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J R Stevens

Publications and source records attributed to J R Stevens.

At least 19 recordsLinked to original sources
PubMed2006

Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets.

Using a unique microarray platform for cytosine methylation profiling, the DNA methylation landscape of the human genome was monitored at more than 21,000 sites, including 79% of the annotated transcriptional start sites (TSS). Analysis of an oligodendroglioma derived cell line LN-18 revealed more than 4000 methylated TSS. The gene-centric analysis indicated a complex pattern of DNA methylation exists along each autosome, with a trend of increasing density approaching the telomeres. Remarkably, 2% of CpG islands (CGI) were densely methylated, and 17% had significant levels of 5 mC, whether or not they corresponded to a TSS. Substantial independent verification, obtained from 95 loci, suggested that this approach is capable of large scale detection of cytosine methylation with an accuracy approaching 90%. In addition, we detected large genomic domains that are also susceptible to DNA methylation reinforced inactivation, such as the HOX cluster on chromosome 7 (CH7). Extrapolation from the data suggests that more than 2000 genomic loci may be susceptible to methylation and associated inactivation, and most have yet to be identified. Finally, we report six new targets of epigenetic inactivation (IRX3, WNT10A, WNT6, RARalpha, BMP7 and ZGPAT). These targets displayed cell line and tumor specific differential methylation when compared with normal brain samples, suggesting they may have utility as biomarkers. Uniquely, hypermethylation of the CGI within an IRX3 exon was correlated with over-expression of IRX3 in tumor tissues and cell lines relative to normal brain samples.

Brain↗
PubMed2006

Amplification of DNA from preserved specimens shows blowflies were preadapted for the rapid evolution of insecticide resistance.

Mutations of esterase 3 confer two forms of organophosphate resistance on contemporary Australasian Lucilia cuprina. One form, called diazinon resistance, is slightly more effective against commonly used insecticides and is now more prevalent than the other form, called malathion resistance. We report here that the single amino acid replacement associated with diazinon resistance and two replacements associated with malathion resistance also occur in esterase 3 in the sibling species Lucilia sericata, suggesting convergent evolution around a finite set of resistance options. We also find parallels between the species in the geographic distributions of the polymorphisms: In both cases, the diazinon-resistance change is absent or rare outside Australasia where insecticide pressure is lower, whereas the changes associated with malathion resistance are widespread. Furthermore, PCR analysis of pinned specimens of Australasian L. cuprina collected before the release of organophosphate insecticides reveals no cases of the diazinon-resistance change but several cases of those associated with malathion resistance. Thus, the early outbreak of resistance in this species can be explained by the preexistence of mutant alleles encoding malathion resistance. The pinned specimen analysis also shows much higher genetic diversity at the locus before organophosphate use, suggesting that the subsequent sweep of diazinon resistance in Australasia has compromised the scope for the locus to respond further to the ongoing challenge of the insecticides.

Adaptation, Physiological↗
PubMed2005

Phylogeny of Trypanosoma ( Megatrypanum ) theileri and related trypanosomes reveals lineages of isolates associated with artiodactyl hosts diverging on SSU and ITS ribosomal sequences.

SSU ribosomal sequences of trypanosomes from Brazilian cattle and water buffalo were used to infer phylogenetic relationships between non-pathogenic T. theileri and allied species parasitic in artiodactyls. T. theileri trypanosomes from distinct geographical regions in Brazil and from other countries were tightly clustered into the 'clade T. theileri' distant from the 'T. brucei clade' of pathogenic parasites of artiodactyls, and also distinct from trypanosomes of other mammals. The existence of this monophyletic assemblage (T. theileri clade) composed only by isolates from artiodactyl species justifies the continued recognition of the subgenus T. (Megatrypanum) with T. theileri as its type species. Phylogenies based on SSU and ITS1 ribosomal sequences produced the same branching pattern with isolates from different mammalian hosts clustered in 5 lineages: A, related to water buffalo; B, C and D, to cattle; E, to fallow deer. The pattern of host specificity allied to some congruence between host and parasite phylogenies suggested association of these trypanosomes with their respective hosts. Segregation of cattle isolates into three lineages revealed an overall geographical structure. Moreover, positioning of trypanosomes infecting tabanids in the T. theileri clade is consistent with the role of these flies as important vectors of these trypanosomes.

Animals↗
PubMed2005

A new lineage of trypanosomes from Australian vertebrates and terrestrial bloodsucking leeches (Haemadipsidae).

