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SpliceProt 2.0 is a public proteogenomics database that aims to list the sequence of known proteins and potential new proteoforms in human, mouse, and rat proteomes. This updated repository provides an even broader range of computationally translated proteins and serves, for example, to aid with proteomic validation of splice variants absent from the reference UniProtKB/SwissProt database. We demonstrate the value of SpliceProt 2.0 to predict orthologous proteins between humans and murines based on transcript reconstruction, sequence annotation and detection at the transcriptome and proteome levels. In this release, the annotation data used in the reconstruction of transcripts based on the methodology of ternary matrices were acquired from new databases such as Ensembl, UniProt, and APPRIS. Another innovation implemented in the pipeline is the exclusion of transcripts predicted to be susceptible to degradation through the NMD pathway. Taken together, our repository and its applications represent a valuable resource for the proteogenomics community.

Aim: To evaluate the quality of podcasts produced by lecturers as pre-class learning material; to verify lecturers' buy-in, after a specific workshop, regarding the practice of producing and using podcasts., Background: The teaching-learning process has undergone significant changes in recent years with the proposal of the flipped classroom strategy, which places the student at the center of the learning process and uses technology that requires adaptation of lecturers, both inside and outside the classroom. Pre-class learning material is one of the features of the flipped classroom model. It provides basic concepts for problem solving in small group discussion in classroom. Podcasts for this educational purpose are a recent technology and their innovative characteristics require deeper understanding in terms of their influence and usability., Design: Prospective, descriptive and quantitative study., Setting and Population: A workshop on the production of educational podcasts was offered to 23 lecturers on the Nursing course., Methods: Data were collected in the second semester of 2021 and the quality analysis was based on criteria available in the literature., Results: Eighteen professors (78 %) participated in the study and 46 podcasts were produced. Most professors being nurses (61 %), followed by biologists (28 %). Most have a doctorate degree (72 %). These podcasts were available for a mean of five days before the classes and their mean access rate by students was 58 %. There was no correlation between the access rate and the period of availability before the relative class. Most podcasts were informative (100 %) and monologues (98 %). The average duration was 6.2 min, which is within the ideal duration recommended in the literature. All of the podcasts included a description of the learning objectives at the beginning and most of them also included a closing message at the end., Conclusion: The nursing lecturers were able to produce their podcasts, which met quality criteria and reached the standards suggested by experts in the field., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Objectives: to map Brazilian undergraduate nursing students' critical thinking level and investigate the correlation between selected sociodemographic data and critical thinking domains., Methods: in this descriptive cross-sectional study, participants' (N=89) critical thinking was assessed using the Health Science Reasoning Test. Correlation between critical thinking domains and sociodemographic data was assessed using the Pearson correlation coefficient., Results: the overall results showed a moderate level of participants' critical thinking (mean = 70.7; standard deviation 5.7). A poor performance was identified in 5 of the 8 critical thinking domains. A significant positive correlation was found between education period and critical thinking (p<.001)., Conclusions: poor level in students critical thinking domains may lead to negative consequences for their learning outcomes. Further studies should be carried out to confirm our results, in addition to investigation of teaching methods that encourage and ensure the development of students' critical thinking skills during nursing education.

RNA sequencing (RNA-Seq) and mass-spectrometry-based proteomics data are often integrated in proteogenomic studies to assist in the prediction of eukaryote genome features, such as genes, splicing, single-nucleotide (SNVs), and single-amino-acid variants (SAAVs). Most genomes of parasite nematodes are draft versions that lack transcript- and protein-level information and whose gene annotations rely only on computational predictions. Angiostrongylus costaricensis is a roundworm species that causes an intestinal inflammatory disease, known as abdominal angiostrongyliasis (AA). Currently, there is no drug available that acts directly on this parasite, mostly due to the sparse understanding of its molecular characteristics. The available genome of A. costaricensis , specific to the Costa Rica strain, is a draft version that is not supported by transcript- or protein-level evidence. This study used RNA-Seq and MS/MS data to perform an in-depth annotation of the A. costaricensis genome. Our prediction improved the reference annotation with (a) novel coding and non-coding genes; (b) pieces of evidence of alternative splicing generating new proteoforms; and (c) a list of SNVs between the Brazilian (Crissiumal) and the Costa Rica strain. To the best of our knowledge, this is the first time that a multi-omics approach has been used to improve the genome annotation of A. costaricensis . We hope this improved genome annotation can assist in the future development of drugs, kits, and vaccines to treat, diagnose, and prevent AA caused by either the Brazil strain (Crissiumal) or the Costa Rica strain.

