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1.
Nat Immunol ; 25(7): 1270-1282, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38877178

RESUMO

The relative and synergistic contributions of genetics and environment to interindividual immune response variation remain unclear, despite implications in evolutionary biology and medicine. Here we quantify interactive effects of genotype and environment on immune traits by investigating C57BL/6, 129S1 and PWK/PhJ inbred mice, rewilded in an outdoor enclosure and infected with the parasite Trichuris muris. Whereas cellular composition was shaped by interactions between genotype and environment, cytokine response heterogeneity including IFNγ concentrations was primarily driven by genotype with consequence on worm burden. In addition, we show that other traits, such as expression of CD44, were explained mostly by genetics on T cells, whereas expression of CD44 on B cells was explained more by environment across all strains. Notably, genetic differences under laboratory conditions were decreased following rewilding. These results indicate that nonheritable influences interact with genetic factors to shape immune variation and parasite burden.


Assuntos
Interação Gene-Ambiente , Camundongos Endogâmicos C57BL , Tricuríase , Trichuris , Animais , Trichuris/imunologia , Tricuríase/imunologia , Tricuríase/parasitologia , Camundongos , Receptores de Hialuronatos/genética , Receptores de Hialuronatos/metabolismo , Linfócitos B/imunologia , Genótipo , Interferon gama/metabolismo , Linfócitos T/imunologia , Feminino , Masculino
2.
Cell ; 173(7): 1755-1769.e22, 2018 06 14.
Artigo em Inglês | MEDLINE | ID: mdl-29754820

RESUMO

High-grade serous ovarian cancer (HGSC) exhibits extensive malignant clonal diversity with widespread but non-random patterns of disease dissemination. We investigated whether local immune microenvironment factors shape tumor progression properties at the interface of tumor-infiltrating lymphocytes (TILs) and cancer cells. Through multi-region study of 212 samples from 38 patients with whole-genome sequencing, immunohistochemistry, histologic image analysis, gene expression profiling, and T and B cell receptor sequencing, we identified three immunologic subtypes across samples and extensive within-patient diversity. Epithelial CD8+ TILs negatively associated with malignant diversity, reflecting immunological pruning of tumor clones inferred by neoantigen depletion, HLA I loss of heterozygosity, and spatial tracking between T cell and tumor clones. In addition, combinatorial prognostic effects of mutational processes and immune properties were observed, illuminating how specific genomic aberration types associate with immune response and impact survival. We conclude that within-patient spatial immune microenvironment variation shapes intraperitoneal malignant spread, provoking new evolutionary perspectives on HGSC clonal dispersion.


Assuntos
Linfócitos do Interstício Tumoral/imunologia , Neoplasias Ovarianas/patologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Antígenos de Neoplasias/genética , Antígenos de Neoplasias/metabolismo , Proteína BRCA1/genética , Proteína BRCA1/metabolismo , Proteína BRCA2/genética , Proteína BRCA2/metabolismo , Antígenos CD8/metabolismo , Análise por Conglomerados , Feminino , Antígenos HLA/genética , Antígenos HLA/metabolismo , Humanos , Perda de Heterozigosidade , Linfócitos do Interstício Tumoral/citologia , Linfócitos do Interstício Tumoral/metabolismo , Pessoa de Meia-Idade , Gradação de Tumores , Neoplasias Ovarianas/classificação , Neoplasias Ovarianas/imunologia , Polimorfismo de Nucleotídeo Único , Receptores de Antígenos de Linfócitos T/genética , Receptores de Antígenos de Linfócitos T/metabolismo , Sequenciamento Completo do Genoma , Adulto Jovem
3.
J Bacteriol ; 206(5): e0007124, 2024 May 23.
Artigo em Inglês | MEDLINE | ID: mdl-38629875

