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1.
The phylogeny of Greya Busck (Lepidoptera: Prodoxidae) was inferred from
nucleotide sequence variation across a 765-bp region in the cytochrome
oxidase I and II genes of the mitochondrial genome. Most parsimonious
relationships of 25 haplotypes from 16 Greya species and two outgroup
genera (Tetragma and Prodoxus) showed substantial congruence with the
species relationships indicated by morphological variation. Differences
between mitochondrial and morphological trees were found primarily in the
positions of two species, G. variabilis and G. pectinifera, and in the
branching order of the three major species groups in the genus. Conflicts
between the data sets were examined by comparing levels of homoplasy in
characters supporting alternative hypotheses. The phylogeny of Greya
species suggests that host-plant association at the family level and larval
feeding mode are conservative characters. Transition/transversion ratios
estimated by reconstruction of nucleotide substitutions on the phylogeny
had a range of 2.0-9.3, when different subsets of the phylogeny were used.
The decline of this ratio with the increase in maximum sequence divergence
among taxa indicates that transitions are masked by transversions along
deeper internodes or long branches of the phylogeny. Among transitions,
substitutions of A-->G and T-->C outnumbered their reciprocal
substitutions by 2-6 times, presumably because of the approximately 4:1
(77%) A+T-bias in nucleotide base composition. Of all transversions,
73%-80% were A<-->T substitutions, 85% of which occurred at third
positions of codons; these estimates did not decrease with an increase in
maximum sequence divergence of taxa included in the analysis. The high
frequency of A<-->T substitutions is either a reflection or an
explanation of the 92% A+T bias at third codon positions.
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2.
A wide-ranging examination of plastid (pt)DNA sequence homologies within
higher plant nuclear genomes (promiscuous DNA) was undertaken. Digestion
with methylation-sensitive restriction enzymes and Southern analysis was
used to distinguish plastid and nuclear DNA in order to assess the extent
of variability of promiscuous sequences within and between plant species.
Some species, such as Gossypium hirsutum (cotton), Nicotiana tabacum
(tobacco), and Chenopodium quinoa, showed homogenity of these sequences,
while intraspecific sequence variation was observed among different
cultivars of Pisum sativum (pea), Hordeum vulgare (barley), and Triticum
aestivum (wheat). Hypervariability of plastid sequence homologies was
identified in the nuclear genomes of Spinacea oleracea (spinach) and Beta
vulgaris (beet), in which individual plants were shown to possess a unique
spectrum of nuclear sequences with ptDNA homology. This hypervariability
apparently extended to somatic variation in B. vulgaris. No sequences with
ptDNA homology were identified by this method in the nuclear genome of
Arabidopsis thaliana.
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3.
A functional analysis of mouse models of cardiac disease through metabolic profiling 总被引:6,自引:0,他引:6
Jones GL Sang E Goddard C Mortishire-Smith RJ Sweatman BC Haselden JN Davies K Grace AA Clarke K Griffin JL 《The Journal of biological chemistry》2005,280(9):7530-7539
Since the completion of the human and mouse genomes, the focus in mammalian biology has been on assessing gene function. Tools are needed for assessing the phenotypes of the many mouse models that are now being generated, where genes have been "knocked out," "knocked in," or mutated, so that gene expression can be understood in its biological context. Metabolic profiling of cardiac tissue through high resolution NMR spectroscopy in conjunction with multivariate statistics has been used to classify mouse models of cardiac disease. The data sets included metabolic profiles from mouse models of Duchenne muscular dystrophy, two models of cardiac arrhythmia, and one of cardiac hypertrophy. The metabolic profiles demonstrate that the strain background is an important component of the global metabolic phenotype of a mouse, providing insight into how a given gene deletion may result in very different responses in diverse populations. Despite these differences associated with strain, multivariate statistics were capable of separating each mouse model from its control strain, demonstrating that metabolic profiles could be generated for each disease. Thus, this approach is a rapid method of phenotyping mouse models of disease. 相似文献
4.
