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M D Collins

Publications and source records attributed to M D Collins.

At least 19 recordsLinked to original sources

Differential teratogenesis of all-trans-retinoic acid administered on gestational day 9.5 to SWV and C57BL/6N mice: emphasis on limb dysmorphology.

BACKGROUND: Mouse strain differences in teratologic response are well documented. However, because retinoids cause similar malformation syndromes across many species, the strain differences may be predicted to be minimal. The goals of this study were to characterize and explain the differences between the C57BL/6N and SWV mouse strains in terms of all-trans-retinoic acid (RA)-induced teratologic effects at the time of gestation that cause postaxial forelimb ectrodactyly. METHODS: Visceral and skeletal malformations were determined by Wilson's sectioning and double-staining techniques, respectively; developmental staging was performed according to the somite count; and retinoid concentrations were assessed by HPLC. RESULTS: C57BL/6N mice were more susceptible than SWV mice to induction of embryolethality, cardiovascular defects, and forelimb ectrodactyly, whereas the opposite was true for the induction of ear, thymus, and tail agenesis, and cleft palate, gastroschisis, and anal atresia. As determined by somite counts, 1 strain intercross was developmentally advanced compared to the parental strains and the reciprocal cross. Retinoid susceptibility was equivalent between the reciprocal crosses for some malformations and determined by the maternal genotype for others. Toxicokinetic experiments showed that whole-embryo peak retinoid concentrations did not differ between the strains, but the area under the curve (AUC) for all-trans-RA was 1.3 times higher in C57BL/6N than in SWV embryos. CONCLUSIONS: The malformation spectrum induced by RA was strain-specific, and the strain sensitivity for forelimb ectrodactyly was consistent with all previously tested teratogenic agents (i.e., C57BL/6N was more sensitive than SWV). The strain differences in teratologic effects were not explained by developmental timing differences or toxicokinetic differences at the whole-embryo level.

Abnormalities, Drug-Induced↗

Uruburuella suis gen. nov., sp. nov., isolated from clinical specimens of pigs.

Five strains of an unusual Gram-negative, catalase-positive, oxidase-positive, coccobacillus-shaped bacterium isolated from the lungs and heart of pigs with pneumonia and pericarditis were characterized by phenotypic and molecular genetic methods. On the basis of cellular morphology and biochemical criteria, the isolates were tentatively assigned to the family Neisseriaceae, although they did not appear to correspond to any recognized genus or species. Comparative 16S rRNA gene sequencing showed that the five unidentified strains were phylogenetically highly related to each other and represent a hitherto unknown subline within the family Neisseriaceae. On the basis of both phenotypic and phylogenetic evidence, it is proposed that the unknown isolates from pigs be classified as a novel genus and species within the family Neisseriaceae, for which the name Uruburuella suis gen. nov., sp. nov. is proposed. The type strain of U. suis is 1258/02(T) (=CCUG 47806(T)=CECT 5685(T)).

Animals↗

Imaging density disturbances in water with a 41.3-attosecond time resolution.

We show that the momentum flexibility of inelastic x-ray scattering may be exploited to invert its loss function, allowing real time imaging of density disturbances in a medium. We show the disturbance arising from a point source in liquid water, with a resolution of 41.3 attoseconds (4.13 x 10(-17) s) and 1.27 A (1.27 x 10(-8) cm). This result is used to determine the structure of the electron cloud around a photoexcited chromophore in solution, as well as the wake generated in water by a 9 MeV gold ion. We draw an analogy with pump-probe techniques and suggest that energy-loss scattering may be applied more generally to the study of attosecond phenomena.

Elasticity↗

Corynebacterium ciconiae sp. nov., isolated from the trachea of black storks (Ciconia nigra).

Eight unidentified Gram-positive, rod-shaped organisms were recovered from the tracheas of apparently healthy black storks (Ciconia nigra) and subjected to a polyphasic taxonomic analysis. Based on cellular morphology and biochemical criteria the isolates were tentatively assigned to the genus Corynebacterium, although three of the organisms did not appear to correspond to any recognized species. Comparative 16S rRNA gene sequencing studies demonstrated that all of the isolates were phylogenetically members of the genus Corynebacterium. Five strains were genotypically identified as representing Corynebacterium falsenii, whereas the remaining three strains represented a hitherto unknown subline, associated with a small subcluster of species that includes Corynebacterium mastitidis and its close relatives. On the basis of phenotypic and phylogenetic evidence, it is proposed that the unknown isolates from black storks represent a novel species within the genus Corynebacterium, for which the Corynebacterium ciconiae sp. nov. is proposed. The type strain is CECT 5779(T) (=BS13(T)=CCUG 47525(T)).

