In silico analysis of mismatches in RT-qPCR assays of 177 SARS-CoV-2 sequences from Brazil.

INTRODUCTION: Quantitative reverse transcription polymerase chain reaction (RT-qPCR) can detect the severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) in a highly specific manner. However, a decrease in the specificity of PCR assays for their targets may lead to false negative results. METHODS: Here, 177 high-coverage complete SARS-CoV-2 genome sequences from 13 Brazilian states were aligned with 15 WHO recommended PCR assays. RESULTS: Only 3 of the 15 completely aligned to all Brazilian sequences. Ten assays had mismatches in up to 3 sequences and two in many sequences. CONCLUSION: These results should be taken into consideration when using PCR-based diagnostics in Brazil.

Application of a cost-effective DNA extraction protocol for screening transgenic and CRISPR-edited primary goat cells.

The genotyping of genetically-modified cells is a crucial step in studies of transgenics and genomic editing with systems such as CRISPR/Cas. The detection of genome editing events can be directly related to the genotyping methodology used, which is influenced by its costs, since many experiments require the analysis of a large number of samples. The aim of this study was to compare the performance of direct lysis methods of genomic DNA (gDNA) extraction for the detection of knockins and knockouts in primary goat cells. Initially, three gDNA extraction protocols (protocol A, heat denaturation/freeze-thaw in water; protocol B, heat denaturation/proteinase K; and protocol C, CellsDirect Kit) were tested using different quantities (1,000, 5,000 and 10,000 cells) and types of goat primary cells (fibroblasts and goat mammary epithelial cells-GMECs) for subsequent validation by PCR amplification of small (GAPDH) and large amplicons (hLF transgene). All protocols were successful in the detection of the small amplicon; however, in GMECs, only protocol B resulted efficient amplification (protocol A-0%, protocol B-93%, protocol C-13.33%, P <0.05). In a proof-of-principle experiment, the TP53 gene was knocked out in GMECs by CRISPR/Cas9-mediated deletion while constructs containing the anti-VEGF monoclonal antibody (pBC-anti-VEGF) and bacterial L-Asparaginase (pBC-ASNase) transgenes were knocked-in separately in fibroblasts. Detection of successful editing was performed using protocol B and PCR. The integration rates of the pBC-ASNase and pBC-anti-VEGF transgenes were 93.6% and 72%, respectively, as per PCR. The efficiency of biallelic editing in GMECs using CRISPR/Cas9 for the TP53 deletion was 5.4%. Our results suggest that protocol B (heat denaturation/proteinase K) can be used as an inexpensive and quick methodology for detecting genetic modifications in different types of primary goat cells, with efficiency rates consistent with values previously described in the literature when using extraction kits or more complex proteinase K formulations.

In silico analysis of mismatches in RT-qPCR assays of 177 SARS-CoV-2 sequences from Brazil

Abstract INTRODUCTION: Quantitative reverse transcription polymerase chain reaction (RT-qPCR) can detect the severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) in a highly specific manner. However, a decrease in the specificity of PCR assays for their targets may lead to false negative results. METHODS: Here, 177 high-coverage complete SARS-CoV-2 genome sequences from 13 Brazilian states were aligned with 15 WHO recommended PCR assays. RESULTS: Only 3 of the 15 completely aligned to all Brazilian sequences. Ten assays had mismatches in up to 3 sequences and two in many sequences. CONCLUSION: These results should be taken into consideration when using PCR-based diagnostics in Brazil.

Caesalpinia pulcherrima seed galactomannan on rheological properties of dairy desserts / Efeito da galactomanana da semente de Caesalpinia pulcherrima sobre as propriedades reológicas de sobremesas lácteas

ABSTRACT: Dairy desserts containing Caesalpinia pulcherrima seed galactomannan were evaluated to determine their static and dynamic rheological behaviors. Variations in consistency index (k), flow behavior (n), yield stress and thixotropy of the desserts indicated that the galactomannan caused an increase in the shear stress and apparent viscosity of the system. All samples exhibited shear-thinning behavior with flow behavior index values (n) between 0.06 and 0.37. Dynamic rheological behavior was evaluated for MD (high solid levels) and MD/2 (half the amount of solids) groups, and both G' and G'' moduli were depended on the frequency. The MD and MD/2 groups showed variations in the elastic modulus (G') throughout the temperature range (mainly at 50 °C), showing greater sensitivity at high temperatures. C. pulcherrima galactomannan was able to promote synergism with starch, milk protein and sucrose and to improve the development of stronger and more resistant gels.

