Sequestration Of Aggregates Research Articles

Elimination of virus-like particles reduces protein aggregation and extends replicative lifespan in Saccharomyces cerevisiae

A major consequence of aging and stress, in yeast to humans, is an increased accumulation of protein aggregates at distinct sites within the cells. Using genetic screens, immunoelectron microscopy, and three-dimensional modeling in our efforts to elucidate the importance of aggregate annexation, we found that most aggregates in yeast accumulate near the surface of mitochondria. Further, we show that virus-like particles (VLPs), which are part of the retrotransposition cycle of Ty elements, are markedly enriched in these sites of protein aggregation. RNA interference-mediated silencing of Ty expression perturbed aggregate sequestration to mitochondria, reduced overall protein aggregation, mitigated toxicity of a Huntington's disease model, and expanded the replicative lifespan of yeast in a partially Hsp104-dependent manner. The results are in line with recent data demonstrating that VLPs might act as aging factors in mammals, including humans, and extend these findings by linking VLPs to a toxic accumulation of protein aggregates and raising the possibility that they might negatively influence neurological disease progression.

Introducing N2-fixing tree species into Eucalyptus plantations promotes soil organic carbon sequestration in aggregates by increasing microbial carbon use efficiency

The conversion of a monoculture plantation into a mixed forest can improve soil properties and increase soil organic carbon (SOC) sequestration. However, the impacts of introducing N2-fixing tree species into Eucalyptus plantations on SOC composition and transformation, as well as the associated changes in microbial properties remain poorly understood. Here, we examined the SOC fractions (LPI-C, LPII-C, and RP-C) in different aggregates (>2.0 mm, 1–2 mm, 0.25–1 mm, and <0.25 mm) from 15-year-old plantations of pure Eucalyptus urophylla (PP) and mixed E. urophylla and Acacia mangium (an N2-fixing tree species) (MP). The results showed that the contents of SOC fractions and the proportion of recalcitrant C pool (fRP-C) in aggregates were significantly higher (P < 0.05) in MP than those in PP. Pearson correlation analysis indicated strong correlations among litter properties, soil properties, and microbial properties. N2-fixing species increased soil aggregate stability and N availability while altering litter quality and quantity; all of these factors strongly impacted microbial properties. Changes in nitrogen availability and microbial properties (e.g. carbon use efficiency) were the drivers of changes in SOC fractions. Our findings highlight the importance of introducing N2-fixing species in regulating soil microbial properties thereby increased SOC sequestration and stability in Eucalyptus plantations, which should be a relatively good option for future afforestation projects in the view of improving the carbon benefits of the ecosystem.

Syntaxin 5-dependent phosphorylation of the small heat shock protein Hsp42 and its role in protein quality control.

The small heat shock protein Hsp42 and the t-SNARE protein Sed5 have central roles in the sequestration of misfolded proteins into insoluble protein deposits in the yeast Saccharomyces cerevisiae. However, whether these proteins/processes interact in protein quality control (PQC) is not known. Here, we show that Sed5 and anterograde trafficking modulate phosphorylation of Hsp42 partially via the MAPK kinase Hog1. Such phosphorylation, specifically at residue S215, abrogated the co-localization of Hsp42 with the Hsp104 disaggregase, aggregate clearance, chaperone activity, and sequestration of aggregates to IPOD and mitochondria. Furthermore, we found that Hsp42 is hyperphosphorylated in old cells leading to a drastic failure in disaggregation. Old cells also displayed a retarded anterograde trafficking, which, together with slow aggregate clearance and hyperphosphorylation of Hsp42, could be counteracted by Sed5 overproduction. We hypothesize that the breakdown of proper PQC during yeast aging may, in part, be due to a retarded anterograde trafficking leading to hyperphosphorylation of Hsp42.

