Direct detection of soil-bound prions

Scrapie and chronic wasting disease are contagious prion diseases affecting sheep and cervids, respectively. Studies have indicated that horizontal transmission is important in sustaining these epidemics, and that environmental contamination plays an important role in this. In the perspective of detecting prions in soil samples from the field by more direct methods than animal-based bioassays, we have developed a novel immuno-based approach that visualises in situ the major component (PrP(Sc)) of prions sorbed onto agricultural soil particles. Importantly, the protocol needs no extraction of the protein from soil. Using a cell-based assay of infectivity, we also report that samples of agricultural soil, or quartz sand, acquire prion infectivity after exposure to whole brain homogenates from prion-infected mice. Our data provide further support to the notion that prion-exposed soils retain infectivity, as recently determined in Syrian hamsters intracerebrally or orally challenged with contaminated soils. The cell approach of the potential infectivity of contaminated soil is faster and cheaper than classical animal-based bioassays. Although it suffers from limitations, e.g. it can currently test only a few mouse prion strains, the cell model can nevertheless be applied in its present form to understand how soil composition influences infectivity, and to test prion-inactivating procedures.     

Resistance of soil-bound prions to rumen digestion

Before prion uptake and infection can occur in the lower gastrointestinal system, ingested prions are subjected to anaerobic digestion in the rumen of cervids and bovids. The susceptibility of soil-bound prions to rumen digestion has not been evaluated previously. In this study, prions from infectious brain homogenates as well as prions bound to a range of soils and soil minerals were subjected to in vitro rumen digestion, and changes in PrP levels were measured via western blot. Binding to clay appeared to protect noninfectious hamster PrP(c) from complete digestion, while both unbound and soil-bound infectious PrP(Sc) proved highly resistant to rumen digestion. In addition, no change in intracerebral incubation period was observed following active rumen digestion of unbound hamster HY TME prions and HY TME prions bound to a silty clay loam soil. These results demonstrate that both unbound and soil-bound prions readily survive rumen digestion without a reduction in infectivity, further supporting the potential for soil-mediated transmission of chronic wasting disease (CWD) and scrapie in the environment.     

An enzymatic treatment of soil-bound prions effectively inhibits replication

Chronic wasting disease (CWD) and scrapie can be transmitted through indirect environmental routes, possibly via soil, and a practical decontamination strategy for prion-contaminated soil is currently unavailable. In the laboratory, an enzymatic treatment under environmentally relevant conditions (22°C, pH 7.4) can degrade soil-bound PrPSc below the limits of Western blot detection. We developed and used a quantitative serial protein misfolding cyclic amplification (PMCA) protocol to characterize the amplification efficiency of treated soil samples relative to controls of known infectious titer. Our results suggest large (10(4)- to >10(6)-fold) decreases in soil-bound prion infectivity following enzyme treatment, demonstrating that a mild enzymatic treatment could effectively reduce the risk of prion disease transmission via soil or other environmental surfaces.     

Replication of prions in differentiated muscle cells

We have demonstrated that prions accumulate to high levels in non-proliferative C2C12 myotubes. C2C12 cells replicate as myoblasts but can be differentiated into myotubes. Earlier studies indicated that C2C12 myoblasts are not competent for prion replication.¹ We confirmed that observation and demonstrated, for the first time, that while replicative myoblasts do not accumulate PrP^Sc, differentiated post-mitotic myotube cultures replicate prions robustly. Here we extend our observations and describe the implication and utility of this system for replicating prions.     

Phosphorus mining efficiency declines with decreasing soil P concentration and varies across crop species

High soil P concentrations hinder ecological restoration of biological communities typical for nutrient-poor soils. Phosphorus mining, i.e., growing crops with fertilization other than P, might reduce soil P concentrations. However, crop species have different P-uptake rates and can affect subsequent P removal in crop rotation, both of which may also vary with soil P concentration. In a pot experiment with three soil-P-levels (High-P: 125–155 mg P_Olsen/kg; Mid-P: 51–70 mg P_Olsen/kg; Low-P: 6–21 mg P_Olsen/kg), we measured how much P was removed by five crop species (buckwheat, maize, sunflower, flax, and triticale). Total P removal decreased with soil-P-level and depended upon crop identity. Buckwheat and maize removed most P from High-P and Mid-P soils and triticale removed less P than buckwheat, maize, and sunflower at every soil-P-level. The difference in P removal between crops was, however, almost absent in Low-P soils. Absolute and relative P removal with seeds depended upon crop species and, for maize and triticale, also upon soil-P-level. None of the previously grown crop species significantly affected P removal by the follow-up crop (perennial ryegrass). We can conclude that for maximizing P removal, buckwheat or maize could be grown.     