Mohammed F. Alum Paul A. Shaw Brian C. Sweatman Baljit K. Ubhi John N. Haselden Susan C. Connor 《Metabolomics : Official journal of the Metabolomic Society》2008,4(2):122-127
Nuclear magnetic resonance (NMR)-based metabolic profiling of biofluids and tissues are of key interest to enhance biomarker
discovery for disease, drug efficacy and toxicity studies. Urine and blood plasma/serum are the biofluids of most interest
as they are the most accessible in both clinical and preclinical studies. However, proteinaceous fluids, such as blood serum
or plasma, represent the greatest technical challenge since the chemical shift (δ) and line-width (ν1/2) of internal standards currently used for aqueous NMR samples are greatly affected by protein binding. We have therefore
investigated the suitability of 4,4-dimethyl-4-silapentane-1-ammonium trifluoroacetate (DSA) as a universal internal standard
for biofluids. Proton (1H) NMR spectroscopy was used to determine the effect of serum pH (3, 7.4 and 10) and DSA concentration on the overall lineshape
and position of the trimethylsilyl resonance of DSA. The results were compared to that of 3-(trimethylsilyl)propionic acid
sodium salt (TSP). Both the chemical shift and line-width of the DSA peak were not significantly affected by pH or DSA concentration,
whereas these parameters for TSP showed large variations due to protein binding. Furthermore, the peak area of DSA correlated
linearly with its concentration under all pH conditions, whilst no linear correlation was observed with TSP. Overall, in contrast
to TSP, these results support the use of DSA as an accurate universal internal chemical shift reference and concentration/normalisation
standard for biofluids. In the case of proteinaceous biofluids such as serum, where no current standard is available, this
offers a considerable saving in both operator and spectrometer time. 相似文献
5.
3-Nitropropionic acid (3-NP)-induced neurotoxicity can be used as a model for the genetic neurodegenerative disorder Huntington’s
disease (HD). A metabolic profiling strategy was adopted to explore the biochemical consequences of 3-NP administered to rats
in specific brain regions. 1H NMR spectroscopy was used to characterize the metabolite composition of several brain regions following 3-NP-intoxication.
Dose-dependent increases in succinate levels were observed in all neuroanatomical regions, resulting from the 3-NP-induced
inhibition of succinate dehydrogenase. Global decreases in taurine and GABA were observed in the majority of brain regions,
whereas altered lipid profiles were observed only in the globus pallidus and dorsal striatum. Depleted phosphatidylcholine
and elevated glycerol levels, which are indicative of apoptosis, were also observed in the frontal cortex of the 3-NP model.
Many of the metabolic anomalies are consistent with those reported in HD. The 3-NP-induced model of HD provides a means of
monitoring potential mechanisms of pathology and therapeutic response for drug interventions, which can be efficiently assessed
using metabolic profiling strategies. 相似文献
6.
Lindon JC Nicholson JK Holmes E Keun HC Craig A Pearce JT Bruce SJ Hardy N Sansone SA Antti H Jonsson P Daykin C Navarange M Beger RD Verheij ER Amberg A Baunsgaard D Cantor GH Lehman-McKeeman L Earll M Wold S Johansson E Haselden JN Kramer K Thomas C Lindberg J Schuppe-Koistinen I Wilson ID Reily MD Robertson DG Senn H Krotzky A Kochhar S Powell J van der Ouderaa F Plumb R Schaefer H Spraul M;Standard Metabolic Reporting Structures working group 《Nature biotechnology》2005,23(7):833-838
7.
