Stopped-flow dynamic light scattering as a method to monitor compaction during protein folding

Kinetic dynamic light scattering is a useful tool to follow compaction during protein folding. In contrast to measurements of the formation of secondary structure and side chain ordering, kinetic measurements of compactness are not well established up to now. This work describes the adaptation of a stopped-flow system (SFM-3) to a dynamic light scattering apparatus, which allows one to monitor the compaction of protein molecules by measuring the hydrodynamic Stokes radius R. The feasibility of such investigations was demonstrated by measuring R and the integrated scattered intensity I during refolding of ribonuclease A and phosphoglycerate kinase from yeast. Refolding was initiated by rapid mixing of protein solutions containing high concentrations of guanidine hydrochloride with buffer. Between 20 and 50 mixing events were performed in these experiments. Measuring both R and I in one and the same experiment is important to distinguish between true folding of individual molecules and cases where folding is accompanied by the appearance of transient oligomers or associated misfolded structures. On refolding of ribonuclease A (0.6 M GuHCl, 25 °C), after a fast phase the Stokes radius decreased from 2.26 nm to 1.95 nm with a time constant of 27 s without detectable aggregates. By contrast, transient and stable oligomers have been observed during the more complex folding of phosphoglycerate kinase. In general, the time-resolution of the method is of the order of 1 s. It can be extended to the subsecond time-range if the number of shots is not limited by the amount of protein available. Received: 8 August 1996 / Accepted: 18 October 1996     

Phenology and Pollination Ecology of Three Brazilian Fig Species (Moraceae)

The phenology and pollination ecology of three native fig species were studied in southeastern Brazil. Populations displayed continual syconia production, with one species showing intra-tree flowering asynchrony. Pollination of the fig flowers was necessary for the development of the syconia; lack of pollination induced abortion of syconia. All three species follow the general pattern of pollination known for figs, but the behavior of the pollinator wasps, Pegoscapus spp., differed in some aspects from those of other neotropical and paleotropical fig wasps, mainly with respect to pollen loading and unloading during pollination. The longevity of Pegoscapus wasps outside the syconium was about two days.     

Matrilins mediate weak cell attachment without promoting focal adhesion formation.

The matrilins form a family of non-collagenous adaptor proteins in the extracellular matrix. The extracellular ligand interactions of matrilins have been studied in some detail, while the potential interplay between matrilins and cells has been largely neglected. Except for matrilin-4, all matrilins mediate cell attachment, but only for matrilin-1 and -3 the binding is clearly dose dependent and seen already at moderate coating concentrations. Even so, much higher concentrations of matrilin-1 or -3 than of fibronectin are required for cell attachment to reach plateau values. Integrins contribute to the matrilin-mediated cell attachment, but the binding does not lead to formation of focal contacts and reorganisation of the actin cytoskeleton. Cells deficient in beta1 integrins are able to adhere, although weaker, and matrilins do not bind the soluble integrin alpha1beta1 and alpha2beta1 ectodomains. Cell surface proteoglycans may promote the attachment, as cells deficient in glycosaminoglycan biosynthesis adhere less well to matrilin-3. Even so, exogenous glycosaminoglycans are not able to compete for the attachment of HaCaT cells to matrilins.     

Appraisal of environmental profiles of pasture-based milk production: a case study of dairy farms in the Waikato region,New Zealand

Purpose

Dairying is a relatively intensive livestock production system and contributes to a range of environmental impacts. In the southern hemisphere, dairy farming systems are based mainly on outdoor grazing of permanent pastures. The objectives of this study were to (i) assess environmental profiles and (ii) to identify environmental hotspots in a pasture-based dairy farming system.

Methods

A cradle-to-farm gate life cycle assessment of 53 dairy farms in the Waikato region, New Zealand, was carried out, using 1 kg of fat- and protein-corrected milk as the functional unit. Twelve environmental impact categories were assessed: climate change (CC), ozone depletion potential (ODP), cancer effects (Cancer), non-cancer effects (non-cancer), particulate matter (PM), ionizing radiation (IR), photochemical ozone formation potential (POFP), acidification potential (AP), terrestrial eutrophication potential (TEP), freshwater eutrophication potential (FEP), marine eutrophication potential (MEP) and ecotoxicity for aquatic freshwater (Ecotox). Contribution and sensitivity analyses were performed to determine key hotspots and investigate potential changes in results due to methodological choices.

