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61.
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Christopher Yau Dmitri Mouradov Robert N Jorissen Stefano Colella Ghazala Mirza Graham Steers Adrian Harris Jiannis Ragoussis Oliver Sieber Christopher C Holmes 《Genome biology》2010,11(9):R92
We describe a statistical method for the characterization of genomic aberrations in single nucleotide polymorphism microarray
data acquired from cancer genomes. Our approach allows us to model the joint effect of polyploidy, normal DNA contamination
and intra-tumour heterogeneity within a single unified Bayesian framework. We demonstrate the efficacy of our method on numerous
datasets including laboratory generated mixtures of normal-cancer cell lines and real primary tumours. 相似文献
63.
J. W. Breneman P. M. Yau R. R. Swiger R. Teplitz H. A. Smith J. D. Tucker E. M. Bradbury 《Chromosoma》1996,105(1):41-49
The expression of genes in mammalian cells depends on many factors including position in the cell cycle, stage of differentiation,
age, and environmental influences. As different groups of genes are expressed, their packaging within chromatin changes and
may be detected at the chromsomal level. The organization of DNA within a chromosome is determined to a large extent by the
positively charged, highly conserved histones. Histone subtypes and the reversible chemical modifications of histones have
been associated with gene activity. Active or potentially active genes have been associated with hyperacetylated histones
and inactive genes with nonacetylated histones. Sodium butyrate increases the acetylation levels of histones in cell cultures
and acts as both an inducer of gene activity and as a cell-cycle block. We describe a method to label the interphase distribution
of DNA associated with various histone acetylation stages on chromosomes. Nucleosomes from untreated and butyrate-treated
HeLa cells were fractionated by their acetylation level and the associated DNA labeled, and hybridized to normal human chromosomes.
In the sodium butyrate-treated cells the resulting banding patterns of the high- and low-acetylated fractions were strikingly
different. DNA from low-acetylated chromatin labeled several pericentric regions, whereas hybridization with DNA from highly
acetylated chromatin resulted in a pattern similar to inverse G-bands on many chromsomes. The results from noninduced cells
at both high and low acetylation levels were noticeably different from their induced counterparts. The capture and hybridization
of DNA from interphase chromatin at different acetylation states provides a “snap-shot” of the distribution of gene activity
on chromosomes at the time of cell harvest.
Edited by: P.B. Moens 相似文献
64.
HengLiang Wu Le Yu Yujin Tong Aimin Ge Shuehlin Yau Masatoshi Osawa Shen Ye 《生物化学与生物物理学报:生物膜》2013,1828(2):642-651
Atomic force microscopy (AFM) is employed to reveal the morphological changes of the supported phospholipid bilayers hydrolyzed by a phospholipase A2 (PLA2) enzyme in a buffer solution at room temperature. Based on the high catalytic selectivity of PLA2 toward l-enantiomer phospholipids, five kinds of supported bilayers made of l- and d-dipalmitoylphosphatidylcholines (DPPC), including l-DPPC (upper leaflet adjacent to solution)/l-DPPC (bottom leaflet) (or l/l in short), l/d, d/l, d/d, and racemic ld/ld, were prepared on a mica surface in gel-phase, to explicate the kinetics and mechanism of the enzyme-induced hydrolysis reaction in detail. AFM observations for the l/l bilayer show that the hydrolysis rate for l-DPPC is significantly increased by PLA2 and most of the hydrolysis products desorb from substrate surface in 40 min. As d-enantiomers are included in the bilayer, the hydrolysis rate is largely decreased in comparison with the l/l bilayer. The time used to hydrolyze the as-prepared bilayers by PLA2 increases in the sequence of l/l, l/d, ld/ld, and d/l (d/d is inert to the enzyme action). d-enantiomers in the enantiomer hybrid bilayers remain on the mica surface at the end of the hydrolysis reaction. It was confirmed that the hydrolysis reaction catalyzed by PLA2 preferentially occurs at the edges of pits or defects on the bilayer surface. The bilayer structures are preserved during the hydrolysis process. Based on these observations, a novel kinetics model is proposed to quantitatively account for the PLA2-catalyzed hydrolysis of the supported phospholipid bilayers. The model simulation demonstrates that PLA2 mainly binds with lipids at the perimeter of defects in the upper leaflet and leads to a hydrolysis reaction, yielding species soluble to the solution phase. The lipid molecules underneath subsequently flip up to the upper leaflet to maintain the hydrophilicity of the bilayer structure. Our analysis shows that d-enantiomers in the hybrid bilayers considerably reduce the hydrolysis rate by its ineffective binding with PLA2. 相似文献
65.
66.