RESUMO: Sobremesas lácteas contendo galactomanana de semente de Caesalpinia pulcherrima tiveram suas propriedades reológicas estáticas e dinâmicas avaliadas. As variações nos índices de consistência (K) e comportamento de fluxo (n), assim como na tensão inicial de fluxo e na tixotropia das sobremesas mostraram o efeito da galactomanana sobre a tensão de cisalhamento e viscosidade aparente dos sistemas lácteos. Todas as sobremesas exibiram comportamento pseudoplástico, com índices de comportamento de fluxo (n) variando entre 0,06 e 0,37. A reologia dinâmica dos grupos MD (alto teor de sólidos) e MD/2 (metade do teor de sólidos), mostrou G' > G'' e módulos dependentes da frequência e da temperatura. Alterações químicas nos componentes das sobremesas foram observadas a 50° C em virtude da maior sensibilidade dos valores de G' e G" a partir dessa temperatura. A galactomanana de C. pulcherrima contribuiu para o desenvolvimento de géis mais fortes e resistentes nas sobremesas lácteas, bem como mostrou sinergismo com amido, proteína do leite e sacarose.

Differences in protein expression associated with ivermectin resistance in Caenorhabditis elegans.

The indiscriminate administration of synthetic anthelmintics such as ivermectin contributes to the selection of subpopulations capable of resisting the drugs' effects. To understand the mechanisms of ivermectin resistance in Caenorhabditis elegans, this study attempted to identify molecular targets. C. elegans lineages that were sensitive and resistant to ivermectin were used. Collected nematodes were added to an extraction buffer and macerated in liquid nitrogen for protein extraction. The extracted proteins were separated according to molecular weight by SDS-PAGE to verify their integrity. Subsequently, proteins from both lineages were separated using two-dimensional electrophoresis. The gels were analyzed and the relevant spots were excised and identified by mass spectrometry (NanoESI-Q-TOF and MASCOT®) and subsequently assessed by GO enrichment and STRING® analyses. The increased expression of proteins associated with high metabolic activity, such as ATP-2 and ENOL-1, which are responsible for ATP synthesis, was observed. Furthermore, proteins with involvement in mediating muscular function (MLC-1, ACT-1, and PDI-2), signaling (FAR-1 and FAR-2), and embryo development (VHA-2) were identified. Protein interaction analysis indicated that the majority of the identified proteins in the resistant lineages participated in the same reaction triggered by ivermectin.

Differences in protein expression associated with ivermectin resistance in Caenorhabditis elegans / Diferenças na expressão de proteínas associadas à resistência à ivermectina em Caenorhabditis elegans

Abstract The indiscriminate administration of synthetic anthelmintics such as ivermectin contributes to the selection of subpopulations capable of resisting the drugs' effects. To understand the mechanisms of ivermectin resistance in Caenorhabditis elegans, this study attempted to identify molecular targets. C. elegans lineages that were sensitive and resistant to ivermectin were used. Collected nematodes were added to an extraction buffer and macerated in liquid nitrogen for protein extraction. The extracted proteins were separated according to molecular weight by SDS-PAGE to verify their integrity. Subsequently, proteins from both lineages were separated using two-dimensional electrophoresis. The gels were analyzed and the relevant spots were excised and identified by mass spectrometry (NanoESI-Q-TOF and MASCOT®) and subsequently assessed by GO enrichment and STRING® analyses. The increased expression of proteins associated with high metabolic activity, such as ATP-2 and ENOL-1, which are responsible for ATP synthesis, was observed. Furthermore, proteins with involvement in mediating muscular function (MLC-1, ACT-1, and PDI-2), signaling (FAR-1 and FAR-2), and embryo development (VHA-2) were identified. Protein interaction analysis indicated that the majority of the identified proteins in the resistant lineages participated in the same reaction triggered by ivermectin.

