Genome-wide protein-DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase.

DNA-protein interactions are central to fundamental cellular processes, yet widely implemented technologies for measuring these interactions on a genome scale in bacteria are laborious and capture only a snapshot of binding events. We devised a facile method for mapping DNA-protein interaction sites in vivo using the double-stranded DNA-specific cytosine deaminase toxin DddA. In 3D-seq (DddA-sequencing), strains containing DddA fused to a DNA-binding protein of interest accumulate characteristic mutations in DNA sequence adjacent to sites occupied by the DNA-bound fusion protein. High-depth sequencing enables detection of sites of increased mutation frequency in these strains, yielding genome-wide maps of DNA-protein interaction sites. We validated 3D-seq for four transcription regulators in two bacterial species, Pseudomonas aeruginosa and Escherichia coli. We show that 3D-seq offers ease of implementation, the ability to record binding event signatures over time and the capacity for single-cell resolution.

An interbacterial DNA deaminase toxin directly mutagenizes surviving target populations.

When bacterial cells come in contact, antagonism mediated by the delivery of toxins frequently ensues. The potential for such encounters to have long-term beneficial consequences in recipient cells has not been investigated. Here, we examined the effects of intoxication by DddA, a cytosine deaminase delivered via the type VI secretion system (T6SS) of Burkholderia cenocepacia. Despite its killing potential, we observed that several bacterial species resist DddA and instead accumulate mutations. These mutations can lead to the acquisition of antibiotic resistance, indicating that even in the absence of killing, interbacterial antagonism can have profound consequences on target populations. Investigation of additional toxins from the deaminase superfamily revealed that mutagenic activity is a common feature of these proteins, including a representative we show targets single-stranded DNA and displays a markedly divergent structure. Our findings suggest that a surprising consequence of antagonistic interactions between bacteria could be the promotion of adaptation via the action of directly mutagenic toxins.

Early Post-operative Weight Change After Roux-en-Y Gastric Bypass Predicts Weight Loss at 12-Month Follow-up.

INTRODUCTION: Sub-optimal weight loss following Roux-en-Y gastric bypass (RYGB) represents an important clinical challenge in a significant number of patients. Early identification of such patients would be advantageous, as it could aid in the selective implementation of targeted adjunct interventions during the first post-operative year. METHODS: Clinical audit data from 1137 patients undergoing RYGB between 2013 and 2016 at the Instituto Sallet in Brazil were prospectively registered in an online database (BOLD) and analyzed. RESULTS: Forty-eight percent of patients achieving less than 5% total weight loss after the first post-operative month achieved a 20% total weight loss at 1 year (n = 626; OR = 0.6 CI = 95%). Eighty-three percent of patients losing between 5 and 10% at 1 month and 95% of patients losing greater than 10% at 1 month had lost at least 20% of total body weight after the first post-operative year. Forty-four percent of patients achieving less than 10% total weight loss after the third post-operative month achieved 20% total weight loss at 1 year (n = 494; OR = 0.3 CI = 95%). CONCLUSION: Total bodyweight reduction after RYGB of < 5% at 1 month and < 10% at 3 months is associated with suboptimal weight loss at 1 year. These results reinforce findings from other studies reporting that patients tend to follow a common weight loss trajectory. Identifying the patients with weight trajectory requiring adjunct therapies early on is crucial so appropriate adjustments can be made to post-operative care.

Investigation of Copaifera genus as a new source of antimycobaterial agents.

AIM: This paper reports on the antimycobacterial activity of the oleoresins and extracts obtained from Copaifera spp. MATERIALS & METHODS: The minimum inhibitory concentration (MIC) and fractional inhibitory concentration index techniques helped to evaluate the effect of these oleoresins and extracts against six strains of mycobacteria that cause tuberculosis. RESULTS & CONCLUSION: Among the assayed oleoresins and plant extracts, the Copaifera langsdorffii, Copaifera duckei, Copaifera reticulata and Copaifera trapezifolia oleoresins provided the lowest MIC values against some of the tested strains. The combination of Copaifera spp. samples with isoniazid did not evidence any synergistic action. Some Copaifera spp. oleoresins may represent a future source for the discovery of new antimycobacterial drugs due to their low MIC values.

