Increased methylation variation in epigenetic domains across cancer types

Tumor heterogeneity is a major barrier to effective cancer diagnosis and treatment. We recently identified cancer-specific differentially DNA-methylated regions (cDMRs) in colon cancer, which also distinguish normal tissue types from each other, suggesting that these cDMRs might be generalized across cancer types. Here we show stochastic methylation variation of the same cDMRs, distinguishing cancer from normal tissue, in colon, lung, breast, thyroid and Wilms' tumors, with intermediate variation in adenomas. Whole-genome bisulfite sequencing shows these variable cDMRs are related to loss of sharply delimited methylation boundaries at CpG islands. Furthermore, we find hypomethylation of discrete blocks encompassing half the genome, with extreme gene expression variability. Genes associated with the cDMRs and large blocks are involved in mitosis and matrix remodeling, respectively. We suggest a model for cancer involving loss of epigenetic stability of well-defined genomic domains that underlies increased methylation variability in cancer that may contribute to tumor heterogeneity.     

Genetic deficiency of tartrate-resistant acid phosphatase associated with skeletal dysplasia, cerebral calcifications and autoimmunity

Vertebral and metaphyseal dysplasia, spasticity with cerebral calcifications, and strong predisposition to autoimmune diseases are the hallmarks of the genetic disorder spondyloenchondrodysplasia. We mapped a locus in five consanguineous families to chromosome 19p13 and identified mutations in ACP5, which encodes tartrate-resistant phosphatase (TRAP), in 14 affected individuals and showed that these mutations abolish enzyme function in the serum and cells of affected individuals. Phosphorylated osteopontin, a protein involved in bone reabsorption and in immune regulation, accumulates in serum, urine and cells cultured from TRAP-deficient individuals. Case-derived dendritic cells exhibit an altered cytokine profile and are more potent than matched control cells in stimulating allogeneic T cell proliferation in mixed lymphocyte reactions. These findings shed new light on the role of osteopontin and its regulation by TRAP in the pathogenesis of common autoimmune disorders.     

The Accuracy of Non‐traditional versus Traditional Methods of Forecasting Lumpy Demand

Forecasting for inventory items with lumpy demand is difficult because of infrequent nonzero demands with high variability. This article developed two methods to forecast lumpy demand: an optimally weighted moving average method and an intelligent pattern‐seeking method. We compare them with a number of well‐referenced methods typically applied over the last 30 years in forecasting intermittent or lumpy demand. The comparison is conducted over about 200,000 forecasts (using 1‐day‐ahead and 5‐day‐ahead review periods) for 24 series of actual product demands across four different error measures. One of the most important findings of our study is that the two non‐traditional methods perform better overall than the traditional methods. We summarize results and discuss managerial implications. Copyright © 2011 John Wiley & Sons, Ltd.     

A large dust/ice ratio in the nucleus of comet 9P/Tempel 1

Comets spend most of their life in a low-temperature environment far from the Sun. They are therefore relatively unprocessed and maintain information about the formation conditions of the planetary system, but the structure and composition of their nuclei are poorly understood. Although in situ and remote measurements have derived the global properties of some cometary nuclei, little is known about their interiors. The Deep Impact mission shot a projectile into comet 9P/Tempel 1 in order to investigate its interior. Here we report the water vapour content (1.5 10(32) water molecules or 4.5 10(6) kg) and the cross-section of the dust (330 km2 assuming an albedo of 0.1) created by the impact. The corresponding dust/ice mass ratio is probably larger than one, suggesting that comets are 'icy dirtballs' rather than 'dirty snowballs' as commonly believed. High dust velocities (between 110 m s(-1) and 300 m s(-1)) imply acceleration in the comet's coma, probably by water molecules sublimated by solar radiation. We did not find evidence of enhanced activity of 9P/Tempel 1 in the days after the impact, suggesting that in general impacts of meteoroids are not the cause of cometary outbursts.     