RESUMO

Bovine mastitis is a frequent infection in lactating cattle, causing great economic losses. Staphylococcus aureus represents the main etiological agent, which causes recurrent and persistent intramammary infections because conventional antibiotics are ineffective against it. Mastoparan-like peptides are multifunctional molecules with broad antimicrobial potential, constituting an attractive alternative. Nevertheless, their toxicity to host cells has hindered their therapeutic application. Previously, our group engineered three mastoparan-L analogs, namely mastoparan-MO, mastoparan-R1, and [I5, R8] MP, to improve cell selectivity and potential. Here, we were interested in comparing the antibacterial efficacy of mastoparan-L and its analogs against bovine mastitis isolates of S. aureus strains, making a correlation with the physicochemical properties and structural arrangement changes promoted by the sequence modifications. As a result, the analog's hemolytic and/or antimicrobial activity was balanced. All the peptides displayed α-helical folding in hydrophobic and membrane-mimetic environments, as determined by circular dichroism. The peptide [I5, R8] MP stood out for its enhanced selectivity and antibacterial features related to mastoparan-L and the other derivatives. Biophysical approaches revealed that [I5, R8] MP rapidly depolarizes the bacterial membrane of S. aureus, causing cell death by subsequent membrane disruption. Our results demonstrated that the [I5, R8] MP peptide could be a starting point for the development of peptide-based drugs for the treatment of bovine mastitis, with the advantage of no residue in milk, which would help reduce the use of classical antibiotics.IMPORTANCEStaphylococcus aureus is a leading cause of mastitis, the world's most important dairy cattle disease. The multidrug resistance and zoonotic potential of S. aureus, besides the likelihood of antibiotic residues in milk, are of critical concern to public and animal health. Antimicrobial peptides offer a novel antimicrobial strategy. Here, we demonstrate that [I5, R8] MP is a potent and selective peptide, which acts on S. aureus by targeting the bacterial membrane. Therefore, understanding the physicochemical determinants and the modes of action of this class of antimicrobials opens novel prospects for peptide development with enhanced activities in the bovine mastitis context.


Assuntos
Antibacterianos , Peptídeos e Proteínas de Sinalização Intercelular , Mastite Bovina , Testes de Sensibilidade Microbiana , Infecções Estafilocócicas , Staphylococcus aureus , Animais , Bovinos , Mastite Bovina/microbiologia , Mastite Bovina/tratamento farmacológico , Staphylococcus aureus/efeitos dos fármacos , Feminino , Antibacterianos/farmacologia , Antibacterianos/química , Peptídeos e Proteínas de Sinalização Intercelular/farmacologia , Infecções Estafilocócicas/microbiologia , Infecções Estafilocócicas/veterinária , Infecções Estafilocócicas/tratamento farmacológico , Peptídeos/farmacologia , Peptídeos/química , Venenos de Vespas/farmacologia , Venenos de Vespas/química
4.
Ann Hum Genet ; 88(2): 113-125, 2024 03.
Artigo em Inglês | MEDLINE | ID: mdl-37807935

RESUMO

INTRODUCTION: Next generation sequencing technology has greatly reduced the cost and time required for sequencing a genome. An approach that is rapidly being adopted as an alternative method for CNV analysis is the low-pass whole genome sequencing (LP-WGS). Here, we evaluated the performance of LP-WGS to detect copy number variants (CNVs) in clinical cytogenetics. MATERIALS AND METHODS: DNA samples with known CNVs detected by chromosomal microarray analyses (CMA) were selected for comparison and used as positive controls; our panel included 44 DNA samples (12 prenatal and 32 postnatal), comprising a total of 55 chromosome imbalances. The selected cases were chosen to provide a wide range of clinically relevant CNVs, the vast majority being associated with intellectual disability or recognizable syndromes. The chromosome imbalances ranged in size from 75 kb to 90.3 Mb, including aneuploidies and two cases of mosaicism. RESULTS: All CNVs were successfully detected by LP-WGS, showing a high level of consistency and robust performance of the sequencing method. Notably, the size of chromosome imbalances detected by CMA and LP-WGS were compatible between the two different platforms, which indicates that the resolution and sensitivity of the LP-WGS approach are at least similar to those provided by CMA. DISCUSSION: Our data show the potential use of LP-WGS to detect CNVs in clinical diagnosis and confirm the method as an alternative for chromosome imbalances detection. The diagnostic effectiveness and feasibility of LP-WGS, in this technical validation study, were evidenced by a clinically representative dataset of CNVs that allowed a systematic assessment of the detection power and the accuracy of the sequencing approach. Further, since the software used in this study is commercially available, the method can easily be tested and implemented in a routine diagnostic setting.


