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While recurrence is frequent in ependymoma, the underlying molecular mechanisms remain to be explored. Here, the authors investigate epigenetic, genetic and tumorigenic changes in 30 patient-matched repeated relapses over 13 years and identify distinct patterns of DNA methylation.

Autophagy plays a major role in the elimination of cellular waste components, the renewal of intracellular proteins and the prevention of the build-up of redundant or defective material. It is fundamental for the maintenance of homeostasis and especially important in post-mitotic neuronal cells, which, without competent autophagy, accumulate protein aggregates and degenerate. Many neurodegenerative diseases are associated with defective autophagy; however, whether altered protein turnover or accumulation of misfolded, aggregate-prone proteins is the primary insult in neurodegeneration has long been a matter of debate. Amyotrophic lateral sclerosis (ALS) is a fatal disease characterized by selective degeneration of motor neurons. Most of the ALS cases occur in sporadic forms (SALS), while 10%–15% of the cases have a positive familial history (FALS). The accumulation in the cell of misfolded/abnormal proteins is a hallmark of both SALS and FALS, and altered protein degradation due to autophagy dysregulation has been proposed to contribute to ALS pathogenesis. In this review, we focus on the main molecular features of autophagy to provide a framework for discussion of our recent findings about the role in disease pathogenesis of the ALS-linked form of the VAPB gene product, a mutant protein that drives the generation of unusual cytoplasmic inclusions.

VAPB is a ubiquitously expressed, ER-resident adaptor protein involved in interorganellar lipid exchange, membrane contact site formation, and membrane trafficking. Its mutant form, P56S-VAPB, which has been linked to a dominantly inherited form of Amyotrophic Lateral Sclerosis (ALS8), generates intracellular inclusions consisting in restructured ER domains whose role in ALS pathogenesis has not been elucidated. P56S-VAPB is less stable than the wild-type protein and, at variance with most pathological aggregates, its inclusions are cleared by the proteasome. Based on studies with cultured cells overexpressing the mutant protein, it has been suggested that VAPB inclusions may exert a pathogenic effect either by sequestering the wild-type protein and other interactors (loss-of-function by a dominant negative effect) or by a more general proteotoxic action (gain-of-function). To investigate P56S-VAPB degradation and the effect of the inclusions on proteostasis and on ER-to-plasma membrane protein transport in a more physiological setting, we used stable HeLa and NSC34 Tet-Off cell lines inducibly expressing moderate levels of P56S-VAPB. Under basal conditions, P56S-VAPB degradation was mediated exclusively by the proteasome in both cell lines, however, it could be targeted also by starvation-stimulated autophagy. To assess possible proteasome impairment, the HeLa cell line was transiently transfected with the ERAD (ER Associated Degradation) substrate CD3δ, while autophagic flow was investigated in cells either starved or treated with an autophagy-stimulating drug. Secretory pathway functionality was evaluated by analyzing the transport of transfected Vesicular Stomatitis Virus Glycoprotein (VSVG). P56S-VAPB expression had no effect either on the degradation of CD3δ or on the levels of autophagic markers, or on the rate of transport of VSVG to the cell surface. We conclude that P56S-VAPB inclusions expressed at moderate levels do not interfere with protein degradation pathways or protein transport, suggesting that the dominant inheritance of the mutant gene may be due mainly to haploinsufficiency.

Composting of municipal solid waste (MSW) was studied in an attempt to characterize concomitant transformations of humic acid (HA). Humic acid and Core‐HA were extracted from MSW at various stages during composting using the following methods: (i) The common IHSS method (HA); and (ii) performing organic solvent and sulfuric acid extractions prior to the alkaline extraction (Core‐HA). Mass balance was calculated for each compost sample during composting, and cross polarization magic angle spinning (CPMAS) 13C‐NMR and fourier transform infrared (FTIR) spectroscopy measurements were employed on the purified HAs and Core‐HAs. The absolute level of HA decreased during composting by 50% whereas the level of Core‐HA was steady throughout the process. The 13C‐NMR and FTIR spectra of the HAs indicated a high rate of change in structure during composting. The aromatic and phenolic C‐containing groups increased by 23 and 16%, respectively. In contrast, the Core‐HA spectra were stable, with only minor changes recorded during composting. The "coating" materials (polysaccharides, peptides, and lipids) bonding to the "core" HA structure degraded during composting, resulting in HA structures of higher aromaticity. The FTIR spectra of both HA and Core‐HA exhibited minor peaks in the carboxyl C, and the high rate of aliphatic C‐containing groups recorded from the 13C‐NMR spectra resembled "young" (type III) humified materials from soils. The mass‐balance data, together with the spectroscopic analyses indicate that one of the major HA transformation processes occurring events during the process is the degradation of the coating materials, yielding the core HA structure. [ABSTRACT FROM AUTHOR]