The contribution of microbial necromass carbon to soil organic carbon in soil aggregates

Microbial necromass is known to be the main component of soil organic carbon (C) sequestration. However, the contribution of microbial necromass to soil aggregates has not been comprehensively studied because of the heterogeneity of microhabitats in different soil aggregates, especially in different ecosystems on a global scale. To address this gap, we conducted a global-scale meta-analysis to investigate the contribution of microbial necromass to carbon sequestration in aggregates and identify the climatic and soil factors that influence necromass carbon in aggregates. The database of fungal and bacterial necromass carbon was based on the glucosamine and muramic acid contents in microaggregates (< 250 μm, 226 samples), medium macroaggregates (250–2000 μm,132 samples), and macroaggregates (> 2000 μm, 66 samples). On average, microbial necromass carbon in microaggregates, medium macroaggregates, and macroaggregates contributed 48.5 %, 40.9 %, and 42.5 % of aggregate carbon sequestration, respectively. The contribution of fungal necromass carbon was significantly higher than that of bacteria (average 30.9 % vs. 13.1 %, respectively). Meanwhile, the ratio of fungal to bacterial necromass carbon increased with the increasing aggregate size, from 2.68 (< 250 μm) to 3.11 (250–2000 μm) to 3.14 (> 2000 μm) for micro, medium size, and macroaggregates, respectively. In addition, the screening method for aggregates and the type of land use significantly affected the contribution of microbial necromass to aggregate carbon sequestration. Specifically, grassland and dry sieving significantly increased the contribution of microbial necromass carbon to aggregate carbon. Finally, the results from PLS-PM showed that climatic factors regulated fungal and bacterial necromass carbon through soil pH, sand, and nutrients in aggregates, thereby enhancing the contribution of microbial necromass to aggregate carbon sequestration. In addition, fungal and bacterial necromass carbon improved with increasing carbon and nitrogen content of the aggregates. Furthermore, a lower soil pH seemingly stimulates the accumulation of fungal and bacterial necromass in soil aggregates. These findings emphasize that the contribution of microbial necromass carbon to aggregate carbon sequestration, especially fungal necromass carbon, is an important method for improving carbon sequestration in soil aggregates.

Influences of 13 Years New Conservation Management on Labile Soil Organic Carbon and Carbon Sequestration in Aggregates in Northeast China

New conservation management (NCM) for summer maize monocultures might cause changes in the organic carbon composition when compared with conventional tillage (CT). To investigate the difference, the soil organic carbon (SOC) under 13 years of NCM and CT was studied in Northeast China. The NCM involved the use of a 40 cm and 160 cm narrow-wide row (maize was planted in the narrow row in two lines) with straw retained, but with no tillage and change in ridge direction. SOC in different soil aggregate size classes and labile organic carbon fractions at 0–10 cm, 10–20 cm and 20–40 cm depths were evaluated. The results showed that there was no significant difference in SOC content at a 0–10 cm depth, with values ranging from 19.9 to 21.1 g·kg−1 between two management systems. The contents of microbial biomass carbon (MBC) and light fraction organic carbon (LFOC) were significantly higher in NCM than in CT in the upper 10 cm. Among the labile organic carbon fractions, the light fraction organic C (LFOC) was the most sensitive to management change. The portion of macroaggregates (&gt;0.25 mm) was higher under NCM than under CT and decreased with the increase in soil depth. NCM improved the organic carbon storage in aggregates 1–0.5 mm and reduced the organic carbon storage in microaggregates. It was concluded that NCM would be an effective and useful management choice for the enhancement of soil C sequestration in maize field systems in Northeast China.

Plant biomass amendment regulates arbuscular mycorrhizal role in organic carbon and nitrogen sequestration in eco-engineered iron ore tailings

Arbuscular mycorrhizal (AM) symbiosis plays an important role in organic matter (OM) stabilization and aggregate formation in eco-engineered Fe-ore tailings technosol, but their role may be influenced by the properties of tailings technosol with different plant biomass amendment and water supply, which has not been addressed. The present study investigated if different plant biomass amendments-- Lucerne hay (LH) (low C: N ratio) and Sugarcane mulch (SM) (high C: N ratio) -- could influence the AM roles in organic carbon (OC) and nitrogen (N) sequestration in tailings under well-watered or water deficit conditions. Sorghum spp. Hybrid cv. Silk with or without AM fungal inoculation was grown in tailings amended with plant biomass (either LH or SM) for 20 weeks under glasshouse conditions. The OC and N distribution among aggregates of various sizes (based on physical fractionation) were examined in the tailings technosol with different treatments. To uncover the mechanisms of OC sequestration, the mineral composition, OC forms, and the Fe phases in organo-mineral association were determined by means of X-ray photoelectron spectroscopy (XPS), attenuated total reflection-Fourier transform infrared analysis (ATR-FTIR), quantitative X-ray diffraction (qXRD), and synchrotron-based Fe K edge X-ray absorption fine structure spectroscopy (Fe K edge XAFS) analysis. AM symbiosis stimulated OC and N sequestration in aggregates formed from the amended tailings, which was regulated by the amendment of plant biomass with different C: N ratios. In LH amended tailings, AM symbiosis enhanced OC sequestration in both particulate OM (POM) and mineral-associated OM (MOM) within macroaggregates. In comparison, AM symbiosis enhanced N sequestration in MOM of both macro- and micro- aggregates in the SM amended tailings. Water deficit generally diminished these AM effects. Furthermore, AM symbiosis enriched carboxyl-rich organics in association with Fe/Si-rich minerals within MOM fraction. These results imply that the AM role in OC and N sequestration in Fe ore tailings is regulated by amendment using plant biomass with different C:N ratio, which should be considered in the eco-engineered pedogenesis for sustainable mine site rehabilitation.