Alternative splicing (AS) may increase the number of proteoforms produced by a gene. Alzheimer's disease (AD) is a neurodegenerative disease with well-characterized AS proteoforms. In this study, we used a proteogenomics strategy to build a customized protein sequence database and identify orthologous AS proteoforms between humans and mice on publicly available shotgun proteomics (MS/MS) data of the corpus callosum (CC) and olfactory bulb (OB). Identical proteotypic peptides of six orthologous AS proteoforms were found in both species: PKM1 (gene PKM/Pkm ), STXBP1a (gene STXBP1/Stxbp1 ), Isoform 3 (gene HNRNPK/Hnrnpk ), LCRMP-1 (gene CRMP1/Crmp1 ), SP3 (gene CADM1/Cadm1 ), and PKCβII (gene PRKCB/Prkcb ). These AS variants were also detected at the transcript level by publicly available RNA-Seq data and experimentally validated by RT-qPCR. Additionally, PKM1 and STXBP1a were detected at higher abundances in a publicly available MS/MS dataset of the AD mouse model APP/PS1 than its wild type. These data corroborate other reports, which suggest that PKM1 and STXBP1a AS proteoforms might play a role in amyloid-like aggregate formation. To the best of our knowledge, this report is the first to describe PKM1 and STXBP1a overexpression in the OB of an AD mouse model. We hope that our strategy may be of use in future human neurodegenerative studies using mouse models.

Objectives: to identify the dominant dimensions of the authentic leadership of nurses in a private hospital network and to verify the association with job satisfaction and accreditation., Methods: cross-sectional, analytical study carried out in 11 hospitals with 282 nurses, of which 94 were leaders and 188 were led. Participants answered the Authentic Leardership Questionnaire and the Job Satisfaction Survey., Results: there was a significant difference between the assessment of leaders and followers in all dimensions of the Authentic Leardership Questionnaire. Regarding the association of authentic leadership and job satisfaction, a significant positive moderate correlation was found among the employees. In hospitals accredited by the Joint Commission International, leaders were perceived as more transparent by their subordinates., Conclusions: there was correlation between authentic leadership and job satisfaction and authentic leadership and the accreditation model among the subordinates.