Results and discussion

The on-farm stage contributed >50 % of the total result for 7 out of 12 indicators (CC, Non-cancer, PM, POFP, AP, TEP, MEP). The off-farm rearing of replacement animals contributed 11–20 % to the total result for all indicators. The production of brought-in (from off-farm) feeds for use on the dairy farms contributed >10 % to the indicator results for Non-cancer (25 %), FEP (15 %), MEP (12 %) and Ecotox (19 %). The manufacturing of agrichemicals for use on the dairy farms contributed >10 % to the indicator results for ODP (26 %), Cancer (26 %), PM (19 %), IR (46 %), FEP (25 %) and Ecotox (42 %). The transportation of off-farm inputs for use on the dairy farms contributed >10 % to the impacts on ODP (15 %), IR (21 %) and POFP (11 %). Sensitivity analysis demonstrated the influence of choices associated with data sources, inventories and impact assessment models on the results.

Conclusions

The off-farm activities together contributed >50 % to 5 out of 12 impact indicator results, >45 % to a further two impact indicator results and 32 % of the CC result. Therefore, environmental improvement options should focus on both on-farm and off-farm activities. A focus on just one impact category (such as CC) risks ignoring the environmental hotspots that are revealed in a more comprehensive environmental assessment.

     

Authors index

In a runoff irrigation system in Northern Kenya, we studied the nutrient interactions of sole cropped and alley cropped Sorghum bicolor (L.) Moench and Acacia saligna (Labill.) H.L. Wendl. The trees were pruned once before the cropping season and the biomass was used as fodder for animals. The nutrient contents in leaf tissue, soil and soil solution were monitored and the uptake of applied tracers (¹⁵N, Sr) was followed. The grain yield of alley cropped sorghum was similar to or slightly higher than in monoculture and did not decrease near the tree-crop interface. Foliar N and Ca contents of the crop were higher in the agroforestry combination than in monoculture, corresponding to higher soil N and Ca contents. Soil solution and soil mineral N dynamics indicate an increase of N under the tree row and unused soil N at the topsoil in the alley of the sole cropped trees as well as below 60 cm depth in the crop monoculture. The N use efficiency of the tree+crop combination was higher than the sole cropped trees or crops. Competition was observed for Zn and Mn of both tree and crop whereas for Ca only the tree contents decreased. P, K, Mg and Fe dynamics were not affected by alley cropping at our site. The lower uptake of applied Sr by trees in alley cropping compared to those of the monoculture stand suggested a lower competitiveness of the acacia than sorghum, which did not show lower Sr contents when intercropped. The study showed the usefulness of combining soil and plant analyses together with tracer techniques identifying nutrient competition, nutrient transfer processes and the complementary use of soil nutrients, as the main features of the tree-crop combination. This revised version was published online in June 2006 with corrections to the Cover Date.     

Abalone (Haliotis tuberculata) hemocyanin type 1 (HtH1). Organization of the approximately 400 kDa subunit, and amino acid sequence of its functional units f, g and h.

We have identified two separate hemocyanin types (HtH1 and HtH2) in the European abalone Haliotis tuberculata. HtH1/HtH2 hybrid molecules were not found. By selective dissociation of HtH2 we isolated HtH1 which, as revealed by electron microscopy and SDS/PAGE, is present as didecamers of a approximately 400 kDa subunit. Immunologically, HtH1 and HtH2 correspond to keyhole limpet hemocyanin (KLH)1 and KLH2, respectively, the two well-studied hemocyanin types of the closely related marine gastropod Megathura crenulata. On the basis of limited proteolytic cleavage, two-dimensional immunoelectrophoresis, SDS/PAGE and N-terminal sequencing, we identified eight different 40-60 kDa functional units in HtH1, termed HtH1-a to HtH1-h, and determined their linear arrangement within the elongated subunit. From Haliotis mantle tissue, rich in hemocyanin-producing pore cells, we isolated mRNA and constructed a cDNA library. By expression screening with HtH-specific rabbit antibodies, a cDNA clone was isolated and sequenced which codes for the three C-terminal functional units f, g and h of HtH1. Their sequences were aligned to those available from other molluscs, notably to functional unit f and functional unit g from the cephalopod Octopus dofleini. HtH1-f, which is the first sequenced functional unit of type f from a gastropod hemocyanin, corresponds to functional unit f from Octopus. Also functional unit g from Haliotis and Octopus correspond to each other. HtH1-h is a gastropod hemocyanin functional unit type which is absent in cephalopods and has not been sequenced previously. It exhibits a unique tail extension of approximately 95 amino acids, which is lacking in functional units a to g and aligns with a published peptide sequence of 48 amino acids from functional unit h of Helix pomatia hemocyanin. The new Haliotis sequences are discussed with respect to their counterparts in Octopus, the 15 A three-dimensional reconstruction of the KLH1 didecamer from electron micrographs, and the recent 2.3 A X-ray structure of functional unit g from Octopus hemocyanin.     