Effects of solution chemistry and aging time on prion protein adsorption and replication of soil-bound prions

Prion interactions with soil may play an important role in the transmission of chronic wasting disease (CWD) and scrapie. Prions are known to bind to a wide range of soil surfaces, but the effects of adsorption solution chemistry and long-term soil binding on prion fate and transmission risk are unknown. We investigated HY TME prion protein (PrP(Sc)) adsorption to soil minerals in aqueous solutions of phosphate buffered saline (PBS), sodium chloride, calcium chloride, and deionized water using western blotting. The replication efficiency of bound prions following adsorption in these solutions was also evaluated by protein misfolding cyclic amplification (PMCA). Aging studies investigated PrP(Sc) desorption and replication efficiency up to one year following adsorption in PBS or DI water. Results indicate that adsorption solution chemistry can affect subsequent prion replication or desorption ability, especially after incubation periods of 30 d or longer. Observed effects were minor over the short-term (7 d or less). Results of long-term aging experiments demonstrate that unbound prions or prions bound to a diverse range of soil surfaces can readily replicate after one year. Our results suggest that while prion-soil interactions can vary with solution chemistry, prions bound to soil could remain a risk for transmitting prion diseases after months in the environment.     

Relationship between conformational stability and amplification efficiency of prions

Recent studies demonstrated that the efficiency, rate, and yield of prion amplification in vitro could be substantially improved by supplementing protein misfolding cyclic amplification (PMCA) with Teflon beads [Gonzalez-Montalban et al. (2011) PLoS Pathog. 7, e1001277]. Here we employed the new PMCA format with beads (PMCAb) to gain insight into the mechanism of prion amplification. Using a panel of six hamster prion strains, the effect of beads on amplification was found to be strain-specific, with the largest improvements in efficiency observed for strains with the highest conformational stability. This result suggests a link between PrP(Sc) conformational stability and its fragmentation rate and that beads improved amplification by assisting fragmentation. Furthermore, while exploring the PrP(Sc)-independent bead effect mechanism, a synergy between the effects of RNA and beads on amplification was observed. Consistent with previous studies, amplification of all six hamster strains tested here was found to be RNA-dependent. Under sonication conditions used for PMCA, large RNA molecules were found to degrade into smaller fragments of a size that was previously shown to be the most effective in facilitating prion conversion. We speculate that sonication-induced changes in RNA size distribution could be one of the rate-limiting steps in prion amplification.     

Biomass-density relationship varies with water use efficiency across an aridity gradient

Accumulating evidence has shown that the scaling exponent (α) of the aboveground biomass-density relationship is not a constant value. Debate continues over what determines the variation in α. By measuring foliar stable carbon isotope, plant morphological traits and α along an aridity gradient from eastern to western China, we confirmed that the variation in α was accounted for by changes in plant morphological traits which are adaptive strategies for enhancing water use efficiency during drought stress. This information can be crucial for understanding and predicting community and ecosystem processes.     

Assembly of vimentin in cultured cells varies with cell type

To examine how vimentin assembles into the cytoskeletons of cultured cells, we used pulse labeling with [35S]methionine, cell fractionation with Triton X-100, and immunoprecipitation with a monoclonal antibody that binds both nascent and full-length vimentin polypeptides. In embryonic muscle cells, fibroblasts, and erythroid cells, we find two populations of newly synthesized vimentin. One population is found on the cytoskeleton immediately after a 2-min pulse with labeled methionine; the other is delayed in its association with the cytoskeleton and has a measurable rate of disappearance from the extractable pool. This rate varies with cell type, being over 3-fold faster in muscle and fibroblast cells than in erythroid cells. By using [3H]puromycin to specifically label nascent chains, we detect nascent vimentin chains that are bound to the cytoskeleton independently of ribosomes. The fraction of newly synthesized, full-length vimentin that associates with the cytoskeleton immediately correlates in these cell types with the fraction of nascent vimentin chains that are not released from the cytoskeleton by puromycin, RNase, or 0.6 M NaCl. Over one-half of the newly synthesized vimentin associates immediately in muscle and fibroblasts, whereas this value is less than 15% in erythroid cells. These data suggest that the process of vimentin assembly may vary both kinetically and mechanistically in different cell types.     