In front of a mirror: visual displays may not be aggressive signals in nocturnal tree frogs

Some evidence indicates that in anuran amphibians, visual signalling can be important during social interactions such as territorial disputes among males, especially in diurnal species. The correct identification of a signal is not a trivial matter. A visual signal provides a visual cue during a social interaction, and to be effective it must elicit an immediate response in the receiver. We tested the hypothesis that visual displays in an agonistic context constitute aggressive signals, in three nocturnal species of Hylidae. We predicted that the production of visual displays would increase in the presence of a conspecific intruder male. Males of Hypsiboas raniceps, Dendropsophus nanus and Lysapsus limellum were submitted to two treatments: (1) Self Image, a reflection in a mirror, simulating the presence of an intruder; and (2) Control, a black rectangle covering the mirror. We observed three visual displays: vocal-sac display (inflate the vocal sac and maintain it inflated for some time), limb lifting (rapid up-and-down movements of one or more limbs), and toe/finger trembling (rapid up-and-down movements of one or more toes and/or fingers). This last display was observed only in H. raniceps males. Contrary to our hypothesis, the emission rates of all visual displays of the focal animals did not differ between treatments; and the behavioural response did not differ among species. Therefore, we suggest that these behaviours could not be used directly for communication in agonistic contexts, and may represent displacement activities (involuntary responses). Alternatively, an aggressive bimodal stimulus may be necessary to trigger a behavioural response by using visual signals during territory defence in these three species.     

Absence of effects of Sir2 overexpression on lifespan in C. elegans and Drosophila

Overexpression of sirtuins (NAD(+)-dependent protein deacetylases) has been reported to increase lifespan in budding yeast (Saccharomyces cerevisiae), Caenorhabditis elegans and Drosophila melanogaster. Studies of the effects of genes on ageing are vulnerable to confounding effects of genetic background. Here we re-examined the reported effects of sirtuin overexpression on ageing and found that standardization of genetic background and the use of appropriate controls abolished the apparent effects in both C. elegans and Drosophila. In C. elegans, outcrossing of a line with high-level sir-2.1 overexpression abrogated the longevity increase, but did not abrogate sir-2.1 overexpression. Instead, longevity co-segregated with a second-site mutation affecting sensory neurons. Outcrossing of a line with low-copy-number sir-2.1 overexpression also abrogated longevity. A Drosophila strain with ubiquitous overexpression of dSir2 using the UAS-GAL4 system was long-lived relative to wild-type controls, as previously reported, but was not long-lived relative to the appropriate transgenic controls, and nor was a new line with stronger overexpression of dSir2. These findings underscore the importance of controlling for genetic background and for the mutagenic effects of transgene insertions in studies of genetic effects on lifespan. The life-extending effect of dietary restriction on ageing in Drosophila has also been reported to be dSir2 dependent. We found that dietary restriction increased fly lifespan independently of dSir2. Our findings do not rule out a role for sirtuins in determination of metazoan lifespan, but they do cast doubt on the robustness of the previously reported effects of sirtuins on lifespan in C. elegans and Drosophila.     

In vivo imaging of Treg cells providing immune privilege to the haematopoietic stem-cell niche

Stem cells reside in a specialized regulatory microenvironment or niche, where they receive appropriate support for maintaining self-renewal and multi-lineage differentiation capacity. The niche may also protect stem cells from environmental insults including cytotoxic chemotherapy and perhaps pathogenic immunity. The testis, hair follicle and placenta are all sites of residence for stem cells and are immune-suppressive environments, called immune-privileged sites, where multiple mechanisms cooperate to prevent immune attack, even enabling prolonged survival of foreign allografts without immunosuppression. We sought to determine if somatic stem-cell niches more broadly are immune-privileged sites by examining the haematopoietic stem/progenitor cell (HSPC) niche in the bone marrow, a site where immune reactivity exists. We observed persistence of HSPCs from allogeneic donor mice (allo-HSPCs) in non-irradiated recipient mice for 30?days without immunosuppression with the same survival frequency compared to syngeneic HSPCs. These HSPCs were lost after the depletion of FoxP3 regulatory T (T(reg)) cells. High-resolution in vivo imaging over time demonstrated marked co-localization of HSPCs with T(reg) cells that accumulated on the endosteal surface in the calvarial and trabecular bone marrow. T(reg) cells seem to participate in creating a localized zone where HSPCs reside and where T(reg) cells are necessary for allo-HSPC persistence. In addition to processes supporting stem-cell function, the niche will provide a relative sanctuary from immune attack.     

