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D M Prescott

Publications and source records attributed to D M Prescott.

At least 19 recordsLinked to original sources
PubMed2006

A model for the origin of internal eliminated segments (IESs) and gene rearrangement in stichotrichous ciliates.

A characteristic feature of ciliates (ciliated protozoans) is their nuclear dimorphism: the presence of two kinds of functionally different nuclei in the same cell--a micronucleus (MIC) and the macronucleus (MAC). In the stichotrichous group of ciliates the organization of DNA in the MIC is dramatically different from that in the MAC. Genes in the MIC consist of the sequence of segments, called MDSs, which are separated by short noncoding pieces of DNA, called IESs. Moreover, the order of MDSs in the MIC may be scrambled compared to their order in the MAC, and also some MDSs may be inverted with respect to each other. In this paper, we consider the evolutionary origin of this bizarre form of MIC genes, and in particular we postulate that the insertion of IESs as well as possible scramblings/inversions have resulted from a repair of one or more breaks in a DNA molecule. We propose a specific repair scheme, and postulate that this repair scheme applied to a coiled structure of a DNA molecule that has undergone multiple breaks can produce IES insertions and/or scrambled/inverted MIC gene patterns. All experimentally demonstrated as well as theoretical MIC gene patterns can be produced in this way.

Animals↗
PubMed2004

Effect of calcitonin gene related peptide vs sodium nitroprusside to increase temperature in spontaneous canine tumours during local hyperthermia.

The objectives of this study were to compare the effects of two vasodilators, sodium nitroprusside (SNP) and calcitonin gene-related peptide (CGRP) on mean arterial pressure (MAP), heart rate (HR) and temperatures in tumour and surrounding normal tissue during local hyperthermia treatment. Eleven tumour-bearing pet dogs with spontaneous soft tissue sarcomas were given SNP intravenously during local hyperthermia. The drug infusion rate was adjusted to maintain a 20% decrease in MAP. The median (95% CI) increase in the temperature distribution descriptors T(90) and T(50) was 0.2 degrees C (0.0-0.4 degrees C, p = 0.02) and 0.4 degrees C (0.1-0.7 degrees C, p = 0.02), respectively, in tumour. Normal subcutaneous tissue temperatures were mildly increased but remained below the threshold for thermal injury. The effects of CGRP were investigated in six tumour-bearing dogs following a protocol similar to that used for SNP. The median (interquartile (IQ) range) decrease in mean arterial pressure was 19% (15-26%) after CGRP administration and a significant increase was seen in tumour but not normal subcutaneous tissue temperatures. The median (95% CI) increase in the temperature distribution descriptors T(90) and T(50) was 0.5 degrees C (0.1-1.6 degrees C, p = 0.03) and 0.8 degrees C (0.1-1.6 degrees C, p = 0.13), respectively. Administration of SNP or CGRP did not result in local or systemic toxicity in tumour-bearing dogs. However, the magnitude of increase in tumour temperatures was not sufficient to improve the likelihood of increased response rates. Therefore, there is little justification for translation of this approach to human trials using conventional local hyperthermia.

Animals↗
PubMed2002

Topological organization of DNA molecules in the macronucleus of hypotrichous ciliated protozoa.

The DNA in the macronucleus of a hypotrichous ciliate occurs as millions of short molecules packed into dense chromatin bodies 0.1-2 microm in diameter. We have studied by electron microscopy the organization of DNA molecules in these chromatin bodies of macronuclei lysed in water at pH 9. Proteinase K treatment of lysed macronuclei progressively releases from chromatin bodies many rosettes of DNA molecules bound at one or both ends to a central core of protein. With longer treatment with proteinase K, rosettes disappear, leaving individual free DNA molecules. We propose that, in the native state, both ends of DNA molecules are bound through telomere-binding protein to a central core to form rosettes. Many rosettes, with collapsed DNA loops, aggregate to form a chromatin body. Chromatin bodies are believed to dissociate into individual collapsed rosettes to form the granules in the forward zone of the replication band. In the rear zone of the band, the rosettes dissociate, presumably as a result of release of telomere-binding protein, which is preliminary to the replication of the DNA molecules.

Animals↗
PubMed2001

Evolution of IESs and scrambling in the actin I gene in hypotrichous ciliates.

