Proteomic characterization of human coronary thrombus in patients with ST-segment elevation acute myocardial infarction

Acute myocardial infarction with ST-segment elevation (STEMI) initiates with intraluminal thrombosis and results in total occlusion of the coronary artery. To date, characterization of the coronary thrombus proteome in STEMI patients has not been yet accomplished. Therefore, we aimed to perform an in-depth proteomic characterization of the human coronary thrombus by means of three different approaches: 2-DE followed by mass spectrometry (MALDI MS/MS), 1-DE combined either with liquid chromatography coupled to mass spectrometry in a MALDI TOF/TOF (LC-MALDI-MS/MS), or in a LTQ-Orbitrap (LC-ESI-MS/MS). This approach allowed us to identify a total of 708 proteins in the thrombus. Expression in coronary thrombi (n=20) of 14 proteins was verified, and the expression of fibrin and 6 cell markers (platelets, monocytes, neutrophils, eosinophils, T-cells and B-cells) quantified by selected reaction monitoring (SRM). A positive correlation of 5 proteins (fermitin homolog 3, thrombospondin-1, myosin-9, beta parvin and ras-related protein Rap-1b) with CD41 was found, pointing out the potential activation of a focal adhesion pathway within thrombus platelets. DIDO1 protein was found to correlate negatively with thrombus fibrin, and was found up-regulated in the plasma of these STEMI patients, which may constitute a starting point for further analyses in the search for biomarkers of thrombosis. BIOLOGICAL SIGNIFICANCE: The proteomic characterization of the human coronary thrombus may contribute to a better understanding of the mechanisms involved in acute coronary syndrome, and thus pave the road for the identification of new therapeutic targets that may help addressing this and other thrombotic diseases. A novel methodology to characterize thrombus composition and expression of a sub-group of proteins is hereby described, which allowed linking protein expression with cellular and ECM matrix composition of the thrombus. Five proteins (fermitin homolog 3, thrombospondin-1, myosin-9, beta parvin and ras-related protein Rap-1b) co-express within the human coronary thrombus with CD41, pointing out the potential activation of a focal adhesion pathway within thrombus platelets during thrombus formation. Besides, the protein death-inducer obliterator 1, found to be expressed within the human coronary thrombus, has been proved to increase in the plasma of STEMI patients, which constitutes an important starting point for further analyses in the search for biomarkers of thrombosis.This work was supported by grants from the Instituto de Salud Carlos III (FIS PI070537, PI11/02239), Fondos Feder, Redes temáticas de Investigación Cooperativa en Salud (RD12/0042/ 0071, RD06/0014/1015), and Fundación para la Investigación Sanitaria de Castilla-La Mancha (FISCAM PI2008-08, PI2008-28, PI2008-52). These results are lined up with the Spanish initiative on the Human Proteome Project (SpHPP). The CNIC is supported by the Spanish Ministerio de Economia y Competitividad and the Fundacion Pro-CNIC. We would like to thank Dr. Gloria Alvarez-Llamas for her kind suggestions for the manuscript; Gemma Barroso from Proteomic Unit, Hospital Nacional de Paraplejicos, for her help and dedication to this work, as well as Veronica Moral and Ana Gallardo from the same Unit, and TamaraSastre andCarmenBermudez for their technical support.S

Biochemical and structural characterization of a novel arginine kinase from the spider <i>Polybetes pythagoricus</i>

Energy buffering systems are key for homeostasis during variations in energy supply. Spiders are the most important predators for insects and therefore key in terrestrial ecosystems. From biomedical interest, spiders are important for their venoms and as a source of potent allergens, such as arginine kinase (AK, EC 2.7.3.3). AK is an enzyme crucial for energy metabolism, keeping the pool of phosphagens in invertebrates, and also an allergen for humans. In this work, we studied AK from the Argentininan spider Polybetes pythagoricus (PpAK), from its complementary DNA to the crystal structure. The PpAK cDNA from muscle was cloned, and it is comprised of 1068 nucleotides that encode a 384-amino acids protein, similar to other invertebrate AKs. The apparent Michaelis-Menten kinetic constant (Km) was 1.7 mM with a kcat of 75 s-1. Two crystal structures are presented, the apoPvAK and PpAK bound to arginine, both in the open conformation with the active site lid (residues 310-320) completely disordered. The guanidino group binding site in the apo structure appears to be organized to accept the arginine substrate. Finally, these results contribute to knowledge of mechanistic details of the function of arginine kinase.Instituto de Investigaciones Bioquímicas de La Plat