Assuntos
Aneuploidia , Variações do Número de Cópias de DNA , Gravidez , Feminino , Humanos , Análise Custo-Benefício , Sequenciamento Completo do Genoma/métodos , DNA
5.
J Antimicrob Chemother ; 79(1): 112-122, 2024 Jan 03.
Artigo em Inglês | MEDLINE | ID: mdl-37966053

RESUMO

BACKGROUND: The synthetic antimicrobial peptide, PaDBS1R1, has been reported as a powerful anti-Klebsiella pneumoniae antimicrobial. However, there is only scarce knowledge about whether K. pneumoniae could develop resistance against PaDBS1R1 and which resistance mechanisms could be involved. OBJECTIVES: Identify via label-free shotgun proteomics the K. pneumoniae resistance mechanisms developed against PaDBS1R1. METHODS: An adaptive laboratory evolution experiment was performed to obtain a PaDBS1R1-resistant K. pneumoniae lineage. Antimicrobial susceptibility was determined through microdilution assay. Modifications in protein abundances between the resistant and sensitive lineages were measured via label-free quantitative shotgun proteomics. Enriched Gene Ontology terms and KEGG pathways were identified through over-representation analysis. Data are available via ProteomeXchange with identifier PXD033020. RESULTS: K. pneumoniae ATCC 13883 parental strain challenged with increased subinhibitory PaDBS1R1 concentrations allowed the PaDBS1R1-resistant K. pneumoniae lineage to emerge. Proteome comparisons between PaDBS1R1-resistant K. pneumoniae and PaDBS1R1-sensitive K. pneumoniae under PaDBS1R1-induced stress conditions enabled the identification and quantification of 1702 proteins, out of which 201 were differentially abundant proteins (DAPs). The profiled DAPs comprised 103 up-regulated proteins (adjusted P value < 0.05, fold change ≥ 2) and 98 down-regulated proteins (adjusted P value < 0.05, fold change ≤ 0.5). The enrichment analysis suggests that PhoPQ-guided LPS modifications and CpxRA-dependent folding machinery could be relevant resistance mechanisms against PaDBS1R1. CONCLUSIONS: Based on experimental evolution and a label-free quantitative shotgun proteomic approach, we showed that K. pneumoniae developed resistance against PaDBS1R1, whereas PhoPQ-guided LPS modifications and CpxRA-dependent folding machinery appear to be relevant resistance mechanisms against PaDBS1R1.


Assuntos
Anti-Infecciosos , Infecções por Klebsiella , Humanos , Antibacterianos/farmacologia , Klebsiella pneumoniae/genética , Peptídeos Antimicrobianos , Proteômica , Lipopolissacarídeos , Anti-Infecciosos/farmacologia , Testes de Sensibilidade Microbiana
6.
Crit Rev Microbiol ; : 1-14, 2024 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-38916977

RESUMO

Bovine mastitis is a mammary gland inflammation that can occur due to infectious pathogens, Staphylococcus aureus and Escherichia coli, which are, respectively, the most prevalent Gram-positive and Gram-negative bacteria associated with this disease. Currently, antibiotic treatment has become more complicated due to the presence of resistant pathogens. This review, therefore, aims to identify the most common resistance genes reported for these strains in the last four years. During the review, it was noted that blaZ, blaSHV, blaTEM, and blaampC are the most reported genes for S. aureus and E. coli, associated with drug inactivation, mainly ß-lactamases. They are characterized by generating bacterial resistance to ß-lactam antibiotics, the most common treatment in animal and human bacterial treatments (penicillins and cephalosporins, among others). Genes associated with efflux systems were also present in the two strains and included norA, tetA, tetC, and tetK, which generate resistance to macrolide and tetracycline antibiotics. Additionally, the effects of spreading resistance between animals and humans through direct contact (such as consumption of contaminated milk) or indirect contact (through environmental contamination) has been deeply discussed, emphasizing the importance of having adequate sanitation and antibiotic control and administration protocols.

7.
Am J Med Genet A ; 194(6): e63544, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38258498

RESUMO

In this pilot study, we aimed to evaluate the feasibility of whole genome sequencing (WGS) as a first-tier diagnostic test for infants hospitalized in neonatal intensive care units in the Brazilian healthcare system. The cohort presented here results from a joint collaboration between private and public hospitals in Brazil considering the initiative of a clinical laboratory to provide timely diagnosis for critically ill infants. We performed trio (proband and parents) WGS in 21 infants suspected of a genetic disease with an urgent need for diagnosis to guide medical care. Overall, the primary indication for genetic testing was dysmorphic syndromes (n = 14, 67%) followed by inborn errors of metabolism (n = 6, 29%) and skeletal dysplasias (n = 1, 5%). The diagnostic yield in our cohort was 57% (12/21) based on cases that received a definitive or likely definitive diagnostic result from WGS analysis. A total of 16 pathogenic/likely pathogenic variants and 10 variants of unknown significance were detected, and in most cases inherited from an unaffected parent. In addition, the reported variants were of different types, but mainly missense (58%) and associated with autosomal diseases (19/26); only three were associated with X-linked diseases, detected in hemizygosity in the proband an inherited from an unaffected mother. Notably, we identified 10 novel variants, absent from public genomic databases, in our cohort. Considering the entire diagnostic process, the average turnaround time from enrollment to medical report in our study was 53 days. Our findings demonstrate the remarkable utility of WGS as a diagnostic tool, elevating the potential of transformative impact since it outperforms conventional genetic tests. Here, we address the main challenges associated with implementing WGS in the medical care system in Brazil, as well as discuss the potential benefits and limitations of WGS as a diagnostic tool in the neonatal care setting.