Animals↗

Corynebacterium spheniscorum sp. nov., isolated from the cloacae of wild penguins.

Twenty unidentified Gram-positive, rod-shaped organisms were recovered from the cloacae of apparently healthy wild penguins (Spheniscus magellanicus) and subjected to a polyphasic taxonomic analysis. On the basis of cellular morphology and biochemical criteria, the isolates were tentatively assigned to the genus Corynebacterium, although the organisms did not appear to correspond to any recognized species. Lipid studies confirmed this generic placement, and comparative 16S rRNA gene sequencing showed that the unidentified organisms represent a hitherto unknown subline, associated with a small subcluster of species that includes Corynebacterium diphtheriae and its close relatives. On the basis of phenotypic and phylogenetic evidence, it is proposed that the unknown isolates from penguins be classified in the genus Corynebacterium, as Corynebacterium spheniscorum sp. nov. The type strain is strain PG 39T (=CCUG 45512T =CECT 5986T).

Animals↗

Psychrobacter pulmonis sp. nov., isolated from the lungs of lambs.

Unusual Gram-negative, catalase- and oxidase-positive, coccus-shaped bacteria isolated from the lungs of two lambs were characterized by phenotypic and molecular-genetic methods. Comparative 16S rRNA gene sequencing studies demonstrated that the unknown isolates were genealogically highly related to each other (99.8% sequence similarity) and represent a novel subline within the genus Psychrobacter. The unknown bacterium was phylogenetically closely related to, but distinct from, Psychrobacter phenylpyruvicus, Psychrobacter immobilis, Psychrobacter glacincola and Psychrobacter urativorans. The novel Psychrobacter isolates were readily distinguished from all other Psychrobacter species and other Gram-negative, oxidase-positive bacteria usually responsible for lung infections in sheep by physiological and biochemical tests. Based on molecular-genetic and phenotypic evidence, it is proposed that the unknown Psychrobacter isolates from lambs be classified as Psychrobacter pulmonis sp. nov. The type strain is strain S-606T (=CECT 5989T =CCUG 46240T).

Animals↗

Corynebacterium sphenisci sp. nov., isolated from wild penguins.

Six unidentified gram-positive, rod-shaped organisms recovered from the cloacae of apparently healthy wild penguins were characterized by phenotypic and molecular taxonomic methods. Chemotaxonomic investigations revealed the presence of a cell wall based on meso-diaminopimelic acid and long-chain cellular fatty acids of the straight-chain saturated and monounsaturated types, consistent with the genus Corynebacterium. Corynomycolic acids, which are characteristic of the genus, were also detected, albeit in small amounts. Comparative 16S rRNA gene sequencing studies showed that the unidentified organisms were phylogenetically related to corynebacteria and represent a novel subline associated with a small subcluster of species that includes Corynebacterium xerosis, Corynebacterium amycolatum and Corynebacterium freneyi. The unknown isolates were readily distinguished from their closest phylogenetic relatives and all other Corynebacterium species with validly published names by using a combination of biochemical and chemotaxonomic criteria. Based on both phenotypic and 16S rRNA gene sequence considerations, it is proposed that the unknown isolates recovered from penguins be classified as a novel species in the genus Corynebacterium, Corynebacterium sphenisci sp. nov. The type strain is CECT 5990T (= CCUG 46398T).

Animals↗

Isolation of Corynebacterium falsenii and description of Corynebacterium aquilae sp. nov., from eagles.

Biochemical, molecular chemical and molecular genetic studies were performed on seven unidentified gram-positive, rod-shaped organisms recovered from eagles. The strains were provisionally identified as Corynebacterium jeikeium with the commercial API Coryne system, but they were able to grow under anaerobic conditions and were non-lipophilic. Comparative 16S rRNA gene sequencing studies demonstrated that the isolates belonged phylogenetically to the genus Corynebacterium. Three strains were identified genotypically as Corynebacterium falsenii; the remaining four strains corresponded to a hitherto unknown lineage within the genus Corynebacterium, associated with a small subcluster of species that included Corynebacterium diphtheriae and its close relatives. The unknown bacterial strains were readily distinguished from these and other species of the genus by biochemical tests. Based on both phenotypic and phylogenetic evidence, it is proposed that the unknown bacterial strains from eagles should be classified as Corynebacterium aquilae sp. nov. (type strain is S-613T = CECT 5993T = CCUG 46511T).

Animals↗

Description of Enterococcus canis sp. nov. from dogs and reclassification of Enterococcus porcinus Teixeira et al. 2001 as a junior synonym of Enterococcus villorum Vancanneyt et al 2001.