Accumulation of 137Cs in aggregated organomineral assemblage in pasture soils 8 years after the accident at the Fukushima Daiichi nuclear power plant

Despite the presence of minerals that allow Cs fixation in soils, 137Cs remains available to crops for several years after its deposition, particularly in pasture soils. Larger amounts of organic matter derived from herbage residues are accumulated in pasture soils than in tilled farmland soils. As the above-ground part of herbage crops initially received airborne 137Cs during the accident at Fukushima Daiich nuclear power plant (FDNPP), the organic matter originated from the contaminated herbage should play an important role in the fate of 137Cs in soils. To evaluate the role of organic matter on 137Cs distribution between potentially mobile and immobile fractions, we compared the distribution of 137Cs and stable 133Cs, which are differently associated with organic matter, by sequential extraction and density fractionation. Soil samples were collected 8 years after the accident from Andosols in pasture fields located about 160 km southwest of FDNPP. More than 90% of 137Cs was not extracted even after oxidative digestion of organic matter, suggesting that most 137Cs was strongly associated with soil minerals. Density fractionation results showed that the 137Cs/133Cs ratio was highest in the density fraction of 1.6–1.8 g cm−3, in which organic matter —including fragmented and decomposed plant detritus —was associated with minerals. Mineral-free organic matter, mostly composed of fresh plant detritus (<1.6 g cm−3), had a higher 137Cs/133Cs ratio than that of crops harvested in the same year of soil sampling. Thus, the transfer of 137Cs from soil to plants decreased with cultivation cycles. Our results demonstrate that plant-available 137Cs in pasture soil decreased with aging time, not only through increased 137Cs fixation in mineral-dominated fractions but also through its physical sequestration in aggregates.

\u0394133p53\u03b2 isoform pro-invasive activity is regulated through an aggregation-dependent mechanism in cancer cells

The p53 isoform, Δ133p53β, is critical in promoting cancer. Here we report that Δ133p53β activity is regulated through an aggregation-dependent mechanism. Δ133p53β aggregates were observed in cancer cells and tumour biopsies. The Δ133p53β aggregation depends on association with interacting partners including p63 family members or the CCT chaperone complex. Depletion of the CCT complex promotes accumulation of Δ133p53β aggregates and loss of Δ133p53β dependent cancer cell invasion. In contrast, association with p63 family members recruits Δ133p53β from aggregates increasing its intracellular mobility. Our study reveals novel mechanisms of cancer progression for p53 isoforms which are regulated through sequestration in aggregates and recruitment upon association with specific partners like p63 isoforms or CCT chaperone complex, that critically influence cancer cell features like EMT, migration and invasion.