Translational control of dosage compensation in Drosophila by Sex-lethal: cooperative silencing via the 5' and 3' UTRs of msl-2 mRNA is independent of the poly(A) tail.

Translational repression of male-specific-lethal 2 (msl-2) mRNA by Sex-lethal (SXL) controls dosage compensation in Drosophila. In vivo regulation involves cooperativity between SXL-binding sites in the 5' and 3' untranslated regions (UTRs). To investigate the mechanism of msl-2 translational control, we have developed a novel cell-free translation system from Drosophila embryos that recapitulates the critical features of mRNA translation in eukaryotes: cap and poly(A) tail dependence. Importantly, tight regulation of msl-2 translation in this system requires cooperation between the SXL-binding sites in both the 5' and 3' UTRs, as seen in vivo. However, in contrast to numerous other developmentally regulated mRNAs, the regulation of msl-2 mRNA occurs by a poly(A) tail-independent mechanism. The approach described here allows mechanistic analysis of translational control in early Drosophila development and has revealed insights into the regulation of dosage compensation by SXL.     

Identification of progesterone and 5α‐dihydroprogesterone (5α‐DHP) in zebras by two‐dimensional high‐performance liquid chromatography and their dependence on the state of reproduction

Because of its low levels in late pregnancy, the relationship of progesterone to pregnancy maintenance in Equidae is not obvious. This study investigated the levels of progesterone (4‐pregnane‐3,20‐dione; P4) and 5α‐dihydroprogesterone (5α‐DHP) during pregnancy in zebras in relation to reproductive state. Blood samples from female zebras (Equus burchelli, E. zebra hartmannae, E. grevyi) were taken at Dvur Kralove Zoo. Progesterone and 5α‐DHP were separated by high‐performance liquid chromatography techniques and detected by cross‐reacting antibodies. Identification of progestins was achieved by comparing the identity of peaks of the samples with a standard. In E. z. hartmannae progesterone, values reached 50 ng/mL at the beginning of pregnancy and dropped to levels below 1 ng/mL during the second half of pregnancy. In contrast, 5α‐DHP increased up to 123 and 183 ng/mL during late pregnancy in E. z. hartmannae and E. burchelli, respectively. In E. grevyi, 5α‐DHP levels of 368 ng/mL were obtained during pregnancy, whereas progesterone values were similar in pregnant and non‐pregnant individuals. These marked differences in the course of progesterone and 5α‐DHP levels point to the importance of 5α‐DHP for pregnancy maintenance in zebras. Zoo Biol 18:325–333, 1999. © 1999 Wiley‐Liss, Inc.     

Distinct thyroid hormone‐dependent expression of trkB and p75NGFR in nonneuronal cells during the critical TH‐dependent period of the cochlea

Analyzing the thyroid hromone (TH)‐dependent period of the inner ear, we observed that the presence of triiodothyronine (T3) between postnatal day 3 (P3) and P12 is sufficient for functional maturation of the auditory system. Within this short time period, an unusual transient TH‐dependent expression of nonneuronal neurotrophin receptors (NT‐R) trkB and p75^NGFR was observed in correlation with neuronal and morphogenetic processes. The availability of thyroid hormone was revealed to be invariably correlated with (a) a transient expression of full‐length trkB in TRα1‐, TRα2‐ and TRβ1‐expressing hair cells concomitant to the segregation of afferent fibers and the synaptogenesis of efferent fibers; and (b) a transient expression of p75^NGFR in TRα1‐ and TRβ1‐expressing great epithelia ridge cells in direct spatiotemporal correlation with the appearance of apoptotic cells and morphogenetic maturation of the organ. For the first time, these data suggest a TH dependency of the expression of neurotrophin receptors in nonneuronal cells. A potential role of these peculiar neurotrophin receptor expression for the conversion of the biological function of TH on innervation patterning and morphogenesis during the critical TH‐dependent period of the inner ear may be considered. © 1999 John Wiley & Sons, Inc. J Neurobiol 38: 338–356, 1999