Multiple realization and multiple “ways” of realization: A progress report

One might have thought that if something has two or more distinct realizations, then that thing is multiply realized. Nevertheless, some philosophers have claimed that two or more distinct realizations do not amount to multiple realization, unless those distinct realizations amount to multiple “ways” of realizing the thing. Corey Maley, Gualtiero Piccinini, Thomas Polger, and Lawrence Shapiro are among these philosophers. Unfortunately, they do not explain why multiple realization requires multiple “ways” of realizing. More significantly, their efforts to articulate multiple “ways” of realizing turn out to be problematic.     

Distribution and three-dimensional structure of AIDS virus envelope spikes

Envelope glycoprotein (Env) spikes on AIDS retroviruses initiate infection of host cells and are therefore targets for vaccine development. Though crystal structures for partial Env subunits are known, the structure and distribution of native Env spikes on virions is obscure. We applied cryoelectron microscopy tomography to define ultrastructural details of spikes. Virions of wild-type human immunodeficiency virus 1 (HIV-1) and a mutant simian immunodeficiency virus (SIV) had approximately 14 and approximately 73 spikes per particle, respectively, with some clustering of HIV-1 spikes. Three-dimensional averaging showed that the surface glycoprotein (gp120) 'head' of each subunit of the trimeric SIV spike contains a primary mass, with two secondary lobes. The transmembrane glycoprotein 'stalk' of each trimer is composed of three independent legs that project obliquely from the trimer head, tripod-like. Reconciling available atomic structures with the three-dimensional whole spike density map yields insights into the orientation of Env spike structural elements and possible structural bases of their functions.     

Molecular architecture of axonemal microtubule doublets revealed by cryo-electron tomography

The axoneme, which forms the core of eukaryotic flagella and cilia, is one of the largest macromolecular machines, with a structure that is largely conserved from protists to mammals. Microtubule doublets are structural components of axonemes that contain a number of proteins besides tubulin, and are usually found in arrays of nine doublets arranged around two singlet microtubules. Coordinated sliding of adjacent doublets, which involves a host of other proteins in the axoneme, produces periodic beating movements of the axoneme. We have obtained a three-dimensional density map of intact microtubule doublets using cryo-electron tomography and image averaging. Our map, with a resolution of about 3 nm, provides insights into locations of particular proteins within the doublets and the structural features of the doublets that define their mechanical properties. We identify likely candidates for several of these non-tubulin components of the doublets. This work offers insight on how tubulin protofilaments and accessory proteins attach together to form the doublets and provides a structural basis for understanding doublet function in axonemes.     

Stratified prokaryote network in the oxic-anoxic transition of a deep-sea halocline

The chemical composition of the Bannock basin has been studied in some detail. We recently showed that unusual microbial populations, including a new division of Archaea (MSBL1), inhabit the NaCl-rich hypersaline brine. High salinities tend to reduce biodiversity, but when brines come into contact with fresher water the natural haloclines formed frequently contain gradients of other chemicals, including permutations of electron donors and acceptors, that may enhance microbial diversity, activity and biogeochemical cycling. Here we report a 2.5-m-thick chemocline with a steep NaCl gradient at 3.3 km within the water column betweeen Bannock anoxic hypersaline brine and overlying sea water. The chemocline supports some of the most biomass-rich and active microbial communities in the deep sea, dominated by Bacteria rather than Archaea, and including four major new divisions of Bacteria. Significantly higher metabolic activities were measured in the chemocline than in the overlying sea water and underlying brine; functional analyses indicate that a range of biological processes is likely to occur in the chemocline. Many prokaryotic taxa, including the phylogenetically new groups, were confined to defined salinities, and collectively formed a diverse, sharply stratified, deep-sea ecosystem with sufficient biomass to potentially contribute to organic geological deposits.     

