Effects of ultra-purified polymerized bovine hemoglobin on local tissue oxygen tension in striated skin muscle - An efficacy study in the hamster

The development of hemoglobin-based oxygen carriers has been propagated for replacement of the oxygen carrying properties of red blood cells for almost one century. Using a Clark-type multi-wire oxygen surface electrode and the dorsal skin fold chamber model of the awake Syrian golden hamster, local tissue pO(2) was analyzed in the thin striated skin muscle before and after administration of an ultrapurified polymerized bovine hemoglobin solution (U-PBHb(R), Biopure Corp., Boston, Mass., USA) under the following experimental conditions: (a) hypervolemic infusion with U-PBHb at similar to 10% of calculated blood volume, and (b) isovolemic exchange transfusion with U-PBHb by replacing similar to50% of calculated blood volume. Control animals of group a received equivalent treatment with either isotonic saline or dextran 60, control animals of group b received dextran 60. Local tissue pO(2) was found slightly decreased after both hypervolemic infusion and isovolemic exchange transfusion with U-PBHb, while frequency distribution curves of local tissue pO(2) were found more narrow (less values 25 mm Hg), suggesting a more homogeneous tissue pO(2) distribution. The data thus indicate that U-PBHb slightly decreases mean tissue pO(2) after both hypervolemic infusion and isovolemic exchange transfusion which is accompanied by an effective homogenization of local tissue pO(2) distribution as compared to dextran 60. Copyright (C) 2002 S. Karger AG, Basel

Corrections to Scaling in the Hydrodynamic Properties of Dilute Polymer Solutions

We discuss the hydrodynamic radius $R_H$ of polymer chains in good solvent, and show that the leading order correction to the asymptotic law $R_H \propto N^\nu$ ($N$ degree of polymerization, $\nu \approx 0.59$) is an ``analytic'' term of order $N^{-(1 - \nu)}$, which is directly related to the discretization of the chain into a finite number of beads. This result is further corroborated by exact calculations for Gaussian chains, and extensive numerical simulations of different models of good--solvent chains, where we find a value of $1.591 \pm 0.007$ for the asymptotic universal ratio $R_G / R_H$, $R_G$ being the chain's gyration radius. For $\Theta$ chains the data apparently extrapolate to $R_G / R_H \approx 1.44$, which is different from the Gaussian value 1.5045, but in accordance with previous simulations. We also show that the experimentally observed deviations of the initial decay rate in dynamic light scattering from the asymptotic Benmouna--Akcasu value can partly be understood by similar arguments.Comment: 13 pages, 10 figures. submitted to J. Chem. Phy

Leptonic decay of the Upsilon(1S) meson at third order in QCD

We present the complete next-to-next-to-next-to-leading order short-distance and bound-state QCD correction to the leptonic decay rate Gamma(Upsilon(1S)->l+l-) of the lowest-lying spin-1 bottomonium state. The perturbative QCD prediction is compared to the measurement Gamma(Upsilon(1S)->e+e-)=1.340(18) keV.Comment: 4 pages, 2 figure

\u3ci\u3eHypsugo stubbei\u3c/i\u3e sp. nov., A Novel Cryptic Bat Species of the Genus \u3ci\u3eHypsugo\u3c/i\u3e (Vespertilionidae, Chiroptera, Mammalia) from Mongolia

The occurrence of two members of the genus Hypsugo, namely H. alaschanicus and H. savii caucasicus, have been reported for Mongolia in the literature. Due to various taxonomic reassignments within and between genera, the number of records for the genus Hypsugo in Mongolia is quite scarce and sometimes not resolved at species or subspecies level. Despite recognition of the two above-mentioned species, recent reports based on genetic analyses describe only new and further records of H. alaschanicus. Thus, it exists a large uncertainty regarding the occurrence and distribution of H. savii caucasicus in Mongolia. Here, our efforts in gaining a deeper understanding towards the occurrence and distribution of Hypsugo species in Mongolia are described. A combination of genetic and morphological analyses of collected material from Hypsugo specimens revealed the existence of a genetically largely distant Hypsugo clade. Therefore, a new and cryptic Hypsugo species is proposed which is named after Prof. Dr. Michael Stubbe for his continuous, long-standing and significant contributions into the biological exploration of Mongolia. Hypsugo stubbei sp. nov. differs by at least 8.4 % and 9 % to the closest Western Palearctic distributed H. cf. darwinii and H. savii as well as at least 11.3 % to the Easter Palearctic (including Mongolia) distributed H. alaschanicus based on the first 798 nucleotides of the gene encoding the mitochondrial ND1 (subunit one of NADH dehydrogenase). Neither a close proximity species based on the gene encoding the mitochondrial COI (cytochrome oxidase subunit one) could be found in publicly accessible nucleotide databases. While the cryptic H. stubbei sp. nov. reveals no obvious cranial and morphological differences, few external characteristics are dissimilar to both H. alaschanicus and H. savii (caucasicus). Currently, Hypsugo stubbei sp. nov. was found at four different locations in Mongolia. Among the 11 specimens captured, six facilitated a genetic assignment. Based on the current scarce data records, the species seems to occur mainly in the far west of Mongolia inhabiting semi-deserts and steppes up to high mountain areas. An overlapping distribution with H. alaschanicus cannot be excluded based on the limited data currently available

