Lipid II-based antimicrobial activity of the lantibiotic plantaricin C

We analyzed the mode of action of the lantibiotic plantaricin C (PlnC), produced by Lactobacillus plantarum LL441. Compared to the well-characterized type A lantibiotic nisin and type B lantibiotic mersacidin, which are both able to interact with the cell wall precursor lipid II, PlnC displays structural features of both prototypes. In this regard, we found that lipid II plays a key role in the antimicrobial activity of PlnC besides that of pore formation. The pore forming activity of PlnC in whole cells was prevented by shielding lipid II on the cell surface. However, in contrast to nisin, PlnC was not able to permeabilize Lactococcus lactis cells or to form pores in 1,2-dioleoyl-sn-glycero-3-phosphocholine liposomes supplemented with 0.1 mol% purified lipid II. This emphasized the different requirements of these lantibiotics for pore formation. Using cell wall synthesis assays, we identified PlnC as a potent inhibitor of (i) lipid II synthesis and (ii) the FemX reaction, i.e., the addition of the first Gly to the pentapeptide side chain of lipid II. As revealed by thin-layer chromatography, both reactions were clearly blocked by the formation of a PlnC-lipid I and/or PlnC-lipid II complex. On the basis of the in vivo and in vitro activities of PlnC shown in this study and the structural lipid II binding motifs described for other lantibiotics, the specific interaction of PlnC with lipid II is discussed.     

RNA interference in J774 macrophages reveals a role for coronin 1 in mycobacterial trafficking but not in actin-dependent processes

Macrophages are crucial for innate immunity, apoptosis, and tissue remodeling, processes that rely on the capacity of macrophages to internalize and process cargo through phagocytosis. Coronin 1, a member of the WD repeat protein family of coronins specifically expressed in leukocytes, was originally identified as a molecule that is recruited to mycobacterial phagosomes and prevents the delivery of mycobacteria to lysosomes, allowing these to survive within phagosomes. However, a role for coronin 1 in mycobacterial pathogenesis has been disputed in favor for its role in mediating phagocytosis and cell motility. In this study, a role for coronin 1 in actin-mediated cellular processes was addressed using RNA interference in the murine macrophage cell line J774. It is shown that the absence of coronin 1 in J774 macrophages expressing small interfering RNA constructs specific for coronin 1 does not affect phagocytosis, macropinocytosis, cell locomotion, or regulation of NADPH oxidase activity. However, in coronin 1-negative J774 cells, internalized mycobacteria were rapidly transferred to lysosomes and killed. Therefore, these results show that in J774 cells coronin 1 has a specific role in modulating phagosome-lysosome transport upon mycobacterial infection and that it is dispensable for most F-actin-mediated cytoskeletal rearrangements.     

Attributional and consequential LCA of milk production

Background, aim and scope  Different ways of performing a life cycle assessment (LCA) are used to assess the environmental burden of milk production. A strong connection exists between the choice between attributional LCA (ALCA) and consequential LCA (CLCA) and the choice of how to handle co-products. Insight is needed in the effect of choice on results of environmental analyses of agricultural products, such as milk. The main goal of this study was to demonstrate and compare ALCA and CLCA of an average conventional milk production system in The Netherlands. Materials and methods  ALCA describes the pollution and resource flows within a chosen system attributed to the delivery of a specified amount of the functional unit. CLCA estimates how pollution and resource flows within a system change in response to a change in output of the functional unit. For an average Dutch conventional milk production system, an ALCA (mass and economic allocation) and a CLCA (system expansion) were performed. Impact categories included in the analyses were: land use, energy use, climate change, acidification and eutrophication. The comparison was based on four criteria: hotspot identification, comprehensibility, quality and availability of data. Results  Total environmental burdens were lower when using CLCA compared with ALCA. Major hotspots for the different impact categories when using CLCA and ALCA were similar, but other hotspots differed in contributions, order and type. As experienced by the authors, ALCA and use of co-product allocation are difficult to comprehend for a consequential practitioner, while CLCA and system expansion are difficult to comprehend for an attributional practitioner. Literature shows concentrates used within ALCA will be more understandable for a feeding expert than the feed used within CLCA. Outcomes of CLCA are more sensitive to uncertainties compared with ALCA, due to the inclusion of market prospects. The amount of data required within CLCA is similar compared with ALCA. Discussion  The main cause of these differences between ALCA and CLCA is the fact that different systems are modelled. The goal of the study or the research question to be answered defines the system under study. In general, the goal of CLCA is to assess environmental consequences of a change in demand, whereas the goal of ALCA is to assess the environmental burden of a product, assuming a status-quo situation. Nowadays, however, most LCA practitioners chose one methodology independent of their research question. Conclusions  This study showed it is possible to perform both ALCA (mass and economic allocation) and CLCA (system expansion) of milk. Choices of methodology, however, resulted in differences in: total quantitative outcomes, hotspots, degree of understanding and quality. Recommendations and perspectives  We recommend LCA practitioners to better distinguish between ALCA and CLCA in applied studies to reach a higher degree of transparency. Furthermore, we recommend LCA practitioners of different research areas to perform similar case studies to address differences between ALCA and CLCA of the specific products as the outcomes might differ from our study.     