马尾松人工林土壤各粒径团聚体湿筛后的有机碳分配

选取25a、45a和65a马尾松人工林为研究对象，采用湿筛法对各粒径土壤团聚体分别湿筛。探究了马尾松人工林各粒径团聚体湿筛后的团聚体有机碳分配，以探讨各粒径团聚体湿筛后分配到同一粒级团聚体有机碳含量及其对团聚体水稳性的贡献差异。结果表明：种植年限增加显著降低土壤团聚体水稳性（P<0.05）；各粒径团聚体湿筛后分配的有机碳随粒级减小含量呈先降后增趋势，以保持原粒级团聚体有机碳（12.96-32.01 g/kg）含量最高，其次是<0.25 mm粒级（8.08-23.53 g/kg）。各粒径团聚体湿筛分配到同一粒级的有机碳以保持原粒级的含量最高（P<0.05）；土壤团聚体水稳性与各粒径团聚体湿筛后保持原粒径的有机碳呈显著或极显著正相关（P<0.05或0.01），分配到越小的粒级正相关性越不显著。此外，团聚体水稳性与各粒径团聚体湿筛分配到同一粒级的有机碳呈正相关，以保持原粒级相关性最高（P<0.01或0.05）；回归方程及相关性系数表明，有机碳与保持原粒径团聚体呈显著呈或极显著正相关（P<0.05或0.01），与消散到其他粒级的团聚体呈负相关或极显著负相关（P>0.05或<0.01）。本研究得出有机碳含量增加促进更大粒径团聚体形成。反之，促使大粒径团聚体向较小粒径团聚体转化。同一粒级团聚体间，保持原粒级团聚体比易转化形成更大粒级团聚体有更高的有机碳含量和更强的水稳性，这对团聚体的固碳提供了新的认识。;Compared with the traditional Elliott wet screen method, the modified wet screen method can be used to analyze the difference in organic carbon for the wet sieving of each particle size aggregate to the same size. This study selected 25a, 45a and 65a Masson Pine plantations as the research objects. Soil aggregates with different particle sizes were wet-screened by wet screening method. The organic carbon distribution of soil aggregates with different particle sizes in Masson Pine plantation was investigated after wet screening. The purpose is to explore the difference of the organic carbon distribution to the same size after wet screening of aggregates of various particle sizes and its influence on the water stability of aggregates. The results showed that the increase of planting years significantly decreased the water stability of soil aggregates (P<0.05); After wet screening, the organic carbon content of each particle size aggregates decreased firstly and then increased with the decrease of grain size, so as to maintain the highest organic carbon content of the original particle size aggregates (12.96-32.01 g/kg), followed by <0.25 mm particle size aggregates (8.08-23.53 g/kg). Wet sieve agglomerates of various particle sizes allocated to the same size of organic carbon to maintain the highest content of the original size (P<0.05); There was significantly or extremely significantly positive correlation between the water stability of soil aggregates and the organic carbon of the aggregates with the original particle size after wet screening (P<0.05 or 0.01). The smaller the particle size was allocated, the less significant the positive correlation was. In addition, the water stability of aggregates was positively correlated with the organic carbon allocated to the same grain size in the wet screen of aggregates with different particle sizes, and it had the strongest correlation with the organic carbon that maintained the original grain size (P<0.01 or 0.05). The regression equation and correlation coefficient showed that the organic carbon had a significantly or extremely significantly positive correlation with the aggregates with original particle size (P<0.05 or 0.01), and an extremely significantly negative correlation with the aggregates dispersed to other particle sizes (P>0.05 or <0.01). This study concludes that organic carbon is an important cementing material for the formation of aggregates, and the increase of organic carbon content can promote the formation of larger size aggregates. On the contrary, it promotes the conversion of large particle size aggregates to small particle size aggregates. In addition, comparison among aggregates of the same grain size, maintaining the original particle size aggregates have higher organic carbon content and stronger water stability than easily transforming into larger particle size aggregates, which provides a new understanding for the carbon sequestration of aggregates.

Carbon sequestration in aggregates from native and cultivated soils as affected by soil stoichiometry

Quantitative influence and underlying mechanisms of nutrient stoichiometry on mineralization of native Soil organic C (SOC) and straw C in different aggregate classes from cultivated and non-cultivated soils are still unclear. Soil samples (Mollisols) from a native woodlot and a farmland converted from woodlot were sieved into three aggregate classes (mega-aggregates (6.3-2 mm), macro-aggregates (2-0.25 mm), and micro-aggregates (< 0.25 mm)) and incubated (180 days) under different nutrient rates (nil, low, and high supplies of N and P) with or without 13C-enriched straw amendment. Significantly higher percentage of native SOC was mineralized from mega- and macro-aggregates (65.8-82.2%) compared with micro-aggregates (48.3-52.0%) in woodlot soil. Nutrient addition significantly increased aggregate-associated C in both soils with straw, and the increase was greater in farmland than in woodlot soil and in large-sized aggregates than in micro-aggregates. These results suggested that large aggregates serve as a C reservoir of labile C, while micro-aggregates that contained C was not easily mineralized even with abundant nutrients. Differences of C mineralization among aggregate size classes were significant in woodlot soil but not in farmland soil. Depletion of SOC was greater with increasing nutrient addition rates in farmland aggregates without straw, while the depletion in woodlot aggregates showed no difference among nutrient treatments, suggesting that microbial activity was nutrient-limited in farmland aggregates. The results improved our knowledge on SOC mineralization in response to residue-nutrient management in different aggregate classes from cultivated and non-cultivated soils, which have important implications for strategies to improve soil fertility or mitigate climate change via increased SOC.