Germ-line (micronuclear) genes in hypotrichous ciliates are interrupted by numerous, short, noncoding, AT-rich segments called internal eliminated segments, or IESs. IESs divide a gene into macronuclear destined segments, or MDSs. IESs are excised from micronuclear genes, and the MDSs are spliced when a micronuclear genome is processed into a macronuclear genome after cell mating. In the micronuclear version of the actin I gene intramolecular recombination between IESs during evolution has put MDSs into a scrambled disorder in some but not all hypotrichs. Studies using rDNA sequences to define phylogenetic relationships among eight hypotrichs suggests that evolution of the micronuclear actin I gene proceeds by successive addition of IESs in earlier diverging species, without MDS scrambling. Continued addition of IESs and recombination among IESs in later diverging species produced actin I genes with scrambled MDSs. Subsequent to MDS scrambling, additional IESs were inserted into the more recently evolved species. Thus, IES insertions and gene scrambling occur in a progressive manner during species evolution to produce micronuclear actin I genes of increasing structural complexity.

Actins↗
PubMed2000

A unique pattern of intrastrand anomalies in base composition of the DNA in hypotrichs.

The 50 non-coding bases immediately internal to the telomeric repeats in the two 5' ends of macronuclear DNA molecules of a group of hypotrichous ciliates are anomalous in composition, consisting of 61% purines and 39% pyrimidines, A>T (ratio of 44:32), and G>C (ratio of 17:7). These ratio imbalances violate parity rule 2, according to which A should equal T and G should equal C within a DNA strand and therefore pyrimidines should equal purines. The purine-rich and base ratio imbalances are in marked contrast to the rest of the non-coding parts of the molecules, which have the theoretically expected purine content of 50%, with A = T and G = C. The ORFs contain an average of 52% purines as a result of bias in codon usage. The 50 bases that flank the 5' ends of macronuclear sequences in micronuclear DNA (12 cases) consist of approximately 50% purines. Thus, the 50 bases in the 5' ends of macronuclear sequences in micronuclear DNA are islands of purine richness in which A>T and G>C. These islands may serve as signals for the excision of macronuclear molecules during macronuclear development. We have found no published reports of coding or non-coding native DNA with such anomalous base composition.

Animals↗
PubMed2000

Temperature-dependent changes in physiologic parameters of spontaneous canine soft tissue sarcomas after combined radiotherapy and hyperthermia treatment.

PURPOSE: The objectives of this study were to evaluate effects of hyperthermia on tumor oxygenation, extracellular pH (pHe), and blood flow in 13 dogs with spontaneous soft tissue sarcomas prior to and after local hyperthermia. METHODS AND MATERIALS: Tumor pO2 was measured using an Eppendorf polarographic device, pHe using interstitial electrodes, and blood flow using contrast-enhanced magnetic resonance imaging (MRI). RESULTS: There was an overall improvement in tumor oxygenation observed as an increase in median pO2 and decrease in hypoxic fraction (% of pO2 measurements <5 mm Hg) at 24-h post hyperthermia. These changes were most pronounced when the median temperature (T50) during hyperthermia treatment was less than 44 degrees C. Tumors with T50 > 44 degrees C were characterized by a decrease in median PO2 and an increase in hypoxic fraction. Similar thermal dose-related changes were observed in tumor perfusion. Perfusion was significantly higher after hyperthermia. Increases in perfusion were most evident in tumors with T50 < 44 degrees C. With T50 > 44 degrees C, there was no change in perfusion after hyperthermia. On average, pHe values declined in all animals after hyperthermia, with the greatest reduction seen for larger T50 values. CONCLUSION: This study suggests that hyperthermia has biphasic effects on tumor physiologic parameters. Lower temperatures tend to favor improved perfusion and oxygenation, whereas higher temperatures are more likely to cause vascular damage, thus leading to greater hypoxia. While it has long been recognized that such effects occur in rodent tumors, this is the first report to tie such changes to temperatures achieved during hyperthermia in the clinical setting. Furthermore, it suggests that the thermal threshold for vascular damage is higher in spontaneous tumors than in more rapidly growing rodent tumors.

Animals↗
PubMed2000

Genome gymnastics: unique modes of DNA evolution and processing in ciliates.

In some ciliates, the DNA sequences of the germline genomes have been profoundly modified during evolution, providing unprecedented examples of germline DNA malleability. Although the significance of the modifications and malleability is unclear, they may reflect the evolution of mechanisms that facilitate evolution. Because of the modifications, these ciliates must perform remarkable feats of cutting, splicing, rearrangement and elimination of DNA sequences to convert the chromosomal DNA in the germline genome (micronuclear genome) into gene-sized DNA molecules in the somatic genome (macronuclear genome). How these manipulations of DNA are guided and carried out is largely unknown. However, the organization and manipulation of ciliate DNA sequences are new phenomena that expand a general appreciation for the flexibility of DNA in evolution and development.

Animals↗
PubMed2000

The relationship between intracellular and extracellular pH in spontaneous canine tumors.