Dual P2Y 12 receptor signaling in thrombin-stimulated platelets--involvement of phosphoinositide 3-kinase beta but not gamma isoform in Ca2+ mobilization and procoagulant activity

During thrombus formation, thrombin, which is abundantly present at sites of vascular injury, activates platelets in part via autocrine-produced ADP. We investigated the signaling pathways by which thrombin and ADP in synergy induced platelet Ca(2+) elevation and procoagulant activity, and we monitored the consequences for the coagulation process. Even at high thrombin concentration, autocrine and added ADP enhanced and prolonged Ca(2+) depletion from internal stores via stimulation of the P2Y(12) receptors. This P2Y(12)-dependent effect was mediated via two distinct signaling pathways. The first is enhanced Ca(2+) mobilization by the inositol 1,4,5-trisphosphate receptors due to inhibition of protein kinase A. The second pathway concerns prolonged activation of phosphoinositide 3-kinase (PI3-K) and phospholipase C. Experiments with phosphoinositide 3-kinase isoform-selective inhibitors and p110gamma deficient platelets demonstrated that the phosphoinositide 3-kinase beta and not the phosphoinositide 3-kinase gamma isoform is responsible for the prolonged Ca(2+) response and for the subsequent increases in procoagulant activity and coagulation. Taken together, these results demonstrate a dual P2Y(12)-dependent signaling mechanism, which increases the platelet-activating effect of thrombin by prolongation of Ca(2+) elevation, thereby facilitating the coagulation process.     

Methods for global sensitivity analysis in life cycle assessment

Purpose

Input parameters required to quantify environmental impact in life cycle assessment (LCA) can be uncertain due to e.g. temporal variability or unknowns about the true value of emission factors. Uncertainty of environmental impact can be analysed by means of a global sensitivity analysis to gain more insight into output variance. This study aimed to (1) give insight into and (2) compare methods for global sensitivity analysis in life cycle assessment, with a focus on the inventory stage.

Methods

Five methods that quantify the contribution to output variance were evaluated: squared standardized regression coefficient, squared Spearman correlation coefficient, key issue analysis, Sobol’ indices and random balance design. To be able to compare the performance of global sensitivity methods, two case studies were constructed: one small hypothetical case study describing electricity production that is sensitive to a small change in the input parameters and a large case study describing a production system of a northeast Atlantic fishery. Input parameters with relative small and large input uncertainties were constructed. The comparison of the sensitivity methods was based on four aspects: (I) sampling design, (II) output variance, (III) explained variance and (IV) contribution to output variance of individual input parameters.

Results and discussion

The evaluation of the sampling design (I) relates to the computational effort of a sensitivity method. Key issue analysis does not make use of sampling and was fastest, whereas the Sobol’ method had to generate two sampling matrices and, therefore, was slowest. The total output variance (II) resulted in approximately the same output variance for each method, except for key issue analysis, which underestimated the variance especially for high input uncertainties. The explained variance (III) and contribution to variance (IV) for small input uncertainties were optimally quantified by the squared standardized regression coefficients and the main Sobol’ index. For large input uncertainties, Spearman correlation coefficients and the Sobol’ indices performed best. The comparison, however, was based on two case studies only.

Conclusions

Most methods for global sensitivity analysis performed equally well, especially for relatively small input uncertainties. When restricted to the assumptions that quantification of environmental impact in LCAs behaves linearly, squared standardized regression coefficients, squared Spearman correlation coefficients, Sobol’ indices or key issue analysis can be used for global sensitivity analysis. The choice for one of the methods depends on the available data, the magnitude of the uncertainties of data and the aim of the study.

     

Bulldog dwarfism in Dexter cattle is caused by mutations in ACAN

Bulldog dwarfism in Dexter cattle is one of the earliest single-locus disorders described in animals. Affected fetuses display extreme disproportionate dwarfism, reflecting abnormal cartilage development (chondrodysplasia). Typically, they die around the seventh month of gestation, precipitating a natural abortion. Heterozygotes show a milder form of dwarfism, most noticeably having shorter legs. Homozygosity mapping in candidate regions in a small Dexter pedigree suggested aggrecan (ACAN) as the most likely candidate gene. Mutation screening revealed a 4-bp insertion in exon 11 (2266_2267insGGCA) (called BD1 for diagnostic testing) and a second, rarer transition in exon 1 (−198C>T) (called BD2) that cosegregate with the disorder. In chondrocytes from cattle heterozygous for the insertion, mutant mRNA is subject to nonsense-mediated decay, showing only 8% of normal expression. Genotyping in Dexter families throughout the world shows a one-to-one correspondence between genotype and phenotype at this locus. The heterozygous and homozygous-affected Dexter cattle could prove invaluable as a model for human disorders caused by mutations in ACAN. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Nucleotide sequence data reported are available in the GenBank database under accession Nos. AY226857–AY226875.     