Assuntos
Testes Genéticos , Unidades de Terapia Intensiva Neonatal , Sequenciamento Completo do Genoma , Humanos , Brasil/epidemiologia , Recém-Nascido , Masculino , Feminino , Testes Genéticos/métodos , Projetos Piloto , Lactente , Doenças Genéticas Inatas/diagnóstico , Doenças Genéticas Inatas/genética
8.
J Immunol ; 209(2): 250-261, 2022 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-35768148

RESUMO

Lipid and cholinergic mediators are inflammatory regulators, but their role in the immunopathology of COVID-19 is still unclear. Here, we used human blood and tracheal aspirate (TA) to investigate whether acetylcholine (Ach), fatty acids (FAs), and their derived lipid mediators (LMs) are associated with COVID-19 severity. First, we analyzed the perturbation profile induced by SARS-CoV-2 infection in the transcriptional profile of genes related to the ACh and FA/LM pathways. Blood and TA were used for metabolomic and lipidomic analyses and for quantification of leukocytes, cytokines, and ACh. Differential expression and coexpression gene network data revealed a unique transcriptional profile associated with ACh and FA/LM production, release, and cellular signaling. Transcriptomic data were corroborated by laboratory findings: SARS-CoV-2 infection increased plasma and TA levels of arachidonic acid, 5-hydroxy-6E,8Z,11Z,14Z-eicosatetraenoic acid, 11-hydroxy-5Z,8Z,12E,14Z-eicosatetraenoic acid, and ACh. TA samples also exhibited high levels of PGE2, thromboxane B2, 12-oxo-5Z,8Z,10E,14Z-eicosatetraenoic acid, and 6-trans-leukotriene B4 Bioinformatics and experimental approaches demonstrated robust correlation between transcriptional profile in Ach and FA/LM pathways and parameters of severe COVID-19. As expected, the increased neutrophil-to-lymphocyte ratio, neutrophil counts, and cytokine levels (IL-6, IL-10, IL-1ß, and IL-8) correlated with worse clinical scores. Glucocorticoids protected severe and critical patients and correlated with reduced Ach levels in plasma and TA samples. We demonstrated that pulmonary and systemic hyperinflammation in severe COVID-19 are associated with high levels of Ach and FA/LM. Glucocorticoids favored the survival of patients with severe/critical disease, and this effect was associated with a reduction in ACh levels.


Assuntos
Acetilcolina , COVID-19 , Ácido Araquidônico , Ácidos Araquidônicos/farmacologia , Ácidos Graxos , Glucocorticoides , Humanos , SARS-CoV-2
9.
Lett Appl Microbiol ; 77(7)2024 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-38942450

RESUMO

The increasing resistance to polymyxins in Acinetobacter baumannii has made it even more urgent to develop new treatments. Anti-virulence compounds have been researched as a new solution. Here, we evaluated the modification of virulence features of A. baumannii after acquiring resistance to polymyxin B. The results showed lineages attaining unstable resistance to polymyxin B, except for Ab7 (A. baumannii polymyxin B resistant lineage), which showed stable resistance without an associated fitness cost. Analysis of virulence by a murine sepsis model indicated diminished virulence in Ab7 (A. baumannii polymyxin B resistant lineage) compared with Ab0 (A. baumannii polymyxin B susceptible lineage). Similarly, downregulation of virulence genes was observed by qPCR at 1 and 3 h of growth. However, an increase in bauE, abaI, and pgAB expression was observed after 6 h of growth. Comparison analysis of Ab0, Ab7, and Pseudomonas aeruginosa suggested no biofilm formation by Ab7. In general, although a decrease in virulence was observed in Ab7 when compared with Ab0, some virulence feature that enables infection could be maintained. In light of this, virulence genes bauE, abaI, and pgAB showed a potential relevance in the maintenance of virulence in polymyxin B-resistant strains, making them promising anti-virulence targets.