Recently, it has been suggested that the cellular uptake of chemotherapeutic drugs may be dependent on the pH gradient between the intracellular (pHi) and extracellular (pHe) compartments. It has been demonstrated in murine tumor models that the extracellular environment is acidic, relative to the intracellular environment, thus favoring preferential accumulation of drugs that are weak acids into cells. However, concomitant measurements of pHi and pHe in spontaneous tumors have not been reported, so it is not certain how well the murine results translate to the clinical scenario. In this study, both types of measurements were performed in dogs with spontaneous malignant soft tissue tumors. On average, pHe was more acidic than pHi, with maintenance of a more physiologically balanced intracellular tumor environment. However, the magnitude of the gradient varied widely, and individual tumors had both positive and negative pH gradients (pHi - pHe). These data suggest that the magnitude and direction of the pH gradient may need to be measured for individual patient tumors and/or that manipulation of pHe may be required if exploitation of the pH gradient is to be achieved for tumor-selective augmentation of intracellular drug delivery.

Animals↗
PubMed1999

Telomeres of polytene chromosomes in a ciliated protozoan terminate in duplex DNA loops.

The end of a telomeric DNA sequence isolated from a polytene chromosome of a hypotrichous ciliate folds back and hybridizes with downstream telomeric sequence to form a t loop that is stable in the absence of protein and DNA cross-linking. The single-stranded, telomeric DNA sequence at the end of a macronuclear molecule does not form a t loop but, instead, is complexed with a heterodimeric, telomere-binding protein. Thus, two mechanisms for capping the ends of DNA molecules are used in the same cell.

Animals↗
PubMed1999

Evolution of DNA organization in hypotrichous ciliates.

Profound changes have been introduced into the germline (micronuclear) and somatic (macronuclear) genomes of hypotrichous ciliates during evolution. First, multiple, short, unique, noncoding sequences, called IESs, have been inserted into micronuclear genes. IESs are spliced out of each gene, and the gene segments, called MDSs, are ligated during conversion of the micronuclear genome to a macronuclear genome after cell mating. The IESs in a particular gene can change dramatically in number, position, length, and sequence during speciation. Once inserted, IESs can shift along the DNA of a gene 1 or 2 bp at a time by a mutational mechanism that does not alter the coding sequence of the gene. Second, the MDSs in the same genes have been rearranged into random or nonrandom, scrambled disorder. The origin of nonrandom scrambling patterns can be explained by a model of simultaneous insertion of multiple IESs into a germline gene during evolution. Subsequent recombinations among the IESs may change the MDS arrangement from a nonrandomly scrambled to a randomly scrambled pattern, including inversions of MDSs. Third, during the conversion of a micronucleus to a macronucleus after cell mating, MDSs are ligated in the unscrambled, orthodox order in association with IES excision, and the genes are then removed from the chromosomes as individual, short DNA molecules. These gene-size molecules are amplified many-fold to produce a mature macronucleus. All of these phenomena attest to a remarkable fluidity of the hypotrich genome both over evolutionary time and in the conversion of a germline genome to a somatic genome. The significance of this fluidity for the life and evolution of these organisms is still obscure. Recombination among IESs could shuffle MDSs and facilitate faster evolution of new genes.

Animals↗
PubMed1999

The evolutionary scrambling and developmental unscrambling of germline genes in hypotrichous ciliates.

Genes in the germline (micronuclear) genome of hypotrichous ciliates are interrupted by multiple, short, non-coding, AT-rich sequences called internal eliminated segments, or IESs. During conversion of a micronucleus to a somatic nucleus (macronucleus) after cell mating, all IESs are excised from the germline genes and the gene segments, called macronuclear-destined segments, or MDSs, are spliced. Excision of the approximately 150 000 IESs from a haploid germline genome in Oxytricha nova requires approximately 150 000 recombinant events. In three of 10 genes the MDSs are scrambled. During macronuclear development the MDSs are unscrambled, possibly by folding of the DNA to allow MDSs to ligate in the correct order. The nine MDSs in the actin I gene of O.nova are scrambled in the random order, 3-4-6-5-7-9-2-1-8, and MDS 2 is inverted. The 14 MDSs in the alphaTP gene of O.nova and Stylonychia mytilus are scrambled in the non-random order, 1-3-5-7-9-11-2-4-6-8-10-12-13-14. The 45 MDSs in the DNA pol alpha gene are non-randomly scrambled into an odd/even series, with an inversion of one-third of the gene. Additional IESs have been inserted into these three genes during evolution of Oxytricha trifallax, slightly modifying scrambling patterns. The non-random scrambled patterns in the alphaTP and DNA pol alpha genes are explained by multiple, simultaneous IES insertions. The randomly scrambled pattern in the actin I gene may arise from an initially non-randomly scrambled pattern by recombination among multiple IESs. Alternatively, IESs inserted sporadically (individually) in a non-scrambled configuration might subsequently recombine, converting a non-scrambled gene into a randomly scrambled one. IESs shift along a DNA molecule, most likely as a result of mutations at MDS/IES junctions. Shifting of IESs has the effect of 'transferring' nucleotides from one MDS to another, but does not change the overall sequence of nucleotides in the combined MDSs. In addition to shifting in position, IESs accumulate mutations at a high rate and increase and decrease in length within a species and during speciation. The phenomena of IESs and of MDS scrambling represent remarkable flexibility of the hypotrich genome, possibly reflecting a process of MDS shuffling that facilitates the evolution of genes.

