The universe of neurotoxic proteins: A study of the conformational space of polyglutamine and β-amyloid

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Física de la Materia Condensada. Fecha de lectura: 16-10-2015Neurodegenerative diseases are considered diseases of the old. These are among the main causes of death after the discovery of vaccination and antibiotics in the late 18th and early 20th century, respectively, pushed the average life expectancy in the developed countries to the current age of about 80. Among them, Alzheimer and Huntington are incurable diseases, even though a great effort has been put in their understanding and several important discoveries have been made about their causal factors. Both diseases are related to specific proteins in the nervous system: β-amyloid (Alzheimer) and polyglutamine expansions in huntingtin (Huntington). Polyglutamine expansions are also present in other proteins, which are in turn involved in several other diseases such as Spinocerebellar Ataxias. The study of these rapidly fluctuating proteins is challenging using the current biophysical techniques, which do not give access to the whole distribution of conformations but average over the whole population of molecules and thereby hide rare events. The advent of single-molecule techniques, as well as their good correlation with computer simulations, has made the atomistic exploration of these proteins possible. In this work, we combine atomic force microscopy with molecular dynamics simulations to study the conformational polymorphism of polyglutamine expansions and β-amyloid. We discover that both proteins have very similar behaviour at the monomeric level even if their amino acid sequences are quite different. When allowed to evolve, these proteins continuously waver between several different conformers that have distinct shapes and properties. Among these conformations, we find some that last longer than others, some that present a high resistance to forced unfolding and, in simulations, some that generate a knot in their structure. With these findings, we propose that high temporal stability, high stability under force and the presence of knots might explain the toxicity of these proteins at the monomeric level, since the proteasomal degradation of some of these species seems to be troublesome and, under certain circumstances, impossibleLas enfermedades neurodegenerativas se consideradan enfermedades de la vejez. Éstas se encuentran entre las mayores causas de mortalidad desde que el descubrimiento de las vacunas y los antibióticos a finales del siglo XVIII y a principios del XX, respectivamente, alargaron la esperanza de vida (en países desarrollados) hasta la edad actual de alrededor de 80 años. Entre ellas, el Alzheimer y el Huntington son enfermedades incurables, a pesar del gran esfuerzo realizado para entenderlas y los distintos descubrimientos realizados acerca de sus factores causales. Ambas enfermedades están relacionadas con proteínas del sistema nervioso: β-amiloide (Alzheimer) y expansiones de poliglutaminas en la huntingtina (Huntington). Las expansiones de poliglutaminas también están presentes en otras proteínas, que a su vez están implicadas en otras enfermedades como las Ataxias Espinocerebelares. El estudio de estas proteínas rápidamente fluctuantes presenta un reto para las técnicas actuales de biofísica, que no dan acceso a la distribución completa de posibilidades sino que promedian sobre la población y con ello esconden eventos raros. El advenimiento de las técnicas de molécula individual, junto con su buena correlación con las simulaciones por ordenador, ha hecho posible la exploración de estas proteínas. En este trabajo combinamos la microscopía de fuerzas atómicas con simulaciones de dinámica molecular para estudiar el polimorfismo conformational de las expansiones de poliglutamina y el β-amiloide. Descubrimos que el comportamiento de ambas es similar a nivel de monómero a pesar de que sus secuencias aminoacídicas son distintas. Cuando se las deja evolucionar, estas proteínas fluctúan rápidamente entre varios confórmeros que presentan formas y propiedades distintas. Entre estas conformaciones, encontramos algunas que duran más que otras, varias con alta resistencia al desplegamiento bajo fuerza y, en simulaciones, algunas que generan un nudo en su estructura. Con estos descubrimientos, proponemos que la estabilidad temporal, la alta estabilidad bajo fuerza y la presencia de nudos podrían explicar la toxicidad de éstas proteínas a nivel de monómero, ya que la degradación de algunas de estas especies en el proteasoma parece ser problemática y, en ciertas condiciones, imposible

Towards Interoperability in E-health Systems: a three-dimensional approach based on standards and semantics

Proceedings of: HEALTHINF 2009 (International Conference on Helath Informatics), Porto (Portugal), January 14-17, 2009, is part of BIOSTEC (Intemational Joint Conference on Biomedical Engineering Systems and Technologies)The interoperability problem in eHealth can only be addressed by mean of combining standards and technology. However, these alone do not suffice. An appropiate framework that articulates such combination is required. In this paper, we adopt a three-dimensional (information, conference and inference) approach for such framework, based on OWL as formal language for terminological and ontological health resources, SNOMED CT as lexical backbone for all such resources, and the standard CEN 13606 for representing EHRs. Based on tha framewok, we propose a novel form for creating and supporting networks of clinical terminologies. Additionally, we propose a number of software modules to semantically process and exploit EHRs, including NLP-based search and inference, wich can support medical applications in heterogeneous and distributed eHealth systems.This work has been funded as part of the Spanish nationally funded projects ISSE (FIT-350300-2007-75) and CISEP (FIT-350301-2007-18). We also acknowledge IST-2005-027595 EU project NeO

Correction : Chaparro et al. Incidence, Clinical Characteristics and Management of Inflammatory Bowel Disease in Spain: Large-Scale Epidemiological Study. J. Clin. Med. 2021, 10, 2885

The authors wish to make the following corrections to this paper [...]