Identification of brassinosteroid-related genes by means of transcript co-response analyses

The comprehensive systems-biology database (CSB.DB) was used to reveal brassinosteroid (BR)-related genes from expression profiles based on co-response analyses. Genes exhibiting simultaneous changes in transcript levels are candidates of common transcriptional regulation. Combining numerous different experiments in data matrices allows ruling out outliers and conditional changes of transcript levels. CSB.DB was queried for transcriptional co-responses with the BR-signalling components BRI1 and BAK1: 301 out of 9694 genes represented in the nasc0271 database showed co-responses with both genes. As expected, these genes comprised pathway-involved genes (e.g. 72 BR-induced genes), because the BRI1 and BAK1 proteins are required for BR-responses. But transcript co-response takes the analysis a step further compared with direct approaches because BR-related non BR-responsive genes were identified. Insights into networks and the functional context of genes are provided, because factors determining expression patterns are reflected in correlations. Our findings demonstrate that transcript co-response analysis presents a valuable resource to uncover common regulatory patterns of genes. Different data matrices in CSB.DB allow examination of specific biological questions. All matrices are publicly available through CSB.DB. This work presents one possible roadmap to use the CSB.DB resources

ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites

<p>Abstract</p> <p>Background</p> <p>In the last decade, techniques were established for the large scale genome-wide analysis of proteins, RNA, and metabolites, and database solutions have been developed to manage the generated data sets. The Golm Metabolome Database for metabolite data (GMD) represents one such effort to make these data broadly available and to interconnect the different molecular levels of a biological system <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>. As data interpretation in the light of already existing data becomes increasingly important, these initiatives are an essential part of current and future systems biology.</p> <p>Results</p> <p>A mass spectral library consisting of experimentally derived tryptic peptide product ion spectra was generated based on liquid chromatography coupled to ion trap mass spectrometry (LC-IT-MS). Protein samples derived from <it>Arabidopsis thaliana</it>, <it>Chlamydomonas reinhardii</it>, <it>Medicago truncatula</it>, and <it>Sinorhizobium meliloti </it>were analysed. With currently 4,557 manually validated spectra associated with 4,226 unique peptides from 1,367 proteins, the database serves as a continuously growing reference data set and can be used for protein identification and quantification in uncharacterized biological samples. For peptide identification, several algorithms were implemented based on a recently published study for peptide mass fingerprinting <abbrgrp><abbr bid="B2">2</abbr></abbrgrp> and tested for false positive and negative rates. An algorithm which considers intensity distribution for match correlation scores was found to yield best results. For proof of concept, an LC-IT-MS analysis of a tryptic leaf protein digest was converted to mzData format and searched against the mass spectral library. The utility of the mass spectral library was also tested for the identification of phosphorylated tryptic peptides. We included <it>in vivo </it>phosphorylation sites of <it>Arabidopsis thaliana </it>proteins and the identification performance was found to be improved compared to genome-based search algorithms. Protein identification by ProMEX is linked to other levels of biological organization such as metabolite, pathway, and transcript data. The database is further connected to annotation and classification services via BioMoby.</p> <p>Conclusion</p> <p>The ProMEX protein/peptide database represents a mass spectral reference library with the capability of matching unknown samples for protein identification. The database allows text searches based on metadata such as experimental information of the samples, mass spectrometric instrument parameters or unique protein identifier like AGI codes. ProMEX integrates proteomics data with other levels of molecular organization including metabolite, pathway, and transcript information and may thus become a useful resource for plant systems biology studies. The ProMEX mass spectral library is available at <url>http://promex.mpimp-golm.mpg.de/</url>.</p