Presents information on a study which detailed a number of compost samples to establish a database for determining the relative quality of composts and their potential use. Categories of compost samples; Categories used in dividing municipal solid waste; Results of the study.

VAPB and VAPA are ubiquitously expressed endoplasmic reticulum membrane proteins that play key roles in lipid exchange at membrane contact sites. A mutant, aggregation-prone, form of VAPB (P56S) is linked to a dominantly inherited form of amyotrophic lateral sclerosis; however, it has been unclear whether its pathogenicity is due to toxic gain of function, to negative dominance, or simply to insufficient levels of the wild-type protein produced from a single allele (haploinsufficiency). To investigate whether reduced levels of functional VAPB, independently from the presence of the mutant form, affect the physiology of mammalian motoneuron-like cells, we generated NSC34 clones, from which VAPB was partially or nearly completely depleted. VAPA levels, determined to be over fourfold higher than those of VAPB in untransfected cells, were unaffected. Nonetheless, cells with even partially depleted VAPB showed an increase in Golgi- and acidic vesicle-localized phosphatidylinositol-4-phosphate (PI4P) and reduced neurite extension when induced to differentiate. Conversely, the PI4 kinase inhibitors PIK93 and IN-10 increased neurite elongation. Thus, for long-term survival, motoneurons might require the full dose of functional VAPB, which may have unique function(s) that VAPA cannot perform., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2019. Published by The Company of Biologists Ltd.)

Autophagy plays a major role in the elimination of cellular waste components, the renewal of intracellular proteins and the prevention of the build-up of redundant or defective material. It is fundamental for the maintenance of homeostasis and especially important in post-mitotic neuronal cells, which, without competent autophagy, accumulate protein aggregates and degenerate. Many neurodegenerative diseases are associated with defective autophagy; however, whether altered protein turnover or accumulation of misfolded, aggregate-prone proteins is the primary insult in neurodegeneration has long been a matter of debate. Amyotrophic lateral sclerosis (ALS) is a fatal disease characterized by selective degeneration of motor neurons. Most of the ALS cases occur in sporadic forms (SALS), while 10%-15% of the cases have a positive familial history (FALS). The accumulation in the cell of misfolded/abnormal proteins is a hallmark of both SALS and FALS, and altered protein degradation due to autophagy dysregulation has been proposed to contribute to ALS pathogenesis. In this review, we focus on the main molecular features of autophagy to provide a framework for discussion of our recent findings about the role in disease pathogenesis of the ALS-linked form of the VAPB gene product, a mutant protein that drives the generation of unusual cytoplasmic inclusions.

VAPB is a ubiquitously expressed, ER-resident adaptor protein involved in interorganellar lipid exchange, membrane contact site formation, and membrane trafficking. Its mutant form, P56S-VAPB, which has been linked to a dominantly inherited form of Amyotrophic Lateral Sclerosis (ALS8), generates intracellular inclusions consisting in restructured ER domains whose role in ALS pathogenesis has not been elucidated. P56S-VAPB is less stable than the wild-type protein and, at variance with most pathological aggregates, its inclusions are cleared by the proteasome. Based on studies with cultured cells overexpressing the mutant protein, it has been suggested that VAPB inclusions may exert a pathogenic effect either by sequestering the wild-type protein and other interactors (loss-of-function by a dominant negative effect) or by a more general proteotoxic action (gain-of-function). To investigate P56S-VAPB degradation and the effect of the inclusions on proteostasis and on ER-to-plasma membrane protein transport in a more physiological setting, we used stable HeLa and NSC34 Tet-Off cell lines inducibly expressing moderate levels of P56S-VAPB. Under basal conditions, P56S-VAPB degradation was mediated exclusively by the proteasome in both cell lines, however, it could be targeted also by starvation-stimulated autophagy. To assess possible proteasome impairment, the HeLa cell line was transiently transfected with the ERAD (ER Associated Degradation) substrate CD3δ, while autophagic flow was investigated in cells either starved or treated with an autophagy-stimulating drug. Secretory pathway functionality was evaluated by analyzing the transport of transfected Vesicular Stomatitis Virus Glycoprotein (VSVG). P56S-VAPB expression had no effect either on the degradation of CD3δ or on the levels of autophagic markers, or on the rate of transport of VSVG to the cell surface. We conclude that P56S-VAPB inclusions expressed at moderate levels do not interfere with protein degradation pathways or protein transport, suggesting that the dominant inheritance of the mutant gene may be due mainly to haploinsufficiency.