Incidence, Clinical Characteristics and Management of Inflammatory Bowel Disease in Spain : Large-Scale Epidemiological Study

(1) Aims: To assess the incidence of inflammatory bowel disease (IBD) in Spain, to describe the main epidemiological and clinical characteristics at diagnosis and the evolution of the disease, and to explore the use of drug treatments. (2) Methods: Prospective, population-based nationwide registry. Adult patients diagnosed with IBD-Crohn's disease (CD), ulcerative colitis (UC) or IBD unclassified (IBD-U)-during 2017 in Spain were included and were followed-up for 1 year. (3) Results: We identified 3611 incident cases of IBD diagnosed during 2017 in 108 hospitals covering over 22 million inhabitants. The overall incidence (cases/100,000 person-years) was 16 for IBD, 7.5 for CD, 8 for UC, and 0.5 for IBD-U; 53% of patients were male and median age was 43 years (interquartile range = 31-56 years). During a median 12-month follow-up, 34% of patients were treated with systemic steroids, 25% with immunomodulators, 15% with biologics and 5.6% underwent surgery. The percentage of patients under these treatments was significantly higher in CD than UC and IBD-U. Use of systemic steroids and biologics was significantly higher in hospitals with high resources. In total, 28% of patients were hospitalized (35% CD and 22% UC patients, p < 0.01). (4) Conclusion: The incidence of IBD in Spain is rather high and similar to that reported in Northern Europe. IBD patients require substantial therapeutic resources, which are greater in CD and in hospitals with high resources, and much higher than previously reported. One third of patients are hospitalized in the first year after diagnosis and a relevant proportion undergo surgery

Treatment with tocilizumab or corticosteroids for COVID-19 patients with hyperinflammatory state: a multicentre cohort study (SAM-COVID-19)

Objectives: The objective of this study was to estimate the association between tocilizumab or corticosteroids and the risk of intubation or death in patients with coronavirus disease 19 (COVID-19) with a hyperinflammatory state according to clinical and laboratory parameters. Methods: A cohort study was performed in 60 Spanish hospitals including 778 patients with COVID-19 and clinical and laboratory data indicative of a hyperinflammatory state. Treatment was mainly with tocilizumab, an intermediate-high dose of corticosteroids (IHDC), a pulse dose of corticosteroids (PDC), combination therapy, or no treatment. Primary outcome was intubation or death; follow-up was 21 days. Propensity score-adjusted estimations using Cox regression (logistic regression if needed) were calculated. Propensity scores were used as confounders, matching variables and for the inverse probability of treatment weights (IPTWs). Results: In all, 88, 117, 78 and 151 patients treated with tocilizumab, IHDC, PDC, and combination therapy, respectively, were compared with 344 untreated patients. The primary endpoint occurred in 10 (11.4%), 27 (23.1%), 12 (15.4%), 40 (25.6%) and 69 (21.1%), respectively. The IPTW-based hazard ratios (odds ratio for combination therapy) for the primary endpoint were 0.32 (95%CI 0.22-0.47; p < 0.001) for tocilizumab, 0.82 (0.71-1.30; p 0.82) for IHDC, 0.61 (0.43-0.86; p 0.006) for PDC, and 1.17 (0.86-1.58; p 0.30) for combination therapy. Other applications of the propensity score provided similar results, but were not significant for PDC. Tocilizumab was also associated with lower hazard of death alone in IPTW analysis (0.07; 0.02-0.17; p < 0.001). Conclusions: Tocilizumab might be useful in COVID-19 patients with a hyperinflammatory state and should be prioritized for randomized trials in this situatio

Debittering activity of peptidases from selected lactobacilli strains in model cheeses

The peptidase activity of 39 Lactobacillus strains isolated from natural sheep and goat cheeses was studied on different substrates. Aminopeptidase and dipeptidyl aminopeptidase activities were generally very low, whereas high dipeptidase, tripeptidase and carboxypeptidase activities were found for some isolates tested. The debittering effect of 2 selected strains, L. plantarum ESI144 and L. paracasei subsp. paracasei ESI207, was investigated in model cheeses elaborated with the addition of Neutrase®. Reduction of the hydrophobic peptides level in the water soluble fraction of Neutrase® cheeses with L. plantarum ESI144 was higher than that obtained with L. paracasei subsp. paracasei ESI207, pointing to its possible use as a debittering starter adjunct in cheese manufacture