Strains from anal swabs and chronic otitis externa in dogs were shown to be phylogenetically related to the Enterococcus faecium species group. They shared a number of phenotypic characteristics with these species, but they could be easily differentiated by biochemical reactions. In addition, the canine strains were unusual in their nearly complete failure to grow on sodium azide-containing enterococci-selective media and in their Voges-Proskauer reactions (usually negative). By using 16S rRNA sequencing and DNA-DNA hybridization of representative strains, as well as tDNA interspacer gene PCR and SDS-PAGE of whole-cell proteins, the group of canine strains was shown to constitute a novel enterococcal species. The name Enterococcus canis sp. nov. is proposed for this species, with LMG 12316T (= CCUG 46666T) as the type strain. Concurrently, the taxonomic situation and nomenclatural position of Enterococcus porcinus were investigated. As no phenotypic or genotypic differences were found between this species and Enterococcus villorum, the name E. porcinus is considered to be a junior synonym of E. villorum.

Animals↗

Corynebacterium suicordis sp. nov., from pigs.

Nineteen strains of Gram-positive, non-motile, non-spore-forming, catalase-positive, rod-shaped bacteria isolated from pigs were characterized by using biochemical, molecular chemical and molecular genetic methods. Two distinct groups of organisms were discerned, based on their colonial morphology, CAMP (Christie-Atkins-Munch-Petersen) reaction and numerical profile by using the API Coryne system. The first group (13 strains) gave a doubtful discrimination between Corynebacterium striatum and Corynebacterium amycolatum, whilst the second group (six strains) were identified tentatively as Corynebacterium urealyticum. Comparative 16S rRNA gene sequencing studies demonstrated that all of the isolates belonged phylogenetically to the genus CORYNEBACTERIUM: The first group of organisms was highly similar to Corynebacterium testudinoris with respect to 16S rRNA gene sequences and physiological characteristics, whereas the remaining six isolates formed a hitherto unknown subline within the genus, associated with a small subcluster of species that included Corynebacterium auriscanis and its close relatives. The unknown Corynebacterium sp. was distinguished readily from these and other species of the genus by biochemical tests. Based on both phenotypic and phylogenetic evidence, it is proposed that the new isolates from pigs should be classified as a novel species, Corynebacterium suicordis sp. nov. The type strain is P81/02(T) (=CECT 5724(T)=CCUG 46963(T)).

Anaerobiosis↗

Bacteriology of the Labrador dog gut: a cultural and genotypic approach.

AIMS: To carry out an extensive study of the microflora composition of the Labrador dog gut. METHODS AND RESULTS: Faecal specimens from four Labradors were collected and plated onto growth media designed to recover total anaerobes, bacteroides, bifidobacteria, lactobacilli, clostridia, Gram-positive cocci, total aerobes and coliforms. Morphologically different isolates were collected from all agars inoculated with faeces from one canine individual (repeated four times). A total of 157 out of 171 isolates were identified using 16S rRNA gene sequencing. Sequence analysis showed that agar selectivity was poor, especially when bacteroides and Gram-positive cocci were the targets. Bifidobacteria were not detected in any of the samples analysed, indicating their presence at low or negligible levels. The gene sequences of many of the isolates (n=45, representing 29% of the total) did not correlate with known species in the Ribosomal Database Project and EMBL databases, suggesting the presence of novel gut diversity. CONCLUSIONS: Traditional culture methods fail to reflect the bacterial diversity present in Labrador dog faeces. SIGNIFICANCE AND IMPACT OF THE STUDY: This study has shown the value of molecular-based methodologies for determining bacterial profiles in the Labrador dog gut microbiota, but has also exposed the limitations of purportedly selective agars.

Animals↗

Molecular biological methods for studying the gut microbiota: the EU human gut flora project.

Seven European laboratories co-operated in a joint project (FAIR CT97-3035) to develop, refine and apply molecular methods towards facilitating elucidation of the complex composition of the human intestinal microflora and to devise robust methodologies for monitoring the gut flora in response to diet. An extensive database of 16S rRNA sequences for tracking intestinal bacteria was generated by sequencing the 16S rRNA genes of new faecal isolates and of clones obtained by amplification with polymerase chain reaction (PCR) on faecal DNA from subjects belonging to different age groups. The analyses indicated that the number of different species (diversity) present in the human gut increased with age. The sequence information generated, provided the basis for design of 16S rRNA-directed oligonucleotide probes to specifically detect bacteria at various levels of phylogenetic hierarchy. The probes were tested for their specificity and used in whole-cell and dot-blot hybridisations. The applicability of the developed methods was demonstrated in several studies and the major outcomes are described.

Adult↗

Streptococcus entericus sp. nov., isolated from cattle intestine.