Soil organic carbon sequestration in soil aggregates in the karst Critical Zone Observatory, Southwest China

Soil organic carbon (SOC) sequestration in aggregates under land use change have been widely concerned due to intimate impacts on the sink (or source) of atmospheric carbon dioxide (CO&lt;sub&gt;2&lt;/sub&gt;). However, the quantitative relationship between soil aggregation and SOC sequestration under land uses change has been poorly studied. Distribution of aggregates, SOC contents in bulk soils and different size aggregates and their contributions to SOC sequestration were determined under different land uses in the Puding Karst Ecosystem Observation and Research Station, karst Critical Zone Observatory (CZO), Southwest China. Soil aggregation and SOC sequestration increased in the processes of farmland abandonment and recovery. SOC contents in micro-aggregates were larger than those in macro-aggregates in restored land soils, while the opposite results in farmland soils were obtained, probably due to the hindrance of the C-enriched SOC transport from macro-aggregate into micro-aggregate by the disturbance of agricultural activities. SOC contents in macro-aggregates exponentially increased with their proportions along successional land uses. Macro-aggregates accounted for over 80% on the SOC sequestration in restored land soils, while they accounted for 31–60% in farmland soils. These results indicated that macro-aggregates have a great potential for SOC sequestration in karst soils.

Targeting CD39 Toward Activated Platelets Reduces Systemic Inflammation and Improves Survival in Sepsis: A Preclinical Pilot Study.

Sepsis is associated with a systemic inflammatory reaction, which can result in a life-endangering organ dysfunction. Pro-inflammatory responses during sepsis are characterized by increased activation of leukocytes and platelets, formation of platelet-neutrophil aggregates, and cytokine production. Sequestration of platelet-neutrophil aggregates in the microvasculature contributes to tissue damage during sepsis. At present no effective therapeutic strategy to ameliorate these events is available. In this preclinical pilot study, a novel anti-inflammatory approach was evaluated, which targets nucleoside triphosphate hydrolase activity toward activated platelets via a recombinant fusion protein combining a single-chain antibody against activated glycoprotein IIb/IIIa and the extracellular domain of CD39 (targ-CD39). Experimental animal study and cell culture study. University-based experimental laboratory. Human dermal microvascular endothelial cells 1, human platelets and neutrophils, and C57BL/6NCrl mice. Platelet-leukocyte-endothelium interactions were evaluated under inflammatory conditions in vitro and in a murine lipopolysaccharide-induced sepsis model in vivo. The outcome of polymicrobial sepsis was evaluated in a murine cecal ligation and puncture model. To evaluate the anti-inflammatory potential of activated platelet targeted nucleoside triphosphate hydrolase activity, we employed a potato apyrase in vitro and in vivo, as well as targ-CD39 and as a control, nontarg-CD39 in vivo. Under conditions of sepsis, agents with nucleoside triphosphate hydrolase activity decreased platelet-leukocyte-endothelium interaction, transcription of pro-inflammatory cytokines, microvascular platelet-neutrophil aggregate sequestration, activation marker expression on platelets and neutrophils contained in these aggregates, leukocyte extravasation, and organ damage. Targ-CD39 had the strongest effect on these variables and retained hemostasis in contrast to nontarg-CD39 and potato apyrase. Most importantly, targ-CD39 improved survival in the cecal ligation and puncture model to a stronger extent then nontarg-CD39 and potato apyrase. Targeting nucleoside triphosphate hydrolase activity (CD39) toward activated platelets is a promising new treatment concept to decrease systemic inflammation and mortality of sepsis. This innovative therapeutic approach warrants further development toward clinical application.

Human DnaJB6 Antiamyloid Chaperone Protects Yeast from Polyglutamine Toxicity Separately from Spatial Segregation of Aggregates.