Resumo A administração indiscriminada de anti-helmínticos sintéticos, como a ivermectina, contribui para a seleção de subpopulações capazes de resistir ao efeito das drogas. Para entender os mecanismos de resistência à ivermectina em Caenorhabditis elegans, este estudo visou identificar alvos moleculares. Portanto, linhagens de C. elegans sensíveis e resistentes à ivermectina foram utilizadas. Os nematóides coletados foram adicionados ao tampão de extração e macerados em nitrogênio líquido para obtenção das proteínas. As proteínas extraídas foram separadas por peso molecular em SDS-PAGE para verificar sua integridade. Posteriormente, as proteínas de ambas as linhagens foram separadas por eletroforese bidimensional. Os géis foram analisados, os spots relevantes foram excisados e identificados por espectrometria de massa (NanoESI-Q-TOF e MASCOT®), em seguida, analisados ​​em seus termos de GO e STRING®. A expressão aumentada de proteínas associadas à alta atividade metabólica, como as proteínas ATP-2 e ENOL-1, responsáveis ​​pela síntese de ATP, foi observada. Além disso, foram identificadas as proteínas responsáveis ​​pelo controle da função muscular (MLC-1, ACT-1 e PDI-2), sinalização (FAR-1 e FAR-2) e desenvolvimento embrionário (VHA-2). A análise das interações proteicas indicou que a maioria das proteínas identificadas na cepa resistente participa da mesma reação desencadeada pela ivermectina.

Angiopoietin-2: A Potential Mediator of the Glycocalyx Injury in Adult Nephrotic Patients.

INTRODUCTION: Glomerulopathy is a group of diseases that affect mainly young adults between the ages of 20 and 40 years. Recently, it has been demonstrated that syndecan-1, a biomarker of endothelial glycocalyx damage, is increased in nephrotic patients with near-normal renal function and it is important to endothelial dysfunction in these patients. Angiopoietin-2 (AGPT2) is an endothelial growth factor that promotes cell derangement. Here we evaluated AGPT2 levels in patients with nephrotic syndrome, near-normal renal function and the possible interaction of AGPT2 with endothelial glycocalyx derangement. METHODS: This was a cross-sectional study performed from January through November 2017. Adult patients (age > 18 years) with nephrotic syndrome and without immunosuppression were included. Blood samples were drawn after a 12 h fast for later measurement of syndecan-1 and AGPT2. Mediation analyses were performed to assess the hypothesized associations of nephrotic syndrome features and AGPT2 with syndecan-1. RESULTS: We included 65 patients, 37 (56.9%) of them female, with primary glomerular disease. Syndecan-1 in nephrotic patients was higher than in control individuals (102.8 ± 36.2 vs. 28.2 ± 9.8 ng/mL, p < 0.001). Correlation of syndecan-1 with the main features of nephrotic syndrome after adjustment for age and estmmated glomerular filtration rate (eGFR) demonstrated that syndecan-1 was significantly associated with 24-h urinary protein excretion, total cholesterol, LDL (low density lipoprotein)-cholesterol, HDL (high-density lipoprotein)-cholesterol, and triglycerides. Angiopoietin-2 was independently associated with serum albumin, 24 h urinary protein excretion, total cholesterol, and LDL-cholesterol, in addition to being strongly associated with syndecan-1 (0.461, p < 0.001). The results of the mediation analyses showed that the direct association between LDL-cholesterol and syndecan-1 was no longer significant after AGPT-2 was included in the mediation analysis. AGPT2 explained 56% of the total observed association between LDL-cholesterol and syndecan-1. CONCLUSION: The association between LDL-cholesterol and glycocalyx derangement in nephrotic patients is possibly mediated by AGPT2.

Action mechanism of naphthofuranquinones against fluconazole-resistant Candida tropicalis strains evidenced by proteomic analysis: The role of increased endogenous ROS.

The increased incidence of candidemia in terciary hospitals worldwide and the cross-resistance frequency require the new therapeutic strategies development. Recently, our research group demonstrated three semi-synthetic naphthofuranquinones (NFQs) with a significant antifungal activity in a fluconazole-resistant (FLC) C. tropicalis strain. The current study aimed to investigate the action's preliminary mechanisms of NFQs by several standardized methods such as proteomic and flow cytometry analyzes, comet assay, immunohistochemistry and confocal microscopy evaluation. Our data showed C. tropicalis 24 h treated with all NFQs induced an expression's increase of proteins involved in the metabolic response to stress, energy metabolism, glycolysis, nucleosome assembly and translation process. Some aspects of proteomic analysis are in consonance with our flow cytometry analysis which indicated an augmentation of intracellular ROS, mitochondrial dysfunction and DNA strand breaks (neutral comet assay and γ-H2AX detection). In conclusion, our data highlights the great contribution of ROS as a key event, probably not the one, associated to anti-candida properties of studied NFQs.