Assuntos
Infecções por Acinetobacter , Acinetobacter baumannii , Antibacterianos , Farmacorresistência Bacteriana , Polimixina B , Polimixina B/farmacologia , Acinetobacter baumannii/efeitos dos fármacos , Acinetobacter baumannii/patogenicidade , Acinetobacter baumannii/genética , Animais , Antibacterianos/farmacologia , Virulência , Camundongos , Infecções por Acinetobacter/microbiologia , Fatores de Virulência/genética , Testes de Sensibilidade Microbiana , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Modelos Animais de Doenças , Sepse/microbiologia , Biofilmes/efeitos dos fármacos , Biofilmes/crescimento & desenvolvimento
10.
Brain Inj ; 38(2): 108-118, 2024 01 28.
Artigo em Inglês | MEDLINE | ID: mdl-38247393

RESUMO

OBJECTIVE: The purpose of this study was to identify the occurrence of AKI, and factors associated with in-hospital mortality and unfavorable outcomes in patients with severe traumatic brain injury (TBI) and acute kidney injury (AKI) severity. METHOD: A retrospective cohort study which analyzed data with severe TBI between 2013 and 2017. We examined demographic and clinical information, and outcome by in-hospital mortality, and the Glasgow Outcome Scale six months after TBI. We associated factors to in-hospital mortality and unfavorable outcome in severe TBI and AKI with an association test. RESULTS: A total of 219 patients were selected, 39.3% had an AKI, and several factors associated with AKI occurrence after severe TBI. Stage 2 or 3 of AKI (OR 12.489; 95% CI = 4.45-37.94) were independent risk for both outcomes in multivariable models, severity injury by the New Trauma Injury Severity Score (OR 0.97; 95% CI = 0.96-0.99) for mortality, and the New Injury Severity Score (OR1.07; 95% CI = 1.04-1.10) and Trauma and Injury Severity Score (OR = 0.98; 95% CI = 0.965-0.997) for unfavorable outcome. CONCLUSION: The findings of our study confirmed that AKI severity and severity of injury was also related to increased mortality and unfavorable outcome after severe TBI.


Assuntos
Injúria Renal Aguda , Lesões Encefálicas Traumáticas , Humanos , Estudos Retrospectivos , Mortalidade Hospitalar , Prognóstico , Lesões Encefálicas Traumáticas/complicações , Injúria Renal Aguda/etiologia , Injúria Renal Aguda/epidemiologia , Fatores de Risco
11.
J Interprof Care ; 38(2): 388-393, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38126193

RESUMO

This short report is based on the 2022 Global IPE Situational Analysis Results e-Book that is available at https://interprofessionalresearch.global/. As an up-to-date global environmental scan of interprofessional education (IPE), this cross-sectional study investigated institutional, administrative, and system-level processes that support IPE program development and implementation globally. Conducted by InterprofessionalResearch.Global (IPR.Global), the survey included 17 quantitative questions that were analyzed at global and regional levels. Three open-text questions were thematically analyzed. In total, 152 institutions from six regions worldwide contributed to this study. Results revealed that only 51.97% of all responding institutions have an established IPE program, with Canada and the USA having the highest (84%) and Africa (26%) having the lowest numbers. Globally, 37.33% of respondents reported no formal leadership positions and 41.33% reported the absence of a designated IPE Director or Coordinator. In addition, IPE funding varies considerably across the world, with 32.65% of institutions reporting no financial support. Over 48.22% of respondents indicated their institutions are rarely or not involved in IPE-related scholarly work or research. The open-text analysis revealed that supportive senior leadership, a culture of collaboration, and recognition of IPE as a strategic direction and/or priority at the institutional level, could foster the successful implementation of IPE. On the other hand, inadequate administrative support, lack of funding, poor attitudes regarding IPE, and limited dedicated time for research, seemed to impair successful implementation of scholarly activities in the field.


Assuntos
Educação Interprofissional , Relações Interprofissionais , Humanos , Estudos Transversais , Atitude , Liderança
12.
J Interprof Care ; : 1-6, 2024 Mar 25.
Artigo em Inglês | MEDLINE | ID: mdl-38527176

RESUMO

The COVID-19 pandemic created global disruption in health professions education and healthcare practice, necessitating an abrupt move to digital delivery. A longitudinal survey was conducted to track the evolution of global responses to the pandemic. During the initial stages, educational and health institutions were forced to adapt quickly without careful consideration of optimal pedagogy, practices, and effectiveness of implemented approaches. In this paper, we report the results of Phase 3 of the global survey that was distributed between November 2021 and February 2022 through InterprofessionalResearch.Global (IPR.Global). The Phase 3 qualitative survey received 27 responses, representing 25 institutions from 13 countries in 6 regions. Using inductive thematic analysis, the data analysis resulted in three emerging themes: Impact of the pandemic on the delivery of interprofessional education and collaborative practice (IPECP); Impact of the pandemic on the healthcare system (team, population/client health, clients); and Sustainability and innovation. This study highlights the evolving nature of health education and collaborative practices in response to the COVID-19 pandemic. IPECP educators need to be resilient and deal with the complexities of face-to-face and digital learning delivery. Preparing for emerging forms of teamwork is essential for new work contexts and optimal health services.