Analysis of the Compartmentalized Metabolome – A Validation of the Non-Aqueous Fractionation Technique

With the development of high-throughput metabolic technologies, a plethora of primary and secondary compounds have been detected in the plant cell. However, there are still major gaps in our understanding of the plant metabolome. This is especially true with regards to the compartmental localization of these identified metabolites. Non-aqueous fractionation (NAF) is a powerful technique for the determination of subcellular metabolite distributions in eukaryotic cells, and it has become the method of choice to analyze the distribution of a large number of metabolites concurrently. However, the NAF technique produces a continuous gradient of metabolite distributions, not discrete assignments. Resolution of these distributions requires computational analyses based on marker molecules to resolve compartmental localizations. In this article we focus on expanding the computational analysis of data derived from NAF. Along with an experimental workflow, we describe the critical steps in NAF experiments and how computational approaches can aid in assessing the quality and robustness of the derived data. For this, we have developed and provide a new version (v1.2) of the BestFit command line tool for calculation and evaluation of subcellular metabolite distributions. Furthermore, using both simulated and experimental data we show the influence on estimated subcellular distributions by modulating important parameters, such as the number of fractions taken or which marker molecule is selected. Finally, we discuss caveats and benefits of NAF analysis in the context of the compartmentalized metabolome

Light quark mass effects in the on-shell renormalization constants

We compute the three-loop relation between the pole and the minimally subtracted quark mass allowing for virtual effects from a second massive quark. We also consider the analogue effects for the on-shell wave function renormalization constant.Comment: 24 page

Halide ion influence on the formation of nickel nanoparticles and their conversion into hollow nickel phosphide and sulphide nanocrystals

A dependence of the formation of tri-n-octylphosphine-capped Ni nanocrystals on the presence of halide ions during their synthesis is shown. For the application-oriented synthesis of Ni particles, this information can be crucial. Furthermore, Ni nanoparticles can be converted to nickel phosphide or sulphide by heating them up in the presence of a phosphorus or sulphur source, resulting in either solid or hollow nanocrystals, formed via the nanoscale Kirkendall effect, depending on the synthesis route. By adjusting the Ni crystallite size in the initial nanoparticles via the halide ion concentration the cavity size of the resulting hollow nanocrystals can be tuned, which is otherwise impossible to realise for particles of a similar total diameter by using this process. The synthesised hollow Ni3S2 nanocrystals exhibit a much sharper localised surface plasmon resonance (LSPR) band than all previously presented particles of this material, which is known to show molar extinction coefficients at the LSPR maximum similar to Au. This narrow linewidth could be explained by the nanoparticles’ high crystallinity resulting from the Kirkendall process and is interesting for various possible optical applications such as surface-enhanced Raman spectroscopy owing to the low cost of the involved materials compared to the widely used noble metals

GMDCSB.DB: the Golm Metabolome Database

Summary: Metabolomics, in particular gas chromatography-mass spectrometry (GC-MS) based metabolite profiling of biological extracts, is rapidly becoming one of the cornerstones of functional genomics and systems biology. Metabolite profiling has profound applications in discovering the mode of action of drugs or herbicides, and in unravelling the effect of altered gene expression on metabolism and organism performance in biotechnological applications. As such the technology needs to be available to many laboratories. For this, an open exchange of information is required, like that already achieved for transcript and protein data. One of the key-steps in metabolite profiling is the unambiguous identification of metabolites in highly complex metabolite preparations from biological samples. Collections of mass spectra, which comprise frequently observed metabolites of either known or unknown exact chemical structure, represent the most effective means to pool the identification efforts currently performed in many laboratories around the world. Here we present GMD, The Golm Metabolome Database, an open access metabolome database, which should enable these processes. GMD provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools, e.g. with regard to methods, spectral information or compounds. The main goal will be the representation of an exchange platform for experimental research activities and bioinformatics to develop and improve metabolomics by multidisciplinary cooperation. Availability: http://csbdb.mpimp-golm.mpg.de/gmd.html Contact: [email protected] Supplementary information: http://csbdb.mpimp-golm.mpg.d