Polyglutamine (polyQ) aggregates are associated with pathology in protein-folding diseases and with toxicity in the yeast Saccharomyces cerevisiae Protection from polyQ toxicity in yeast by human DnaJB6 coincides with sequestration of aggregates. Gathering of misfolded proteins into deposition sites by protein quality control (PQC) factors has led to the view that PQC processes protect cells by spatially segregating toxic aggregates. Whether DnaJB6 depends on this machinery to sequester polyQ aggregates, if this sequestration is needed for DnaJB6 to protect cells, and the identity of the deposition site are unknown. Here, we found DnaJB6-driven deposits share characteristics with perivacuolar insoluble protein deposition sites (IPODs). Binding of DnaJB6 to aggregates was necessary, but not enough, for detoxification. Focal formation required a DnaJB6-Hsp70 interaction and actin, polyQ could be detoxified without sequestration, and segregation of aggregates alone was not protective. Our findings suggest DnaJB6 binds to smaller polyQ aggregates to block their toxicity. Assembly and segregation of detoxified aggregates are driven by an Hsp70- and actin-dependent process. Our findings show sequestration of aggregates is not the primary mechanism by which DnaJB6 suppresses toxicity and raise questions regarding how and when misfolded proteins are detoxified during spatial segregation.

Selective aggregation of the splicing factor Hsh155 suppresses splicing upon genotoxic stress.

Upon genotoxic stress, dynamic relocalization events control DNA repair as well as alterations of the transcriptome and proteome, enabling stress recovery. How these events may influence one another is only partly known. Beginning with a cytological screen of genome stability proteins, we find that the splicing factor Hsh155 disassembles from its partners and localizes to both intranuclear and cytoplasmic protein quality control (PQC) aggregates under alkylation stress. Aggregate sequestration of Hsh155 occurs at nuclear and then cytoplasmic sites in a manner that is regulated by molecular chaperones and requires TORC1 activity signaling through the Sfp1 transcription factor. This dynamic behavior is associated with intron retention in ribosomal protein gene transcripts, a decrease in splicing efficiency, and more rapid recovery from stress. Collectively, our analyses suggest a model in which some proteins evicted from chromatin and undergoing transcriptional remodeling during stress are targeted to PQC sites to influence gene expression changes and facilitate stress recovery.

Carbon sequestration and mineralization of aggregate-associated carbon in an intensively cultivated Anthrosol in north China as affected by long term fertilization

Understanding organic carbon (OC) sequestration in aggregates and OC stability under different fertilization practices is of key importance in improving soil quality and crop productivity and in mitigating the causes of climate change. A long-term field experiment established in 1990 was used to assess the influence of organic and inorganic fertilizers on aggregate-associated OC and its mineralization and on the SOC stock at a soil depth of 0–20cm under an intensive wheat-maize cropping system on Anthrosol in North China. The study involved three treatments: CK, control without fertilization; NPK, nitrogen (N), phosphorus (P) and potassium (K) fertilizers; MNPK, manure (M) combined with N, P and K fertilizers. Soil samples were collected and analyzed to determine the size distribution of aggregates, which were separated by dry sieving; the concentrations of OC and N in aggregates (>2, 0.25–2 and <0.25mm) and bulk soils; and respiration from aggregates and bulk soils in the 0–10 and 10–20cm layers after 21years. Fertilization did not affect the size distribution of aggregates in the surface soil layer, but there was a significant change in the subsurface layer in response to manure addition. Application of NPK and MNPK significantly and evenly augmented OC and N sequestration in the three aggregate classes tested. However, the OC mineralization rate was substantially higher in micro- than in macro-aggregates. Application of NPK and MNPK considerably increased OC mineralization in both aggregates and bulk soils; MNPK yielded the highest values. OC mineralization rates in bulk soils were comparable among the three treatments for the surface layer, but they increased in the subsurface layer because of adding manure. Overall, soils treated for 21years with NPK and MNPK showed increases in the OC pools in the top 20cm of 7.42 and 22.83MgCha−1, respectively, compared with the control treatment, and had average sequestration rates of 353 and 1087kgCha−1yr−1 respectively. Thus, appropriate application of NPK, alone or in combination with manure, can lead to improved OC sequestration by evenly augmenting aggregate-associated OC and providing the same degree of protection for OC in both macro-aggregates and micro-aggregates under a winter wheat-summer maize rotation on Anthrosol.