清洁能源处理中的实验研究在工业放大的作用

实验室规模(小试规模)实验能够迅速的、廉价的完成.它们对于设计和发展中试规模和商业规模的实验设备是有帮助的,特别是当有问题需要解决时小试实验非常有用.这些设备可以提供不同燃料在不同的反应条件下的基础数据,帮助建立实验结果的趋势和发展新的设计.笔者简单回顾了实验室规模的丝网反应器和高压流化床反应器系统的设计和操作,基于这两个研究平台,能够进行各式热解、气化和燃烧方面的实验.这两套系统温度可达到2 000℃,压力达到150MPa.在小试实验上准确模拟中试和工业规模设备上的条件需要精心设计.笔者试图综述在设计实验规模和设备上所面对的挑战,这其中固体燃料(包括可再生和化石燃料)的热过程扮演了一个重要的角色.重点放在特征化固体燃料潜在的自身行为上,关于样品或反应器结构几乎没有任何可参考的文献.本文将讨论几个实例.首先是关于"中国煤在气流床条件下的反应性和可操作性"的研究项目,该项目由中国科技部和英国贸工部联合资助,由西安热工研究院和伦敦帝国理工学院执行.我们在西安热工研究院新的两段式气流床气化炉上比较了不同中国煤样的反应性.实验在一高压丝网反应器上进行,反应条件为氦气气氛、3 MPa、2 000℃,或CO2气氛下温度为1 500℃;用热天平测定剩余焦的相关反应性,这两种方法被证明对于气流床中煤的行为研究有效.发现1 500℃以上足以气化绝大多数合适的煤--但并不能气化所有煤样.在两段式气化炉中,较高反应活性的煤可在温度较低的上段反应.另外一个高压丝网反应器的应用是估计鼓风炉的鼓风口和通道上所注入煤颗粒的燃烧程度.可以测定在鼓风口和通道上煤燃尽的程度,得到煤在空气鼓风处的燃烧动力学.作为反应条件和水蒸气的输入速率的函数,一个直径34 mm的高压流化床反应器被用于监测在煤和生物质气化过程中氨的形成,得出了水蒸气浓度和氨形成速率关系.在生物质热化学过程中,描述了一个在小型反应器上的实验,该反应器能够提供焦油破坏趋势的数据,该结果解决了下吸式生物质气化炉的主要操作问题之一.结论:对于在可再生能源生物质和煤等其它化石燃料的洁净转化过程中发展新技术,还有许多尚待研究的问题.这些问题中的大多数都可以凭借实验室规模的反应器研究得到有效、快速和廉价的解决.小型反应器实验研究可用于如下领域:诊断产品及其趋势;焦油的产生和/或破坏;反应器的效率和燃料的反应性;氨的去除,HCN和有毒微量元素的释放;钙基固相沉积物检测.     

Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK

First identified as histone-modifying proteins, lysine acetyltransferases (KATs) and deacetylases (KDACs) antagonize each other through modification of the side chains of lysine residues in histone proteins. Acetylation of many non-histone proteins involved in chromatin, metabolism or cytoskeleton regulation were further identified in eukaryotic organisms, but the corresponding enzymes and substrate-specific functions of the modifications are unclear. Moreover, mechanisms underlying functional specificity of individual KDACs remain enigmatic, and the substrate spectra of each KDAC lack comprehensive definition. Here we dissect the functional specificity of 12 critical human KDACs using a genome-wide synthetic lethality screen in cultured human cells. The genetic interaction profiles revealed enzyme-substrate relationships between individual KDACs and many important substrates governing a wide array of biological processes including metabolism, development and cell cycle progression. We further confirmed that acetylation and deacetylation of the catalytic subunit of the adenosine monophosphate-activated protein kinase (AMPK), a critical cellular energy-sensing protein kinase complex, is controlled by the opposing catalytic activities of HDAC1 and p300. Deacetylation of AMPK enhances physical interaction with the upstream kinase LKB1, leading to AMPK phosphorylation and activation, and resulting in lipid breakdown in human liver cells. These findings provide new insights into previously underappreciated metabolic regulatory roles of HDAC1 in coordinating nutrient availability and cellular responses upstream of AMPK, and demonstrate the importance of high-throughput genetic interaction profiling to elucidate functional specificity and critical substrates of individual human KDACs potentially valuable for therapeutic applications.