Exploring the mechanism of formation of native-like and precursor amyloid oligomers for the native acylphosphatase from Sulfolobus solfataricus

Over 40 human diseases are associated with the formation of well-defined proteinaceous fibrillar aggregates. Since the oligomers precursors to the fibrils are increasingly recognized to be the causative agents of such diseases, it is important to elucidate the mechanism of formation of these early species. The acylphosphatase from Sulfolobus solfataricus is an ideal system as it was found to form, under conditions in which it is initially native, two types of prefibrillar aggregates: (1) initial enzymatically active aggregates and (2) oligomers with characteristics reminiscent of amyloid protofibrils, with the latter originating from the structural reorganization of the initial assemblies. By studying a number of protein variants with a variety of biophysical techniques, we have identified the regions of the sequence and the driving forces that promote the first aggregation phase and show that the second phase consists in a cooperative conversion involving the entire globular fol

The regions of the sequence most exposed to the solvent within the amyloidogenic state of a protein initiate the aggregation process.

Formation of misfolded aggregates is an essential part of what proteins can do. The process of protein aggregation is central to many human diseases and any aggregating event needs to be prevented within a cell and in protein design. In order to aggregate, a protein needs to unfold its native state, at least partially. The conformational state that is prone to aggregate is difficult to study, due to its aggregating potential and heterogeneous nature. Here, we use a systematic approach of limited proteolysis, in combination with electrospray ionisation mass spectrometry, to investigate the regions that are most flexible and solvent-exposed within the native, ligand-bound and amyloidogenic states of muscle acylphosphatase (AcP), a protein previously shown to form amyloid fibrils in the presence of trifluoroethanol. Seven proteases with different degrees of specificity have been used for this purpose. Following exposure to the aggregating conditions, a number of sites along the sequence of AcP become susceptible to proteolytic digestion. The pattern of proteolytic cleavages obtained under these conditions is considerably different from that of the native and ligand-bound conformations and includes a portion within the N-terminal tail of the protein (residues 6-7), the region of the sequence 18-23 and the position 94 near the C terminus. There is a significant overlap between the regions of the sequence found to be solvent-exposed from the present study and those previously identified to be critical in the rate-determining steps of aggregation from protein engineering approaches. This indicates that a considerable degree of solvent exposure is a feature of the portions of a protein that initiate the process of aggregation

Bounds for the relative n-th nilpotency degree in compact groups

The line of investigation of the present paper goes back to a classical work of W. H. Gustafson of the 1973, in which it is described the probability that two randomly chosen group elements commute. In the same work, he gave some bounds for this kind of probability, providing information on the group structure. We have recently obtained some generalizations of his results for finite groups. Here we improve them in the context of the compact groups.Comment: 9 pages; to appear in Asian-European Journal of Mathematics with several improvement

Does degradation from selective logging and illegal activities differently impact forest resources? A case study in Ghana

Degradation, a reduction of the ecosystem’s capacity to supply goods and services, is widespread in tropical forests and mainly caused by human disturbance. To maintain the full range of forest ecosystem services and support the development of effective conservation policies, we must understand the overall impact of degradation on different forest resources. This research investigates the response to disturbance of forest structure using several indicators: soil carbon content, arboreal richness and biodiversity, functional composition (guild and wood density), and productivity. We drew upon large field and remote sensing datasets from different forest types in Ghana, characterized by varied protection status, to investigate impacts of selective logging, and of illegal land use and resources extraction, which are the main disturbance causes in West Africa. Results indicate that functional composition and the overall number of species are less affected by degradation, while forest structure, soil carbon content and species abundance are seriously impacted, with resources distribution reflecting the protection level of the areas. Remote sensing analysis showed an increase in productivity in the last three decades, with higher resiliency to change in drier forest types, and stronger productivity correlation with solar radiation in the short dry season. The study region is affected by growing anthropogenic pressure on natural resources and by an increased climate variability: possible interactions of disturbance with climate are also discussed, together with the urgency to reduce degradation in order to preserve the full range of ecosystem functions