Biochemical and structural characterization of a novel arginine kinase from the spider <i>Polybetes pythagoricus</i>

Energy buffering systems are key for homeostasis during variations in energy supply. Spiders are the most important predators for insects and therefore key in terrestrial ecosystems. From biomedical interest, spiders are important for their venoms and as a source of potent allergens, such as arginine kinase (AK, EC 2.7.3.3). AK is an enzyme crucial for energy metabolism, keeping the pool of phosphagens in invertebrates, and also an allergen for humans. In this work, we studied AK from the Argentininan spider Polybetes pythagoricus (PpAK), from its complementary DNA to the crystal structure. The PpAK cDNA from muscle was cloned, and it is comprised of 1068 nucleotides that encode a 384-amino acids protein, similar to other invertebrate AKs. The apparent Michaelis-Menten kinetic constant (Km) was 1.7 mM with a kcat of 75 s-1. Two crystal structures are presented, the apoPvAK and PpAK bound to arginine, both in the open conformation with the active site lid (residues 310-320) completely disordered. The guanidino group binding site in the apo structure appears to be organized to accept the arginine substrate. Finally, these results contribute to knowledge of mechanistic details of the function of arginine kinase.Instituto de Investigaciones Bioquímicas de La Plat

A method for automatically extracting infectious disease-related primers and probes from the literature

BACKGROUND: Primer and probe sequences are the main components of nucleic acid-based detection systems. Biologists use primers and probes for different tasks, some related to the diagnosis and prescription of infectious diseases. The biological literature is the main information source for empirically validated primer and probe sequences. Therefore, it is becoming increasingly important for researchers to navigate this important information. In this paper, we present a four-phase method for extracting and annotating primer/probe sequences from the literature. These phases are: (1) convert each document into a tree of paper sections, (2) detect the candidate sequences using a set of finite state machine-based recognizers, (3) refine problem sequences using a rule-based expert system, and (4) annotate the extracted sequences with their related organism/gene information. RESULTS: We tested our approach using a test set composed of 297 manuscripts. The extracted sequences and their organism/gene annotations were manually evaluated by a panel of molecular biologists. The results of the evaluation show that our approach is suitable for automatically extracting DNA sequences, achieving precision/recall rates of 97.98% and 95.77%, respectively. In addition, 76.66% of the detected sequences were correctly annotated with their organism name. The system also provided correct gene-related information for 46.18% of the sequences assigned a correct organism name. CONCLUSIONS: We believe that the proposed method can facilitate routine tasks for biomedical researchers using molecular methods to diagnose and prescribe different infectious diseases. In addition, the proposed method can be expanded to detect and extract other biological sequences from the literature. The extracted information can also be used to readily update available primer/probe databases or to create new databases from scratch.The present work has been funded, in part, by the European Commission through the ACGT integrated project (FP6-2005-IST-026996) and the ACTION-Grid support action (FP7-ICT-2007-2-224176), the Spanish Ministry of Science and Innovation through the OntoMineBase project (ref. TSI2006-13021-C02-01), the ImGraSec project (ref. TIN2007-61768), FIS/AES PS09/00069 and COMBIOMED-RETICS, and the Comunidad de Madrid, Spain.S