A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing.

Bacterial toxins represent a vast reservoir of biochemical diversity that can be repurposed for biomedical applications. Such proteins include a group of predicted interbacterial toxins of the deaminase superfamily, members of which have found application in gene-editing techniques1,2. Because previously described cytidine deaminases operate on single-stranded nucleic acids3, their use in base editing requires the unwinding of double-stranded DNA (dsDNA)-for example by a CRISPR-Cas9 system. Base editing within mitochondrial DNA (mtDNA), however, has thus far been hindered by challenges associated with the delivery of guide RNA into the mitochondria4. As a consequence, manipulation of mtDNA to date has been limited to the targeted destruction of the mitochondrial genome by designer nucleases9,10.Here we describe an interbacterial toxin, which we name DddA, that catalyses the deamination of cytidines within dsDNA. We engineered split-DddA halves that are non-toxic and inactive until brought together on target DNA by adjacently bound programmable DNA-binding proteins. Fusions of the split-DddA halves, transcription activator-like effector array proteins, and a uracil glycosylase inhibitor resulted in RNA-free DddA-derived cytosine base editors (DdCBEs) that catalyse C•G-to-T•A conversions in human mtDNA with high target specificity and product purity. We used DdCBEs to model a disease-associated mtDNA mutation in human cells, resulting in changes in respiration rates and oxidative phosphorylation. CRISPR-free DdCBEs enable the precise manipulation of mtDNA, rather than the elimination of mtDNA copies that results from its cleavage by targeted nucleases, with broad implications for the study and potential treatment of mitochondrial disorders.

Adaptability and stability of Coffea canephora Pierre ex Froehner genotypes in the Western Amazon / Adaptabilidade e estabilidade de genótipos de Coffea canephora Pierre ex Froehner na Amazônia Ocidental

ABSTRACT: The development of Coffea canephora cultivars is based on the characterization of genotype × environment interaction, which is interpreted to quantify the differential behavior of clones at different cultivation sites. The objective of this research was to study the genotype x environment interaction aiming to select clones of broad and specific adaptation to different environments of the Western Amazon. Twelve clones with hybrid characteristics of the botanical varieties Conilon and Robusta and four open pollinated clones, had their performance evaluated in comparison with four controls. The genotype × environment interaction was interpreted based on the environmental quality index, the non-parametric estimator of Lin and Binns, 1988 and on the dispersion of the centroid method. Effects of the genotypes, environment, and genotype × environment interaction were all significant (p<0.01). The environmental quality index (Ij) classified three environments as favorable for coffee production. In terms of the Lin and Binn's estimator (Pi), hybrid genotypes 16, 10, 13, 09 and 14 presented lower Pi indices than others, and were classified as being more stable. Five clones of low adaptability, seven clones of specific adaptability to favorable or unfavorable environments and two clones of broad adaptability to all environments were identified interpreting the dispersion of the centroid method.

RESUMO: O desenvolvimento de novas cultivares de Coffea canephora fundamenta-se na caracterização do comportamento diferenciado dos clones em diferentes locais de cultivo. O objetivo deste trabalho foi estudar a interação genótipo x ambientes visando selecionar clones de adaptação ampla e específica à diferentes ambientes da Amazônia Ocidental. Doze clones com características híbridas das variedades botânicas Conilon e Robusta e quatro clones provenientes de polinização aberta tiveram seu desempenho avaliado em comparação com quatro testemunhas. Os métodos utilizados para quantificar a interação genótipo x ambientes foram o estimador não paramétrico de Lin & Binns e a dispersão do método centroide. A análise de variância indicou que os efeitos de genótipos, de ambiente e da interação G x A foram significativos (p<0,01). O índice de qualidade ambiental (Ij) permitiu classificar três ambientes favoráveis em relação a sua contribuição para o desempenho das plantas. Os genótipos híbridos 16, 10, 13, 9 e 14 apresentaram menores índices de Pi, tendo sido ranqueados como mais estáveis, apresentando produtividade média superior ao desempenho das testemunhas. Cinco clones de baixa adaptabilidade, sete clones de adaptabilidade específica a ambientes favoráveis ou desfavoráveis e dois clones de ampla adaptabilidade foram identificados interpretando a dispersão no plano do método centroide.