13.
J Environ Sci Health B ; 59(3): 88-97, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38189415

RESUMO

The relationship between bacterial diversity and the bioavailability of nutrients, toxic metals and the herbicide oxyfluorfen in a tropical vegetable growing area was evaluated. The study was conducted in a vegetable growing area located in the mountainous region of Rio de Janeiro (Brazil), and samples were collected in areas of vegetable cultivation and areas of environmental reserve. Fertility analyses and determination of the pseudototal levels of toxic metals in the soil samples were performed. The profile of the soil bacterial community was determined by amplification of the 16S rRNA gene and separation by DGGE. The results showed that the levels of toxic metals and elements associated with soil fertility were higher in vegetable production areas. These differences in the physical and chemical characteristics of the soil favored the presence of a greater number of OTUs in the cultivation areas (17.3-27 OTUs) than in the areas of environmental reserve (13-22 OTUs). Therefore, this study demonstrates that the presence of toxic metals and the herbicide oxyfluorfen and the increase in fertility in soils in areas with intensive vegetable cultivation resulting from the intensive management adopted in these areas promotes a differentiation of the bacterial profiles in soils in tropical vegetable growing areas.


Assuntos
Éteres Difenil Halogenados , Poluentes do Solo , Solo , Solo/química , Verduras , RNA Ribossômico 16S/genética , Brasil , Nutrientes/análise , Microbiologia do Solo , Poluentes do Solo/toxicidade , Poluentes do Solo/análise
14.
Bioinformatics ; 38(9): 2619-2620, 2022 04 28.
Artigo em Inglês | MEDLINE | ID: mdl-35258549

RESUMO

SUMMARY: SomaticSiMu is an in silico simulator of single and double base substitutions, and single base insertions and deletions in an input genomic sequence to mimic mutational signatures. SomaticSiMu outputs simulated DNA sequences and mutational catalogues with imposed mutational signatures. The tool is the first mutational signature simulator featuring a graphical user interface, control of mutation rates and built-in visualization tools of the simulated mutations. Simulated datasets are useful as a ground truth to test the accuracy and sensitivity of DNA sequence classification tools and mutational signature extraction tools under different experimental scenarios. The reliability of SomaticSiMu was affirmed by (i) supervised machine learning classification of simulated sequences with different mutation types and burdens, and (ii) mutational signature extraction from simulated mutational catalogues. AVAILABILITY AND IMPLEMENTATION: SomaticSiMu is written in Python 3.8.3. The open-source code, documentation and tutorials are available at https://github.com/HillLab/SomaticSiMu under the terms of the CreativeCommonsAttribution4.0InternationalLicense. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Genômica , Software , Reprodutibilidade dos Testes , Mutação , Genoma
15.
Heredity (Edinb) ; 131(1): 25-32, 2023 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-37157025

RESUMO

Most theoretical studies on epistatic QTL mapping have shown that this procedure is powerful, efficient to control the false positive rate (FPR), and precise to localize QTLs. The objective of this simulation-based study was to show that mapping epistatic QTLs is not an almost-perfect process. We simulated 50 samples of 400 F2 plants/recombinant inbred lines, genotyped for 975 SNPs distributed in 10 chromosomes of 100 cM. The plants were phenotyped for grain yield, assuming 10 epistatic QTLs and 90 minor genes. Adopting basic procedures of r/qtl package, we maximized the power of detection for QTLs (56-74%, on average) but associated with a very high FPR (65%) and a low detection power for the epistatic pairs (7%). Increasing the average detection power for epistatic pairs (14%) highly increased the related FPR. Adopting a procedure to find the best balance between power and FPR, there was a significant decrease in the power of QTL detection (17-31%, on average), associated with a low average detection power for epistatic pairs (8%) and an average FPR of 31% for QTLs and 16% for epistatic pairs. The main reasons for these negative results are a simplified specification of the coefficients of epistatic effects, as theoretically proved, and the effects of minor genes since 2/3 of the FPR for QTLs were due to them. We hope that this study, including the partial derivation of the coefficients of epistatic effects, motivates investigations on how to increase the power of detection for epistatic pairs, effectively controlling the FPR.