Animals↗
PubMed1998

Magnetic resonance thermometry during hyperthermia for human high-grade sarcoma.

PURPOSE: To determine the feasibility of measuring temperature noninvasively with magnetic resonance imaging during hyperthermia treatment of human tumors. METHODS: The proton chemical shift detected using phase-difference magnetic resonance imaging (MRI) was used to measure temperature in phantoms and human tumors during treatment with hyperthermia. Four adult patients having high-grade primary sarcoma tumors of the lower leg received 5 hyperthermia treatments in the MR scanner using an MRI-compatible radiofrequency heating applicator. Prior to each treatment, an average of 3 fiberoptic temperature probes were invasively placed into the tumor (or phantom). Hyperthermia was applied concurrent with MR thermometry. Following completion of the treatment, regions of interest (ROI) were defined on MR phase images at each temperature probe location, in bone marrow, and in gel standards placed outside the heated region. The median phase difference (compared to pretreatment baseline images) was calculated for each ROI. This phase difference was corrected for phase drift observed in standards and bone marrow. The observed phase difference, with and without corrections, was correlated with the fiberoptic temperature measurements. RESULTS: The phase difference observed with MRI was found to correlate with temperature. Phantom measurements demonstrated a linear regression coefficient of 4.70 degrees phase difference per degree Celsius, with an R2 = 0.998. After human images with artifact were excluded, the linear regression demonstrated a correlation coefficient of 5.5 degrees phase difference per degree Celsius, with an R2 = 0.84. In both phantom and human treatments, temperature measured via corrected phase difference closely tracked measurements obtained with fiberoptic probes during the hyperthermia treatments. CONCLUSIONS: Proton chemical shift imaging with current MRI and hyperthermia technology can be used to monitor and control temperature during treatment of large tumors in the distal lower extremity.

Adult↗
PubMed1998

Evolution of the scrambled germline gene encoding alpha-telomere binding protein in three hypotrichous ciliates.

The micronuclear genes encoding alpha-telomere-binding protein (alphaTP) in Oxytricha trifallax and Stylonychia mytilus contain multiple internal eliminated segments, or IESs, that divide the gene into multiple parts called macronuclear destined segments, or MDSs. The MDSs have become disordered, or scrambled, during evolution. The scrambled structures of the alphaTP genes in Oxytricha trifallax and S. mytilus have been compared with the previously published scrambled structure of the alphaTP gene in O. nova. The scrambled patterns of the alphaTP gene in the three species are similar but show significant differences. The micronuclear genes in O. nova and S. mytilus consist of 13 IESs and 14 MDSs, but the gene in O. trifallax is divided into three additional MDSs by the presence of three additional IESs, believed to have been inserted into the O. trifallax alphaTP gene after divergence of O. trifallax from the other two species. Corresponding IESs among the three species have shifted along the DNA during evolution, presumably by a mutational mechanism that changes the short repeat sequences that flank IESs. The IESs also have changed markedly in length by insertion and/or deletion of nucleotides. Comparison of the putative alphaTP amino acid sequences in the three species reveals three conserved and three nonconserved domains. The 5' nontranslated regions of the gene-sized molecules encoding alphaTP contain several conserved segments, and the 3' nontranscribed trailer contains one conserved segment.

Amino Acid Sequence↗
PubMed1997

Evolution of internal eliminated segments and scrambling in the micronuclear gene encoding DNA polymerase alpha in two Oxytricha species.