In Colombia, Lachesis acrochorda causes 2-3% of all snake envenomations. The accidents promote a high mortality rate (90%) due to blood and cardiovascular complications. Here, the effects of the snake venom of L. acrochorda (SVLa) were analyzed on human blood cells and on cardiovascular parameters of rats. SVLa induced blood coagulation, as measured by the prothrombin time test, but did not reduce the cell viability of neutrophils and platelets evaluated by the 3-(4,5-dimethylthiazol-2yl)-2,5-diphenyl tetrazolium bromide (MTT) reduction assay and by the lactate dehydrogenase (LDH) enzyme assay. In fact, SVLa increased the absorbance in tests made with platelets subjected to the MTT assay. SVLa induced platelet aggregation whose magnitude was comparable to that of the positive control adenosine diphosphate (ADP), and occurred earlier with increasing SVLa concentration. Acetylsalicylic acid (ASA, a cyclooxygenase inhibitor) or clopidogrel (an ADP receptor blocker) inhibited the aggregating effect of SVLa. Inhibition of SVLa-elicited platelet aggregation also resulted from the treatment with disodium ethylenediaminetetraacetate (Na 2 -EDTA; metalloproteinase inhibitor) and with 4-(2-aminoethyl) benzenesulfonyl fluoride hydrochloride (AEBSF, serine protease inhibitor). In isolated right atrium of rats, SVLa increased slightly, but significantly, the magnitude of the spontaneous contractions and, in isolated rat aorta, SVLa relaxed KCl- or phenylephrine-induced contractions. In vivo, SVLa induced hypotension and bradycardia in rats, with detection of hemorrhage in pulmonary and renal tissues. Altogether, under experimental conditions, SVLa induced blood coagulation, platelet aggregation, hypotension and bradycardia. Part of the effects presented here may be explained by the presence of snake venom metalloproteinases (SVMPs) and snake venom serine proteases (SVSPs), constituents of SVLa., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Background: Worldwide, breast cancer is the main cause of cancer mortality in women. Most cases originate in mammary ductal cells that produce the nipple aspirate fluid (NAF). In cancer patients, this secretome contains proteins associated with the tumor microenvironment. NAF studies are challenging because of inter-individual variability. We introduced a paired-proteomic shotgun strategy that relies on NAF analysis from both breasts of patients with unilateral breast cancer and extended PatternLab for Proteomics software to take advantage of this setup., Methods: The software is based on a peptide-centric approach and uses the binomial distribution to attribute a probability for each peptide as being linked to the disease; these probabilities are propagated to a final protein p-value according to the Stouffer's Z-score method., Results: A total of 1227 proteins were identified and quantified, of which 87 were differentially abundant, being mainly involved in glycolysis (Warburg effect) and immune system activation (activated stroma). Additionally, in the estrogen receptor-positive subgroup, proteins related to the regulation of insulin-like growth factor transport and platelet degranulation displayed higher abundance, confirming the presence of a proliferative microenvironment., Conclusions: We debuted a differential bioinformatics workflow for the proteomic analysis of NAF, validating this secretome as a treasure-trove for studying a paired-organ cancer type.

Objective: The objective of this study was to analyze the association between consumption of alcoholic drinks and adoption of other risky forms of behavior in traffic among motorcyclists involved in accidents. Methods: This was an exploratory cross-sectional study among injured motorcyclists who were hospitalized in the traumatology department of the "Governador Paulo Guerra" Restoration Hospital (Hospital da Restauração Governador Paulo Guerra), Recife, Pernambuco, Brazil. A questionnaire containing items relating to sociodemographic, occupational, and behavioral factors and aspects of the accident and road conditions was applied. Descriptive and bivariate analyses were performed and odds ratios (ORs) and 95% confidence intervals (CIs) were calculated. The significance level was set at 5%. Results: One hundred seventy individuals were investigated. Consumption of alcohol prior to the accident was reported by 32.9% of motorcyclists. This behavior was positively associated with the following risky forms of behavior in traffic: speeding (OR = 4.08; 95% CI, 1.15-9.48); failure to use a helmet (OR = 2.41; 95% CI, 1.15-5.02); and not having a motorcycle driver's license (OR = 2.68; 95% CI, 1.31-5.45). Conclusion: This study showed that, in the population studied, riding a motorcycle under the effects of alcoholic drinks was associated with other risky forms of behavior in traffic: speeding, not using a helmet, and not having a motorcycle driver's license. We believe that the interaction between these behaviors may lead to greater occurrence and greater severity of accidents.

