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Biomedical subjects

J Cullum

Publications and source records attributed to J Cullum.

At least 19 recordsLinked to original sources
PubMed2004

High levels of untreated distress and fatigue in cancer patients.

The purpose of the study was to assess a large representative sample of cancer patients on distress levels, common psychosocial problems, and awareness and use of psychosocial support services. A total of 3095 patients were assessed over a 4-week period with the Brief Symptom Inventory-18 (BSI-18), a common problems checklist, and on awareness and use of psychosocial resources. Full data was available on 2776 patients. On average, patients were 60 years old, Caucasian (78.3%), and middle class. Approximately, half were attending for follow-up care. Types of cancer varied, with the largest groups being breast (23.5%), prostate (16.9%), colorectal (7.5%), and lung (5.8%) cancer patients. Overall, 37.8% of all patients met criteria for general distress in the clinical range. A higher proportion of men met case criteria for somatisation, and more women for depression. There were no gender differences in anxiety or overall distress severity. Minority patients were more likely to be distressed, as were those with lower income, cancers other than prostate, and those currently on active treatment. Lung, pancreatic, head and neck, Hodgkin's disease, and brain cancer patients were the most distressed. Almost half of all patients who met distress criteria had not sought professional psychosocial support nor did they intend to in the future. In conclusion, distress is very common in cancer patients across diagnoses and across the disease trajectory. Many patients who report high levels of distress are not taking advantage of available supportive resources. Barriers to such use, and factors predicting distress and use of psychosocial care, require further exploration.

Adult↗
PubMed2000

The pyrroloquinoline quinone synthesis genes of Gluconobacter oxydans.

A Tn5-induced glucose dehydrogenase (GDH) deficient mutant of Gluconobacter oxydans IFO 3293 was characterised. DNA sequencing showed that the insertion site occurred in an open reading frame with homology to the pqqE gene. It was shown that acid production could be restored by addition of the coenzyme pyrroloquinoline quinone (PQQ) to the medium. The pqq cluster of G. oxydans ATCC 9937 was cloned and sequenced. It has five genes pqqA-E. The cluster could complement the Tn5-induced mutation in IFO 3293. Pulsed-field gel electrophoresis suggested that the pqq genes are not closely linked to the ribF gene that produces the riboflavin cofactor for the gluconic acid dehydrogenase.

Bacterial Proteins↗
PubMed2000

Isolation and cloning of Streptomyces terminal fragments.

Streptomyces species have a linear chromosome of approximately 8 Mb in size. Many strains also carry linear plasmids. Most of these linear elements contain terminal proteins covalently bound to the 5' ends of the DNA. Using a method for the visualisation of terminal DNA fragments in agarose gels, it was possible to see three fragments in S. rimosus and five fragments in S. avermitilis. The method was also used to clone the 298 bp BamHI fragment carrying the left end of plasmid SLP2. Analysis of the sequence showed that the end resembled other Streptomyces chromosome and plasmid ends, but there were eight palindromes (instead of seven) and a tandem duplication of a 14 bp sequence.

Base Sequence↗
PubMed2000

A complex insertion sequence cluster at a point of interaction between the linear plasmid SCP1 and the linear chromosome of Streptomyces coelicolor A3(2).

The giant linear plasmid SCP1 can integrate into the central region of the linear chromosome of Streptomyces coelicolor A3(2). Nucleotide sequence analysis around the target site for SCP1 integration in strain M145 identified a total of five copies of four insertion sequences (ISs) in a 6.5-kb DNA stretch. Three of the four (IS468, IS469, and IS470) are new IS elements, and the other is IS466. All of these elements contain one open reading frame which encodes a transposase-like protein. Two copies of IS468 (IS468A and -B) are tandemly aligned at the left end of the cluster. Following these, IS469 and IS466 are located in a tail-to-tail orientation with 69.3% identity to each other. IS470 is located at the right end of the cluster. The activities of IS466 and IS468 were demonstrated by transposition experiments and sequence comparison of several copies, respectively.

Amino Acid Sequence↗
PubMed1999

A mutant of gluconobacter oxydans deficient in gluconic acid dehydrogenase

Gluconobacter oxydans ATCC 9937 was subjected to transposon mutagenesis using Tn5. A non-pigmented mutant was shown to be defective in gluconic acid dehydrogenase and to produce gluconic acid from glucose, whereas the parent strain produced 2, 5-diketogluconic acid. Cloning and sequencing of the region containing the Tn5 insertion showed that the insertion point occurred in an open reading frame homologous (42% amino acid identity) to the ribF genes of Pseudomonas fluorescens and Escherichia coli. The resulting lack of a riboflavin cofactor would explain the loss of enzyme activity.

Journal Article↗
PubMed1998

Recombination between the linear plasmid pPZG101 and the linear chromosome of Streptomyces rimosus can lead to exchange of ends.