Little is known about the trypanosomes of indigenous Australian vertebrates and their vectors. We surveyed a range of vertebrates and blood-feeding invertebrates for trypanosomes by parasitological and PCR-based methods using primers specific to the small subunit ribosomal RNA (SSU rRNA) gene of genus Trypanosoma. Trypanosome isolates were obtained in culture from two common wombats, one swamp wallaby and an Australian bird (Strepera sp.). By PCR, blood samples from three wombats, one brush-tailed wallaby, three platypuses and a frog were positive for trypanosome DNA. All the blood-sucking invertebrates screened were negative for trypanosomes both by microscopy and PCR, except for specimens of terrestrial leeches (Haemadipsidae). Of the latter, two Micobdella sp. specimens from Victoria and 18 Philaemon sp. specimens from Queensland were positive by PCR. Four Haemadipsa zeylanica specimens from Sri Lanka and three Leiobdella jawarerensis specimens from Papua New Guinea were also PCR positive for trypanosome DNA. We sequenced the SSU rRNA and glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH) genes in order to determine the phylogenetic positions of the new vertebrate and terrestrial leech trypanosomes. In trees based on these genes, Australian vertebrate trypanosomes fell in several distinct clades, for the most part being more closely related to trypanosomes outside Australia than to each other. Two previously undescribed wallaby trypanosomes fell in a clade with Trypanosoma theileri, the cosmopolitan bovid trypanosome, and Trypanosoma cyclops from a Malaysian primate. The terrestrial leech trypanosomes were closely related to the wallaby trypanosomes, T. cyclops and a trypanosome from an Australian frog. We suggest that haemadipsid leeches may be significant and widespread vectors of trypanosomes in Australia and Asia.

Amphibians↗
PubMed2005

Antibacterial properties of larval secretions of the blowfly, Lucilia sericata.

The antibacterial properties of secretions aseptically collected from larvae of the greenbottle fly Lucilia sericata (Meigen) (Diptera: Calliphoridae) were examined. These investigations revealed the presence of small (<1 kDa) antibacterial factor(s) within the larval secretions, active against a range of bacteria. These include the Gram-positive Staphylococcus aureus, both methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-sensitive Staphylococcus aureus (MSSA), Streptococcus pyogenes and to a lesser extent the Gram-negative Pseudomonas aeruginosa. These secretions were shown to be highly stable as a freeze-dried preparation and, considering the activity against organisms typically associated with clinical infection, may be a source of novel antibiotic-like compounds that may be used for infection control and in the fight against MRSA.

Animals↗
PubMed2005

Morphological and molecular comparison of host-derived populations of parasitic Psoroptes mites.

Infestation by parasitic Psoroptes mites (Acari: Psoroptidae) is an important cause of economic loss and welfare problems in livestock in many areas of the world. At least five species within this genus have been recognized, based on the host infested, the infestation site and differences in length of the opisthosomal setae of adult male mites. Here the integrity of these species is considered by subjecting populations of mites from a range of host species and geographical locations to simultaneous morphological and molecular genetic analyses. Morphological analysis showed that there were significant differences in shape and size between mite populations from different hosts, and that length of the outer opisthosomal setae in males and the homologous seta in females were the most important distinguishing character in adults. However, considerable variation in outer opisthosomal seta length was evident within and between populations of mites, and differences were not clearly related to host-species or geographical origin and did not support the accepted species differences. Molecular characterization using sequence data from the mitochondrial second internal transcribed spacer (ITS-2) region and microsatellite markers found little or no consistent host-related variation between the mite population samples. The results suggest that there is no case for considering the Psoroptes mites from the different hosts examined as separate species and that the morphological variation observed therefore may represent phenotypic adaptation to the local microenvironment on particular species of host.

Animal Structures↗
PubMed2005

The inadvertent introduction into Australia of Trypanosoma nabiasi, the trypanosome of the European rabbit (Oryctolagus cuniculus), and its potential for biocontrol.