Safety and efficacy of bentonite as a feed additive for all animal species

The EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) received a request from the European Commission to assess the safety and efficacy of bentonite when used as a technological feed additive (substances for reduction of the contamination of feed by mycotoxins) for all animal species. The applicant, EUBA aisbl (European Bentonite Association) representing six companies, submitted to EFSA a technical dossier to support the application. The applicant proposes to use bentonite at the maximum level of 20,000 mg/kg complete feed. The additive apparently interferes with the analysis of aflatoxin B1 in feed. The safety of the additive was already evaluated by the Panel in an opinion delivered in 2012. Bentonites are safe for all animal species, the consumers and the environment when used at a maximum level of 20,000 mg/kg complete feed. The results of a new genotoxicity study reinforced the previous conclusion that smectites are non-genotoxic. Bentonites are not skin irritants but might be mildly irritant to the eye; based on a new study submitted, the additive is not a skin sensitiser. Owing to its silica content, the additive is a hazard by inhalation for the users. The in vitro study showed that the di- and tri-octahedral smectites tested can adsorb aflatoxin B1 at different concentrations and at pH 5; however, no adequate in vivo studies were available. Therefore, the Panel cannot draw conclusions on the additive\u2019s efficacy. The Panel further considers the safety and efficacy conclusions to apply equally to the di- and tri-octahedral smectites under assessment. The FEEDAP Panel posted some recommendations regarding the maximum content of other minerals in the additive and the incompatibilities of the additive with other medicinal substances. The Panel also drew a remark concerning the denomination of the additive and the current regulatory definition of Bentonite

High levels of population genetic differentiation in the American crocodile (Crocodylus acutus)

The American crocodile (Crocodylus acutus) is a widely distributed species across coastal and brackish areas of the Neotropical region of the Americas and the Greater Antilles. Available information on patterns of genetic differentiation in C. acutus shows a complex structuring influenced by interspecific interactions (mainly hybridization) and anthropogenic actions (mostly historical hunting, recent poaching, habitat loss and fragmentation, and unintentional translocation of individuals). In this study, we used data on mitochondrial DNA control region and 11 nuclear polymorphic microsatellite loci to assess the degree of population structure of C. acutus in South America, North America, Central America and the Greater Antilles. We used traditional genetic differentiation indices, Bayesian clustering and multivariate methods to create a more comprehensive picture of the genetic relationships within the species across its range. Analyses of mtDNA and microsatellite loci show evidence of a strong population genetic structure in the American crocodile, with unique populations in each sampling locality. Our results support previous findings showing large degrees of genetic differentiation between the continental and the Greater Antillean C. acutus. We report three new haplotypes unique to Venezuela, which are considerably less distant from the Central and North American haplotypes than to the Greater Antillean ones. Our findings reveal genetic population differentiation between Cuban and Jamaican C. acutus and offer the first evidence of strong genetic differentiation among the populations of Greater Antillean C. acutus

Nanoinformatics: developing new computing applications for nanomedicine

Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also offer breakthrough perspectives for the prevention, diagnosis and treatment of diseases. In this paper, we analyze the different aspects of nanoinformatics and suggest five research topics to help catalyze new research and development in the area, particularly focused on nanomedicine. We also encompass the use of informatics to further the biological and clinical applications of basic research in nanoscience and nanotechnology, and the related concept of an extended ?nanotype? to coalesce information related to nanoparticles. We suggest how nanoinformatics could accelerate developments in nanomedicine, similarly to what happened with the Human Genome and other -omics projects, on issues like exchanging modeling and simulation methods and tools, linking toxicity information to clinical and personal databases or developing new approaches for scientific ontologies, among many others

Correction to: Usefulness of Genetic Testing in Hypertrophic Cardiomyopathy: an Analysis Using Real-World Data

post-print123 K

MRI Investigation of the Differential Impact of Left Ventricular Ejection Fraction After Myocardial Infarction in Elderly vs. Nonelderly Patients to Predict Readmission for Heart Failure