I. G. Priede L. M. Williams H.-J. Wagner A. Thom I. Brierley M. A. Collins S. P. Collin N. R. Merrett C. Yau 《Proceedings. Biological sciences / The Royal Society》1999,266(1435):2295
Relative eye size, gross brain morphology and central localization of 2-[125I]iodomelatonin binding sites and melatonin receptor gene expression were compared in six gadiform fish living at different depths in the north-east Atlantic Ocean: Phycis blennoides (capture depth range 265 to 1260 m), Nezumia aequalis (445 to 1512 m), Coryphaenoides rupestris (706 to 1932 m), Trachyrincus murrayi (1010 to 1884 m), Coryphaenoides guentheri (1030 m) and Coryphaenoides (Nematonurus) armatus (2172 to 4787 m). Amongst these, the eye size range was 0.15 to 0.35 of head length with a value of 0.19 for C. (N.) armatus, the deepest species. Brain morphology reflected behavioural differences with well-developed olfactory regions in P. blennoides, T. murrayi and C. (N.) armatus and evidence of olfactory deficit in N. aequalis, C. rupestris and C. guentheri. All species had a clearly defined optic tectum with 2-[125I]iodomelatonin binding and melatonin receptor gene expression localized to specific brain regions in a similar pattern to that found in shallow-water fish. Melatonin receptors were found throughout the visual structures of the brains of all species. Despite living beyond the depth of penetration of solar light these fish have retained central features associated with the coupling of cycles of growth, behaviour and reproduction to the diel light–dark cycle. How this functions in the deep sea remains enigmatic. 相似文献
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69.
A thioredoxin NbTRXh2 from Nicotiana benthamiana negatively regulates the movement of Bamboo mosaic virus 下载免费PDF全文
I‐Hsuan Chen Hui‐Ting Chen Ying‐Ping Huang Hui‐Chen Huang Lin‐Ling Shenkwen Yau‐Heiu Hsu Ching‐Hsiu Tsai 《Molecular Plant Pathology》2018,19(2):405-417
An up‐regulated gene derived from Bamboo mosaic virus (BaMV)‐infected Nicotiana benthamiana plants was cloned and characterized in this study. BaMV is a single‐stranded, positive‐sense RNA virus. This gene product, designated as NbTRXh2, was matched with sequences of thioredoxin h proteins, a group of small proteins with a conserved active‐site motif WCXPC conferring disulfide reductase activity. To examine how NbTRXh2 is involved in the infection cycle of BaMV, we used the virus‐induced gene silencing technique to knock down NbTRXh2 expression in N. benthamiana and inoculated the plants with BaMV. We observed that, compared with control plants, BaMV coat protein accumulation increased in knockdown plants at 5 days post‐inoculation (dpi). Furthermore, BaMV coat protein accumulation did not differ significantly between NbTRXh2‐knockdown and control protoplasts at 24 hpi. The BaMV infection foci in NbTRXh2‐knockdown plants were larger than those in control plants. In addition, BaMV coat protein accumulation decreased when NbTRXh2 was transiently expressed in plants. These results suggest that NbTRXh2 plays a role in restricting BaMV accumulation. Moreover, confocal microscopy results showed that NbTRXh2‐OFP (NbTRXh2 fused with orange fluorescent protein) localized at the plasma membrane, similar to AtTRXh9, a homologue in Arabidopsis. The expression of the mutant that did not target the substrates failed to reduce BaMV accumulation. Co‐immunoprecipitation experiments revealed that the viral movement protein TGBp2 could be the target of NbTRXh2. Overall, the functional role of NbTRXh2 in reducing the disulfide bonds of targeting factors, encoded either by the host or virus (TGBp2), is crucial in restricting BaMV movement. 相似文献
70.
Activation of hypothalamic RIP‐Cre neurons promotes beiging of WAT via sympathetic nervous system 下载免费PDF全文
Baile Wang Ang Li Xiaomu Li Philip WL Ho Donghai Wu Xiaoqi Wang Zhuohao Liu Kelvin KL Wu Sonata SY Yau Aimin Xu Kenneth KY Cheng 《EMBO reports》2018,19(4)
Activation of brown adipose tissue (BAT) and beige fat by cold increases energy expenditure. Although their activation is known to be differentially regulated in part by hypothalamus, the underlying neural pathways and populations remain poorly characterized. Here, we show that activation of rat‐insulin‐promoter‐Cre (RIP‐Cre) neurons in ventromedial hypothalamus (VMH) preferentially promotes recruitment of beige fat via a selective control of sympathetic nervous system (SNS) outflow to subcutaneous white adipose tissue (sWAT), but has no effect on BAT. Genetic ablation of APPL2 in RIP‐Cre neurons diminishes beiging in sWAT without affecting BAT, leading to cold intolerance and obesity in mice. Such defects are reversed by activation of RIP‐Cre neurons, inactivation of VMH AMPK, or treatment with a β3‐adrenergic receptor agonist. Hypothalamic APPL2 enhances neuronal activation in VMH RIP‐Cre neurons and raphe pallidus, thereby eliciting SNS outflow to sWAT and subsequent beiging. These data suggest that beige fat can be selectively activated by VMH RIP‐Cre neurons, in which the APPL2–AMPK signaling axis is crucial for this defending mechanism to cold and obesity. 相似文献