FCS cell surface measurements--photophysical limitations and consequences on molecular ensembles with heterogenic mobilities.

BACKGROUND: Fluorescence Correlation Spectroscopy is a powerful method to analyze densities and diffusive behavior of molecules in membranes, but effects of photodegradation can easily be overlooked. METHOD: Based on experimental photophysical parameters, calculations were performed to analyze the consequences of photobleaching in fluorescence correlation spectroscopy (FCS) cell surface experiments, covering a range of standard measurement conditions. RESULTS: Cumulative effects of photobleaching can be prominent, although an absolute majority of the fluorescent molecules would pass the laser excitation beam without being photo-bleached. Given a distribution of molecules on a cell surface with different diffusive properties, the fraction of molecules that is actually analyzed depends strongly on the excitation intensities and measurement times, as well as on the size of the reservoir of freely diffusing molecules. Both the slower and the faster diffusing molecules can be disfavored. CONCLUSIONS: Apart from quantifying photobleaching effects, the calculations suggest that the effects can be used to extract additional information, for instance about the size of the reservoirs of free diffusion. By certain choices of measurement conditions, it may be possible to more specifically analyze certain species within a population, based on their different diffusive properties, different areas of free diffusion, or different kinetics of possible transient binding.     

Disruption of the Cytokeratin Cytoskeleton and Inhibition of Hepatocytic Autophagy by Okadaic Acid

To learn whether autophagy might be dependent on any of the major cytoskeletal elements, the effect of various cytoskeleton inhibitors on autophagy and cytoskeletal organization was studied in isolated rat hepatocytes. Autophagy, measured as the sequestration of endogenous lactate dehydrogenase, was completely inhibited in isolated rat hepatocytes by the protein phosphatase inhibitor okadaic acid (30 nM). Only small effects were seen with vinblastine (10 μM) or cytochalasin D (10 μM). Indirect immunofluorescence microscopy with antibody to a 55-kDa cytokeratin, corresponding to human cytokeratin 8 (CK8), revealed that whereas control cells contained a well-organized network of cytokeratin intermediate filaments, okadaic acid disrupted this network into small spherical aggregates. Treatment with cytochalasin D or vinblastine, which disrupt microfilaments and microtubules, respectively, had no detectable effect on the cytokeratin filament distribution. Neither the microtubule network (detected by indirect immunofluorescence with antibodies against α- and β-tubulin) nor the actin microfilament network (detected by rhodamine-palloidin) was disrupted by okadaic acid. Naringin (100 μM), a putative protein kinase-inhibitory flavonoid, offered complete protection against the autophagy-inhibitory and cytokeratin-disruptive effects of okadaic acid. Two other flavonoids, genistein (100 μM) and prunin (100 μM) as well as KN-62 (10 μM), a specific inhibitor of Ca²⁺/calmodulin-dependent kinase II), likewise displayed a good ability to protect against the effect of okadaic acid upon cytokeratin organization, while no such protection was seen with H-89 (20 μM), an inhibitor of the cyclic nucleotide-dependent protein kinases, or with H-7 (100 μM), which in addition inhibits protein kinase C. The results suggest that the cytokeratin cytoskeleton of hepatocytes is subject to rapid control by phosphorylation and dephosphorylation and that cytokeratin filaments may somehow be involved in the autophagic process.     

Linker insertion analysis of the FimH adhesin of type 1 fimbriae in an Escherichia coli fimH-null background

Abstract The gene encoding the Escherichia coli FimH adhesin of type 1 fimbriae has been subjected to linker insertion mutagenesis. Amino acid changes were introduced at a number of positions spanning the entire sequence in order to probe the structure-function relationship of the FimH protein. The effect of these mutations on the ability of bacteria to express a D-mannose binding phenotype was assessed in a fimH null mutant (MS4) constructed by allelic exchange in the E. coli K-12 strain PC31. Mutations mapping at amino acid residues 36, 58 and 279 of the mature FimH protein were shown to completely abolish binding to D-mannose receptors. Differences in the level of fimbriation were also observed as a result of some of the mutations in the fimH gene. These mutants may prove useful in dissecting receptor-ligand interactions by defining regions of the FimH protein that are important in erythrocyte binding.     