Acute heart failure; Acute myocardial infarction; ElderlyInsuficiència cardíaca aguda; Infart agut de miocardi; Gent granInsuficiencia cardíaca aguda; Infarto agudo de miocardio; AncianoBackground Patients with ST-segment elevation myocardial infarction (STEMI), especially elderly individuals, have an increased risk of readmission for acute heart failure (AHF). Purpose To study the impact of left ventricular ejection fraction (LVEF) by MRI to predict AHF in elderly (>70 years) and nonelderly patients after STEMI. Study Type Prospective. Population Multicenter registry of 759 reperfused STEMI patients (23.3% elderly). Field Strength/Sequence 1.5-T. Balanced steady-state free precession (cine imaging) and segmented inversion recovery steady-state free precession (late gadolinium enhancement) sequences. Assessment One-week MRI-derived LVEF (%) was quantified. Sequential MRI data were recorded in 579 patients. Patients were categorized according to their MRI-derived LVEF as preserved (p-LVEF, ≥50%), mildly reduced (mr-LVEF, 41%–49%), or reduced (r-LVEF, ≤40%). Median follow-up was 5 [2.33–7.54] years. Statistical Tests Univariable (Student's t, Mann–Whitney U, chi-square, and Fisher's exact tests) and multivariable (Cox proportional hazard regression) comparisons and continuous-time multistate Markov model to analyze transitions between LVEF categories and to AHF. Hazard ratios (HR) with 95% confidence intervals (CIs) were computed. P < 0.05 was considered statistically significant. Results Over the follow-up period, 79 (10.4%) patients presented AHF. MRI-LVEF was the most robust predictor in nonelderly (HR 0.94 [0.91–0.98]) and elderly patients (HR 0.94 [0.91–0.97]). Elderly patients had an increased AHF risk across the LVEF spectrum. An excess of risk (compared to p-LVEF) was noted in patients with r-LVEF both in nonelderly (HR 11.25 [5.67–22.32]) and elderly patients (HR 7.55 [3.29–17.34]). However, the mr-LVEF category was associated with increased AHF risk only in elderly patients (HR 3.66 [1.54–8.68]). Less transitions to higher LVEF states (n = 19, 30.2% vs. n = 98, 53%) and more transitions to AHF state (n = 34, 53.9% vs. n = 45, 24.3%) were observed in elderly than nonelderly patients. Data Conclusion MRI-derived p-LVEF confers a favorable prognosis and r-LVEF identifies individuals at the highest risk of AHF in both elderly and nonelderly patients. Nevertheless, an excess of risk was also found in the mr-LVEF category in the elderly group. Evidence Level 2. Technical Efficacy Stage 2.Grant sponsor: This work was supported by “Instituto de Salud Carlos III” and “Fondos Europeos de Desarrollo Regional FEDER” (grant numbers PI20/00637, PI15/00531, and CIBERCV16/11/00486, CIBERCV16/11/00420, CIBERCV16/11/00479, and CM21/00175 to V.M.-G.), Fundació La Marató TV3 (grant 20153030-31-32), La Caixa Banking Foundation (HR17-00527) and by Conselleria de Educación – Generalitat Valenciana (PROMETEO/2021/008). J.G. acknowledges financial support from the “Agencia Estatal de Investigación” (grant FJC2020-043981-I/AEI/10.13039/501100011033)

Safety and efficacy of a preparation of algae interspaced bentonite as a feed additive for all animal species

Following a request from the European Commission, the EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP Panel) was asked to deliver a scientific opinion on the safety and efficacy of a preparation of algae interspaced bentonite when used as a flatoxin B1 binder for all animal species. The additive is composed of bentonite and algae belonging to Ulva spp. The additive is considered safe for weaned piglets, dairy cows and chickens for fattening at the maximum recommended dose of 125 mg/kg complete feed (a wide margin of safety is established in weaned piglets and dairy cows); this conclusion is extrapolated to all animal species. The additive is not genotoxic. As bentonite is essentially not absorbed from the gut lumen and algae from Ulva spp. are not expected to be of concern for human consumption, the FEEDAP Panel considers that the use of the additive in animal nutrition is safe for consumers. The additive is not an irritant to the skin or the eyes and it is considered to have low inhalation toxicity. However, the additive has a high dusting potential and contains a high proportion offine particles. A high level of inhalation exposure to an inert dust may be hazardous. In the absence of data, the Panel could not conclude on dermal sensitisation. As the components of the additive are of natural origin (soil and marine environment), it is not expected that the use of the additive in animal nutrition would adversely affect the environment. The FEEDAP Panel could not conclude on the efficacy of the additive for all animal species