Ron R. Kopito: Unfolding the Secrets of Protein Aggregation

Today the mechanism of protein aggregation is an intensely investigated subject in cell biology. We know that protein aggregation can occur due to a variety of causes including mutations in proteins easily misfolded or disruption of components of protein homeostasis machinery such as chaperones or components of the ubiquitin⿿proteasome system. Moreover, these aggregates are known to increase with age and to be associated with a variety of neurodegenerative disease. But not long ago, our understanding of the fate and function of protein aggregates in cells remained a mystery. Seminal studies revealed that protein aggregates could be sequestered into inclusion bodies called aggresomes through a highly regulated process that relies on dynein-dependent retrograde transport on microtubules. In 2000, Ron R. Kopito from Stanford University described recent insights into the mechanisms of aggregate sequestration and proposed potential benefits of this sequestration for the cell [ 1 Kopito R.R. Aggresomes, inclusion bodies and protein aggregation. Trends Cell Biol. 2000; 10: 524-530 Abstract Full Text Full Text PDF PubMed Scopus (1599) Google Scholar ]. Dr Kopito shares his thoughts on where the field of protein aggregation has come since publication of this review and the outstanding questions that remain.

Ataxin-3, DNA damage repair, and SCA3 cerebellar degeneration: on the path to parsimony?

Ataxin-3, DNA damage repair, and SCA3 cerebellar degeneration: on the path to parsimony?

Self-restoration of post-agrogenic soils of Calcisol–Solonetz complex: Soil development, carbon stock dynamics of carbon pools

This chronosequential study focusses on the vegetation succession, pedogenesis, carbon stocks and different carbon pools of post-agrogenic Calcisol–Solonetz complexes in the dry steppe zone of Russia. The sites were comparable in terms of climate, soil texture and land-use history, but differed in the duration of agricultural abandonment, covering 1, 7, 12, 17 and 42years of self-restoration. During self-restoration without direct human impact, the vegetation developed towards a steppe with dominance of Artemisia lercheana/pauciflora and Stipa pennata. After 17years, the abundance of Artemisia pauciflora indicated again the Solonetz locations within the Calcisol–Solonetz complex, which were not visible during arable land use. Pedogenesis resulted in the recovery of the natural soil structure—fine subangular polyhedral for Calcisol and crumble fine platy for Solonetz. The recovery of soil structure of Solonetz was in accordance with a decline of water-stable aggregates from 84% to 68%. The plow features were still well visible after 42years of self-restoration in both soil groups. Partial integration of Btn materials into the plow layer induced a pH increase during cultivation of the Solonetzes, while slight pH decreases were observed during self-restoration afterwards. Other chemical properties of both soil groups remained unchanged. Post-agrogenic Solonetzes showed an exchange sodium percentage (ESP) below 5.0% and an electrical conductivity (ECe) below 50mSm−1 at the topsoil during the period of self-restoration. The development towards natural soils was observed in terms of soil organic carbon (SOC) dynamics. SOC stocks of the Calcisols increased slowly from 2.0 to 3.5kgm−2 in the upper 0–0.5m, comprising 64% of the natural soil. SOC stocks of the Solonetzes grew from 1.7 to 3.1kgm−2 in the upper 0–0.5m and almost reached the level of natural soil already after 12years of self-restoration. The long-term modelling showed a recovery of SOC stocks almost after 100years for the Calcisol and the Solonetz chronosequences. The nutrient dynamics traced SOC dynamics during the self-restoration. The investigation of different carbon pools showed a significant organic carbon (OC) enrichment of the density fractions <1.8gcm−3 (free particulate organic material (POM) and occluded POM) and the density fractions >1.8gcm−3 (sand coarse/medium silt, fine silt, clay) following an increase of total SOC during self-restoration. In the Calcisol chronosequence, the dynamics of all fractions was close to the dynamics of total SOC with the exception of free POM showing a moderate accumulation rate in relation to total SOC. Post-agrogenic Solonetzes showed a more intensive accumulation of free POM and a slower OC sequestration in aggregates compared to total SOC. Both chronosequences showed comparable recovery rates for the passive SOC pool and total SOC. Despite all these alterations the study showed no full restoration for many parameters within the chronosequential time scale of 42years.

