Guidelines for consistent reporting of exchanges/to nature within life cycle inventories (LCI)

Data availability and data quality are still critical factors for successful LCA work. The SETAC-Europe LCA Working Group ‘Data Availability and Data Quality’ has therefore focused on ongoing developments toward a common data exchange format, public databases and accepted quality measures to find science-based solutions than can be widely accepted. A necessary prerequisite for the free flow and exchange of life cycle inventory (LCI) data and the comparability of LCIs is the consistent definition, nomenclature, and use of inventory parameters. This is the main subject of the subgroup ‘Recommended List of Exchanges’ that presents its results and findings here:

Early Tertiary out-of-India dispersal of Crypteroniaceae: evidence from phylogeny and molecular dating

Abstract.— Pylogenetic analyses and molecular dating estimates based on chloroplast DNA sequences were used to establish the relationships of the southern and Southeast Asian Crypteroniaceae and elucidate their biogeographic history. Maximum parsimony and likelihood analyses of rbc L sequences suggested that Crypteroniaceae should be restricted to Crypteronia , Axinandra , and Dactylocladus and that Crypteroniaceae, so defined, are sister to a clade formed by three small African taxa (Oliniaceae, Penaeaceae, and Rhynchocalycaceae) and the monotypic Central and South American Alzateaceae. Three molecular dating approaches (maximum-likelihood under a molecular clock, Langley-Fitch, and penalized-likelihood) were used to infer the age of Crypteroniaceae using both paleobotanic and geologic calibrations. Comparisons among these three methods revealed significant lineage effects in rbc L sequences. Clock-independent dating estimates suggested that divergence of Crypteroniaceae from its African and South American relatives coincided with the breakup of Gondwana, and that India likely served as a "raft" transporting Crypteroniaceae to Asia, with later expansion to Southeast Asia. To our knowledge, Crypteroniaceae are the first plant group for which the out-of-India hypothesis is well corroborated by molecular-based estimates of divergence times.     

Structural requirements for mutational lutropin/choriogonadotropin receptor activation

Different activation mechanisms of glycoprotein hormone receptors, which are members of the G protein-coupled receptor superfamily, have been proposed. For example, the large ectodomain of glycoprotein hormone receptors may function as an inverse agonist keeping the transmembrane domain in an inactive conformation. To provide support for this hypothesis, we have generated different lutropin/choriogonadotropin receptor (LHR) constructs lacking the ectodomain. Although some ectodomain-deficient LHR constructs were targeted to the cell surface, cAMP levels remained unchanged under basal conditions and agonist application but could be increased by a mutation within the transmembrane domain 6 (D578H). Taking advantage of a constitutive activating mutation (S277N) located in the extracellular domain, we showed that the intact leucine-rich repeat-containing ectodomain is essential for constitutive activation of the LHR by mutation of the hinge region. Our findings support an activation scenario in which agonist binding or mutational alterations expose a structure within the ectodomain, which then activates the transmembrane core.     

Toward reconstitution of in vivo microtubule dynamics in vitro

The transition from interphase to mitosis is marked by a dramatic change in microtubule dynamics resulting in the reorganization of the microtubule network that culminates in mitotic spindle formation. While the molecular basis for this change in microtubule organization remains obscure, it is currently thought that a balance in the activity of microtubule stabilizing and destabilizing factors regulates how dynamic cellular microtubules are. By mixing the microtubule stabilizer XMAP215 and the microtubule destabilizer XKCM1, reconstitution of in vivo-like microtubule dynamics has now been achieved in vitro.     

Two different lantibiotic-like peptides originate from the ericin gene cluster of Bacillus subtilis A1/3

A lantibiotic gene cluster was identified in Bacillus subtilis A1/3 showing a high degree of homology to the subtilin gene cluster and occupying the same genetic locus as the spa genes in B. subtilis ATCC 6633. The gene cluster exhibits diversity with respect to duplication of two subtilin-like genes which are separated by a sequence similar to a portion of a lanC gene. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analyses of B. subtilis A1/3 culture extracts confirmed the presence of two lantibiotic-like peptides, ericin S (3,442 Da) and ericin A (2,986 Da). Disruption of the lanB-homologous gene eriB resulted in loss of production of both peptides, demonstrating that they are processed in an eriB-dependent manner. Although precursors of ericins S and A show only 75% of identity, the matured lantibiotic-like peptides reveal highly similar physical properties; separation was only achieved after multistep, reversed-phase high-performance liquid chromatography. Based on Edman and peptidase degradation in combination with MALDI-TOF MS, for ericin S a subtilin-like, lanthionine-bridging pattern is supposed. For ericin A two C-terminal rings are different from the lanthionine pattern of subtilin. Due to only four amino acid exchanges, ericin S and subtilin revealed similar antibiotic activities as well as similar properties in response to heat and protease treatment. For ericin A only minor antibiotic activity was found.     