Cross-linking/Mass spectrometry (XLMS) is a consolidated technique for structural characterization of proteins and protein complexes. Despite its success, the cross-linking chemistry currently used is mostly based on N-hydroxysuccinimide (NHS) esters, which react primarily with lysine residues. One way to expand the current applicability of XLMS into several new areas is to increase the number of cross-links obtainable for a target protein. We introduce a multiplex chemistry (denoted XPlex) that targets Asp, Glu, Lys, and Ser residues. XPlex can generate significantly more cross-links with reactions occurring at lower temperatures and enables targeting proteins that are not possible with NHS ester-based cross-linkers. We demonstrate the effectiveness of our approach in model proteins as well as a target Lys-poor protein, SalBIII. Identification of XPlex spectra requires a search engine capable of simultaneously considering multiple cross-linkers on the same run; to achieve this, we updated the SIM-XL search algorithm with a search mode tailored toward XPlex. In summary, we present a complete chemistry/computational solution for significantly increasing the number of possible distance constraints by mass spectrometry experiments, and thus, we are convinced that XPlex poses as a real complementary approach for structural proteomics studies.

Snake venoms are sources of molecules with proven and potential therapeutic applications. However, most activities assayed in venoms (or their components) are of hemorrhagic, hypotensive, edematogenic, neurotoxic or myotoxic natures. Thus, other relevant activities might remain unknown. Using functional genomics coupled to the connectivity map (C-map) approach, we undertook a wide range indirect search for biological activities within the venom of the South American pit viper Bothrops jararaca . For that effect, venom was incubated with human breast adenocarcinoma cell line (MCF7) followed by RNA extraction and gene expression analysis. A list of 90 differentially expressed genes was submitted to biosimilar drug discovery based on pattern recognition. Among the 100 highest-ranked positively correlated drugs, only the antihypertensive, antimicrobial (both antibiotic and antiparasitic), and antitumor classes had been previously reported for B. jararaca venom. The majority of drug classes identified were related to (1) antimicrobial activity; (2) treatment of neuropsychiatric illnesses (Parkinson's disease, schizophrenia, depression, and epilepsy); (3) treatment of cardiovascular diseases, and (4) anti-inflammatory action. The C-map results also indicated that B. jararaca venom may have components that target G-protein-coupled receptors (muscarinic, serotonergic, histaminergic, dopaminergic, GABA, and adrenergic) and ion channels. Although validation experiments are still necessary, the C-map correlation to drugs with activities previously linked to snake venoms supports the efficacy of this strategy as a broad-spectrum approach for biological activity screening, and rekindles the snake venom-based search for new therapeutic agents., Competing Interests: The authors declare no conflict of interest.

Snakebite envenomation is a neglected condition that constitutes a public health problem in tropical and subtropical countries, including Brazil. Interestingly, some animals are resistant to snake envenomation due to the presence of inhibitory glycoproteins in their serum that target toxic venom components. DM64 is an acidic glycoprotein isolated from Didelphis aurita (opossum) serum that has been characterized as an inhibitor of the myotoxicity induced by bothropic toxins bearing phospholipase A2 (PLA2) structures. This antitoxic protein can serve as an excellent starting template for the design of novel therapeutics against snakebite envenomation, particularly venom-induced local tissue damage. Therefore, the aim of this work was to produce a recombinant DM64 (rDM64) in the methylotrophic yeast Pichia pastoris and to compare its biological properties with those of native DM64. Yeast fermentation in the presence of Pefabloc, a serine protease inhibitor, stimulated cell growth (~1.5-fold), increased the rDM64 production yield approximately 10-fold and significantly reduced the susceptibility of rDM64 to proteolytic degradation. P. pastoris fermentation products were identified by mass spectrometry and Western blotting. The heterologous protein was efficiently purified from the culture medium by affinity chromatography (with immobilized PLA2 myotoxin) and/or an ion exchange column. Although both native and recombinant DM64 exhibit different glycosylation patterns, they show very similar electrophoretic mobilities after PNGase F treatment. rDM64 formed a noncovalent complex with myotoxin II (Lys49-PLA2) from Bothrops asper and displayed biological activity that was similar to that of native DM64, inhibiting the cytotoxicity of myotoxin II by 92% at a 1:1 molar ratio.