The ecosystem carbon sink implications of mountain forest expansion into abandoned grazing land: The role of subsoil and climatic factors

Woody encroachment is a widespread phenomenon resulting from the abandonment of mountain agricultural and pastoral practices during the last century. As a result, forests have expanded, increasing biomass and necromass carbon (C) pools. However, the impact on soil organic carbon (SOC) is less clear. The main aim of this study was to investigate the effect of woody encroachment on SOC stocks and ecosystem C pools in six chronosequences located along the Italian peninsula, three in the Alps and three in the Apennines. Five stages along the chronosequences were identified in each site. Considering the topsoil (0 30 cm), subsoil (30 cm-bedrock) and whole soil profile, the temporal trend in SOC stocks was similar in all sites, with an initial increment and subsequent decrement in the intermediate phase. However, the final phase of the woody encroachment differed significantly between the Alps (mainly conifers) and the Apennines (broadleaf forests) sites, with a much more pronounced increment in the latter case. Compared to the previous pastures, after mature forest (>62 years old) establishment, SOC stocks increased by: 2.1(mean) ± 18.1(sd) and 50.1 ± 25.2 Mg C·ha -1 in the topsoil, 7.3 ± 17.4 and 93.2 ± 29.7 Mg C·ha -1 in the subsoil, and 9.4 ± 24.4 and 143.3 ± 51.0 Mg C·ha -1 in the whole soil profile in Alps and Apennines, respectively. Changes in SOC stocks increased with mean annual air temperature and average minimum winter temperature, and were negatively correlated with the sum of summer precipitation. At the same time, all other C pools (biomass and necromass) increased by 179.1 ± 51.3 and 304.2 ± 67.6 Mg C·ha -1 in the Alps and the Apennines sites, respectively. This study highlights the importance of considering both the subsoil, since deep soil layers contributed 38% to the observed variations in carbon stocks after land use change, and the possible repercussions for the carbon balance of large areas where forests are expanding, especially under pressing global warming scenarios. © 2019 Elsevier B.V.The project of this work is part of the research activities of the PhD in science, technology and biotechnology for sustainability. The first author received a fully founded scholarship partially by the University of Tuscia (Viterbo - Italy) and partially by the University of Molise . Tommaso Chiti participated in the project by conducting his work with the funding obtained through the LIFE MediNet project (grant number LIFE15 PRE IT/732295 ). Jorge Curiel Yuste was financed in part by the Basque Government through the BERC 2018-2021 (grant code) program and by Spanish Ministry of Economy and Competitiveness (MINECO) through BC3 María de Maeztu excellence accreditation MDM-2017-0714. I.C (grant code)

"The difference that makes a difference": highlighting the role of variable contexts within an HIV Prevention Community Randomised Trial (HPTN 071/PopART) in 21 study communities in Zambia and South Africa.

This paper explores contextual heterogeneity within a community randomised trial HPTN 071 (Population Effects of Antiretroviral Treatment to Reduce HIV Transmission) carried out in 21 study communities (12 Zambian, 9 South African). The trial evaluates the impact of a combination HIV prevention package (including household-based HIV counselling and testing and anti-retroviral treatment (ART) eligibility regardless of CD4-count) on HIV incidence. The selection, matching and randomisation of study communities relied on key epidemiological and demographic variables and community and stakeholder support. In 2013, following the selection of study communities, a "Broad Brush Survey" (BBS) approach was used to rapidly gather qualitative data on each study community, prior to the implementation of the trial intervention. First-year process indicator intervention data (2014-2015) were collected during the household-based intervention by community lay workers. Using an open/closed typology of urban communities (indicating more or less heterogeneity), this qualitative inquiry presents key features of 12 Zambian communities using a list of four meta-indicators (physical features, social organisation, networks and community narratives). These indicators are then compared with four intervention process indicators in a smaller set of four study communities. The process indicators selected for this analysis indicate response to the intervention (uptake) amongst adults. The BBS qualitative data are used to interpret patterns of similarity and variability in the process indicators across four communities. We found that meta-indicators of local context helped to interpret patterns of similarity and variability emerging across and within the four communities. Features especially significant for influencing heterogeneity in process indicators include proportion of middle-class residents, proximity to neighbouring communities and town centre, the scale of the informal economy, livelihood-linked mobility, presence of HIV stakeholders over time and commitment to community action. Future interdisciplinary analysis is needed to explore if these patterns of difference continue to hold up over the full intervention period and all intervention communities

