Species of Borrelia distinguished by restriction site polymorphisms in 16S rRNA genes

Abstract Three phyletic groups of Borrelia associated with Lyme disease, B. burgdorferi, B. garinii and group VS461 can be distinguished from each other and other species of Borrelia by Bfa I restriction site polymorphisms in PCR amplified 16S rRNA genes. One strain isolated from an Ixodes pacificus tick in California that was previously unclassifiable was distinguishable from B. burgdorferi by an Mnl I restriction site polymorphism.     

Solvent‐dependent conformation of a regioselective amylose carbamate: Amylose‐2‐acetyl‐3,6‐bis(phenylcarbamate)

Six amylose‐2‐acetyl‐3,6‐bis(phenylcarbamate) (AAPC) samples ranging in weight‐average molar mass M_w from 1.8 × 10⁴ g mol^?1 to 1.1 × 10⁶ g mol^?1 have been prepared from enzymatically synthesized amylose samples. Static light scattering, small‐angle X‐ray scattering, sedimentation equilibrium, and viscosity measurements were made for the samples in 1,4‐dioxane (DIOX), 2‐ethoxyethanol (2EE), and 2‐butanone (MEK) all at 25°C to determine particle scattering functions, z‐average radii of gyration, intrinsic viscosities, as well as M_w. The data were analyzed in terms of the wormlike cylinder model mainly to yield the helix pitch per residue h and the Kuhn segment length λ^?1, which corresponds to twice of the persistence length. The latter parameters (λ^?1) in 2EE (11 nm) and MEK (12 nm) are quite smaller than those for amylose tris(phenylcarbamate) (ATPC) in the same solvent (16 nm in 2EE and 18 nm in MEK) whereas those for AAPC (21 nm) and ATPC (22 nm) in DIOX are essentially the same as each other. This indicates that the chain stiffness of AAPC is more strongly influenced by the solvents since the number of intramolecular H‐bonds of AAPC is more changeable than that for ATPC. © 2012 Wiley Periodicals, Inc. Biopolymers 97:1010–1017, 2012.     

Birds are tracking climate warming, but not fast enough

Range shifts of many species are now documented as a response to global warming. But whether these observed changes are occurring fast enough remains uncertain and hardly quantifiable. Here, we developed a simple framework to measure change in community composition in response to climate warming. This framework is based on a community temperature index (CTI) that directly reflects, for a given species assemblage, the balance between low- and high-temperature dwelling species. Using data from the French breeding bird survey, we first found a strong increase in CTI over the last two decades revealing that birds are rapidly tracking climate warming. This increase corresponds to a 91 km northward shift in bird community composition, which is much higher than previous estimates based on changes in species range edges. During the same period, temperature increase corresponds to a 273 km northward shift in temperature. Change in community composition was thus insufficient to keep up with temperature increase: birds are lagging approximately 182 km behind climate warming. Our method is applicable to any taxa with large-scale survey data, using either abundance or occurrence data. This approach can be further used to test whether different delays are found across groups or in different land-use contexts.     

Cell-free synthesis of membrane proteins: Tailored cell models out of microsomes

Incorporation of proteins in biomimetic giant unilamellar vesicles (GUVs) is one of the hallmarks towards cell models in which we strive to obtain a better mechanistic understanding of the manifold cellular processes. The reconstruction of transmembrane proteins, like receptors or channels, into GUVs is a special challenge. This procedure is essential to make these proteins accessible to further functional investigation. Here we describe a strategy combining two approaches: cell-free eukaryotic protein expression for protein integration and GUV formation to prepare biomimetic cell models. The cell-free protein expression system in this study is based on insect lysates, which provide endoplasmic reticulum derived vesicles named microsomes. It enables signal-induced translocation and posttranslational modification of de novo synthesized membrane proteins. Combining these microsomes with synthetic lipids within the electroswelling process allowed for the rapid generation of giant proteo-liposomes of up to 50 μm in diameter. We incorporated various fluorescent protein-labeled membrane proteins into GUVs (the prenylated membrane anchor CAAX, the heparin-binding epithelial growth factor like factor Hb-EGF, the endothelin receptor ETB, the chemokine receptor CXCR4) and thus presented insect microsomes as functional modules for proteo-GUV formation. Single-molecule fluorescence microscopy was applied to detect and further characterize the proteins in the GUV membrane. To extend the options in the tailoring cell models toolbox, we synthesized two different membrane proteins sequentially in the same microsome. Additionally, we introduced biotinylated lipids to specifically immobilize proteo-GUVs on streptavidin-coated surfaces. We envision this achievement as an important first step toward systematic protein studies on technical surfaces.     