The 387kb linear plasmid pPZG101 of Streptomyces rimosus R6 can integrate into the chromosome or form a prime plasmid carrying the oxytetracycline biosynthesis cluster. The integration of plasmid pPZG101 into the linear chromosome of S. rimosus R6-501 in mutant MV25 was shown to be due to a single cross-over at a 4 bp common sequence. pPZG101 had integrated into a 250 kb DNA sequence that was reiterated at a low level. This sequence includes the oxytetracycline biosynthesis cluster, so that homologous recombination generated a mixed population carrying different copy numbers of the region. The 1 Mb linear plasmid pPZG103 in mutant MV17 had also arisen from a cross-over between pPZG101 and the chromosome, so that one end of pPZG103 consists of c. 850 kb of chromosomal sequence including the oxytetracycline biosynthesis cluster. The plasmid pPZG101 was shown to consist of a unique central region of about 30 kb flanked by terminal inverted repeats of about 180 kb. Analysis of a presumed ancestor plasmid pPZG102 suggested that the long terminal repeats had arisen by a recombination event during the strain development programme.

Base Sequence↗
PubMed1996

A set of ordered cosmids and a detailed genetic and physical map for the 8 Mb Streptomyces coelicolor A3(2) chromosome.

A Supercos-1 library carrying chromosomal DNA of a plasmid-free derivative of Streptomyces coelicolor A3(2) was organized into an ordered encyclopaedia of overlapping clones by hybridization. The minimum set of overlapping clones representing the entire chromosome (with three short gaps) consists of 319 cosmids. The average insert size is 37.5 kb and the set of clones therefore divides the chromosome into 637 alternating unique and overlapping segments which have an average length of approx. 12.5 kb. More than 170 genes, gene clusters and other genetic markers were mapped to their specific segment by hybridization to the encyclopaedia. Genes could be cloned by direct transformation and complementation of S. coelicolor mutants with cosmids isolated from Escherichia coli, selecting for insertion into the chromosome by homologous recombination. As in other streptomycetes, the ends of the chromosome have long terminal inverted repeats.

Chromosome Mapping↗
PubMed1995

DNA amplifications and deletions in Streptomyces lividans 66 and the loss of one end of the linear chromosome.

Thirty-two 2-deoxygalactose-resistant mutants with DNA amplifications were isolated from Streptomyces lividans 66 strains carrying plasmid pMT664, which carries an agarase gene (dagA) and IS466. Thirty-one of the mutants carried amplified DNA sequences from a 70 kb region about 300 kb from one end of the linear chromosome in this species. In 28 of the mutants, all the wild-type sequences between the amplified region and the start of the 30 kb inverted repeat that forms the chromosome end were deleted. Thus, there appeared to be loss of one chromosome end and its replacement by the DNA amplification. In some mutants there amplification of a previously characterised 5.7 kb sequence that lies about 600 kb from the other chromosome end was also noted.

Blotting, Southern↗
PubMed1994

Analysis of putative DNA amplification genes in the element AUD1 of Streptomyces lividans 66.

The amplifiable AUD1 element of Streptomyces lividans 66 consists of two copies of a 4.7 kb sequence flanked by three copies of a 1 kb sequence. The DNA sequences of the three 1 kb repeats were determined. Two copies (left and middle repeats) were identical: (1009 bp in length) and the right repeat was 1012 bp long and differed at 63 positions. The repeats code for open reading frames (ORFs) with typical Streptomyces codon usage, which would encode proteins of about 36 kD molecular weight. The sequences of these ORFs suggest that they specify DNA-binding proteins and potential palindromic binding sites are found adjacent to the genes. The putative amplification protein encoded by the right repeat was expressed in Escherichia coli.

Base Sequence↗
PubMed1994

Characterisation of plasmids from diketogluconic acid producing strains of Gluconobacter oxydans.

Gluconobacter oxydans ATCC 9937, which produces 2,5-diketogluconic acid, an intermediate in vitamin C synthesis, has three plasmids of sizes 27.7 kb (pVJ1), 12.3 kb (pVJ2) and 18 kb (pVJ4). A restriction map was constructed of pVJ1. A potential glucose dehydrogenase gene was located on pVJ1 using the polymerase chain reaction with heterologous primers. Two other G. oxydans strains had no detectable plasmid DNA (IFO 12258) and a plasmid (pVJ3) of 9.4 kb (IFO 3293), respectively.

Base Sequence↗
PubMed1994

The 387 kb linear plasmid pPZG101 of Streptomyces rimosus and its interactions with the chromosome.

The linear plasmid pPZG101 of Streptomyces rimosus R6 was restriction mapped with the enzymes AseI, BfrI, DraI and XbaI. It is 387 kb in size and the ends are inverted repeats of at least 95 kb in length. Twenty spontaneous morphological variants and seventeen auxotrophic mutants were screened for changes in the plasmid. Two strains were found that had lost all plasmid sequences. Four strains had integrated parts of the plasmid into the chromosome. Restriction analysis suggested that at least three of the integrated strains had retained free plasmid ends. If it is assumed that the chromosome of S. rimosus R6 is linear, this might be explained by replacement of one or both chromosome ends by a plasmid end. One strain, which overproduced oxytetracycline, carried an enlarged linear plasmid of 1 Mb in size that had acquired chromosomal sequences from the oxytetracycline biosynthesis cluster.