Osteogenesis imperfecta in Brazilian patients.

Osteogenesis Imperfecta (OI) is a heterogeneous genetic disorder characterized by bone fragility and fracture. Mutations in 20 distinct genes can cause OI, and therefore, the genetic diagnosis of OI is frequently difficult to obtain because of the great number of genes that can be related with this disease. Studies that report the most frequently mutated genes in OI patients can help to improve molecular strategies for diagnosis of the disease. In order to characterize the mutation profile of OI in Brazilian patients, we analyzed 30 unrelated patients through SSCP screening, NGS gene panel, and/or Sanger sequencing for the 11 most frequently mutated genes in the database of mutations, including COL1A1, COL1A2, P3H1, CRTAP, PPIB, SERPINH1, SERPINF1, FKBP10, SP7, WNT1 and IFITM5. Disease-causing variants were identified in COL1A1, COL1A2, FKBP10, P3H1, and IFITM5. A total of 28 distinct mutations were identified, including seven novel changes. Our data show that the analysis of these five genes is able to detect at least 95% of causative mutations in OI disorder from Brazilian population. However, it has to be taken into considerations that distinct populations can have different frequencies of disease-causing variants. Hence, it is important to replicate this study in other groups.

Exploring diseases and syndromes in neurology case reports from 1955 to 2017 with text mining.

BACKGROUND: A large number of neurology case reports have been published, but it is a challenging task for human medical experts to explore all of these publications. Text mining offers a computational approach to investigate neurology literature and capture meaningful patterns. The overarching goal of this study is to provide a new perspective on case reports of neurological disease and syndrome analysis over the last six decades using text mining. METHODS: We extracted diseases and syndromes (DsSs) from more than 65,000 neurology case reports from 66 journals in PubMed over the last six decades from 1955 to 2017. Text mining was applied to reports on the detected DsSs to investigate high-frequency DsSs, categorize them, and explore the linear trends over the 63-year time frame. RESULTS: The text mining methods explored high-frequency neurologic DsSs and the relationships between them from 1955 to 2017. We detected more than 18,000 unique DsSs and found 10 categories of neurologic DsSs. While the trend analysis showed the increasing trends in the case reports for top-10 high-frequency DsSs, the categories had mixed trends. CONCLUSION: Our study provided new insights into the application of text mining methods to investigate DsSs in a large number of medical case reports that occur over several decades. The proposed approach can be used to provide a macro level analysis of medical literature by discovering interesting patterns and tracking them over several years to help physicians explore these case reports more efficiently.

Inflammatory lung injury in rabbits: effects of high-frequency oscillatory ventilation in the prone position.

OBJECTIVE: To compare the effects that prone and supine positioning during high-frequency oscillatory ventilation (HFOV) have on oxygenation and lung inflammation, histological injury, and oxidative stress in a rabbit model of acute lung injury (ALI). METHODS: Thirty male Norfolk white rabbits were induced to ALI by tracheal saline lavage (30 mL/kg, 38°C). The injury was induced during conventional mechanical ventilation, and ALI was considered confirmed when a PaO2/FiO2 ratio < 100 mmHg was reached. Rabbits were randomly divided into two groups: HFOV in the supine position (SP group, n = 15); and HFOV with prone positioning (PP group, n = 15). For HFOV, the mean airway pressure was initially set at 16 cmH2O. At 30, 60, and 90 min after the start of the HFOV protocol, the mean airway pressure was reduced to 14, 12, and 10 cmH2O, respectively. At 120 min, the animals were returned to or remained in the supine position for an extra 30 min. We evaluated oxygenation indices and histological lung injury scores, as well as TNF-α levels in BAL fluid and lung tissue. RESULTS: After ALI induction, all of the animals showed significant hypoxemia, decreased respiratory system compliance, decreased oxygenation, and increased mean airway pressure in comparison with the baseline values. There were no statistically significant differences between the two groups, at any of the time points evaluated, in terms of the PaO2 or oxygenation index. However, TNF-α levels in BAL fluid were significantly lower in the PP group than in the SP group, as were histological lung injury scores. CONCLUSIONS: Prone positioning appears to attenuate inflammatory and histological lung injury during HFOV in rabbits with ALI.

Inflammatory lung injury in rabbits: effects of high-frequency oscillatory ventilation in the prone position / Lesão inflamatória pulmonar em coelhos: efeitos da ventilação oscilatória de alta frequência em posição prona

ABSTRACT Objective: To compare the effects that prone and supine positioning during high-frequency oscillatory ventilation (HFOV) have on oxygenation and lung inflammation, histological injury, and oxidative stress in a rabbit model of acute lung injury (ALI). Methods: Thirty male Norfolk white rabbits were induced to ALI by tracheal saline lavage (30 mL/kg, 38°C). The injury was induced during conventional mechanical ventilation, and ALI was considered confirmed when a PaO2/FiO2 ratio < 100 mmHg was reached. Rabbits were randomly divided into two groups: HFOV in the supine position (SP group, n = 15); and HFOV with prone positioning (PP group, n = 15). For HFOV, the mean airway pressure was initially set at 16 cmH2O. At 30, 60, and 90 min after the start of the HFOV protocol, the mean airway pressure was reduced to 14, 12, and 10 cmH2O, respectively. At 120 min, the animals were returned to or remained in the supine position for an extra 30 min. We evaluated oxygenation indices and histological lung injury scores, as well as TNF-α levels in BAL fluid and lung tissue. Results: After ALI induction, all of the animals showed significant hypoxemia, decreased respiratory system compliance, decreased oxygenation, and increased mean airway pressure in comparison with the baseline values. There were no statistically significant differences between the two groups, at any of the time points evaluated, in terms of the PaO2 or oxygenation index. However, TNF-α levels in BAL fluid were significantly lower in the PP group than in the SP group, as were histological lung injury scores. Conclusions: Prone positioning appears to attenuate inflammatory and histological lung injury during HFOV in rabbits with ALI.

RESUMO Objetivo: Comparar os efeitos das posições prona e supina durante ventilação oscilatória de alta frequência (VOAF) sobre oxigenação e inflamação pulmonar, lesão histológica e estresse oxidativo em um modelo de lesão pulmonar aguda (LPA) em coelhos. Métodos: Trinta coelhos Norfolk machos brancos foram submetidos à LPA por meio de lavagem traqueal com salina (30 ml/kg, 38°C). A lesão foi induzida durante a ventilação mecânica convencional, e a LPA foi considerada confirmada na presença de relação PaO2/FiO2 < 100 mmHg. Os coelhos foram aleatoriamente divididos em dois grupos: VOAF em posição supina (grupo PS, n = 15); e VOAF em posição prona (grupo PP, n = 15). Para a VOAF, a pressão média das vias aéreas foi inicialmente estabelecida em 16 cmH2O. No 30º, 60º e 90º min após o início do protocolo de VOAF, a pressão média das vias aéreas foi reduzida para 14, 12 e 10 cmH2O, respectivamente. No 120º min, os animais foram recolocados ou permaneceram na posição supina por mais 30 min. Foram avaliados os índices de oxigenação e escores histológicos de lesão pulmonar, bem como os níveis de TNF-α em lavado broncoalveolar e tecido pulmonar. Resultados: Após a indução da LPA, todos os animais apresentaram hipoxemia significativa, diminuição da complacência do sistema respiratório, diminuição da oxigenação e aumento da pressão média das vias aéreas em comparação aos valores basais. Não houve diferenças estatisticamente significativas entre os dois grupos, em nenhum dos momentos avaliados, quanto a PaO2 e índice de oxigenação. Entretanto, os níveis de TNF-α no lavado broncoalveolar foram significativamente menores no grupo PP que no grupo PS, assim como os escores histológicos de lesão pulmonar. Conclusões: A posição prona parece atenuar a lesão pulmonar inflamatória e histológica durante a VOAF em coelhos com LPA.

