Algorithmic compression of empirical data: reply to Twardy, Gardner, and Dowe

This discussion note responds to objections by Twardy, Gardner, and Dowe to my earlier claim that empirical data sets are algorithmically incompressible. Twardy, Gardner, and Dowe hold that many empirical data sets are compressible by Minimum Message Length technique and offer this as evidence that these data sets are algorithmically compressible. I reply that the compression achieved by Minimum Message Length technique is different from algorithmic compression. I conclude that Twardy, Gardner, and Dowe fail to establish that empirical data sets are algorithmically compressible.     

Studies on muscle fibre splitting in skeletal muscle

Summary Autoradiographic, stereological and histological studies have been carried out to determine the origin of muscle fibre splitting which supposedly occurs during muscle hypertrophy. The results obtained clearly indicate that the supposedly split fibres are a transient response probably derived from satellite cells and are not derived from pre-existing fibres by true splitting. Similarly, increases in muscle fibre size are not achieved by recruitment of satellite structures as indicated by lack of myonuclear recruitment.Acknowledgment. This work was carried out with the aid of a grant from the Medical Research Council of Great Britain. The authors are grateful for the excellent technical assistance of Miss H. Caulton, M.J. Wild and M. Fenner.     

Structure,biosynthesis and functions of glycoprotein glycans

Since the pioneering work on structure and function of heteroglycans compiled in the classical books edited by A. Gottschalk in 1972¹, there have been several promising developments in glycoconjugate research, as reviewed in this article.In Part 1, contributed by A. Kobata, current knowledge on heteroglycan structures is presented and representative examples taken from higher organisms are given. Part 2, written by J. F. G. Vliegenthart and J. P. Kamerling, covers the most important achievements in methodology: procedures to obtain pure glycans and to analyze their structures. Part 3, contributed by J. Paulson, is devoted to biosynthesis of glycans now describable as pathways since several of the glycosyltransferases have been isolated and analyzed for specificity. In Part 4, contributed by E. Buddecke, current knowledge on functional roles of glycans is presented. It will become apparent that the prerequisite for valid work either in biosynthetic or functional context depends on solid structural information. This is particularly true whenever glycosyltransferase reaction products are being analyzed, or glycans involved in biological functions are investigated. Although in past years, a great deal of important knowledge has been gathered by use of crude glycosidase or glycosyltransferase activities (a notable example is found in reference 2), one may now postulate that glycans implicated in biological reactions should be thoroughly analyzed.This review may familiarize newcomers with the field of glycoconjugate research with special emphasis on glycoprotein glycans. Glycolipids are not included in this article as they have recently been reviewed by S. I. Hakomori³. The reader is also referred to several excellent monographs^4,5 and the Proceedings of the Glycoconjugate Symposia held biannually^6–8.     

Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration

We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically interpreted translocations and inversions. We confirm that the recently described phenomenon of 'chromothripsis' (massive chromosomal shattering and reorganization) is not unique to cancer cells but also occurs in the germline, where it can resolve to a relatively balanced state with frequent inversions. We detected a high incidence of complex rearrangements (19.2%) and substantially less reliance on microhomology (31%) than previously observed in benign copy-number variants (CNVs). We compared these results to experimentally generated DNA breakage-repair by sequencing seven transgenic animals, revealing extensive rearrangement of the transgene and host genome with similar complexity to human germline alterations. Inversion was the most common rearrangement, suggesting that a combined mechanism involving template switching and non-homologous repair mediates the formation of balanced complex rearrangements that are viable, stably replicated and transmitted unaltered to subsequent generations.     

Anthropogenic ocean acidification over the twenty-first century and its impact on calcifying organisms

Today's surface ocean is saturated with respect to calcium carbonate, but increasing atmospheric carbon dioxide concentrations are reducing ocean pH and carbonate ion concentrations, and thus the level of calcium carbonate saturation. Experimental evidence suggests that if these trends continue, key marine organisms--such as corals and some plankton--will have difficulty maintaining their external calcium carbonate skeletons. Here we use 13 models of the ocean-carbon cycle to assess calcium carbonate saturation under the IS92a 'business-as-usual' scenario for future emissions of anthropogenic carbon dioxide. In our projections, Southern Ocean surface waters will begin to become undersaturated with respect to aragonite, a metastable form of calcium carbonate, by the year 2050. By 2100, this undersaturation could extend throughout the entire Southern Ocean and into the subarctic Pacific Ocean. When live pteropods were exposed to our predicted level of undersaturation during a two-day shipboard experiment, their aragonite shells showed notable dissolution. Our findings indicate that conditions detrimental to high-latitude ecosystems could develop within decades, not centuries as suggested previously.     

Angiotensin-converting enzyme 2 is an essential regulator of heart function

Cardiovascular diseases are predicted to be the most common cause of death worldwide by 2020. Here we show that angiotensin-converting enzyme 2 (ace2) maps to a defined quantitative trait locus (QTL) on the X chromosome in three different rat models of hypertension. In all hypertensive rat strains, ACE2 messenger RNA and protein expression were markedly reduced, suggesting that ace2 is a candidate gene for this QTL. Targeted disruption of ACE2 in mice results in a severe cardiac contractility defect, increased angiotensin II levels, and upregulation of hypoxia-induced genes in the heart. Genetic ablation of ACE on an ACE2 mutant background completely rescues the cardiac phenotype. But disruption of ACER, a Drosophila ACE2 homologue, results in a severe defect of heart morphogenesis. These genetic data for ACE2 show that it is an essential regulator of heart function in vivo.     

四生散对肺癌细胞增殖的抑制作用及毒性研究

主要探讨中药制剂四生散对人肺癌A5 4 9细胞株的增殖抑制作用以及其急性毒性.应用改进的MTT法测定四生散对肺癌细胞增殖的影响;采用琼脂糖凝胶电泳测定四生散对诱导肿瘤细胞凋亡的影响;再用分剂量组灌胃小鼠的方法,鉴定四生散的急性毒性.实验结果表明,四生散对人肺癌A5 4 9细胞株的增殖有较强的抑制作用,并具有明显的量效和时效相关性;经四生散处理后的A5 4 9细胞呈现凋亡特征性电泳条带;在3 2倍于人的剂量时,小鼠饮食和体重均在正常水平,并无异常,证实口服四生散无急性毒性.     

Genome sequencing in microfabricated high-density picolitre reactors

The proliferation of large-scale DNA-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. Here we describe a scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments. The apparatus uses a novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99% or better accuracy, in one four-hour run. To achieve an approximately 100-fold increase in throughput over current Sanger sequencing technology, we have developed an emulsion method for DNA amplification and an instrument for sequencing by synthesis using a pyrosequencing protocol optimized for solid support and picolitre-scale volumes. Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine.