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J E Newbold

Publications and source records attributed to J E Newbold.

33 records · Page 2Linked to original sources
PubMed1980

Physical mapping of adeno-associated virus serotype 4 DNA.

The organization of adeno-associated virus serotype 4 (AAV 4) DNA was probed by using restriction enzymes. The cleavage sites of the following enzymes were mapped: BglII, BamI, HincII, KpnI, PstI, SalI, SstI, and XhoI. The orientation of transcription on the physical cleavage map was determined by locating the fragments which contain the 3' end of the mRNA. Strand separation gels were run for HinII fragments of AAV 4 DNA. By hybridizing AAV 4 mRNA to the resolved strands, the polarity of the DNA strands was identified. Restriction digestion of AAV 4 DNA sometimes produced terminal fragments which migrated in agarose gels as doublets. However, when AAV 4 DNA was prepared devoid of any single-stranded nicks, these terminal doublet bands were not observed upon subsequent restriction analysis. During these studies, the molecular weights of both AAV 4 and AAV 2 duplex DNA were measured and were found to be somewhat larger than previously reported (3.18 x 10(6) and 3.10 x 10(6), respectively).

DNA Restriction Enzymes↗
PubMed1977

Two-dimensional restriction analysis of the Bacillus subtilis genome: gene purification and ribosomal ribonucleic acid gene organization.

With two-dimensional restriction enzyme analysis we have been able to cleave the Bacillus subtilis genome and resolve the resulting deoxyribonucleic acid (DNA) segments into discrete bands on agarose gels. A general procedure for gene purification has been developed by coupling multidimensional restriction analysis with a biological assay for gene detection. The organization of ribosomal ribonucleic acid (rRNA) genes was studied by hybridizing 16S and 23S rRNA probes to the two-dimensional DNA banding patterns.

Bacillus subtilis↗
PubMed1975

Specific cleavage analysis of mammalian mitochondrial DNA.

Mitochondrial DNA from several mammalian species has been digested with a site-specific restriction endonuclease (HaeIII) from Haemophilus aegyptius. A quantitative analysis of the resulting specific fragments indicates that the mtDNA of any individual mammal is predominantly a single molecular clone. Gel analysis of specific cleavage products has proven quite sensitive in detecting differences in mtDNA: mtDNAs from the more distantly related mammals studied (e.g., donkey and dog) are found to have few bands in common and very closely related mammals (e.g., donkey and horse) share only about 50% of their bands. This procedure has detected several intraspecies mtDNA differences. Six distinct human patterns have been found, with one pattern usually differing from another in two or three bands. mtDNAs from different organs of single individuals have also been analyzed, and no differences have been found.

Animals↗
PubMed1974

Simian virus 40 transcription in productively infected and transformed cells.

Several independent cell lines transformed by simian virus 40 carry a species of viral RNA of 900,000 to 1,000,000 daltons. A viral RNA species of similar size is found early in the lytic cycle. Late in the viral lytic cycle, two prominent viral RNA species of about 600,000 and 900,000 daltons are seen. The larger late species shares nucleotide sequences with, and is less stable than, the smaller. These RNA species are located in the cytoplasm of the infected cell. The regions of the viral genome coding for these RNA species are mapped by hybridization of lytic RNA species to fragments of the genome produced by cleavage with Haemophilus aegyptius endonuclease.

Animals↗
PubMed1973

Analysis of simian virus 40 DNA with the restriction enzyme of Haemophilus aegyptius, endonuclease Z.

Limited digestion of simian virus 40 (SV40) DNA from both small- and large- plaque strains with the restriction endonuclease Z from Haemophilus aegyptius yielded 10 specific fragments. The number of nucleotide pairs for each fragment, determined by co-electrophoresis with phiX174 RF fragments produced by endonuclease Z, ranges from 2,050 to 80. The difference in the pattern between the large- and small-plaque strains is the disappearance of one fragment containing approximately 255 nucleotide pairs and the appearance of a new fragment with 145 nucleotide pairs. This finding can be explained either by deletions or insertions totaling 110 nucleotide pairs. Complementary RNA synthesized in vitro from the adeno-SV40 hybrid virus, strain ND-1, hybridized preferentially to four of the fragments of SV40 DNA.

Adenoviridae↗
PubMed1970

Process of infection with bacteriophage phi-X174. XXXIV. Kinetic of the attachment and eclipse steps of the infection.

The products of phiX cistrons II, III, and VII are demonstrated to affect the attachment of the phage to its host Escherichia coli C; therefore, by inference, these cistrons influence, directly or indirectly, the structure of proteins in the virus particle. Two of the mutations which alter attachment kinetics, ts79 in cistron III and h in cistron VII, also affect the electrophoretic mobility of the virus and emphasize the role of charge in the attachment interaction with the host. The kinetics for attached phage to go into "eclipse" are first-order and biphasic; about 85% of the phage eclipse at one rate (k(e) = 0.86 min(-1)) and the remainder do so at a distinctly lower rate (k(e) = 0.21 min(-1)). No phiX cistrons yet identified affect the eclipse process. The lowest temperature at which eclipse is detected is 19 C. The Arrhenius activation energy for phage eclipse has the high value of 36.6 kcal/mole, indicating the cooperative nature of the event.

Coliphages↗
PubMedDate not supplied

Intraspecific nucleotide sequence variability surrounding the origin of replication in human mitochondrial DNA.

We have cloned the major noncoding region of human mitochondrial DNA (mtDNA) from 11 human placentas. Partial nucleotide sequences of five of these clones have been determined and they share a maximum of 900 bp around the origin of H-strand replication. Alignment of these sequences with others previously determined has revealed a striking pattern of nucleotide substitutions and insertion/deletion events. The level of sequence divergence significantly exceeds the reported estimates of divergence in coding regions. Two particularly hypervariable regions have also been defined. More than 96% of the base changes are transitions, and length alterations have occurred exclusively by addition or deletion of mono-or dinucleotide segments within serially repeating stretches. This region of the mitochondrial genome, which contains the initiation sites for replication and transcription, is the least conserved among species with respect to both sequence and length (Anderson et al., 1981; Walberg and Clayton, 1981). Despite this overall lack of primary sequence conservation, several consistencies appear among the available mammalian mtDNA sequences within this region. Between species, a conserved linear array of characteristic stretches exists which nonetheless differ in primary sequence. Among humans, several conserved blocks of nucleotides appear within domains deleted from the mtDNA of other species. These observations are consistent with both a species-specificity of nucleotide sequence, and a preservation of the necessary genetic functions among species. This provides a model for the evolution of protein-nucleic acid interactions in mammalian mitochondria.

Amino Acid Sequence↗
PubMedDate not supplied

A teratoma in a duck infected congenitally with duck hepatitis B virus.

A teratoma was diagnosed in an 8-month-old pekin duck based on the presence of tissue derived from embryonic ectoderm, mesoderm, and endoderm in the neoplasm. The neoplasm was examined for the presence of duck hepatitis B virus, because the duck was congenitally infected with the virus, a member of the hepadnavirus family that is associated with hepatic neoplasms in hepadnavirus-infected mammals. Persistent infection occurred in the liver, but no evidence of viral infection was found in the neoplasm.

Animals↗