Surgery is unlikely to be enough for a patient to stop smoking 24 h prior to hospital admission / É improvável que a cirurgia seja suficiente para que o paciente pare de fumar 24 horas antes da internação hospitalar

Abstract Introduction The need for surgery can be a decisive factor for long-term smoking cessation. On the other hand, situations that precipitate stress could precipitate smoking relapse. The authors decided to study the impact of a surgery on the patient's effort to cease smoking for, at least, 24 h before hospital admission and possible relapse on the last 24 h before hospital admission for ex-smokers. Methods Smoker, ex-smokers and non-smokers adults, either from pre-anesthetic clinic or recently hospital admitted for scheduled elective surgeries that were, at most, 6 h inside the hospital buildings were included in the study. The patients answered a questionnaire at the ward or at the entrance of the operating room (Admitted group) or at the beginning of the first pre-anesthetic consultation (Clinic group) and performed CO measurements. Results 241 patients were included, being 52 ex-smokers and 109 never smokers and 80 non-smokers. Smokers had higher levels of expired carbon monoxide than non-smokers and ex-smokers (9.97 ± 6.50 vs. 2.26 ± 1.65 vs. 2.98 ± 2.69; p = 0.02). Among the smokers, the Clinic group had CO levels not statistically different of those on the Admitted group (10.93 ± 7.5 vs. 8.65 ± 4.56; p = 0.21). The ex-smokers presented with no significant differences for the carbon monoxide levels between the Clinic and Admitted groups (2.9 ± 2.3 vs. 2.82 ± 2.15; p = 0.45). Conclusion A medical condition, such as a surgery, without proper assistance is unlikely to be enough for a patient to stop smoking for, at least, 24 h prior to admission. The proximity of a surgery was not associated with smoking relapse 24 h before the procedure.

Resumo Introdução A necessidade de cirurgia pode ser um fator decisivo para a cessação do tabagismo em longo prazo. Por outro lado, situações que precipitam o estresse podem precipitar a recaída do tabagismo. Decidimos avaliar o impacto de uma cirurgia no esforço do paciente para deixar de fumar durante pelo menos 24 horas antes da internação hospitalar e a possível recaída nas últimas 24 horas anteriores à internação em ex-fumantes. Métodos Fumantes, ex-fumantes e não fumantes adultos, quer de clínica pré-anestésica ou recentemente internados para cirurgias eletivas programadas que ficariam, no máximo, seis horas dentro das unidades hospitalares, foram incluídos no estudo. Os pacientes responderam um questionário na enfermaria ou na entrada da sala de operação (Grupo Internação) ou no início da primeira consulta pré-anestesia (Grupo Clínico) e fizeram mensurações dos níveis de CO. Resultados No total, 241 pacientes foram incluídos: 52 ex-fumantes, 109 que nunca fumaram e 80 não fumantes. Os fumantes apresentaram níveis mais elevados de monóxido de carbono expirado que os não fumantes e ex-fumantes (9,97 ± 6,50 vs. 2,26 ± 1,65 vs. 2,98 ± 2,69;p = 0,02). Entre os fumantes, o Grupo Clínico apresentou níveis de CO não estatisticamente diferentes daqueles do Grupo Internação (10,93 ± 7,5 vs. 8,65 ± 4,56; p = 0,21). Os ex-fumantes não apresentaram diferenças significativas entre os grupos Clínico e Internação para os níveis de monóxido de carbono (2,9 ± 2,3 vs. 2,82 ± 2,15; p = 0,45). Conclusão É improvável que uma condição médica, como uma cirurgia, sem assistência adequada seja suficiente para que um paciente pare de fumar, pelo menos, 24 horas antes da internação. A proximidade de uma cirurgia não foi associada à recaída do tabagismo nas 24 horas anteriores ao procedimento.

Genome-Wide Comparative Functional Analyses Reveal Adaptations of Salmonella sv. Newport to a Plant Colonization Lifestyle.

Outbreaks of salmonellosis linked to the consumption of vegetables have been disproportionately associated with strains of serovar Newport. We tested the hypothesis that strains of sv. Newport have evolved unique adaptations to persistence in plants that are not shared by strains of other Salmonella serovars. We used a genome-wide mutant screen to compare growth in tomato fruit of a sv. Newport strain from an outbreak traced to tomatoes, and a sv. Typhimurium strain from animals. Most genes in the sv. Newport strain that were selected during persistence in tomatoes were shared with, and similarly selected in, the sv. Typhimurium strain. Many of their functions are linked to central metabolism, including amino acid biosynthetic pathways, iron acquisition, and maintenance of cell structure. One exception was a greater need for the core genes involved in purine metabolism in sv. Typhimurium than in sv. Newport. We discovered a gene, papA, that was unique to sv. Newport and contributed to the strain's fitness in tomatoes. The papA gene was present in about 25% of sv. Newport Group III genomes and generally absent from other Salmonella genomes. Homologs of papA were detected in the genomes of Pantoea, Dickeya, and Pectobacterium, members of the Enterobacteriacea family that can colonize both plants and animals.