Molecular Phylogeny of Some European Heteronemertean (Nemertea) Species and the Monophyletic Status ofRiseriellus, Lineus,andMicrura

The 16S rRNA mitochondrial gene was used to reconstruct the relationships among 10 heteronemertean species (subclass Heteronemertea, phylum Nemertea);Lineus ruberandL. viridisare represented by more than one specimen to assess intraspecific variation in these enigmatic species, and the analysis includes in total 14 terminal taxa incorporating one palaeonemertean species (Tubulanus annulatus) for outgroup rooting. The aligned sequences were subjected to maximum parsimony, maximum-likelihood, and neighbor-joining analyses to estimate the phylogenetic relationship of the species. The results were concordant from all analyses and indicate that neitherLineusnorMicruraare monophyletic taxa, and that there is no support from a phylogenetic point of view to establish the monotypic genusRiseriellus.     

Effect of grazing by a neotropical copepod, Notodiaptomus, on a natural cyanobacterial assemblage and on toxic and non-toxic cyanobacterial strains

The neotropical, freshwater copepod Notodiaptomus iheringi decreasedthe growth of small colonies in cyanobacteria-dominated plankton,indicating that they can be efficiently ingested and that theymay represent an important food source for this copepod in reservoirsdominated by cyanobacteria. Cultured, colonial, toxic Microcystisaeruginosa was not affected, indicating that toxicity may causea decrease in its ingestion by N. iheringi.     

Prenatal and postnatal transfer of fatty acids from mother to pup in the hooded seal

Unlike most mammals, hooded seal (Cystophora cristata) pups are born with a substantial layer of adipose tissue. Subsequently, during the brief lactation period of only 4 days, fasting mothers mobilize enormous amounts of lipid from blubber and secrete milk (60% fat) at rates of 10 kg·day^-1. Pups gain 7 kg·day^-1 due primarily to the deposition of fat in blubber. We measured blubber content and fatty acid composition of blubber and milk in hooded seal mother-pup pairs at birth and over the 4-day lactation period to examine the nature and source of fetal lipids, the incorporation of maternal blubber fatty acids into milk lipid, and patterns of fatty acid deposition in suckling young. The fatty acid composition of the blubber of the newborn was notably different from that of its mother. Fetal deposition was likely due to a combination of both fetal synthesis and direct placental transfer of maternal circulating fatty acids. The blubber of the newborn was characterized by high levels (>90% of total fatty acids) of saturated and monounsaturated fatty acids of primarily endogenous origin. In particular, the fetus appeared to have high Δ-9 desaturase activity as evidenced by the large amounts of 14:1n-5 (4.2%) and 16:1n-7 (37.0%) in newborn blubber compared to maternal blubber (0.2% and 14.1%, respectively). Nevertheless, essential and long-chain polyunsaturated fatty acids of the n-3 and n-6 families, which could only have originated by direct transfer from the mother, comprised>7% of pup blubber fatty acids and indicated greater rates of placental transfer than found in humans. In hooded seal mothers, rapid lipid transfer during the brief lactation period appeared to be facilitated by direct incorporation of mobilized fatty acids into milk. Although some differences in proportions of specific fatty acids were found between milk and maternal blubber, most of these differences declined over the course of lactation. However, selective mobilization of 20:5n-3 from maternal blubber into milk was apparent throughout lactation and resulted in elevated levels in pup blubber at weaning compared to maternal blubber. Ingested fatty acids were deposited directly and without modification into the blubber of pups, and by 4 days the fatty acid composition of pup blubber was virtually identical to that of the milk consumed.     

Nitrogen mineralization and denitrification as influenced by crop residue particle size