Ultra high-resolution fMRI in monkeys with implanted RF coils

Spatiotemporally resolved functional MRI (fMRI) in animals can reveal how wide-spread neural networks are organized and accompanying electrophysiological recordings can show how small neural assemblies contribute to this organization. Here we present a novel technique that yields high-resolution structural and functional images of the monkey brain with small, tissue-compatible, intraosteally implantable radiofrequency coils. Voxel sizes as small as 0.0113 microl with high signal-to-noise and contrast-to-noise ratios were obtained, revealing both structural and functional cortical architecture in great detail. Up to a certain point, contrast sensitivity increased with decreasing voxel size, probably because of the decreased partial volume effects. Spatial specificity was demonstrated by the lamina-specific activation in experiments comparing responses to moving and flickering stimuli. The implications of this technique for combined fMRI/electrophysiology experiments and its limitations in terms of spatial coverage are discussed.     

Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS

Novel algorithms are presented for automated NOESY peak picking and NOE signal identification in homonuclear 2D and heteronuclear-resolved 3D [¹H,¹H]-NOESY spectra during de novoprotein structure determination by NMR, which have been implemented in the new software ATNOS (automated NOESY peak picking). The input for ATNOS consists of the amino acid sequence of the protein, chemical shift lists from the sequence-specific resonance assignment, and one or several 2D or 3D NOESY spectra. In the present implementation, ATNOS performs multiple cycles of NOE peak identification in concert with automated NOE assignment with the software CANDID and protein structure calculation with the program DYANA. In the second and subsequent cycles, the intermediate protein structures are used as an additional guide for the interpretation of the NOESY spectra. By incorporating the analysis of the raw NMR data into the process of automated de novoprotein NMR structure determination, ATNOS enables direct feedback between the protein structure, the NOE assignments and the experimental NOESY spectra. The main elements of the algorithms for NOESY spectral analysis are techniques for local baseline correction and evaluation of local noise level amplitudes, automated determination of spectrum-specific threshold parameters, the use of symmetry relations, and the inclusion of the chemical shift information and the intermediate protein structures in the process of distinguishing between NOE peaks and artifacts. The ATNOS procedure has been validated with experimental NMR data sets of three proteins, for which high-quality NMR structures had previously been obtained by interactive interpretation of the NOESY spectra. The ATNOS-based structures coincide closely with those obtained with interactive peak picking. Overall, we present the algorithms used in this paper as a further important step towards objective and efficient de novoprotein structure determination by NMR.     

Impact of integrating clinical and genetic information

To assess the relevance of molecular markers it is required to combine clinical and genetic information. For reliable assessment of parameters relevant to diagnostics and therapy large patient collectives must be characterized both with respect to phenotype and genotype. Matching of genetic data like gene expression profiles, molecular genetics and cytogenetics with clinical data like follow-up, morphological findings and diagnoses involves integration of complex databases. In the context of a nationwide leukemia research network in Germany we designed an integrated database covering both genetic and clinical data of patients. The system contains follow-up data and relevant laboratory modalities, i. e. cytomorphology, cytogenetics, molecular genetics, FISH, immunophenotyping and gene expression profiling. So far 13,541 cases from 7,746 patients treated by 1,225 physicians are documented. The data structure consists of up to 888 variables per case. From our experience, integration of clinical and genetic information requires significant efforts - including data protection issues -, but is feasible and improves data quality leading to faster and more reliable research results for the benefit of the patients.     

Monoseptic cultivation of phototrophic microorganisms--development and scale-up of a photobioreactor system with thermal sterilization

The use of phototrophic microorganisms as sources of biological active substances in photoautotrophic and mixotrophic cultivation modes requires an adequate cultivation system with thermal sterilization. A corresponding photobioreactor system in the 10, 25 and 100 l scales was developed. This "Medusa"-photobioreactor system represents a concept based on the air-lift loop principle, whose working volume is irradiated by external light sources. The incident irradiation can be varied by a light control system. An effective CO(2)/O(2) gas exchange is enabled due to the efficient supply with process gas by several gas supply nozzles within the system and a large degassing surface. Using a model to describe the growth characteristics of the organisms, the volumetric irradiation coefficient I(DX) was defined as scale-up parameter. On this basis the scale-up from 1 l bubble columns to the 10 and 100 l scales was realized. The scale-up was performed successfully with Chlorella salina as model organism. A maximum biomass concentration of 7.89 g (dry weight) l(-1) at a maximum specific growth rate of 0.058 h(-1) and a yield of 35 mg l(-1) h(-1) was obtained in a batch cultivation in the 100 l scale under photoautotrophic conditions with an initial biomass concentration of approx. 0.03 g l(-1).