The quantity and quality of plant litter in the soil play an important role in the soil organic matter balance. Besides other pedo-climatic aspects, the content of recalcitrant molecules of plant residues and their chemical composition play a major role in the preservation of plant residues. In this study, we report that intrinsically resistant alkali-soluble bio-macromolecules extracted from maize plant (plant-humic acid) (plant-HA) contribute directly to the soil organic matter (OM) by its addition and conservation in the soil. Furthermore, we also observed that a high syringyl/guaiacyl (S/G) ratio in the lignin residues comprising the plant tissue, which modifies the microscopic structure of the alkali-soluble plant biopolymers, enhances their recalcitrance because of lower accessibility of molecules to degrading enzymes. These results are in agreement with a recent study, which showed that the humic substance of soil consists of a mixture of identifiable biopolymers obtained directly from plant tissues that are added annually by maize plant residues.

The transformation of organic matter during anaerobic digestion of mixtures of energetic crops, cow slurry, agro-industrial waste and organic fraction of municipal solid waste (OFMSW) was studied by analysing different samples at diverse points during the anaerobic digestion process in a full-scale plant. Both chemical (fiber analysis) and spectroscopic approaches ((13)C CPMAS NMR) indicated the anaerobic digestion process proceeded by degradation of more labile fraction (e.g. carbohydrate-like molecules) and concentration of more recalcitrant molecules (lignin and non-hydrolysable lipids). These modifications determined a higher degree of biological stability of digestate with respect to the starting mixture, as suggested, also, by the good correlations found between the cumulative oxygen uptake (OD(20)), and the sum of (cellulose+hemicellulose+cell soluble) contents of biomasses detected by fiber analysis (r=0.99; P<0.05), and both O-alkyl-C (r=0.98; P<0.05) and alkyl-C (r=-0.99; P<0.05) measured by (13)C CPMAS NMR.

We investigated the effect of a single compost application at two rates (50 and 85Mgha(-1)) on carbon (C) degradation and retention in an agricultural soil cropped with maize after 150d. We used both C mass balance and soil respiration data to trace the fate of compost C. Our results indicated that compost C accumulated in the soil after 150d was 4.24Mgha(-1) and 6.82Mg C ha(-1) for 50 and 85Mg ha(-1) compost rate, respectively. Compost C was sequestered at the rate of 623 and 617g C kg(-1) compost TOC for 50 and 85Mgha(-1) compost dose, respectively. These results point to a linear response between dose of application and both C degradation and retention. The amount of C sequestered was similar to the total recalcitrant C content of compost, which was 586g C kg(-1) compost TOC, indicating that, probably, during the short experiment, the labile C pool of compost (414g C kg(-1) of compost TOC) was completely degraded. Soil respiration measured at different times during the crop growth cycle was stable for soils amended with compost (CO2 flux of 0.96+/-0.11g CO2 m(-2) h(-1) and 1.07+/-0.10g CO2 m(-2) h(-1), respectively, for 50 and 85Mgha(-1)), whereas it increased in the control. The CO2 flux due to compost degradation only, though not statistically significant, was always greatest for the highest compost doses applied (0.22+/-0.40g CO2 m(-2) h(-1) and 0.33+/-0.25g CO2 m(-2) h(-1) for the 50 and 85Mgha(-1) compost dose, respectively). This seems to confirm the highest C degradation for the 85Mgha(-1) compost dose as a consequence of the presence of more labile C. Unlike other studies, the results show a slight increase in the fraction of carbon retained with the increase in compost application rate. This could be due to the highly stable state of the compost prior to application, although it could also be due to sampling uncertainty. Further investigations are needed to better explain how the compost application rate affects carbon sequestration, and how characterization into labile and recalcitrant C can predict the amount of C sequestered in the soil.