Waters NJ Garrod S Farrant RD Haselden JN Connor SC Connelly J Lindon JC Holmes E Nicholson JK 《Analytical biochemistry》2000,282(1):16-23
High-resolution magic angle spinning (MAS) (1)H NMR spectroscopy has been used to investigate the biochemical composition of whole rat renal cortex and liver tissue samples. The effects of a number of sample preparation procedures and experimental variables have been investigated systematically in order to optimize spectral quality and maximize information recovery. These variables include the effects of changing the sample volume in the MAS rotor, snap-freezing the samples, and the effect of organ perfusion with deuterated saline solution prior to MAS NMR analysis. Also, the overall biochemical stability of liver and kidney tissue MAS NMR spectra was investigated under different temperature conditions. We demonstrate improved resolution and line shape of MAS NMR spectra obtained from small spherical tissue volume (12 microl) rotor inserts compared to 65 microl cylindrical samples directly inserted into the MAS rotors. D(2)O saline perfusion of the in situ afferent vascular tree of the tissue immediately postmortem also improves line shape in MAS NMR spectra. Snap-freezing resulted in increased signal intensities from alpha-amino acids (e.g., valine) in tissue together with decreases in renal osmolytes, such as myo-inositol. A decrease in triglyceride levels was observed in renal cortex following stasis on ice and in the MAS rotor (303 K for 4 h). This work indicates that different tissues have differential metabolic stabilities in (1)H MAS NMR experiments and that careful attention to sample preparation is required to minimize artifacts and maintain spectral quality. 相似文献
8.
JN Matthiessen 《Australian Journal of Entomology》1999,38(4):348-353
In field and laboratory studies, mortality of African black beetle, Heteronychus arator, in the winter-rainfall, Mediterranean-type climate region of south-western Australia was higher in the late immature stages during summer than in the early immature stages that occur during spring, a contrast to summer-rainfall climatic regions. Greatest mortality occurred around the pupal stage in contrasting soil types, despite drying differences in summer and supplementary watering in some plots. Sampling of natural populations confirmed experimental results that mortality in late immature stages is the major factor limiting H. arator populations under a Mediterranean-type climate. Inter-generation increase in H. arator abundance was uncommon, explaining the consistent abundance typically observed between years in south-western Australia. Random dispersal of newly emerged adults in autumn was inferred to restore uniformity in adult abundance between areas of varying favourability for immature survival. 相似文献
9.
Susan C Connor Mark P Hodson Stephanie Ringeissen Brian C Sweatman Paul J McGill Catherine J Waterfield John N Haselden 《Biomarkers》2004,9(4-5):364-385
A previous report of this work (Ringeissen et al. 2003) described the use of nuclear magnetic resonance (NMR) spectroscopy coupled with multivariate statistical data analysis (MVDA) to identify novel biomarkers of peroxisome proliferation (PP) in Wistar Han rats. Two potential biomarkers of peroxisome proliferation in the rat were described, N-methylnicotinamide (NMN) and N-methyl-4-pyridone-3-carboxamide (4PY). The inference from these results was that the tryptophan-nicotinamide adenine dinucleotide (NAD(+)) pathway was altered in correlation with peroxisome proliferation, a hypothesis subsequently confirmed by TaqMan analysis of the relevant genes encoding two key enzymes in the pathway, aminocarboxymuconate-semialdehyde decarboxylase (EC 4.1.1.45) and quinolinate phosphoribosyltransferase (EC 2.4.2.19). The objective of the present study was to investigate these data further and identify other metabolites in the NMR spectrum correlating equally with PP. MVDA Partial Least Squares (PLS) models were constructed that provided a better prediction of PP in Wistar Han rats than levels of 4PY and NMN alone. The resulting Wistar Han rat predictive models were then used to predict PP in a test group of Sprague Dawley rats following administration of fenofibrate. The models predicted the presence or absence of PP (above on arbitrary threshold of >2-fold mean control) in all Sprague Dawley rats in the test group. 相似文献
10.
BRCA1 C-terminal (BRCT) domains are integral signaling modules in the DNA damage response (DDR). Aside from their established roles as phospho-peptide binding modules, BRCT domains have been implicated in phosphorylation-independent protein interactions, DNA binding and poly(ADP-ribose) (PAR) binding. These numerous functions can be attributed to the diversity in BRCT domain structure and architecture, where domains can exist as isolated single domains or assemble into higher order homo- or hetero-domain complexes. In this review, we incorporate recent structural and biochemical studies to demonstrate how structural features allow single and tandem BRCT domains to attain a high degree of functional diversity.Key words: BRCT domain, DNA repair, phosphorylation, phospho-peptide interaction, protein interaction, DNA binding, DNA damage response 相似文献