Conformational plasticity of the Gerstmann-Sträussler-Scheinker disease peptide as indicated by its multiple aggregation pathways

The existence of several prion strains and their capacity of overcoming species barriers seem to point to a high conformational adaptability of the prion protein. To investigate this structural plasticity, we studied here the aggregation pathways of the human prion peptide PrP82-146, a major component of the Gerstmann-Sträussler-Scheinker amyloid disease.By Fourier transform infrared (FT-IR) spectroscopy, electron microscopy, and atomic force microscopy (AFM), we monitored the time course of PrP82-146 fibril formation. After incubation at 37 °C, the unfolded peptide was found to aggregate into oligomers characterized by intermolecular β-sheet infrared bands. At a critical oligomer concentration, the emergence of a new FT-IR band allowed to detect fibril formation. A different intermolecular β-sheet interaction of the peptides in oligomers and in fibrils is, therefore, detected by FT-IR spectroscopy, which, in addition, suggests a parallel orientation of the cross β-sheet structures of PrP82-146 fibrils. By AFM, a wide distribution of PrP82-146 oligomer volumes—the smallest ones containing from 5 to 30 peptides—was observed. Interestingly, the statistical analysis of AFM data enabled us to detect a quantization in the oligomer height values differing by steps of ∼ 0.5 nm that could reflect an orientation of oligomer β-strands parallel with the sample surface. Different morphologies were also detected for fibrils that displayed high heterogeneity in their twisting periodicity and a complex hierarchical assembly.Thermal aggregation of PrP82-146 was also investigated by FT-IR spectroscopy, which indicated for these aggregates an intermolecular β-sheet interaction different from that observed for oligomers and fibrils. Unexpectedly, random aggregates, induced by solvent evaporation, were found to display a significant α-helical structure as well as several β-sheet components.All these results clearly point to a high plasticity of the PrP82-146 peptide, which was found to be capable of undergoing several aggregation pathways, with end products displaying different secondary structures and intermolecular interactions.     

Comparing bird assemblages in large and small fragments of the Atlantic Forest hotspots

The Atlantic Forest (AF) is one of the five most threatened and megadiverse world hotspots. It is arguably the most devastated and highly threatened ecosystem on the planet. The vast scope of habitat loss and extreme fragmentation in the AF hotspots has left intact very few extensive and continuous forested fragments. We compared bird assemblages between small (<100 ha) and large (>6,000 ha) forest remnants, in one of the largest AF remnants in Argentina. We performed 84 point-counts of birds in four large fragments (LF) and 67 points in 25 small fragments (SF). We recorded 4,527 bird individuals belonging to 173 species; 2,632 belonging to 153 species in LF and 1,897 in 124 species in SF. Small fragments suffered a significant loss of bird richness, mainly forest dependent species, but the birds abundance did not decrease, due to an increase in abundance of forest independent and semi-dependent bird species (edge and non forest species) that benefit from forest fragmentation. The bird guilds of frugivores, undestory, terrestrial and midstory insectivores, nectarivores and raptors, and the endemic species of AF were area sensitive, decreasing significantly in richness and abundance in the SF. Terrestrial granivores were the only guild positively affected by forest fragmentation, containing mainly edge species, which forage in open areas or borders including crops. Our first observations on fragmentation effects on bird assemblages in the southernmost Argentinean Atlantic Forests did not validate the hypothesis on pre-adaptation to human disturbances in the bird communities of AF. On the contrary, we observed that forest dependent, endemic and several sensitive bird guilds were strongly affected by fragmentation, putting in evidence the vulnerability to the fragmentation process and the necessity to conserve large remnants to avoid reduction of the high biodiversity of AF birds.     

Schwannomas of the peroneal nerves: Clinical and functional results of surgical treatment

Objectives:Peroneal nerves Schwannomas are rare benign tumors. Literature is still poor of studies about clinical and functional outcomes after surgical treatment. We evaluated the pre-operative presentation of the disease and assessed clinical and functional outcomes after surgery.Methods:We collected all the cases of peroneal nerves’ neurinoma treated surgically between June 2016 and June 2020. We analyzed each patients’ personal data and carried out accurate clinical examinations before and after surgery. MRI was performed both pre-operatively and post-operatively.Results:We reported 9 cases of peroneal nerves schwannomas: five arising from the common peroneal nerve and four arising from the deep or superficial branches alone. Their mean size was 22.6 mm. Each patient showed sensation deficits before surgery; pre-operative MRC score was 4.2. Pre-Operative MSTS and LEFS scores were 23.6 and 64.4. Surgery was successful in each case. No local recurrence nor major complication occurred. Tumor size was significantly associated with both diagnostic delay and development of pre-operative deficits. Surgery was proven to be globally successful: post-operative evaluations highlighted a marked reduction of neurological signs and overall functional limitations.Conclusions:Surgical treatment at early stages of the disease represents a reliable and relatively safe therapeutic option.     