Assuntos
Plantas , Locos de Características Quantitativas , Mapeamento Cromossômico/métodos , Fenótipo , Simulação por Computador , Genótipo , Plantas/genética , Epistasia Genética
16.
Am J Bot ; 110(7): e16186, 2023 07.
Artigo em Inglês | MEDLINE | ID: mdl-37183532

RESUMO

PREMISE: Flower damage caused by florivores often has negative consequences for plant reproduction. However, the factors affecting plant-florivore interactions are still poorly understood, especially the role of abiotic factors and interspecific variation in florivory within ecosystems. Thus, the patterns of florivory levels and its consequences for plant communities need to be investigated further. METHODS: We assessed the influence of abiotic factors related to climatic seasonality, of phylogenetic relationships among plants, and of functional attributes associated with attractiveness to pollinators on florivory incidence and intensity in the Pantanal, the world's largest tropical wetland. Between December 2020 and November 2021, the percentage of flowers attacked (incidence) and petal area removed (intensity) by florivores were examined in 51 species from 25 families, considering flowering season, the substrate where the plants occur, and flower attributes as potentially determining factors on florivory levels. RESULTS: Phylogeny and environmental factors did not have a significant influence on florivory. The only determinant of interspecific variation in florivory incidence and intensity was flower size, where larger flowers experienced higher florivory levels regardless of season and substrate, while flower arrangement and color were not significant factors. CONCLUSIONS: Our study is one of the first to estimate the community-wide effects of biotic and abiotic factors on both the incidence and the intensity of florivory. The magnitude of this plant-florivore interaction may reduce reproductive success and entail selective pressures on plant attractiveness to pollinators.


Assuntos
Ecossistema , Áreas Alagadas , Filogenia , Flores , Reprodução , Plantas , Polinização
17.
Microb Ecol ; 86(2): 1292-1306, 2023 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-36166070

RESUMO

The importance of species that connect the different types of interactions is becoming increasingly recognized, and this role may be related to specific attributes of these species. Multilayer networks have two or more layers, which represent different types of interactions, for example, between different parasites and hosts that are nonetheless connected. The understanding of the ecological relationship between bats, ectoparasites, and vector-borne bacteria could shed some light on the complex transmission cycles of these pathogens. In this study, we investigated a multilayer network in Brazil formed by interactions between bat-bacteria, bat-ectoparasite, and ectoparasite-bacteria, and asked how these interactions overlap considering different groups and transmission modes. The multilayer network was composed of 31 nodes (12 bat species, 14 ectoparasite species, and five bacteria genera) and 334 links, distributed over three layers. The multilayer network has low modularity and shows a core-periphery organization, that is, composed of a few generalist species with many interactions and many specialist species participating in few interactions in the multilayer network. The three layers were needed to accurately describe the multilayer structure, while aggregation leads to loss of information. Our findings also demonstrated that the multilayer network is influenced by a specific set of species that can easily be connected to the behavior, life cycle, and type of existing interactions of these species. Four bat species (Artibeus lituratus, A. planirostris, Phyllostomus discolor, and Platyrrhinus lineatus), one ectoparasite species (Steatonyssus) and three bacteria genera (Ehrlichia, hemotropic Mycoplasma and Neorickettsia) are the most important species for the multilayer network structure. Finally, our study brings an ecological perspective under a multilayer network approach on the interactions between bats, ectoparasites, and pathogens. By using a multilayer approach (different types of interactions), it was possible to better understand these different ecological interactions and how they affect each other, advancing our knowledge on the role of bats and ectoparasites as potential pathogen vectors and reservoirs, as well as the modes of transmission of these pathogens.


Assuntos
Quirópteros , Ácaros , Animais , Quirópteros/microbiologia , Brasil
18.
Nutr Neurosci ; : 1-11, 2023 Aug 31.
Artigo em Inglês | MEDLINE | ID: mdl-37650777