Quantitative trait loci mapping in dairy cattle: review and meta-analysis

From an extensive review of public domain information on dairy cattle quantitative trait loci (QTL), we have prepared a draft online QTL map for dairy production traits. Most publications (45 out of 55 reviewed) reported QTL for the major milk production traits (milk, fat and protein yield, and fat and protein concentration (%)) and somatic cell score. Relatively few QTL studies have been reported for more complex traits such as mastitis, fertility and health. The collated QTL map shows some chromosomal regions with a high density of QTL, as well as a substantial number of QTL at single chromosomal locations. To extract the most information from these published records, a meta-analysis was conducted to obtain consensus on QTL location and allelic substitution effect of these QTL. This required modification and development of statistical methodologies. The meta-analysis indicated a number of consensus regions, the most striking being two distinct regions affecting milk yield on chromosome 6 at 49 cM and 87 cM explaining 4.2 and 3.6 percent of the genetic variance of milk yield, respectively. The first of these regions (near marker BM143) affects five separate milk production traits (protein yield, protein percent, fat yield, fat percent, as well as milk yield).     

Role of lipid-bound peptidoglycan precursors in the formation of pores by nisin, epidermin and other lantibiotics

It is generally assumed that type A lantibiotics primarily kill bacteria by permeabilization of the cytoplasmic membrane. As previous studies had demonstrated that nisin interacts with the membrane-bound peptidoglycan precursors lipid I and lipid II, we presumed that this interaction could play a role in the pore formation process of lantibiotics. Using a thin-layer chromatography system, we found that only nisin and epidermin, but not Pep5, can form a complex with [¹⁴C]-lipid II. Lipid II was then purified from Micrococcus luteus and incorporated into carboxyfluorescein-loaded liposomes made of phosphatidylcholine and cholesterol (1:1). Liposomes supplemented with 0.05 or 0.1 mol% of lipid II did not release any marker when treated with Pep5 or epilancin K7 (peptide concentrations of up to 5 mol% were tested). In contrast, as little as 0.01 mol% of epidermin and 0.1 mol% of nisin were sufficient to induce rapid marker release; phosphatidylglycerol-containing liposomes were even more susceptible. Controls with moenomycin-, undecaprenol- or dodecaprenolphosphate-doped liposomes demonstrated the specificity of the lantibiotics for lipid II. These results were correlated with intact cells in an in vivo model. M. luteus and Staphylococcus simulans were depleted of lipid II by preincubation with the lipopeptide ramoplanin and then tested for pore formation. When applied in concentrations below the minimal inhibitory concentration (MIC) and up to 5–10 times the MIC, the pore formation by nisin and epidermin was blocked; at higher concentrations of the lantibiotics the protective effect of ramoplanin disappeared. These results demonstrate that, in vitro and in vivo , lipid II serves as a docking molecule for nisin and epidermin, but not for Pep5 and epilancin K7, and thereby facilitates the formation of pores in the cytoplasmic membrane.     

Purification and characterization of the tungsten enzyme aldehyde:ferredoxin oxidoreductase from the hyperthermophilic denitrifier Pyrobaculum aerophilum

A tungsten-containing aldehyde:ferredoxin oxidoreductase (AOR) has been purified to homogeneity from Pyrobaculum aerophilum. The N-terminal sequence of the isolated enzyme matches a single open reading frame in the genome. Metal analysis and electron paramagnetic resonance (EPR) spectroscopy indicate that the P. aerophilum AOR contains one tungsten center and one [4Fe-4S]^2+/1+ cluster per 68-kDa monomer. Native AOR is a homodimer. EPR spectroscopy of the purified enzyme that has been reduced with the substrate crotonaldehyde revealed a W(V) species with g_zyx values of 1.952, 1.918, 1.872. The substrate-reduced AOR also contains a [4Fe-4S]¹⁺ cluster with S=3/2 and zero field splitting parameters D=7.5 cm^–1 and E/D=0.22. Molybdenum was absent from the enzyme preparation. The P. aerophilum AOR lacks the amino acid sequence motif indicative for binding of mononuclear iron that is typically found in other AORs. Furthermore, the P. aerophilum AOR utilizes a 7Fe ferredoxin as the putative physiological redox partner, instead of a 4Fe ferredoxin as in Pyrococcus furiosus. This 7Fe ferredoxin has been purified from P. aerophilum, and the amino acid sequence has been identified using mass spectrometry. Direct electrochemistry of the ferredoxin showed two one-electron transitions, at –306 and –445 mV. In the presence of 55 M ferredoxin the AOR activity is 17% of the activity obtained with 1 mM benzyl viologen as an electron acceptor.