Binding of transforming growth factor-beta to cell surface proteins varies with cell type

Transforming growth factor-beta (TGF beta 1 and TGF beta 2) bind to several different cell surface proteins, including a high Mr proteoglycan. We found that on primary and early passage cultures of fibroblasts, chondroblasts, and osteoblasts TGF beta 1 binds to both the high Mr proteoglycan and to lower Mr components, whereas on epithelial, endothelial, and lymphoid-derived cells TGF beta 1 only binds to the lower Mr species. With cell lines, this distinction is lost. Further analysis indicated that binding to the high Mr proteoglycan is not necessary for TGF beta 1 induced regulation of DNA, collagen and fibronectin synthesis, change in cell morphology, or reorganization of the actin cytoskeleton. We propose that the lower Mr components are the active receptors mediating these events.     

Chimeric yeast prions with unstable inheritance

The Saccharomyces cerevisiae [PSI] factor, a cytoplasmic omnipotent nonsense suppressor, is a conformationally changed (prion) form of translation termination factor eRF3 (Sup35p). Induction and maintenance of the [PSI] factor depend on the prionizing peptide located in the N domain of Sup35p. The N domain of Sup35p was fused with phosphoribosylaminoimidazole carboxylase (Ade2p), a purine biosynthesis enzyme, and the hybrid protein (NM-Sup35p::Ade2p) was tested for induction of the [PSI] factor. Transformation with a centromeric plasmid carrying the gene for NM-Sup35p::Ade2p induced a [PSI]-like factor in yeast cells, which was evident from efficient nonsense suppression. The suppressory effect depended on the presence of the prionizing peptide both in the hybrid protein and in Sup35p synthesized from the chromosomal gene, as well as on the presence of the prion-like [PIN] factor in the cell.     

Transcription efficiency of human apolipoprotein A-I promoter varies with naturally occurring A to G transition.

In human, the gene coding for apolipoprotein A-I (apo A-I), a protein of the plasma lipid transport system, is expressed only in the liver and the intestine. A naturally occurring A to G substitution in the promoter at position -78 was shown to be associated with high density lipoproteins (HDL) in females. We have studied the effect of this mutation on promoter activity using various lengths of promoter sequences and the CAT reporter gene system. Transient expression studies after introduction of these constructs into Hep 3B cells revealed that in the region spanning -330 to +1 of the promoter an A to G substitution increases the activity approximately twofold. On the other hand, when further upstream region (-1469 to +397) is also included, the promoter activity seems comparable in both alleles. Our results show how minimal sequence variations can affect the in vitro analysis of promoter activity.     

Synthetic prions with novel strain-specified properties

Prions are infectious proteins that possess multiple self-propagating structures. The information for strains and structural specific barriers appears to be contained exclusively in the folding of the pathological isoform, PrP^Sc. Many recent studies determined that de novo prion strains could be generated in vitro from the structural conversion of recombinant (rec) prion protein (PrP) into amyloidal structures. Our aim was to elucidate the conformational diversity of pathological recPrP amyloids and their biological activities, as well as to gain novel insights in characterizing molecular events involved in mammalian prion conversion and propagation. To this end we generated infectious materials that possess different conformational structures. Our methodology for the prion conversion of recPrP required only purified rec full-length mouse (Mo) PrP and common chemicals. Neither infected brain extracts nor amplified PrP^Sc were used. Following two different in vitro protocols recMoPrP converted to amyloid fibrils without any seeding factor. Mouse hypothalamic GT1 and neuroblastoma N2a cell lines were infected with these amyloid preparations as fast screening methodology to characterize the infectious materials. Remarkably, a large number of amyloid preparations were able to induce the conformational change of endogenous PrP^C to harbor several distinctive proteinase-resistant PrP forms. One such preparation was characterized in vivo habouring a synthetic prion with novel strain specified neuropathological and biochemical properties.     

Mutability of prions

Murine prions transferred from brain to cultured cells gradually adapt to the new environment. Brain-derived 22L prions can infect neuroblastoma-derived PK1 cells in the presence of swainsonine (swa); that is, they are 'swa resistant'. PK1 cell-adapted 22L prions are swa sensitive; however, propagation in swa results in selection of swa-resistant substrains. Cloned, PK1 cell-adapted 22L prions were initially unable to develop swa resistance ('swa incompetent'); however, after serial propagation for 30-90 doublings, four of nine clones became swa competent, showing that swa-resistant 'mutants' arose during replication. Mutations in the case of prions are attributed to heritable changes in PrP(Sc) conformation. One clone remained swa incompetent even after 10(35)-fold expansion; surprisingly, after propagation in brain, it yielded swa-resistant prions, indistinguishable from the original 22L population. Thus, cell-adapted 22L prions assumed either mutable or virtually immutable conformations; however, when passaged through the brain all became mutable. Mutability is thus a substrain-specific attribute.     