Wild rabbits (Oryctolagus cuniculus) in Australia are the descendents of 24 animals from England released in 1859. We surveyed rabbits and rabbit fleas (Spilopsyllus cuniculi) in Australia for the presence of trypanosomes using parasitological and PCR-based methods. Trypanosomes were detected in blood from the European rabbits by microscopy, and PCR using trypanosome-specific small subunit ribosomal RNA (SSU rRNA) gene primers and those in rabbit fleas by PCR. This is the first record of trypanosomes from rabbits in Australia. We identified these Australian rabbit trypanosomes as Trypanosoma nabiasi, the trypanosome of the European rabbit, by comparison of morphology and SSU rRNA gene sequences of Australian and European rabbit trypanosomes. Phylogenetic analysis places T. nabiasi in a clade with rodent trypanosomes in the subgenus Herpetosoma and their common link appears to be transmission by fleas. Despite the strict host specificity of trypanosomes in this clade, phylogenies presented here suggest that they have not strictly cospeciated with their vertebrate hosts. We suggest that T. nabiasi was inadvertently introduced into Australia in the 1960s in its flea vector Spilopsyllus cuniculi, which was deliberately introduced as a potential vector of the myxoma virus. In view of the environmental and economic damage caused by rabbits in Australia and other islands, the development of a virulent or genetically modified T. nabiasi should be considered to control rabbits.

Animals↗
PubMed2004

Phylogeny, taxonomy and grouping of Trypanosoma rangeli isolates from man, triatomines and sylvatic mammals from widespread geographical origin based on SSU and ITS ribosomal sequences.

Phylogenetic relationships among Trypanosoma rangeli isolates from man, wild mammals and triatomine bugs from widespread geographical origin were inferred by comparison of the small subunit of ribosomal gene sequences. The phylogenetic trees indicated that the subgenus Herpetosoma is polyphyletic and strongly supported division of this group into two monophyletic lineages, one made up of T. rangeli, T. rangeli-like and allied species and other consisting of T. lewisi and related taxa. Based on phylogenetic analysis, morphology, behaviour in vertebrate and invertebrate hosts and epidemiology we propose: a) the validation of Herpetosoma as a taxon comprised only for species of group lewisi and the maintenance of T. lewisi as the type-species of this subgenus; b) the classification of T. rangeli, T. rangeli-like and allied species into a 'T. rangeli-clade' more closely related to Schizotrypanum than to T. lewisi or T. brucei. The phylogenetic tree disclosed at least 4 groups within the clade T. rangeli, all confirmed by polymorphism of the internal transcribed spacer, thus conferring for the first time phylogenetic support to groups of T. rangeli and corroborating the high complexity of this taxon. Grouping was independent of their mammalian host-species and geographical origin, indicating that other factors are determining this segregation.

Animals↗
PubMed2003

Molecular characterization of the mitochondrial cytochrome oxidase I gene of Oestridae species causing obligate myiasis.

A 688-bp region of the mitochondrial cytochrome oxidase I gene was sequenced from larvae of 18 species of Oestridae causing obligate myiasis. Larvae belonged to the four Oestridae subfamilies (Cuterebrinae, Gasterophilinae, Hypodermatinae and Oestrinae), which are commonly found throughout the world. Analysis of both nucleotide and amino acid data was performed. Nucleotide sequences included 385 conserved sites and 303 variable sites; mean nucleotide variation between all species was 18.1% and variation within each subfamily ranged from 5.3% to 13.34%. Intraspecific pairwise divergences ranged from 0.14% to 1.59%, and interspecific variation ranged from 0.7% to 27%. Of the 229 amino acids, 76 were variable (60 of which were phylogenetically informative), with some highly conserved residues identified within each subfamily. Phylogenetic analysis showed a strong divergence among the four subfamilies, concordant with classical taxonomy based on morphological and biological features. This study provides the first molecular data set for myiasis-causing Oestridae species, providing an essential database for the molecular identification of these parasites and the assessment of phylogenetic relationships within family Oestridae.

Animals↗
PubMed2003

Species identification of Hypoderma affecting domestic and wild ruminants by morphological and molecular characterization.

Cuticular structures and the sequence of the cytochrome oxidase I gene were compared for Hypoderma bovis (Linnaeus), Hypoderma lineatum (De Villers), Hypoderma actaeon Brauer, Hypoderma diana Brauer and Hypoderma tarandi (Linnaeus) (Diptera, Oestridae). Third-stage larvae of each species were examined by scanning electron microscopy revealing differences among species in the pattern and morphology of spines on the cephalic and thoracic segments, by spine patterns on the tenth abdominal segment, and by morphology of the spiracular plates. The morphological approach was supported by the molecular characterization of the most variable region of the cytochrome oxidase I (COI) gene of these species, which was amplified by polymerase chain reaction and analysed. Amplicons were digested with the unique restriction enzyme, BfaI, providing diagnostic profiles able to simultaneously differentiate all Hypoderma species examined. These findings confirm the utility of morphological characters for differentiating the most common Hypoderma larvae and reconfirm the power of the COI gene for studying insect identification and systematics.