Quantification of prior impact in terms of effective current sample size

Bayesian methods allow borrowing of historical information through prior distributions. The concept of prior effective sample size (prior ESS) facilitates quantification and communication of such prior information by equating it to a sample size. Prior information can arise from historical observations; thus, the traditional approach identifies the ESS with such a historical sample size. However, this measure is independent of newly observed data, and thus would not capture an actual “loss of information” induced by the prior in case of prior-data conflict. We build on a recent work to relate prior impact to the number of (virtual) samples from the current data model and introduce the effective current sample size (ECSS) of a prior, tailored to the application in Bayesian clinical trial designs. Special emphasis is put on robust mixture, power, and commensurate priors. We apply the approach to an adaptive design in which the number of recruited patients is adjusted depending on the effective sample size at an interim analysis. We argue that the ECSS is the appropriate measure in this case, as the aim is to save current (as opposed to historical) patients from recruitment. Furthermore, the ECSS can help overcome lack of consensus in the ESS assessment of mixture priors and can, more broadly, provide further insights into the impact of priors. An R package accompanies the paper.     

Conformational changes of yeast plasma membrane H(+)-ATPase during activation by glucose: role of threonine-912 in the carboxy-terminal tail

Yeast Pma1 H(+)-ATPase, which belongs to the P-type family of cation-transporting ATPases, is activated up to 10-fold by growth on glucose, and indirect evidence has linked the activation to Ser/Thr phosphorylation within the C-terminal tail. We have now used limited trypsinolysis to map glucose-induced conformational changes throughout the 100 kDa ATPase. In the wild-type enzyme, trypsin cleaves first at Lys-28 and Arg-73 in the extended N-terminal segment (sites T1 and T2); subsequent cleavages occur at Arg-271 between the A domain and M3 (site T3) and at Lys-749 or Lys-754 in the M6-M7 cytoplasmic loop (site T4). Activation by glucose leads to a striking increase in trypsin sensitivity. At the C-terminal end of the protein, the Arg- and Lys-rich tail is shielded from trypsin in membranes from glucose-starved cells (GS) but becomes accessible in membranes from glucose-metabolizing cells (GM). In the presence of orthovanadate, Lys-174 at the boundary between M2 and the A domain also becomes open to cleavage in GM but not GS samples (site T5). Significantly, this global conformational change can be suppressed by mutations at Thr-912, a consensus phosphorylation site near the C-terminus. Substitution by Ala at position 912 leads to a GS-like (trypsin-resistant) state, while substitution by Asp leads to a GM-like (trypsin-sensitive) state. Thus, the present results help to dissect the intramolecular movements that result in glucose activation.     

How well does presence‐only‐based species distribution modelling predict assemblage diversity? A case study of the Tenerife flora

Prediction error is considered an important problem in species distribution models. To address this issue, we here examined the accuracy of overlays of presence‐only‐based models for many individual species in representing patterns of assemblage diversity. For this purpose, we used a database of 977 160 records of seed plant occurrences on an intensively surveyed, species‐rich island (Tenerife, Canary Islands) for modelling the distribution of all its 841 native plant species individually. The modelling was done using Maxent, one of the best‐performing presence‐only modelling techniques, using various thresholds to convert the estimated suitability values into predicted presence or absence. Distribution models for each individual species were overlaid to predict species richness and composition, which were then compared to the observed values for well‐surveyed grid cells. We found high levels of compositional error, when the best performing suitability threshold for predicting species richness was applied. Our best prediction had a mean species richness error of 24% and a mean compositional error of 60% relative to the observed values for the well‐surveyed cells; >50% of all species were included erroneously in >25% of the well‐surveyed cells. Hence, large quantities of data are not necessarily enough to obtain reliable predictions of assemblage diversity, limiting the usefulness of this methodology in conservation planning.     

CNF1 improves astrocytic ability to support neuronal growth and differentiation in vitro

Modulation of cerebral Rho GTPases activity in mice brain by intracerebral administration of Cytotoxic Necrotizing Factor 1 (CNF1) leads to enhanced neurotransmission and synaptic plasticity and improves learning and memory. To gain more insight into the interactions between CNF1 and neuronal cells, we used primary neuronal and astrocytic cultures from rat embryonic brain to study CNF1 effects on neuronal differentiation, focusing on dendritic tree growth and synapse formation, which are strictly modulated by Rho GTPases. CNF1 profoundly remodeled the cytoskeleton of hippocampal and cortical neurons, which showed philopodia-like, actin-positive projections, thickened and poorly branched dendrites, and a decrease in synapse number. CNF1 removal, however, restored dendritic tree development and synapse formation, suggesting that the toxin can reversibly block neuronal differentiation. On differentiated neurons, CNF1 had a similar effacing effect on synapses. Therefore, a direct interaction with CNF1 is apparently deleterious for neurons. Since astrocytes play a pivotal role in neuronal differentiation and synaptic regulation, we wondered if the beneficial in vivo effect could be mediated by astrocytes. Primary astrocytes from embryonic cortex were treated with CNF1 for 48 hours and used as a substrate for growing hippocampal neurons. Such neurons showed an increased development of neurites, in respect to age-matched controls, with a wider dendritic tree and a richer content in synapses. In CNF1-exposed astrocytes, the production of interleukin 1β, known to reduce dendrite development and complexity in neuronal cultures, was decreased. These results demonstrate that astrocytes, under the influence of CNF1, increase their supporting activity on neuronal growth and differentiation, possibly related to the diminished levels of interleukin 1β. These observations suggest that the enhanced synaptic plasticity and improved learning and memory described in CNF1-injected mice are probably mediated by astrocytes.