Chromosomes, Bacterial↗
PubMed1993

The Streptomyces lividans 66 chromosome contains a 1 MB deletogenic region flanked by two amplifiable regions.

Genetic instability in Streptomyces species often involves large deletions sometimes accompanied by DNA amplification. Two such systems in Streptomyces lividans 66 involve the production of mutants sensitive to chloramphenicol and the production of mutants resistant to the galactose analogue 2-deoxygalactose, respectively. Overlapping cosmids were isolated that span the ca. 1 Mb region between the two amplifiable regions. The structure of the region was confirmed by restriction mapping using the rarely cutting enzymes AseI, BfrI and DraI and pulsed-field gel electrophoresis. The region contains a non-clonable gap flanked by inverted repeats; the structure is consistent with the presence of a physical gap, i.e. a linear chromosome.

Chloramphenicol↗
PubMed1993

The temperate phages RP2 and RP3 of Streptomyces rimosus.

The oxytetracycline-producing Streptomyces rimosus strains R6-65 and R7 (ATCC 10970) are lysogenic for the two narrow-host-range phages RP2 and RP3. Both phages are released at low frequency from the lysogenic strains and form plaques on 'cured' S. rimosus strains. RP2 and RP3 are of similar shape with flexible tails and contain double-stranded DNA of about 70% G+C with cohesive ends (group B1 of bacteriophage classification). The two phages also have identical, very slow, growth kinetics in S. rimosus, with a latent phase of about 6 h and a rise period of about 4 h. RP2 and RP3 are heteroimmune and they differ slightly in their size of phage particles and length of DNA (64.7 and 62.4 kb for RP2 and RP3, respectively). The restriction maps of the two phages are completely different, and hybridization experiments showed only one short region of sequence similarity (less than 430 bp); the two phages are thus essentially unrelated. Both phages lysogenize their hosts by recombination via defined attachment (att) sites. The positions of the attP sites have been localized on the restriction maps of RP2 and RP3 to restriction fragments of 800 and 300 bp, respectively. The prophages did not affect the level of oxytetracycline production or the genetic instability of this trait.

Attachment Sites, Microbiological↗
PubMed1993

Genetic instability and strain degeneration in Streptomyces rimosus.

During a strain selection program to improve oxytetracycline production in Streptomyces rimosus R6, isolates that showed extreme morphological instability appeared. Propagation via spores gave much higher instability than did propagation via mycelial fragments. Five phenotypic traits were affected: sporulation, pigmentation, colony morphology, oxytetracycline production, and oxytetracycline resistance. The variants were classified on the basis of oxytetracycline resistance into three classes. Class I variants (99% of variants) showed parental levels of resistance but were very heterogeneous regarding the other phenotypes. No DNA rearrangements were detected in primary class I variants. Class II variants (1% of variants, oxytetracycline sensitive) were phenotypically uniform, and most variants carried the same large deletion of ca. 455 kb, including the oxytetracycline resistance gene otrB. Class III variants (0.1% of variants, increased oxytetracycline resistance) were phenotypically uniform and overproduced a brown pigment and oxytetracycline. Most of these variants also showed a reproducible large-scale DNA rearrangement, which probably included deletion and a low-level reiteration (three or four copies) of a DNA fragment. "Revertants" of some class I variants show a similar DNA rearrangement to the class III variants, but there is extensive reiteration of sequences of about 200 kb, including the otrB gene. The significance of these results for the problem of strain degeneration and overproduction of antibiotics is discussed.

DNA, Bacterial↗
PubMed1993

Physical map of the Streptomyces lividans 66 genome and comparison with that of the related strain Streptomyces coelicolor A3(2).

A physical map of the chromosome of Streptomyces lividans 66 ZX7 was constructed by ordering the macrorestriction fragments generated from the genomic DNA with the restriction enzymes AseI and DraI. AseI and DraI linking cosmids (i.e., recombinant cosmids including either AseI or DraI sites) were isolated from a gene bank and used as hybridization probes against Southern transfers of pulsed-field gel electrophoresis (PFGE) restriction patterns. The DraI sites were precisely mapped by PFGE analyses of AseI-DraI double digests and hybridization with the AseI junctions. The 16 AseI and 7 DraI fragments were aligned as a single chromosome of about 8,000 kb. The data supported the interpretation that the chromosome is a linear structure. The related strain Streptomyces coelicolor A3(2) M145, recently mapped by H. Kieser, T. Kieser, and D. A. Hopwood (J. Bacteriol. 174:5496-5507, 1992), was compared with S. lividans at the level of the genomic structure by hybridizing the linking cosmids to Southern transfers of PFGE patterns. In spite of little apparent similarity in their restriction patterns, the comparison of the physical maps revealed a common structure with an identical ordering of the cosmid sequences. This conservation of the map order was further confirmed by assigning genetic markers (i.e., cloned genes and DNA elements relevant to the unstable region) to the AseI fragments.

DNA, Bacterial↗