植被类型变化对土壤微生物碳利用效率的影响研究进展

植被类型变化强烈影响着土壤碳循环。土壤微生物碳利用效率（CUE）是微生物将从环境中获取的碳分配给自身生长的比例,是土壤碳循环的综合指标。研究植被类型变化对CUE的影响有助于从微生物视角理解该过程中的土壤碳动态,可以为评估植被类型变化对土壤质量及生态系统碳循环的影响提供基础,具有重要的理论及实际价值。通过系统查阅相关文献,综述了植被类型变化导致的CUE变化情况,以及该过程中影响CUE的因子与机制。目前,相关研究主要涉及以林地、草地和农业用地为起点或终点的植被变化类型。天然林（原生林、次生林）变化为人工林、林地变化为草地后CUE普遍下降,随终点植被的发展CUE可能恢复至起点水平。植被成熟度越高,发生转变时CUE变化越剧烈。植被类型变化以农业用地为起点或终点时,CUE变化方向的不确定性及幅度的变异性均增加。植被类型变化导致的CUE变化主要受到植被、土壤、微生物因子及其交互作用的驱动,指示CUE的指标、采样季节和土层也会一定程度上影响CUE的变化。今后相关研究应采用直接的CUE测定方法,拓宽研究气候区及植被变化类型,关注植被变化过程中CUE变化的土层差异及动态监测,深入对植被类型变化导致的生态环境因子变化与CUE的关系及作用机制的研究。     

ATP modulation of ATP-sensitive potassium channel ATP sensitivity varies with the type of SUR subunit

ATP-sensitive potassium (K(ATP)) channels comprise Kir and SUR subunits. Using recombinant K(ATP) channels expressed in Xenopus oocytes, we observed that MgATP (100 microm) block of Kir6.2/SUR2A currents gradually declined with time, whereas inhibition of Kir6.2/SUR1 or Kir6.2DeltaC36 currents did not change. The decline in Kir6.2/SUR2A ATP sensitivity was not observed in Mg(2+) free solution and was blocked by the phosphatidylinositol (PI) 3-kinase inhibitors LY 294002 (10 microm) and wortmannin (100 microm), and by neomycin (100 microm). These results suggest that a MgATP-dependent synthesis of membrane phospholipids produces a secondary decrease in the ATP sensitivity of Kir6.2/SUR2A. Direct application of the phospholipids PI 4,5-bisphosphate and PI 3,4,5-trisphosphate in the presence of 100 microm MgATP activated all three types of channel, but the response was faster for Kir6.2/SUR2A. Chimeric studies indicate that the different responses of Kir6.2/SUR2A and Kir6.2/SUR1 are mediated by the first six transmembrane domains of SUR. The MgATP-dependent loss of ATP sensitivity of Kir6.2/SUR2A was enhanced by the actin filament disrupter cytochalasin and blocked by phalloidin (which stabilizes the cytoskeleton). Phalloidin did not block the effect of PI 3,4,5-trisphosphate. This suggests that MgATP may cause disruption of the cytoskeleton, leading to enhanced membrane phospholipid levels (or better targeting to the K(ATP) channel) and thus to decreased channel ATP sensitivity.     

Access to organic and insoluble sources of phosphorus varies among soil Chytridiomycota

The sources of minerals accessed by fungi in the Chytridiomycota (chytrid) in soil are largely unknown. The ability of ten species of soil chytrids to use various sources of phosphorus was examined in vitro. While all grew on orthophosphate, fifty per cent of isolates grew on phytic acid, and one isolate grew on DNA as the sole source of phosphorus. All isolates solubilised and utilised CaHPO₄. Most isolates utilised hydroxyapatite when NH₄⁺ was the nitrogen source. When ammonium was omitted, 50% of isolates solubilised hydroxyapatite. Many soil chytrids may utilise phosphomonoesters as the sole source of phosphorus, and access to DNA appears limited. We suggest that the capacity to use different sources of phosphorus may influence the diversity of chytrids found in Australian soils.