The distillation and volatility of ionic liquids

It is widely believed that a defining characteristic of ionic liquids (or low-temperature molten salts) is that they exert no measurable vapour pressure, and hence cannot be distilled. Here we demonstrate that this is unfounded, and that many ionic liquids can be distilled at low pressure without decomposition. Ionic liquids represent matter solely composed of ions, and so are perceived as non-volatile substances. During the last decade, interest in the field of ionic liquids has burgeoned, producing a wealth of intellectual and technological challenges and opportunities for the production of new chemical and extractive processes, fuel cells and batteries, and new composite materials. Much of this potential is underpinned by their presumed involatility. This characteristic, however, can severely restrict the attainability of high purity levels for ionic liquids (when they contain poorly volatile components) in recycling schemes, as well as excluding their use in gas-phase processes. We anticipate that our demonstration that some selected families of commonly used aprotic ionic liquids can be distilled at 200-300 degrees C and low pressure, with concomitant recovery of significant amounts of pure substance, will permit these currently excluded applications to be realized.     

Transiting extrasolar planetary candidates in the Galactic bulge

More than 200 extrasolar planets have been discovered around relatively nearby stars, primarily through the Doppler line shifts owing to reflex motions of their host stars, and more recently through transits of some planets across the faces of the host stars. The detection of planets with the shortest known periods, 1.2-2.5 days, has mainly resulted from transit surveys which have generally targeted stars more massive than 0.75 M(o), where M(o) is the mass of the Sun. Here we report the results from a planetary transit search performed in a rich stellar field towards the Galactic bulge. We discovered 16 candidates with orbital periods between 0.4 and 4.2 days, five of which orbit stars of masses in the range 0.44-0.75 M(o). In two cases, radial-velocity measurements support the planetary nature of the companions. Five candidates have orbital periods below 1.0 day, constituting a new class of ultra-short-period planets, which occur only around stars of less than 0.88 M(o). This indicates that those orbiting very close to more-luminous stars might be evaporatively destroyed or that jovian planets around stars of lower mass might migrate to smaller radii.     

双循环，对集和树

令Ｇ＝（Ｖ，Ｅ）为一个图，它的节点数为ｎ，不仅是一个双循环也是一个上循环．记β（Ｇ）为Ｇ的双循环空间的维数．对于Ｇ的一个子图Ｈ，用φ（Ｇ，Ｈ）表示Ｇ的支撑森数目，使得它的每个树均恰含Ｈ的一条边．图Ｇ的Ｈ扩张Ｘ（Ｇ，Ｈ）在Ｇ上增添一个新节点ν，连ν与Ｈ的每一个奇次节点以一边所得到的图．本文证明，φ（Ｇ，Ｈ）是个偶数，要么Ｘ（Ｇ，Ｈ）不连通，要么Ｘ（Ｇ，Ｈ）有一个非零双循环．对于一个欧拉图Ｇ，令λ（Ｇ）为Ｇ中这样边的最小数目，使得在将它们从Ｇ中收缩掉而得到的图Ｇ中，所有那些落在奇数个完满对集上的边，形成一个非零双循环．同时还得到，在Ｇ的最大对集中边数为μ（Ｇ）的一个下界，即μ（Ｇ）≥（ｎ－｜β（Ｇ）－１｜）／２．对于非欧拉图Ｇ，令ψ（Ｇ）＝β（Ｘ（Ｇ，Ｇ）），和用γ（Ｇ）表示这样边的最小数目，使得在将它们从Ｇ中收缩掉而得到的图上，有边属于奇数个完满对集．我们证明，γ（Ｇ）＝ψ（Ｇ）以及μ（Ｇ）≥（ｎ－ψ（Ｇ））／２．     

In situ analyses of genome instability in breast cancer

Transition through telomere crisis is thought to be a crucial event in the development of most breast carcinomas. Our goal in this study was to determine where this occurs in the context of histologically defined breast cancer progression. To this end, we assessed genome instability (using fluorescence in situ hybridization) and other features associated with telomere crisis in normal ductal epithelium, usual ductal hyperplasia, ductal carcinoma in situ and invasive cancer. We modeled this process in vitro by measuring these same features in human mammary epithelial cell cultures during ZNF217-mediated transition through telomere crisis and immortalization. Taken together, the data suggest that transition through telomere crisis and immortalization in breast cancer occurs during progression from usual ductal hyperplasia to ductal carcinoma in situ.