Animals↗
PubMed2002

Discounting and reciprocity in an Iterated Prisoner's Dilemma.

The Iterated Prisoner's Dilemma (IPD) is a central paradigm in the study of animal cooperation. According to the IPD framework, repeated play (repetition) and reciprocity combine to maintain a cooperative equilibrium. However, experimental studies with animals suggest that cooperative behavior in IPDs is unstable, and some have suggested that strong preferences for immediate benefits (that is, temporal discounting) might explain the fragility of cooperative equilibria. We studied the effects of discounting and strategic reciprocity on cooperation in captive blue jays. Our results demonstrate an interaction between discounting and reciprocity. Blue jays show high stable levels of cooperation in treatments with reduced discounting when their opponent reciprocates, but their levels of cooperation decline in all other treatment combinations. This suggests that stable cooperation requires both reduced discounting and reciprocity, and it offers an explanation of earlier failures to find cooperation in controlled payoff games.

Animals↗
PubMed2002

Paraphyly in Hawaiian hybrid blowfly populations and the evolutionary history of anthropophilic species.

Complementary nuclear (28S rRNA) and mitochondrial (COI + II) gene markers were sequenced from the blowflies, Lucilia cuprina and Lucilia sericata, from Europe, Africa, North America, Australasia and Hawaii. Populations of the two species were phylogenetically distinct at both genes, with one exception. Hawaiian L. cuprina possessed typical L. cuprina-type rRNA, but had L. sericata-type mitochondrial (COI + II) sequences. An explanation for this pattern is that Hawaiian flies are hybrids and comparison of observed levels of sequence divergence to possible introduction events, e.g. Polynesian colonization, suggests that Hawaiian L. cuprina may be evolving rapidly. Moreover, the monophyly of these flies also suggests that the L. sericata mtDNA haplotype was apparently fixed in Hawaiian L. cuprina by lineage sorting, indicating a population bottleneck in the evolutionary history of these island flies.

Animals↗
PubMed2001

The molecular evolution of Trypanosomatidae.

In the absence of a fossil record, theories relating to the evolution of protozoa have, for most of the twentieth century, been based on morphological and life cycle data despite their known limitations. However, recent advances in molecular methodology, notably the wide availability of accurate, automated DNA sequencing, have made it possible to deduce the evolutionary relationships of extant species from their genes. This paper focuses on new findings concerning the evolution of the Trypanosomatidae, based on the ever-expanding body of molecular data now available. Classically, the evolution of digenetic parasitism in kinetoplastids has centred around two opposing theories--invertebrate first or vertebrate first--depending on which was the original host of the monogenetic parasite. However, data supporting a close phylogenetic relationship between genera of monogenetic insect parasites and digenetic vertebrate parasites challenge the simplicity of these hypotheses and suggest that the transition may not have been a major evolutionary barrier. The implications of these observations for the evolution of parasitism within the group are discussed. Phylogenetic analysis of a diverse selection of trypanosomatid species suggests that the genus Trypanosoma is monophyletic and that the human parasites, T. brucei, T. cruzi and Leishmania spp., have fundamentally different patterns of evolution. T. brucei clusters with mammalian trypanosomes of African origin, suggesting an evolutionary history confined to Africa. T. cruzi shows association with trypanosomes from bats, T. rangeli, and trypanosomes from a range of South American mammals and an Australian kangaroo. The origins of most parasites within this clade lie in South America and Australia, suggesting an ancient southern super-continent origin for T. cruzi, possibly in marsupials. The divergence between the Leishmania and Trypanosoma lineages is also ancient. The topology of Leishmania phylogenies suggests an independent transition to digenetic parasitism, a neotropical origin and an early tertiary radiation of the parasite.

Animals↗
PubMed2001

Unravelling the phylogenetic relationships of African trypanosomes of suids.