Multivariate multiple test procedures based on nonparametric copula estimation

Multivariate multiple test procedures have received growing attention recently. This is due to the fact that data generated by modern applications typically are high‐dimensional, but possess pronounced dependencies due to the technical mechanisms involved in the experiments. Hence, it is possible and often necessary to exploit these dependencies in order to achieve reasonable power. In the present paper, we express dependency structures in the most general manner, namely, by means of copula functions. One class of nonparametric copula estimators is constituted by Bernstein copulae. We extend previous statistical results regarding bivariate Bernstein copulae to the multivariate case and study their impact on multiple tests. In particular, we utilize them to derive asymptotic confidence regions for the family‐wise error rate (FWER) of multiple test procedures that are empirically calibrated by making use of Bernstein copulae approximations of the dependency structure among the test statistics. This extends a similar approach by Stange et al. (2015) in the parametric case. A simulation study quantifies the gain in FWER level exhaustion and, consequently, power that can be achieved by exploiting the dependencies, in comparison with common threshold calibrations like the Bonferroni or ?idák corrections. Finally, we demonstrate an application of the proposed methodology to real‐life data from insurance.     

Maximizing antibody production in a targeted integration host by optimization of subunit gene dosage and position

Historically, therapeutic protein production in Chinese hamster ovary (CHO) cells has been accomplished by random integration (RI) of expression plasmids into the host cell genome. More recently, the development of targeted integration (TI) host cells has allowed for recombination of plasmid DNA into a predetermined genomic locus, eliminating one contributor to clone-to-clone variability. In this study, a TI host capable of simultaneously integrating two plasmids at the same genomic site was used to assess the effect of antibody heavy chain and light chain gene dosage on antibody productivity. Our results showed that increasing antibody gene copy number can increase specific productivity, but with diminishing returns as more antibody genes are added to the same TI locus. Random integration of additional antibody DNA copies in to a targeted integration cell line showed a further increase in specific productivity, suggesting that targeting additional genomic sites for gene integration may be beneficial. Additionally, the position of antibody genes in the two plasmids was observed to have a strong effect on antibody expression level. These findings shed light on vector design to maximize production of conventional antibodies or tune expression for proper assembly of complex or bispecific antibodies in a TI system.     

Synchrony in tritrophic food chain metacommunities

The synchronous behaviour of interacting communities is studied in this paper. Each community is described by a tritrophic food chain model, and the communities interact through a network with arbitrary topology, composed of patches and migration corridors. The analysis of the local synchronization properties (via the master stability function approach) shows that, if only one species can migrate, the dispersal of the consumer (i.e., the intermediate trophic level) is the most effective mechanism for promoting synchronization. When analysing the effects of the variations of demographic parameters, it is found that factors that stabilize the single community also tend to favour synchronization. Global synchronization is finally analysed by means of the connection graph method, yielding a lower bound on the value of the dispersion rate that guarantees the synchronization of the metacommunity for a given network topology.     

Estimation of Tissue Construction Cost from Heat of Combustion and Organic Nitrogen Content

Abstract. We present a method for estimating the construction costs of plant tissues from measurements of heat of combustion, ash content, and organic nitrogen content. The method predicts glucose equivalents, the amount of glucose required to provide carbon skeletons and reductant to synthesize a quantity of organic product. Glucose equivalents have previously been calculated from the elemental composition of tissue. We define construction cost as the amount of glucose required to provide carbon skeletons, reductant and ATP for synthesizing the organic compounds in a tissue via standard biochemical pathways. The fraction of the total construction cost of a compound or tissue (excluding costs of transporting compounds) that is reflected in its glucose equivalents is the biosynthetic efficiency ( E _B). This quantity varies between 0.84 and 0.95 for tissues with a wide range of compositions. Using the new method, total construction cost can be estimated to ± 6% of the value obtained from biochemical pathway analysis.
Construction costs of leaves of three chaparral species were estimated using the proposed method and compared to previously published values, derived using different methods. Agreement among methods was generally good. Differences were probably due to a combination of inaccuracy in the estimated biosynthetic efficiency and technical difficulties with biochemical analysis, one of the older methods of determining construction cost.     

野生田头菇菌株的驯化及其子实体营养成分分析

采自湖南洞庭湖大通湖区芦苇湿地的野生菌株,经鉴定为田头菇Agrocybe praecox。通过驯化实现人工栽培,栽培原料以芦苇屑为主,使用液体菌种和覆土栽培方式,初潮菇平均生物转化率为45.6%。营养成分分析表明：以芦苇屑为栽培培养基,子实体中矿物元素含量分别为K（2 190mg/kg）、Fe（16.2mg/kg）、Mg（59.7mg/kg）、Ca（33.4mg/kg）,必需氨基酸含量占比高达44.85%,谷氨酸、蛋氨酸、天冬氨酸含量高,是一种高蛋白、低脂肪、高钾低钠的食用菌。     

Concepts and analysis of mass extinction with the late Ordovician event as an example

Twelve groups of fossils, including graptolites, brachiopods, nautiloids, trilobites, corals, crinoids, bryozoans, conodonts, ostracods, gastropods, chitinozoans, and acritarchs expired in different but substantial magnitude and global extent during the late Caradoc to latest Ashgill. It indicates a multiple‐episodic mass extinction containing the possible Prologue (late Caradoc), Climax episode (Rawtheyan) and Epilogue (late Hirnantian). The main causes of this mass extinction are recognized as a global sea‐level lowering in the climax and remarkable rapid rise at the final, and global cooling. The Chinese data, especially from the South China Paleoplate, are evaluated first. They are significant for explaining this global bioevent.