Managing the crop residue particle size has the potential to affect N conservation in agricultural systems. We investigated the influence of barley (Hordeum vulgare) and pea (Pisum sativum) crop residue particle size on N mineralization and denitrification in two laboratory experiments. Experiment 1: ¹⁵N-labelled ground (3 mm) and cut (25 mm) barley residue, and microcrystalline cellulose+glucose were mixed into a sandy loam soil with additional inorganic N. Experiment 2: inorganic¹⁵ N and C₂H₂ were added to soils with barley and pea material after 3, 26, and 109 days for measuring gross N mineralization and denitrification.Net N immobilization over 60 days in Experiment 1 cumulated to 63 mg N kg^-1 soil (ground barley), 42 (cut barley), and 122 (cellulose+glucose). More N was seemingly net mineralized from ground barley (3.3 mg N kg^-1 soil) than from cut barley (2.7 mg N kg^-1 soil). Microbial biomass peaked at day 4 with the barley treatments and at day 14 with the cellulose+glucose whereafter the biomass leveled out at values 79 mg C kg^-1 (ground), 104 (cut), and 242 (cellulose+glucose) higher than for the control soil. Microbial growth yields were similar for the two barley treatments, ca. 60 mg C g^-1 substrate C added, which was lower than the 142 mg C g^-1 C added with cellulose+glucose. This suggests that the 75% (w/w) holocelluloses and sugars contained with the barley material remained physically protected despite grinding. In Experiment 2 gross mineralization on day 3 was 4.8 mg N kg^-1 d^-1 with ground pea, twice as much as for all other treatments. On day 26 the treatment with ground barley had the greatest gross N mineralization. In static cores ground barley denitrified 11-fold more than did cut barley, whereas denitrification was similar for the two pea treatments. In suspensions denitrification was similar for the two treatments both with barley and pea residue.We conclude that the higher microbial activity associated with the initial decomposition of ground plant material is due to a more intimate plant residue-soil contact. On the long term, grinding the plant residues has no significant effect on N dynamics.     

Structure and Mode-of-Action of the Two-Peptide (Class-IIb) Bacteriocins

This review focuses on the structure and mode-of-action of the two-peptide (class-IIb) bacteriocins that consist of two different peptides whose genes are next to each other in the same operon. Optimal antibacterial activity requires the presence of both peptides in about equal amounts. The two peptides are synthesized as preforms that contain a 15–30 residue double-glycine-type N-terminal leader sequence that is cleaved off at the C-terminal side of two glycine residues by a dedicated ABC-transporter that concomitantly transfers the bacteriocin peptides across cell membranes. Two-peptide bacteriocins render the membrane of sensitive bacteria permeable to a selected group of ions, indicating that the bacteriocins form or induce the formation of pores that display specificity with respect to the transport of molecules. Based on structure–function studies, it has been proposed that the two peptides of two-peptide bacteriocins form a membrane-penetrating helix–helix structure involving helix–helix-interacting GxxxG-motifs that are present in all characterized two-peptide bacteriocins. It has also been suggested that the membrane-penetrating helix–helix structure interacts with an integrated membrane protein, thereby triggering a conformational alteration in the protein, which in turn causes membrane-leakage. This proposed mode-of-action is similar to the mode-of-action of the pediocin-like (class-IIa) bacteriocins and lactococcin A (a class-IId bacteriocin), which bind to a membrane-embedded part of the mannose phosphotransferase permease in a manner that causes membrane-leakage and cell death.     

Time‐dependent climate impact and energy efficiency of combined heat and power production from short‐rotation coppice willow using pyrolysis or direct combustion

A life cycle assessment of a Swedish short‐rotation coppice willow bioenergy system generating electricity and heat was performed to investigate how the energy efficiency and time‐dependent climate impact were affected when the feedstock was converted into bio‐oil and char before generating electricity and heat, compared with being combusted directly. The study also investigated how the climate impact was affected when part of the char was applied to soil as biochar to act as a carbon sequestration agent and potential soil improver. The energy efficiencies were calculated separately for electricity and heat as the energy ratios between the amount of energy service delivered by the system compared to the amount of external energy inputs used in each scenario after having allocated the primary energy related to the inputs between the two energy services. The energy in the feedstock was not included in the external energy inputs. Direct combustion had the highest energy efficiency. It had energy ratios of 10 and 36 for electricity and heat, respectively. The least energy‐efficient scenario was the pyrolysis scenario where biochar was applied to soils. It had energy ratios of 4 and 12 for electricity and heat, respectively. The results showed that pyrolysis with carbon sequestration might be an option to counteract the current trend in global warming. The pyrolysis system with soil application of the biochar removed the largest amount of from the atmosphere. However, compared with the direct combustion scenario, the climate change mitigation potential depended on the energy system to which the bioenergy system delivered its energy services. A system expansion showed that direct combustion had the highest climate change mitigation potential when coal or natural gas were used as external energy sources to compensate for the lower energy efficiency of the pyrolysis scenario.