Radiocarbon dating reveals different past managements of adjacent forest soils in the Campine region, Belgium

The soils of adjacent first generation monospecific stands of Scots pine (Pinus sylvestris L.) and pedunculate oak (Quercus robur L.) in the Campine region, Belgium, apparently developed under the same forming factors, were studied for carbon dynamics to disentangle eventual different past land uses. In fact, visual observations suggested that the soil under pine experienced substantial addition of organic matter and ploughing, such to be considered a plaggen, opposite to the soil under oak, which is inexplicably much poorer in C. In order to prove this hypothesis, the soil organic carbon was quantified by horizons and, both bulk soil organic matter (SOM) and the least mobile SOM fractions - the humic acid and the unextractable fractions - were radiocarbon dated. Surprising was the marked difference between the mean SOM age from the two stands. In fact, while under oak this age is a few years or decades, under pine it amounts to more than a millennium, so confirming the hypothesis of a confined C supply occurred mainly in the Middle Age, or later using partly humified matter. The mean residence time (MRT) of SOM in the organic layers matches almost perfectly with that estimated via a mass balance approach and, as expected, was much lower in the oaks than in the pines. The humic acid fraction, generally the most stable fraction of SOM, in terms of both mobility and degradability, reflects the behaviour of the bulk SOM, showing higher radiocarbon ages under pine. The findings of this work indicate that the large human-induced additions of organic material in the area now occupied by the pine stand, probably occurred in the Middle Age and it continues to strongly affect the present soil C pools and their dynamics. Any study dealing with budgets and dynamics of C in soil should avail itself of a careful reconstruction of the land uses and management history, in order to provide reliable conclusions about the real role of the current vegetation on soil carbon. Crown Copyright (c) 2008 Published by Elsevier B.V. All rights reserved

Two isoperimetric inequalities for the Sobolev constant

In this note we prove two isoperimetric inequalities for the sharp constant in the Sobolev embedding and its associated extremal function. The first such inequality is a variation on the classical Schwarz Lemma from complex analysis, similar to recent inequalities of Burckel, Marshall, Minda, Poggi-Corradini, and Ransford, while the second generalises an isoperimetric inequality for the first eigenfunction of the Laplacian due to Payne and Rayner.Comment: 11 page

Full-length TDP-43 and its C-terminal domain form filamentsin vitrohaving non-amyloid properties

Accumulation of ubiquitin-positive, tau- and α-synuclein-negative intracellular inclusions of TDP-43 in the central nervous system represents the major hallmark correlated to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLD-U). Such inclusions have variably been described as amorphous aggregates or more structured deposits having amyloid properties. Here we have purified full-length TDP-43 (FL TDP-43) and its C-terminal domain (Ct TDP-43) to investigate the morphological, structural and tinctorial features of aggregates formed in vitro by them at pH 7.4 and 37 °C. AFM images indicate that both protein variants show a tendency to form filaments. Moreover, we show that both FL TDP-43 and Ct TDP-43 filaments possess a largely disordered secondary structure, as ascertained by far-UV circular dichroism and Fourier transform infra-red spectroscopy, do not bind Congo red and induce a very weak increase of thioflavin T fluorescence, indicating the absence of a clear amyloid-like signature