To learn about the evolution of internal eliminated segments (IESs) and gene scrambling in hypotrichous ciliates we determined the structure of the micronuclear (germline) gene encoding DNA polymerasealpha(DNA polalpha) in Oxytricha trifallax and compared it to the previously published structure of the germline DNA polalphagene in Oxytricha nova . The DNA polalphagene of O.trifallax contains 51 macronuclear-destined segments (MDSs) separated by 50 IESs, compared to 45 MDSs and 44 IESs in the O.nova gene. This means that IESs and MDSs have been gained and/or lost during evolutionary divergence of the two species. Most of the MDSs are highly scrambled in a similar non-random pattern in the two species. We present a model to explain how IESs, non-scrambled MDSs and scrambled MDSs may be added and/or eliminated during evolution. Corresponding IESs in the two species differ totally in sequence, and junctions between MDSs and IESs are shifted by 1-18 bp in O.trifallax compared to the O.nova gene. In both species a short region of the gene is distantly separated from the main part of the gene. Comparison of the gene in the two species shows that IESs and scrambling are highly malleable over evolutionary time.

Animals↗
PubMed1997

Phylogenetic relationships among hypotrichous ciliates determined with the macronuclear gene encoding the large, catalytic subunit of DNA polymerase alpha.

The complete macronuclear DNA polymerase alpha gene, previously sequenced in Oxytricha nova, has been cloned from a genomic macronuclear library and sequenced for the hypotrich O. trifallax. Macronuclear DNA clones of DNA polymerase alpha encoding approximately 1000 amino acids, or approximately two-thirds of the open reading frame, have been obtained by PCR and sequenced for Halteria grandinella, Holosticha species, Paraurostyla viridis, Pleurotricha lanceolata, Stylonychia lemnae Teller, Sty. mytilus, Uroleptus gallina, and Urostyla grandis. Phylogenetic relationships inferred from DNA polymerase alpha amino acid sequences have been used to clarify taxonomic relationships previously determined by morphology of the cell cortex. Hypotrich phylogenies based on DNA polymerase alpha amino acid sequences are incongruent with morphological and other molecular phylogenies. Based upon these data, we assert that, contrary to morphological data, O. nova and O. trifallax are different species, and we propose that the oligotrich Halteria grandinella be reclassified as a hypotrich. This work also extends the available data base of eukaryotic DNA polymerase alpha sequences, and suggests new amino acid sequence targets for mutagenesis experiments to continue the functional dissection of DNA pol alpha biochemistry at the molecular level.

Amino Acid Sequence↗
PubMed1997

Origin, evolution, and excision of internal elimination segments in germline genes of ciliates.

Three hypothesis on the evolutionary/molecular origin of internal eliminated segments (IESs) in the germline of hypotrichous ciliates are discussed in the context of the high rate of mutation accumulation in IESs, shifting of IESs during speciation, and evolutionary scrambling of segments within some hypotrich germline genes. Developmental excision of IESs from the germline in Paramecium suggests that the parental macronucleus may provide nucleic acid sequence information to guide excision of IESs and splicing of macronuclear-destined sequences. In ciliates of the oxytrichid/stylonychid group, such a mechanism could explain the precision of excision of IESs and gene unscrambling. Recently initiated molecular/genetic studies may eventually clarify the role of the parental macronucleus in IES excision and gene unscrambling as well as the molecular mechanisms of these events.

Animals↗
PubMed1997

Volatility of internal eliminated segments in germ line genes of hypotrichous ciliates.

Germ line micronuclear genes in ciliated protozoa contain two types of interrupting sequences. Some genes contain introns, but internal eliminated segments (IESs) are much more prevalent. IESs are AT-rich DNA segments that separate macronucleus-destined segments (MDSs) in micronuclear genes. All IESs are excised and destroyed when a micronucleus develops into a macronucleus after each cell mating. IESs have no discernible function. Therefore, an investigation of the behavior of IESs in evolution has been undertaken to assess their possible significance. The IESs in the micronuclear gene encoding the beta-subunit of the telomere-binding protein (beta-TP) are not conserved in number, position, sequence, or length during the evolution of four oxytrichid ciliates. In contrast, the scrambled pattern of MDSs and IESs of the micronuclear actin I gene has been conserved during evolution; however, the precise positions, sequences, and lengths of the IESs differ among species, and in some organisms the actin I gene contains an additional IES and MDS. Corresponding IESs in the actin I genes among the different organisms have shifted positions by 1 to 14 bp, presumably by a mutation-shifting mechanism, creating differences in the repeat sequences flanking IESs. Thus, conservation of a particular repeat sequence among species is not required for IES excision. The changes in IES number and position in the beta-TP genes among ciliates are in sharp contrast to the stability of the intron position. Therefore, IESs are volatile, hypermutable elements that are inserted, removed, shifted, and modified continuously in the germ line through evolutionary time.

Actins↗