African trypanosomes of the subgenera Nannomonas and Pycnomonas have been recorded from both wild and domestic suids. However, complete descriptions of some of these trypanosomes with regard to host range, pathogenicity, transmission and distribution are still lacking. Neither the recently described Trypanosoma (Nannomonas) godfreyi nor Trypanosoma (Nannomonas) congolense Tsavo have been isolated from mammalian hosts, while Trypanosoma (Pycnomonas) suis remains the rarest of the Salivarian trypanosomes. The only isolate presumed to be of the latter species is maintained at the Kenya Trypanosomiasis Research Institute, Nairobi. We present here the results of characterization of this isolate by morphology, tsetse transmission, the use of species-specific DNA probes and DNA sequence analysis. Morphology in stained blood smears revealed a small trypanosome with a free flagellum. Experimental transmission through Glossina morsitans morsitans showed a developmental cycle typical of subgenus Nannomonas A positive identification was obtained with species-specific PCR primers for T. congolense Tsavo; moreover, the sequence of the SSU rRNA gene was almost identical to that of T. congolense Tsavo on database. In phylogenetic analysis of the SSU rRNA genes of Salivarian trypanosomes, T. congolense Tsavo grouped with T. simiae rather than T. congolense, suggesting that the name T. simiae Tsavo is more appropriate.

Animals↗
PubMed2000

A dielectric analysis of liquid and glassy solid glucose/water solutions.

Dielectric relaxation data covering a temperature range from above room temperature to below the glass transition for 40% (w/w) and 75% (w/w) glucose/water solutions in the frequency range between 5 and 13 MHz are presented. These data are used to obtain correlation times for the dielectric relaxation in the viscous liquid and the glass and are compared with correlation times determined from deuterium nuclear spin relaxation times [J. Chem. Phys., 110 (1999) 3472-3483]. The two sets of results have the same temperature dependence, but differ in magnitude by a factor of 3, implying that the relaxation is a small-step rotational diffusion. Both the structural relaxation (alpha process) and the slow beta process are present. In the 40% glucose/water sample, there is a dielectric relaxation attributable to the ice that forms at low temperature. It is shown that the reciprocal of the viscosity, the correlation time derived from the dielectric relaxation, and the dc conductivity have a similar dependence on temperature.

Electric Conductivity↗
PubMed1999

Epilepsy, schizophrenia, and the extended amygdala.

Propagation and prolongation of rapid neuronal discharge underlies the epilepsies. However, episodic focal rapid neuronal discharges limited to discrete nuclei and pathways of the amygdala-hippocampal-septal-hypothalamic networks are the language of physiologic message systems for endocrine regulation and reproductive activities vital to the survival of the organism and the species. To prevent prolongation and propagation of physiologic pulsed excitation to areas outside specific networks and resultant epileptic seizures, these discharges must be limited in extent and time by powerful inhibitory processes. The nucleus accumbens, a unit of the extended amygdala, and the monoamines and GABA are components of the inhibitory networks that restrict physiologic rapid discharge in duration and in location. In parallel to the relationship of excessive neuronal excitation to epilepsy, evidence will be presented that excessive inhibition via one or more components of these inhibitory networks or diminished excitation underlies development of some psychoses, including schizophrenia.

Amygdala↗
PubMed1999

A nested PCR for the ssrRNA gene detects Trypanosoma binneyi in the platypus and Trypanosoma sp. in wombats and kangaroos in Australia.

Trypanosome infections in their natural hosts are frequently difficult to detect by microscopy, and culture methods are unreliable and not suitable for all species of Trypanosoma. A nested PCR strategy for detecting and identifying Trypanosoma species, suitable for detecting both known and unknown trypanosomes, is presented. Thirty-two blood samples from 23 species of Australian birds and mammals were screened by a nested PCR for the presence of Trypanosoma sp. ssrRNA. Three infections were detected, one in an eastern grey kangaroo (Macropus giganteus), one in a common wombat (Vombatus ursinus) and one in a platypus (Ornithorhynchus anatinus). The kangaroo and wombat are new host records for Trypanosoma sp.; the platypus parasite was Trypanosoma hinneyi. The three parasites could be distinguished by restriction fragment length polymorphisms of the amplified fragment of the ssrRNA gene. The kangaroo and wombat parasites were also isolated in a semi-solid blood agar medium. The culture forms of the kangaroo trypanosome had an expanded flagellar sheath in which structures similar to hemidesmosomes were detected by EM. The nested PCR was at least as sensitive as culture, and analysis of the PCR products gave parasite-specific fingerprints. Therefore this method could be suitable for rapidly screening host animals for the presence of trypanosomes and identifying the infecting strain.

Animals↗