[Surgery is unlikely to be enough for a patient to stop smoking 24h prior to hospital admission]. / É improvável que a cirurgia seja suficiente para que o paciente pare de fumar 24 horas antes da internação hospitalar.

INTRODUCTION: The need for surgery can be a decisive factor for long-term smoking cessation. On the other hand, situations that precipitate stress could precipitate smoking relapse. The authors decided to study the impact of a surgery on the patient's effort to cease smoking for, at least, 24h before hospital admission and possible relapse on the last 24h before hospital admission for ex-smokers. METHODS: Smoker, ex-smokers and non-smokers adults, either from pre-anesthetic clinic or recently hospital admitted for scheduled elective surgeries that were, at most, 6h inside the hospital buildings were included in the study. The patients answered a questionnaire at the ward or at the entrance of the operating room (Admitted group) or at the beginning of the first pre-anesthetic consultation (Clinic group) and performed CO measurements. RESULTS: 241 patients were included, being 52 ex-smokers and 109 never smokers and 80 non-smokers. Smokers had higher levels of expired carbon monoxide than non-smokers and ex-smokers (9.97±6.50 vs. 2.26±1.65 vs. 2.98±2.69; p=0.02). Among the smokers, the Clinic group had CO levels not statistically different of those on the Admitted group (10.93±7.5 vs. 8.65±4.56; p=0.21). The ex-smokers presented with no significant differences for the carbon monoxide levels between the Clinic and Admitted groups (2.9±2.3 vs. 2.82±2.15; p=0.45). CONCLUSION: A medical condition, such as a surgery, without proper assistance is unlikely to be enough for a patient to stop smoking for, at least, 24h prior to admission. The proximity of a surgery was not associated with smoking relapse 24h before the procedure.

Of Mice and Men....and Plants: Comparative Genomics of the Dual Lifestyles of Enteric Pathogens.

Outbreaks of gastrointestinal illness, linked to the consumption of fruits, vegetables, and sprouts, continue to capture the attention of the general public and scientists. The recurrence of these outbreaks, despite heightened producer and consumer awareness, combined with improved sanitation protocols and technology, can be explained by the hypothesis that enteric pathogens, such as nontyphoidal Salmonella spp. and enterovirulent Escherichia coli, have evolved to exploit plants as alternative hosts. This review explores the genetic and genomic context for this hypothesis. Even though gastroenteritis outbreaks associated with the consumption of produce have been caused by a limited number of strains or serovars, robust evidence in support of the polymorphism hypothesis is lacking. While some housekeeping genes with additional virulence functions in animal models contribute to the fitness of enterics within plants, canonical virulence determinants required for animal infections, such as the type III secretion system (T3SS) and effectors, by and large, are of little consequence in interactions with plants. Conversely, despite possessing some functions more commonly found in phytobacteria, human enteric pathogens do not appear to rely on the same strategies for plant colonization. Instead, it is likely that nontyphoidal Salmonella and enterovirulent E. coli have evolved a set of functions distinct from its virulence regulon and from those used by phytopathogens.

Interactions of Salmonella enterica Serovar Typhimurium and Pectobacterium carotovorum within a Tomato Soft Rot.