This work represents the first attempt to evaluate the precision of the specific oxygen uptake rate method expressed in terms of repeatability (r) and reproducibility limits (R). Three laboratories were involved in an inter-laboratory test for the validation of respiration analyses on six biomass samples (three composts and three biostabilized products) having different degrees of biological stability. Both the maximum specific oxygen uptake rate peak (SOUR) and the cumulative oxygen demand after 12 h (OD(12)) and 20 h (OD(20)) of respiration test were investigated. Precisions expressed as the relative standard deviation were in the range of 9-41%. Linear regressions found for r and R, versus OD(12) and OD(20), enabled derivation of precision values (r and R) for all respirometric levels within the operating range. The OD(12) and OD(20) indices were found to be more adequate to indicate biological stability since they were less influenced by random errors than the SOUR index.

Two soil plots, 1 ha each, were amended yearly for 4 years, respectively, with 35.8 and 71.6 Mg ha(-1) yr(-1) of mature compost (CM) obtained from food and vegetable residues. The compost, amended soils, and a control soil plot after 4 years (S4), were analyzed for humin (HUC), humic acid (HAC), fulvic acid (FAC), and non-humic carbon (NHC) content. Compared to S4, the amended soil contained more humified C (HAC, FAC and HUC) and less NHC. Further evidence of the effect of compost on soil organic matter was obtained by the analysis of the humic acid (HA) fractions isolated from both the compost and the soils. These were characterized by elemental analyses and Diffuse Reflectance Infrared Fourier Transformed spectroscopy. The HAs isolated from CM and from S4 were significantly different. The HAs isolated from the amended plots were more similar to HA isolated from CM than to HA isolated from S4. The experimental data of this work indicate that the compost application may affect significantly the soil organic matter composition, and that the approach used in this work allows one to trace the fate of compost organic matter in soil.

The humic acid (HA) fraction of a food and vegetable residues compost (CM) was taken as indicator to trace the fate of CM organic matter in four years CM amended soil. (1)H and (13)C NMR spectroscopy were used to investigate the nature of the HA isolates from CM, control soil (S(4)) and amended soil. The result indicated a significant structural difference between CM HA and S(4) HA, and supported the presence of both HA fractions in soil at the end of the amendment trials. However, the nature and content of CM HA in soil did not fully explain the increase of soil cation exchange capacity (CEC) after amendment. All CM humic fractions (i.e., fulvic acid, humic acid and humin) were found to contribute to the change of the soil organic matter composition. It is concluded that although CM HA is a suitable indicator of the survival of compost organic matter in soil during amendment, all three humic fractions should be monitored and analyzed to fully understand changes in the composition and properties of amended soil.

Humic acid consists of a recalcitrant (unhydrolysed fraction) (the core) and labile (hydrolysable fraction) fraction. Core-humic acid (core-HA) isolation was performed by treating source material with apolar and polar solvents (organic solvents+acid hydrolysis) before alkaline extraction. Leonardite, soil Ah horizont and dry blood were chosen for this study because of their different origin and degree of humification. Chemical analysis (elemental analysis, total acidity, E(4):E(6)), spectroscopic analysis (DRIFT and (1)H NMR), and complete mass balance were used to investigate the effect of purifying humic acids. The results obtained showed that purification produced a slight modification of Leonardite humic acids as was expected for these highly humified organic matrices. On the other hand, about 500 g kg(-1) of soil humic acids were lost by purification. The fractions lost mainly consisted of carbohydrates. Dry blood showed the presence of humic acids that contrasted with its origin, thus indicating the limitations of the common analytical methods used for HA extraction. Nevertheless, in practice, purification caused the complete disappearance (914 g kg(-1) of HA was lost) of these HAs. The results obtained in this work suggest that the HA fraction isolated (named core-HA) effectively represents the HA structure proposed by the existing literature, since the purification proposed was able to eliminate the adsorbed organic molecules (interference materials) coating the HA structure.