RESUMO

Nutritional status during critical windows in early development can challenge metabolic functions and physiological responses to immune stress in adulthood, such as the systemic inflammation induced by lipopolysaccharide (LPS). The aim of this study was to investigate the long-term effects of post-natal over- and undernutrition on the anorexigenic effect of LPS and its association with neuronal activation in the brainstem and hypothalamus of male rats. Animals were raised in litters of 3 (small - SL), 10 (normal - NL), or 16 (large - LL) pups per dam. On post-natal day 60, male rats were treated with LPS (500 µg/Kg) or vehicle for the evaluation of food intake and c-Fos expression in the area postrema (AP), nucleus of solitary tract (NTS), and paraventricular (PVN), arcuate (ARC), ventromedial (VMH), and dorsomedial (DMH) nuclei of the hypothalamus. SL, NL, and LL animals showed a decreased food consumption after LPS treatment. In under- and normonourished animals, peripheral LPS induced an increase in neuronal activation in the brainstem, PaV, PaMP, and ARC and a decrease in the number of c-Fos-ir neurons in the DMH. Overnourished rats showed a reduced hypophagic response, lower neuron activation in the NTS and PaMP, and no response in the DMH induced by LPS. These results indicate that early nutritional programming displays different responses to LPS, by means of neonatal overnutrition decreasing LPS-mediated anorexigenic effect and neuronal activation in the NTS and hypothalamic nuclei.

19.
Cell Biochem Funct ; 41(8): 1252-1262, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37787620

RESUMO

Insulin (INS) resistance is often found in cancer-bearing, but its correlation with cachexia development is not completely established. This study investigated the temporal sequence of the development of INS resistance and cachexia to establish the relationship between these factors in Walker-256 tumor-bearing rats (TB rats). INS hepatic sensitivity and INS resistance-inducing factors, such as free fatty acids (FFA) and tumor necrosis factor-α (TNF-α), were also evaluated. Studies were carried out on Days 2, 5, 8, and/or 12 after inoculation of tumor cells in rats. The peripheral INS sensitivity was assessed by the INS tolerance test and the INS hepatic sensitivity in in situ liver perfusion. TB rats with 5, 8, and 12 days of tumor, but not 2 days, showed decreased peripheral INS sensitivity (INS resistance), retroperitoneal fat, and body weight, compared to healthy rats, which were more pronounced on Day 12. Gastrocnemius muscle wasting was observed only on Day 12 of tumor. The peripheral INS resistance was significantly correlated (r = -.81) with weight loss. Liver INS sensitivity of TB rats with 2 and 5 days of tumor was unchanged, compared to healthy rats. TB rats with 12 days of tumor showed increased plasma FFA and increased TNF-α in retroperitoneal fat and liver, but not in the gastrocnemius, compared to healthy rats. In conclusion, peripheral INS resistance is early, starts along with fat and weight loss and before muscle wasting, progressive, and correlated with cachexia, suggesting that it may play an important role in the pathogenesis of the cachectic process in TB rats. Therefore, early correction of INS resistance may be a therapeutic approach to prevent and treat cancer cachexia.


Assuntos
Resistência à Insulina , Neoplasias , Ratos , Animais , Caquexia/etiologia , Caquexia/patologia , Insulina , Fator de Necrose Tumoral alfa , Ratos Wistar , Redução de Peso , Neoplasias/complicações
20.
Lett Appl Microbiol ; 76(1)2023 Jan 23.
Artigo em Inglês | MEDLINE | ID: mdl-36688746

RESUMO

Bacterial resistance is a threat to health worldwide, mainly due to reduced effective treatment. In this context, the search for strategies to control such infections and suppress antimicrobial resistance is necessary. One of the strategies that has been used is combination therapy. In the present work, we investigated the in vitro efficacy of the antimicrobials diminazene aceturate (DA), chloramphenicol (CHL), and streptomycin (STP) alone and in combination against Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus clinical isolates. DA was capable of inhibiting all strains with MIC of 25-400 µg mL-1, while STP and CHL showed antibacterial activity with minimum inhibitory concentration (MICs) of ≤3.12-400 µg mL-1. The combination of aceturate with STP showed synergism toward almost all Gram-negative bacteria, with fractional inhibitory concentration index (FICIs) of 0.09-0.37. In addition, for CHL and aceturate, synergisms for Gram-negative and -positive strains were observed. A time-kill assay against E. coli revealed that the aceturate and STP combination can inhibit bacterial growth in a shorter time when compared with single antibiotics. In addition, antimicrobials did not show hemolytic activity even at the highest concentrations used. Therefore, the antimicrobial combinations presented in this work showed important results, demonstrating that combined therapy can be used as an alternative strategy for pathogen control.


Assuntos
Anti-Infecciosos , Cloranfenicol , Cloranfenicol/farmacologia , Estreptomicina/farmacologia , Escherichia coli , Antibacterianos/farmacologia , Bactérias , Anti-Infecciosos/farmacologia , Testes de Sensibilidade Microbiana
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