Salmonella spp. are remarkably adaptable pathogens, and this adaptability allows these bacteria to thrive in a variety of environments and hosts. The mechanisms with which these pathogens establish within a niche amid the native microbiota remain poorly understood. Here, we aimed to uncover the mechanisms that enable Salmonella enterica serovar Typhimurium strain ATCC 14028 to benefit from the degradation of plant tissue by a soft rot plant pathogen, Pectobacterium carotovorum The hypothesis that in the soft rot, the liberation of starch (not utilized by P. carotovorum) makes this polymer available to Salmonella spp., thus allowing it to colonize soft rots, was tested first and proven null. To identify the functions involved in Salmonella soft rot colonization, we carried out transposon insertion sequencing coupled with the phenotypic characterization of the mutants. The data indicate that Salmonella spp. experience a metabolic shift in response to the changes in the environment brought on by Pectobacterium spp. and likely coordinated by the csrBC small regulatory RNA. While csrBC and flhD appear to be of importance in the soft rot, the global two-component system encoded by barA sirA (which controls csrBC and flhDC under laboratory conditions) does not appear to be necessary for the observed phenotype. Motility and the synthesis of nucleotides and amino acids play critical roles in the growth of Salmonella spp. in the soft rot.IMPORTANCE Outbreaks of produce-associated illness continue to be a food safety concern. Earlier studies demonstrated that the presence of phytopathogens on produce was a significant risk factor associated with increased Salmonella carriage on fruits and vegetables. Here, we genetically characterize some of the requirements for interactions between Salmonella and phytobacteria that allow Salmonella spp. to establish a niche within an alternate host (tomato). Pathways necessary for nucleotide synthesis, amino acid synthesis, and motility are identified as contributors to the persistence of Salmonella spp. in soft rots.

Comparison between conventional protective mechanical ventilation and high-frequency oscillatory ventilation associated with the prone position. / Comparação entre ventilação mecânica convencional protetora e ventilação oscilatória de alta frequência associada à posição prona.

OBJECTIVE: To compare the effects of high-frequency oscillatory ventilation and conventional protective mechanical ventilation associated with the prone position on oxygenation, histology and pulmonary oxidative damage in an experimental model of acute lung injury. METHODS: Forty-five rabbits with tracheostomy and vascular access were underwent mechanical ventilation. Acute lung injury was induced by tracheal infusion of warm saline. Three experimental groups were formed: healthy animals + conventional protective mechanical ventilation, supine position (Control Group; n = 15); animals with acute lung injury + conventional protective mechanical ventilation, prone position (CMVG; n = 15); and animals with acute lung injury + high-frequency oscillatory ventilation, prone position (HFOG; n = 15). Ten minutes after the beginning of the specific ventilation of each group, arterial gasometry was collected, with this timepoint being called time zero, after which the animal was placed in prone position and remained in this position for 4 hours. Oxidative stress was evaluated by the total antioxidant performance assay. Pulmonary tissue injury was determined by histopathological score. The level of significance was 5%. RESULTS: Both groups with acute lung injury showed worsening of oxygenation after induction of injury compared with the Control Group. After 4 hours, there was a significant improvement in oxygenation in the HFOG group compared with CMVG. Analysis of total antioxidant performance in plasma showed greater protection in HFOG. HFOG had a lower histopathological lesion score in lung tissue than CMVG. CONCLUSION: High-frequency oscillatory ventilation, associated with prone position, improves oxygenation and attenuates oxidative damage and histopathological lung injury compared with conventional protective mechanical ventilation.

OBJETIVO: Comparar os efeitos da ventilação oscilatória de alta frequência e da ventilação mecânica convencional protetora associadas à posição prona quanto à oxigenação, à histologia e ao dano oxidativo pulmonar em modelo experimental de lesão pulmonar aguda. MÉTODOS: Foram instrumentados com traqueostomia, acessos vasculares e ventilados mecanicamente 45 coelhos. A lesão pulmonar aguda foi induzida por infusão traqueal de salina aquecida. Foram formados três grupos experimentais: animais sadios + ventilação mecânica convencional protetora, em posição supina (Grupo Controle; n = 15); animais com lesão pulmonar aguda + ventilação mecânica convencional protetora, posição prona (GVMC; n = 15); animais com lesão pulmonar aguda + ventilação oscilatória de alta frequência, posição prona (GVAF; n = 15). Após 10 minutos do início da ventilação específica de cada grupo, foi coletada gasometria arterial, sendo este momento denominado tempo zero, após o qual o animal foi colocado em posição prona, permanecendo assim por 4 horas. O estresse oxidativo foi avaliado pelo método de capacidade antioxidante total. A lesão tecidual pulmonar foi determinada por escore histopatológico. O nível de significância adotado foi de 5%. RESULTADOS: Ambos os grupos com lesão pulmonar aguda apresentaram piora da oxigenação após a indução da lesão comparados ao Grupo Controle. Após 4 horas, houve melhora significante da oxigenação no grupo GVAF comparado ao GVMC. A análise da capacidade antioxidante total no plasma mostrou maior proteção no GVAF. O GVAF apresentou menor escore de lesão histopatológica no tecido pulmonar que o GVMC. CONCLUSÃO: A ventilação oscilatória de alta frequência, associada à posição prona, melhora a oxigenação, e atenua o dano oxidativo e a lesão pulmonar histopatológica, comparada com ventilação mecânica convencional protetora.