Biochemical, molecular chemical and molecular genetic studies were performed on an unknown gram-positive, catalase-negative, coccus-shaped organism isolated from the intestine of a cow affected with catarrhal enteritis. The organism was tentatively identified as a streptococcal species based on results of cellular morphological and biochemical tests. 16S rRNA gene sequencing studies confirmed its provisional identification as a member of the genus Streptococcus, but the organism did not correspond to any recognized species of this genus. The nearest phylogenetic relatives of the unknown coccus from a calf were Streptococcus acidominimus and Streptococcus suis. The unknown bacterium, however, was distinguished from these species and other animal streptococci by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on both phenotypic and phylogenetic findings, it is proposed that the unknown bacterium be classified as a novel species of the genus Streptococcus, Streptococcus entericus sp. nov. The type strain is CECT 5353T (= CCUG 44616T).

Animals↗

Clostridium hathewayi sp. nov., from human faeces.

A strictly anoxic, Gram-positive, sporeforming, rod-shaped bacterium was isolated from a chemostat inoculated with human faeces. The bacterium used carbohydrate as fermentable substrates, producing acetate, ethanol, carbon dioxide and hydrogen as the major products of glucose metabolism, and possessed a G + C content of 50.7 to 50.9 mol%. Comparative 16S rRNA gene sequencing showed that the unidentified bacterium represents a previously unrecognised sub-line within the Clostridium coccoides rRNA group of organisms. The nearest relatives of the unknown bacterium corresponded to Clostridium algidixylanolyticum, C. aerotolerans, C. celerecrescens, C. indolis, C. sphenoides, C. methoxybenzovorans and C. xylanolyticum but 16S rRNA sequence divergence values of >4% demonstrated that it represents a novel species. Based on the presented findings a new species, Clostridium hathewayi, is described. The type strain of Clostridium hathewayi is DSM = 13479T (= CCUG 43506 T).

Clostridium↗

Characterization of some strains from human clinical sources which resemble "Leptotrichia sanguinegens": description of Sneathia sanguinegens sp. nov., gen. nov.

Three strains of a gram-negative, blood or serum requiring, rod-shaped bacterium recovered from human clinical specimens were characterised by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing showed the unknown rod-shaped strains are members of the same species as some fastidious isolates recovered from human blood specimens and previously designated "Leptotrichia sanguinegens". Based on phylogenetic and phenotypic evidence, it is proposed that the isolates from human sources be classified in a new genus Sneathia, as Sneathia sanguinegens gen. nov., sp. nov. The type strain of Sneathia sanguinegens is CCUG 41628T.

Adult↗

Intracellular S-adenosylhomocysteine concentrations predict global DNA hypomethylation in tissues of methyl-deficient cystathionine beta-synthase heterozygous mice.

Because S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) are the substrate and product of essential methyltransferase reactions; the ratio of SAM:SAH is frequently used as an indicator of cellular methylation potential. However, it is not clear from the ratio whether substrate insufficiency, product inhibition or both are required to negatively affect cellular methylation capacity. A combined genetic and dietary approach was used to modulate intracellular concentrations of SAM and SAH. Wild-type (WT) or heterozygous cystathionine beta-synthase (CBS +/-) mice consumed a control or methyl-deficient diet for 24 wk. The independent and combined effect of genotype and diet on SAM, SAH and the SAM:SAH ratio were assessed in liver, kidney, brain and testes and were correlated with relative changes in tissue-specific global DNA methylation. The combined results from the different tissues indicated that a decrease in SAM alone was not sufficient to affect DNA methylation in this model, whereas an increase in SAH, either alone or associated with a decrease in SAM, was most consistently associated with DNA hypomethylation. A decrease in SAM:SAH ratio was predictive of reduced methylation capacity only when associated with an increase in SAH; a decrease in the SAM:SAH ratio due to SAM depletion alone was not sufficient to affect DNA methylation in this model. Plasma homocysteine levels were positively correlated with intracellular SAH levels in all tissues except kidney. These results support the possibility that plasma SAH concentrations may provide a sensitive biomarker for cellular methylation status.

Analysis of Variance↗

Actinomyces marimammalium sp. nov., from marine mammals.

Three strains of a previously undescribed Actinomyces-like bacterium were isolated from samples taken from two dead seals and a porpoise. Biochemical testing and PAGE analysis of whole-cell proteins indicated the strains were phenotypically similar to each other but different from previously described Actinomyces and Arcanobacterium species. Comparative 16S rRNA gene sequencing studies showed the organisms from marine animals were genetically closely related and represent a hitherto unknown subline within the genus Actinomyces (sequence divergence values > 6% with recognized species). Based on phylogenetic and phenotypic evidence it is proposed that the unknown bacterium from the seals and a porpoise should be classified as Actinomyces marimammalium sp. nov. The type strain is CCUG 41710T.

Actinomyces↗