Streptococcus thermophilus as adjunct culture for a semi-hard cows' milk cheese

The influence of the addition of Streptococcus thermophilus as adjunct to the mesophilic starter on chemical, textural and sensory characteristics of a semi-hard cows' milk cheese was studied. Addition of the thermophilic adjunct increased αs1-casein hydrolysis and the level of N soluble at pH 4.6 after 30 d of ripening, reduced the level of N soluble in TCA and did not affect the level of N soluble in PTA. Lower apparent elastic modulus, breaking force and hardness were recorded for cheeses with thermophilic adjunct, as a consequence of the lower dry matter and the slightly enhanced casein hydrolysis. Flavour quality, flavour intensity and cheese bitterness were not affected by S. thermophilus addition. In cheese made from milk with Bacillus subtilis neutral proteinase added to accelerate ripening and induce bitter flavour formation, the use of S. thermophilus as adjunct enhanced proteolysis and produced a considerably higher concentration of N soluble in PTA. Textural characteristics were not affected. Flavour quality was improved and cheese bitterness significantly reduced by the addition of the thermophilic adjunct. ©Inra/Elsevier, Paris

Effect of Lactobacillus plantarum as adjunct starter on the flavour and texture of a semi-hard cheese made from pasteurised cows' milk

The effect of Lactobacillus plantarum ESI 144 as starter adjunct on the chemical, textural and sensory characteristics of a semi-hard cows' milk cheese was investigated. Lactobacilli lowered cheese pH during early manufacture, reducing casein degradation and formation of soluble N. Higher apparent elastic modulus, breaking force and hardness values were recorded for cheeses with added lactobacilli, as a consequence of the less pronounced proteolysis. In cheese made from milk to which Bacillus subtilis neutral proteinase was added to induce bitter flavour formation, the use of L plantarum as adjunct starter resulted in lower levels of hydrophobic peptides from day 1 and lower bitterness scores throughout ripening

Proteolysis, texture, and sensory characteristics of Serrano hams from Duroc and Large White pigs during dry-curing

Proteolysis, texture, physicochemical, and sensory characteristics of Serrano hams from Duroc and Large White pigs at 5, 7, 9, 12, and 15 m of curing (3 hams per breed per curing time) were investigated. Higher concentrations of some sarcoplasmic and myofibrillar proteins, peptides with molecular mass in the ranges 3700 to 12000 Da, 700 to 2000 Da, and below 450 Da, and total free amino acids were recorded for Large White hams, while hydrophobic peptides were at higher levels in Duroc hams. A 40 kDa peak in the low-ionic-strength soluble protein fraction and 2 peaks of 40 and 45 kDa in the high-ionic-strength soluble protein fraction found only in Duroc hams could be of use in discriminating products from different breeds. Physicochemical and textural characteristics of both types of hams evolved similarly during curing and differences in organoleptic traits between breeds were negligible. Flavor intensity and flavor quality of hams were strongly correlated to curing time, with r2 values over 0.95 for flavor intensity and over 0.90 for flavor quality, and to the concentration of total free amino acids, with r2 values over 0.90 for both flavor intensity and flavor quality. The sensory evaluation scores of Duroc hams, at least as high as those of Large White hams, make the production of high-quality Serrano ham from pure breed Duroc pigs feasible. © 2013 Institute of Food Technologists®

Proteolysis and flavor characteristics of Serrano ham processed under different ripening temperature conditions

Physicochemical, proteolysis and sensory characteristics of Serrano hams processed under low, medium and high ripening temperature conditions (RTC), with respective average temperatures of 9.3, 14.3, and 19.1 °C, were determined throughout a 15-mo period. In addition, quantitative relationships among variables were calculated. Medium and high RTC hams showed lower moisture contents and lower levels of low- and high-ionic-strength soluble proteins than low RTC hams. At 15 mo, aldolase was the most abundant low-ionic-strength soluble protein and actin the most abundant high-ionic-strength soluble protein in all hams while creatine kinase was no longer detected and H-meromyosin was detected only in low and medium RTC hams. Levels of all the molecular-weight peptide fractions increased during ripening, with higher factors of increase for the fractions of lower molecular weight. Total free amino acids were at significantly higher concentrations in medium and high RTC hams than in low RTC hams from month 7 onwards. The correlations of flavor preference and flavor intensity with ripening time, thermal integral, total free amino acids and most individual free amino acids were highly significant, while raw-meat taste was negatively correlated with all those variables. From month 5 to month 9 of ripening, development of a high quality flavor evolved more rapidly in medium RTC hams, flavor intensity increased at a faster rate in high RTC hams and raw-meat taste declined more rapidly in medium and high RTC hams. Medium and high RTC may be applied to accelerate the ripening process of Serrano ham without impairing flavor preference. Practical application Medium and high ripening temperature conditions (RTC) may be applied to Serrano ham in order to enhance the phenomena associated with ripening, without loss of product quality. Moisture loss, degradation of proteins and formation of free amino acids were accelerated in medium and high RTC hams. From month 5 to month 9 of ripening, development of a high quality flavor evolved more rapidly in medium RTC hams, flavor intensity increased at a faster rate in high RTC hams, and raw-meat taste declined more rapidly in medium and high RTC hams. © 2015 Institute of Food Technologists®