Comparação entre ventilação mecânica convencional protetora e ventilação oscilatória de alta frequência associada à posição prona / Comparison between conventional protective mechanical ventilation and high-frequency oscillatory ventilation associated with the prone position

RESUMO Objetivo: Comparar os efeitos da ventilação oscilatória de alta frequência e da ventilação mecânica convencional protetora associadas à posição prona quanto à oxigenação, à histologia e ao dano oxidativo pulmonar em modelo experimental de lesão pulmonar aguda. Métodos: Foram instrumentados com traqueostomia, acessos vasculares e ventilados mecanicamente 45 coelhos. A lesão pulmonar aguda foi induzida por infusão traqueal de salina aquecida. Foram formados três grupos experimentais: animais sadios + ventilação mecânica convencional protetora, em posição supina (Grupo Controle; n = 15); animais com lesão pulmonar aguda + ventilação mecânica convencional protetora, posição prona (GVMC; n = 15); animais com lesão pulmonar aguda + ventilação oscilatória de alta frequência, posição prona (GVAF; n = 15). Após 10 minutos do início da ventilação específica de cada grupo, foi coletada gasometria arterial, sendo este momento denominado tempo zero, após o qual o animal foi colocado em posição prona, permanecendo assim por 4 horas. O estresse oxidativo foi avaliado pelo método de capacidade antioxidante total. A lesão tecidual pulmonar foi determinada por escore histopatológico. O nível de significância adotado foi de 5%. Resultados: Ambos os grupos com lesão pulmonar aguda apresentaram piora da oxigenação após a indução da lesão comparados ao Grupo Controle. Após 4 horas, houve melhora significante da oxigenação no grupo GVAF comparado ao GVMC. A análise da capacidade antioxidante total no plasma mostrou maior proteção no GVAF. O GVAF apresentou menor escore de lesão histopatológica no tecido pulmonar que o GVMC. Conclusão: A ventilação oscilatória de alta frequência, associada à posição prona, melhora a oxigenação, e atenua o dano oxidativo e a lesão pulmonar histopatológica, comparada com ventilação mecânica convencional protetora.

ABSTRACT Objective: To compare the effects of high-frequency oscillatory ventilation and conventional protective mechanical ventilation associated with the prone position on oxygenation, histology and pulmonary oxidative damage in an experimental model of acute lung injury. Methods: Forty-five rabbits with tracheostomy and vascular access were underwent mechanical ventilation. Acute lung injury was induced by tracheal infusion of warm saline. Three experimental groups were formed: healthy animals + conventional protective mechanical ventilation, supine position (Control Group; n = 15); animals with acute lung injury + conventional protective mechanical ventilation, prone position (CMVG; n = 15); and animals with acute lung injury + high-frequency oscillatory ventilation, prone position (HFOG; n = 15). Ten minutes after the beginning of the specific ventilation of each group, arterial gasometry was collected, with this timepoint being called time zero, after which the animal was placed in prone position and remained in this position for 4 hours. Oxidative stress was evaluated by the total antioxidant performance assay. Pulmonary tissue injury was determined by histopathological score. The level of significance was 5%. Results: Both groups with acute lung injury showed worsening of oxygenation after induction of injury compared with the Control Group. After 4 hours, there was a significant improvement in oxygenation in the HFOG group compared with CMVG. Analysis of total antioxidant performance in plasma showed greater protection in HFOG. HFOG had a lower histopathological lesion score in lung tissue than CMVG. Conclusion: High-frequency oscillatory ventilation, associated with prone position, improves oxygenation and attenuates oxidative damage and histopathological lung injury compared with conventional protective mechanical ventilation.