Degradation mechanisms of the Tomato yellow leaf curl virus coat protein following inoculation of tomato plants by the whitefly Bemisia tabaci

Tomato yellow leaf curl virus (TYLCV) is a begomovirus infecting tomato cultures worldwide. TYLCV is transmitted to plants by the whitefly Bemisia tabaci. Once in the plant, the virus is subjected to attack by the host-plant defences, which may include sequestration in aggregates, proteolysis, ubiquitination, 26S proteasome degradation and autophagy. Elucidating how the virus avoids destruction will make it possible to understand infection and possibly devise countermeasures. The accumulation of viral coat protein (CP) and of viral DNA in plants is a marker of a successful virus transmission by B. tabaci. In response to infection, tomato tissues display multiple ways of degrading TYLCV proteins and DNA. In this study it is shown that CP (in soluble and insoluble states) is the target of protease digestion, 26S proteasome degradation and autophagy. The highest degradation capacity was detected among soluble proteins and proteins in large aggregates/inclusion bodies; cytoplasmic extracts displayed higher activity than nuclear fractions. The very same fractions possessed the highest capacity to degrade viral genomic DNA. Separately, 26S proteasome degradation was associated with large aggregates (more pronounced in the nuclear than in the cytoplasmic fractions), which are indicators of a successful abduction of plants by viruses. Autophagy/lysosome/vacuole degradation was a characteristic of intermediate aggregates, sequestering the CP in the cytoplasm and retarding the development of large aggregates. Chloroplast proteases were active in soluble as well as in insoluble protein extracts. To the best of the authors' knowledge, this study is the first attempt to identify elements of the virus-targeted degradation machinery, which is a part of the plant response to virus invasion.

Long-Term Impacts of Organic and Inorganic Fertilizers on Carbon Sequestration in Aggregates of an Entisol in Mediterranean Turkey

Soil management practices significantly impact soil aggregation and carbon (C) dynamics. Organic fertilizer and mycorrhizal inoculation also affect aggregate stability and soil C pool. Thus, this study was designed to assess the effects of inorganic and organic fertilizer treatments (control, chemical fertilizer, animal manure, compost, and compost + mycorrhizal inoculation) on bulk density (ρ b ), C and N concentrations, soil organic C (SOC) pool, C sequestration, total N, aggregate fractions, water-stable aggregates (WSA), and mean weight diameter (MWD) in the long-term field experiment initiated in 1996 on the Mediterranean coast of Turkey. Disturbed and undisturbed soil samples were collected from the 0- to 0.15-m and 0.15- to 0.30-m depths after wheat (Triticum aestivum) harvest in June 2010 to determine the soil physical and chemical characteristics. Soils that received animal manure, compost, and compost + mycorrhizae contained more C (in percent), N (in percent), SOC, and total N concentrations than control. In comparison with control, chemical fertilizers also affected soil C and N concentrations and pools by increasing plant biomass production. The C/N ratio of soil was less than 10 in control and chemical fertilizer treatments but more than 10 in animal manure, compost, and compost + mycorrhizae treatments. Organic fertilizers significantly reduced ρ b and increased porosity (in percent). Total amounts and rate of C and N sequestration increased with application of organic fertilizers. The rate (kg C ha ―1 year ―1 ) of C sequestration in 0- to 0.15-m depth was 7.19 for control, 329.6 for animal manure, and 273.4 for the compost + mycorrhizae treatment. Furthermore, organic fertilizers significantly increased the SOC concentrations in different aggregate size fractions. The C and N concentrations in the 0.25- to 1.0-mm aggregate size were higher than those in the less than 0.25-mm fraction. Concentrations of C and N decreased significantly with the decrease in aggregate size less than 0.25 mm (P < 0.0009). Application of organic fertilizers impacted soil ρ b , WSA, and MWD. Compost + mycorrhizae―treated soil had the highest MWD (3.09 mm), and the control treatment had the least (1.49 mm). Decline in aggregate size decreased WSA in compost and mycorrhizae treatments. The high values of MWD were associated with mycorrhizal inoculation rather than with application of organic fertilizer. Application of organic fertilizers including mycorrhizal inoculation contributed considerably to soil aggregation and soil C sequestration. There was more C concentration in 1- to 2-mm and 0.5- to 1-mm aggregate sizes than in the less than 0.25-mm size range. Additional research is needed to assess the role of mycorrhizae on macroaggregate development and C sequestration under long-term soil and crop management systems.