both the echinoid and the asteroid mtDNA gene maps. Florometra serratissima has a novel genome organization in a segment containing most of the tRNA genes, large and small rRNA genes, and the NADH dehydrogenase subunit 1 and 2 genes. Potential pathways and mechanisms for gene rearrangements between mitochondrial gene maps of echinoderm classes and vertebrates are discussed as indicators of early deuterostome phylogeny.

Animals↗

PubMed1972

Properties of a R factor which originated in Pseudomonas aeruginosa 1822.

RP1, a group of genes specifying resistance to carbenicillin, neomycin, kanamycin, and tetracycline and originating in a strain of Pseudomonas aeruginosa, was freely transmissible between strains of P. aeruginosa, Escherichia coli, and Proteus mirabilis. Acquisition of the multiple drug resistance specified by RP1 by these strains was accompanied by acquisition of an extrachromosomal satellite of covalently closed circular deoxyribonucleic acid of molecular weight about 40 million daltons and of buoyant density 1.719 g/cm(3) (60% guanine plus cytosine).

Bromides↗

PubMed1980

Genome organization of retroviruses. V. In vitro-synthesized Moloney murine leukemia viral DNA has long terminal redundancy.

Purified virions of Moloney murine leukemia virus can synthesize genome-length double-stranded DNA in vitro. Two predominant species of long DNA transcripts, with average sizes of 9.1 and 8.5 kilobases (kb) can be identified. Both species of DNA contain the negative (complementary to viral RNA) and positive (same polarity as viral RNA) strands. However, only the negative strand of the 8.5-kb species can be identified if the synthesis of DNA is carried out in the presence of the drug actinomycin D. The 9.1-kb species appears to be slightly larger than the genomic RNA. If the linear double-stranded 9.1-kb species is treated with Escherichia coli exonuclease III and allowed to anneal, circular DNA molecules can be observed. Furthermore, polyadenylate-containing short genomic RNA fragments (0.5 to 1.0 kb) can anneal to both the 5' and the 3' termini of 9.1-kb complementary DNA. The polyadenylate moiety of the RNA fragments can be identified by tagging it with circular polyoma DNA containing polydeoxybromouridylic acid tails. Thus, the 9.1-kb complementary DNA transcript with two circular polyoma DNA molecules at its termini can be observed. However, when similar annealings are performed with 8.5-kb complementary DNA species, only one end of the resulting molecule has circular polyoma DNA. We conclude that the 9.1-kb complementary DNA species has a large terminal redundancy. The sequences involved in terminal redundancy appear to be derived from the 3' end of the genomic RNA.

Cell-Free System↗

PubMed1989

Identification, sequence, and transcriptional mapping of the major capsid protein gene of the baculovirus Autographa californica nuclear polyhedrosis virus.

The gene encoding the major capsid protein of the baculovirus Autographa californica nuclear polyhedrosis virus (AcMNPV) was identified, sequenced, and transcriptionally mapped. The location of the gene was determined by immunological screening of an expression library of AcMNPV open reading frame-beta-galactosidase fusions with an antibody raised to virus structural proteins. The DNA sequence of the corresponding region, which mapped within 56.6 and 58.0 map units on the AcMNPV genome, revealed a 1,040-base-pair open reading frame capable of encoding a 39-kilodalton polypeptide. The identity of the polypeptide was determined by Western blot (immunoblot) analysis of purified empty capsids with an antibody raised to the capsid-beta-galactosidase fusion protein. The identity of the peptide encoded by the gene was confirmed by immunoprecipitation of an in vitro translation product with RNA selected by hybridization to DNA sequences from the coding region of the gene. Transcripts of the capsid gene were analyzed by Northern (RNA) blots and mapped by nuclease protection and primer extension analysis. The capsid gene is transcribed maximally at 12 and 24 h postinfection but not in the presence of cycloheximide, a protein synthesis inhibitor, or aphidicolin, a viral DNA synthesis inhibitor, and is therefore classified as a late gene. The gene is transcribed in a counterclockwise direction with respect to the circular map. There are three transcriptional start sites, all containing the AGTAAG consensus sequence found at the start site of all late AcMNPV genes.

Amino Acid Sequence↗

PubMed1991

Leishmania (Viannia) braziliensis: comparative pathology of golden hamsters infected with isolates from cutaneous and mucosal lesions of patients residing in Tres Bracos, Bahia, Brazil.

The histopathology of primary forepaw and metastatic lymph node, spleen, and liver lesions produced in golden hamsters infected with cutaneous leishmaniasis (CL) strains (LTB 111 and LTB558) and mucocutaneous leishmaniasis (MCL) strains (LTB12 and LTB201) of Leishmania (Viannia) braziliensis isolated from patients residing in Tres Bracos, Bahia, Brazil is described. No pathological features providing clear differentiation of the CL and MCL strains were found. Although amastigotes were plentiful early in the development of primary forepaw lesions, they were either absent or could not be identified with certainty in sections of late stage lesions. Similarly, amastigotes were not found in histologic lesions at metastatic sites; however, leishmanial DNA was detected in both early and late stage forepaw lesions and metastatic lesions using Leishmania kinetoplast DNA and the gene coding for gp63 as hybridization probes. The DNA recovered from metastatic lesions was extracted from formalin-fixed paraffin-embedded tissues that had been stored at room temperature for prolonged periods.

Animals↗

PubMed2005

Cloning, sequence analysis, and characterization of a novel beta-glucosidase-like activity from Pichia etchellsii.

Genomic DNA fragment encoding a novel beta-glucosidase-like activity of the yeast Pichia etchellsii was cloned and expressed in Escherichia coli. An open-reading frame of 1515bp, termed mugA, coding for a protein of predicted molecular mass of approximately 54kDa was confirmed for this activity. The sequence of the deduced protein did not show homology with the generic beta-glucosidases but a high degree of identity was seen with several Ser-Asp (SD)-rich cell-surface-associated proteins. The secondary structure prediction program 3D-PSSM indicated the protein to be composed of largely helical and coiled structures, which was confirmed by circular dichroism spectroscopy. The encoded protein, MUGA, was purified by about 53-fold and characterized as a monomer of 52.1kDa by SDS-PAGE and MALDI-TOF. The protein displayed high hydrolytic activity on methylumbelliferyl beta-d-glucoside but relatively very little hydrolysis of p-nitrophenyl beta-d-glucoside and gentiobiose, characteristic substrates for beta-glucosidases. The binding experiments performed between P. etchellsii cells and the purified E. coli expressed MUGA indicated binding with the cell surface, which was monitored by fluorescence microscopy. In competition experiments with the SD dipeptide, less protein was shown to bind to the cell surface, in a concentration-dependent manner.

Amino Acid Sequence↗