Research Design and the Politics of Abstraction: Unpacking the Environmentality of Scientific Practice in Socioecological Assessments

Scientific assessments of socio-ecological systems are becoming mainstays in guiding policymaking and other interventions in response to global environmental change. The environmentality literature emphasizes the institutional architecture of emergent science-policy regimes and how scientific research is used in political settings, creating new modes of governance and subjectivities. However, there has been relatively little attention to domain-level socio-ecological assessments as socially produced technologies where specific scientific choices are mechanisms connecting governance architecture and popular subjectivities.Combining empirical case study and literature review, assessment technologies are analyzed in three domains: vulnerability assessment, ecosystem services assessment, life-cycle assessment. Using conceptualization, operationalization, and institutionalization as analytical lenses, the cases illustrate ways that scientific choices simplify complex socio-ecological relationships with implications for both governance practices and subjectivities. Furthermore, findings explore the possibility for assessments to be more inclusive of diverse social values and practices, enabling more empowering subjectivities.     

Emerging roles of PPARdelta in metabolism

PPARdelta differs from the other two PPAR isotypes (alpha and gamma) by its more wide-spread tissue-specific expression pattern, its involvement in developmental processes and its profound impact on muscle and heart fat metabolism. Activation of PPARdelta modulates inflammatory responses of macrophages and is linked to altered lipoprotein metabolism, most importantly a significant raise of HDL cholesterol. PPARdelta activation in the liver decreases hepatic glucose output, thereby contributing to improved glucose tolerance and insulin sensitivity. Several studies have shown that PPARdelta polymorphisms are associated with plasma lipid levels, body mass index and the risk for diabetes and coronary heart disease. These findings support that high affinity PPARdelta agonists may be promising drugs of the future to treat the metabolic syndrome which is an expanding overweight-related health threat characterized by insulin resistance, hyperglycemia, dyslipidemia, hypertension, and accelerated atherosclerosis.     

Translation initiation factor 3 antagonizes authentic start codon selection on leaderless mRNAs

In this study, we have examined the influence of initiation factors on translation initiation of leaderless mRNAs whose 5'-terminal residues are the A of the AUG initiating codon. A 1:1 ratio of initiation factors to ribosomes abolished ternary complex formation at the authentic start codon of different leaderless mRNAs. Supporting this observation, in vitro translation assays using limiting ribosome concentrations with competing leaderless λ c I and Escherichia coli ompA mRNAs, the latter containing a canonical ribosome binding site, revealed reduced cI synthesis relative to OmpA in the presence of added initiation factors. Using in vitro toeprinting and in vitro translation assays, we show that this effect can be attributed to IF3. Moreover, in vivo studies revealed that the translational efficiency of a leaderless reporter gene is decreased with increased IF3 levels. These studies are corroborated by the observed increased translational efficiency of a leaderless reporter construct in an infC mutant strain unable to discriminate against non-standard start codons. These results suggest that, in the absence of a leader or a Shine–Dalgarno sequence, the function(s) of IF3 limits stable 30S ternary complex formation.     

Preparation and crystallization of a cross-linked complex of bovine adrenodoxin and adrenodoxin reductase

Bovine adrenodoxin was cross-linked to adrenodoxin reductase with 1-ethyl-3-(3-dimethyl-aminopropyl) carbodiimide. Mass spectrometry showed the reaction product to be a 1:1 complex of the two proteins with M_r = 64,790 ± 50. The cross-linked complex showed cytochrome c reductase activity and could be crystallized by hanging-drop vapor diffusion. Crystals of the adrenodoxin-adrenodoxin reductase complex are hexagonal, space group P6₁22 or P6₅22, with a = 93.26 Å and c= 612.20 Å and diffract to 2.9 Å resolution at 100 K. Assuming two cross-linked complexes per asymmetric unit yields a reasonable V_M of 2.97 ų/Da. Proteins 28:289–292, 1997. © 1997 Wiley-Liss Inc.     

Downstream processing of serinol from a glycerol‐based fermentation broth and transfer to other amine containing molecules

A possible application of glycerol, which is produced in large amounts as a by‐product from the biodiesel industry, is its fermentation to serinol (2‐amino‐1,3‐propanediol), a glycerol derivative. The downstream processing of this glycerol‐based fermentation broth was investigated. The challenge of the isolation of serinol was the complex media and the solubility of the desired substance in aqueous media. In this study, the isolation of serinol was investigated by an appropriate reversible derivatization method. Serinol was isolated by protecting the amino group with diethyl ethoxymethylenemalonate directly in the aqueous phase, followed by extraction of the 2,2‐bis(ethoxycarbonyl)vinyl‐serinol (BECV‐serinol) with ethyl acetate resulting in an isolated yield of 63%. We demonstrate the possibility of isolation of a hydroscopic amino alcohol from the fermentation broth and the comparison of the products in water as well as the cleavage of the 2,2‐bis(ethoxycarbonyl)vinyl group (BECV group). The procedure can also be used for other amino group containing molecules, such as serine, glucosamine, hexylamine and amino methyl laureate.     