Produção de anticorpos policlonais anti-ricina / Production of polyclonal anti-ricin antibodies

A ricina é uma proteína bastante tóxica presente nas sementes de mamona que impossibilita o uso da torta de mamona "in natura", como ração. A torta de mamona destoxificada necessita ainda de métodos de análise que garantam a ausência de traços dessa proteína. Objetivou-se, neste trabalho, produzir e avaliar a sensibilidade e especificidade de anticorpos policlonais anti-ricina, para serem empregados como possíveis componentes de métodos sorológicos na detecção de ricina em torta de mamona destoxificada. Foram avaliadas três doses da proteína: 400, 180 e 100 µg cada uma dividida em duas aplicações em coelhos. A primeira dose foi injetada no animal no início do experimento e a segunda após 21 dias. O método de ELISA indicou que as duas doses menores (100 e 180 µg) induziram respostas imunológicas primária e secundária com produção de anticorpos específicos. Enquanto a dose maior (400 µg) de ricina apresentou uma resposta primária com elevação dos títulos de anticorpos, seguida de uma supressão da resposta. Esse perfil é sugestivo de tolerância imunológica. Pela técnica de Western blotting verificou-se que os anticorpos policlonais produzidos são bastante específicos para a ricina, no entanto, por detectarem ricina na forma nativa e desnaturada não são recomendados para o monitoramento de ricina em torta de mamona destoxificada por tratamento térmico.

Ricin is a very toxic protein found in castor bean plants, making it impossible to use natural castor cake as animal food. The detoxificated castor cake needs to be analyzed by methods that ensure the absence of traces of this protein. This work had the objective to produce and to evaluate the sensitivity and specificity of anti-ricin polyclonal antibodies, to be employed as component of sorologic methods as the ELISA in the detection of ricin in detoxificated castor cake. Three doses of protein, 400, 180 and 100 µg were evaluated each one injected twice into rabbit, with one half in the begin of the experiment and the other half after 21 days of immunization. The ELISA method indicated that the lower doses (100 e 180 µg) induced primary and secondary immunological response with production of specific antibodies, while the higher dose of ricin (400 µg) showed a primary response with increase of the antibody titre, followed of immunological suppression. This profile suggests immunological tolerance. By Western blotting technique it was verified that polyclonal antibodies are too specific to ricin, however, they detected ricin in native and denaturated form and are not recommended for the monitoring of ricin in detoxificated castor bean cake by heat treatment.

Proline accumulation and glutamine synthetase activity are increased by salt-induced proteolysis in cashew leaves.

In this study cashew (Anacardium occidentale) plants were exposed to a short- and long-term exposure to NaCl in order to establish the importance of the salt-induced proteolysis and the glutamine synthetase activity on the proline accumulation. The cashew leaf showed a prominent proline accumulation in response to salt stress. In contrast, the root tissue had no significant changes in proline content even after the drastic injury caused by salinity on the whole plant. The leaf proline accumulation was correlated to protease activity, accumulation of free amino acid and ammonia, and decrease of both total protein and chlorophyll contents. The leaf GS activity was increased by the salt stress whereas in the roots it was slightly lowered. Although the several amino acids in the soluble pool of leaf tissue have showed an intense increment in its concentrations in the salt-treated plants, proline was the unique to show a proportional increment from 50 to 100 mol m-3 NaCl exposure (16.37 to 34.35 mmol kg-1 DM, respectively). Although the leaf glutamate concentration increased in the leaves of the salt-stressed cashew plants, as compared to control, its relative contribution to the total amino acid decreased significantly in stressed leaves when compared to other amino acids. In addition, when the leaf discs were incubated with NaCl in the presence of exogenous precursors (Glu, Gln, Orn or Arg) involved in the proline synthesis pathways, the glutamate was unique in inducing a significant enhancement of the proline accumulation compared to those discs with precursor in the absence of NaCl. These results, together with the salt-induced increase in the GS activity, suggest an increase in the de novo synthesis of proline probably associated with the increase of the concentration of glutamate. Moreover, the prominent salt-induced proline accumulation in the leaves was associated with the higher salt-sensitivity in terms of proteolysis and salt-induced senescence as compared to the roots. In conclusion, the leaf-proline accumulation was due, at least in part, to the increase in the salt-induced proteolysis associated with the increments in the GS activity and hence the increase in the concentration of glutamate precursor in the soluble amino acid pool.