An approach to quality management in structural biology: biophysical selection of proteins for successful crystallization

Aggregation, incorrect folding and low stability are common obstacles for protein structure determination, and are often discovered at a very late state of protein production. In many cases, however, the reasons for failure to obtain diffracting crystals remain entirely unknown. We report on the contribution of systematic biophysical characterization to the success in structural determination of human proteins of unknown fold. Routine analysis using dynamic light scattering (DLS), differential scanning calorimetry (DSC) and Fourier-transform infrared spectroscopy (FTIR) was employed to evaluate fold and stability of 263 purified protein samples (98 different human proteins). We found that FTIR-monitored temperature scanning may be used to detect incorrect folding and discovered a positive correlation between unfolding enthalpy measured with DSC and the size of small, globular proteins that may be used to estimate the quality of protein preparations. Furthermore, our work establishes that the risk of aggregation during concentration of proteins may be reduced through DLS monitoring. In summary, our study demonstrates that biophysical characterization provides an ideal tool to facilitate quality management for structural biology and many other areas of biological research.     

The alternative sigma factor sigma B of Staphylococcus aureus modulates virulence in experimental central venous catheter-related infections

The impact of the alternative sigma factor sigma B (SigB) on pathogenesis of Staphylococcus aureus is not conclusively clarified. In this study, a central venous catheter (CVC) related model of multiorgan infection was used to investigate the role of SigB for the pathogenesis of S. aureus infections and biofilm formation in vivo. Analysis of two SigB-positive wild-type strains and their isogenic mutants revealed uniformly that the wild-type was significantly more virulent than the SigB-deficient mutant. The observed difference in virulence was apparently not linked to the capability of the strains to form biofilms in vivo since wild-type and mutant strains were able to produce biofilm layers inside of the catheter. The data strongly indicate that the alternative sigma factor SigB plays a role in CVC-associated infections caused by S. aureus.     

Biochemical and functional characterization of anti-HIV antibody-ELP fusion proteins from transgenic plants

The stability and recovery of recombinant proteins expressed in plants are improved by fusion to elastin-like peptides (ELPs). In order to test the suitability of ELP for the production of pharmaceutical proteins, transgenic plants were created that individually expressed the light and heavy chains of the broadly neutralizing anti-human immunodeficiency virus type 1 (anti-HIV-1) monoclonal antibody 2F5, which is being evaluated as a microbicide component. The antibody chains were expressed both with and without a C-terminal ELP fusion. Crossing these plants in all combinations resulted in transgenic lines producing the full antibody in four formats, with ELP on either the light or heavy chains, on both or on neither. Characterization of the affinity-purified antibodies by surface plasmon resonance spectroscopy showed that the kinetic binding parameters were identical to those of a Chinese hamster ovary (CHO) cell counterpart lacking ELP. N -Glycan analysis showed that all four derivatives contained predominantly oligo-mannose-type N -glycans and that the ELP fusions had no significant effect on N -glycan structure. It was concluded that ELP fusion to the light chain, heavy chain or both chains of a plant-derived antibody had no adverse affects on protein quality, but had a positive impact on the yield. ELP fusions do not interfere with folding, assembly, trafficking in the secretory pathway or post-translational modification, but enhance stability whilst at the same time simplifying recovery.     

A short-oligonucleotide microarray that allows improved detection of gastrointestinal tract microbial communities

Background  

The human gastrointestinal (GI) tract contains a diverse collection of bacteria, most of which are unculturable by conventional microbiological methods. Increasingly molecular profiling techniques are being employed to examine this complex microbial community. The purpose of this study was to develop a microarray technique based on 16S ribosomal gene sequences for rapidly monitoring the microbial population of the GI tract.     

Inhibition of hyaluronan export attenuates cell migration and metastasis of human melanoma

When secreted from malignant cells, hyaluronan facilitates tumor invasion and metastasis, as inhibition of its export by zaprinast inhibited metastasis formation in mice. However, the precise steps of the metastatic cascade, which were influenced by zaprinast, have not been identified as yet. Here we analyzed the cell biological effects of the inhibitor on three human melanoma cell lines that differed in their hyaluronan production and their metastatic capability when xenografted into SCID mice. We measured the influence of zaprinast on cellular hyaluronan export, surface coat formation, proliferation, random migration, colony formation in soft agar, adhesion, and transepithelial resistance. Concentrations of zaprinast not affecting cell proliferation, adhesion and transepithelial resistance, nevertheless reduced hyaluronan export by 50%, surface coat formation, random migration, and colony formation in soft agar. These results indicate that hyaluronan enhances metastasis formation primarily in those steps of the metastatic cascade, which involves tumor cell migration.