CNN application for automated determination of the patient's size to obtain the size-specific dose estimated in CT.

Introduction. The currently available dosimetry techniques in computed tomography can be inaccurate which overestimate the absorbed dose. Therefore, we aimed to provide an automated and fast methodology to more accurately calculate the SSDE usingDwobtained by using CNN from thorax and abdominal CT study images.Methods. The SSDE was determined from the 200 records files. For that purpose, patients' size was measured in two ways: (a) by developing an algorithm following the AAPM Report No. 204 methodology; and (b) using a CNN according to AAPM Report No. 220.Results. The patient's size measured by the in-house software in the region of thorax and abdomen was 27.63 ± 3.23 cm and 28.66 ± 3.37 cm, while CNN was 18.90 ± 2.6 cm and 21.77 ± 2.45 cm. The SSDE in thorax according to 204 and 220 reports were 17.26 ± 2.81 mGy and 23.70 ± 2.96 mGy for women and 17.08 ± 2.09 mGy and 23.47 ± 2.34 mGy for men. In abdomen was 18.54 ± 2.25 mGy and 23.40 ± 1.88 mGy in women and 18.37 ± 2.31 mGy and 23.84 ± 2.36 mGy in men.Conclusions. Implementing CNN-based automated methodologies can contribute to fast and accurate dose calculations, thereby improving patient-specific radiation safety in clinical practice.

Bacillus subtilis stress-associated mutagenesis and developmental DNA repair.

SUMMARYThe metabolic conditions that prevail during bacterial growth have evolved with the faithful operation of repair systems that recognize and eliminate DNA lesions caused by intracellular and exogenous agents. This idea is supported by the low rate of spontaneous mutations (10-9) that occur in replicating cells, maintaining genome integrity. In contrast, when growth and/or replication cease, bacteria frequently process DNA lesions in an error-prone manner. DNA repairs provide cells with the tools needed for maintaining homeostasis during stressful conditions and depend on the developmental context in which repair events occur. Thus, different physiological scenarios can be anticipated. In nutritionally stressed bacteria, different components of the base excision repair pathway may process damaged DNA in an error-prone approach, promoting genetic variability. Interestingly, suppressing the mismatch repair machinery and activating specific DNA glycosylases promote stationary-phase mutations. Current evidence also suggests that in resting cells, coupling repair processes to actively transcribed genes may promote multiple genetic transactions that are advantageous for stressed cells. DNA repair during sporulation is of interest as a model to understand how transcriptional processes influence the formation of mutations in conditions where replication is halted. Current reports indicate that transcriptional coupling repair-dependent and -independent processes operate in differentiating cells to process spontaneous and induced DNA damage and that error-prone synthesis of DNA is involved in these events. These and other noncanonical ways of DNA repair that contribute to mutagenesis, survival, and evolution are reviewed in this manuscript.

8-OxoG-Dependent Regulation of Global Protein Responses Leads to Mutagenesis and Stress Survival in Bacillus subtilis.

The guanine oxidized (GO) system of Bacillus subtilis, composed of the YtkD (MutT), MutM and MutY proteins, counteracts the cytotoxic and genotoxic effects of the oxidized nucleobase 8-OxoG. Here, we report that in growing B. subtilis cells, the genetic inactivation of GO system potentiated mutagenesis (HPM), and subsequent hyperresistance, contributes to the damaging effects of hydrogen peroxide (H2O2) (HPHR). The mechanism(s) that connect the accumulation of the mutagenic lesion 8-OxoG with the ability of B. subtilis to evolve and survive the noxious effects of oxidative stress were dissected. Genetic and biochemical evidence indicated that the synthesis of KatA was exacerbated, in a PerR-independent manner, and the transcriptional coupling repair factor, Mfd, contributed to HPHR and HPM of the ΔGO strain. Moreover, these phenotypes are associated with wider pleiotropic effects, as revealed by a global proteome analysis. The inactivation of the GO system results in the upregulated production of KatA, and it reprograms the synthesis of the proteins involved in distinct types of cellular stress; this has a direct impact on (i) cysteine catabolism, (ii) the synthesis of iron-sulfur clusters, (iii) the reorganization of cell wall architecture, (iv) the activation of AhpC/AhpF-independent organic peroxide resistance, and (v) increased resistance to transcription-acting antibiotics. Therefore, to contend with the cytotoxic and genotoxic effects derived from the accumulation of 8-OxoG, B. subtilis activates the synthesis of proteins belonging to transcriptional regulons that respond to a wide, diverse range of cell stressors.

Trends in Low-Value Care Among Children's Hospitals.

BACKGROUND AND OBJECTIVES: Longitudinal pediatric low-value care (LVC) trends are not well established. We used the Pediatric Health Information System LVC Calculator, which measures utilization of 30 nonevidenced-based services, to report 7-year LVC trends. METHODS: This retrospective cohort study applied the LVC Calculator to emergency department (ED) and hospital encounters from January 1, 2016, to December 31, 2022. We used generalized estimating equation models accounting for hospital clustering to assess temporal changes in LVC. RESULTS: There were 5 265 153 eligible ED encounters and 1 301 613 eligible hospitalizations. In 2022, of 21 LVC measures applicable to the ED cohort, the percentage of encounters with LVC had increased for 11 measures, decreased for 1, and remained unchanged for 9 as compared with 2016. Computed tomography for minor head injury had the largest increase (17%-23%; P < .001); bronchodilators for bronchiolitis decreased (22%-17%; P = .001). Of 26 hospitalization measures, LVC increased for 6 measures, decreased for 9, and was unchanged for 11. Inflammatory marker testing for pneumonia had the largest increase (23%-38%; P = .003); broad-spectrum antibiotic use for pneumonia had the largest decrease (60%-48%; P < .001). LVC remained unchanged or decreased for most medication and procedure measures, but remained unchanged or increased for most laboratory and imaging measures. CONCLUSIONS: LVC improved for a minority of services between 2016 and 2022. Trends were more favorable for therapeutic (medications and procedures) than diagnostic measures (imaging and laboratory studies). These data may inform prioritization of deimplementation efforts.

Pediatric Respiratory Illnesses: An Update on Achievable Benchmarks of Care.

BACKGROUND AND OBJECTIVES: Pediatric respiratory illnesses (PRI): asthma, bronchiolitis, pneumonia, croup, and influenza are leading causes of pediatric hospitalizations, and emergency department (ED) visits in the United States. There is a lack of standardized measures to assess the quality of hospital care delivered for these conditions. We aimed to develop a measure set for automated data extraction from administrative data sets and evaluate its performance including updated achievable benchmarks of care (ABC). METHODS: A multidisciplinary subject-matter experts team selected quality measures from multiple sources. The measure set was applied to the Public Health Information System database (Children's Hospital Association, Lenexa, KS) to cohorts of ED visits and hospitalizations from 2017 to 2019. ABC for pertinent measures and performance gaps of mean values from the ABC were estimated. ABC were compared with previous reports. RESULTS: The measure set: PRI report includes a total of 94 quality measures. The study cohort included 984 337 episodes of care, and 82.3% were discharged from the ED. Measures with low performance included bronchodilators (19.7%) and chest x-rays (14.4%) for bronchiolitis in the ED. These indicators were (34.6%) and (29.5%) in the hospitalized cohort. In pneumonia, there was a 57.3% use of narrow spectrum antibiotics. In general, compared with previous reports, there was improvement toward optimal performance for the ABCs. CONCLUSIONS: The PRI report provides performance data including ABC and identifies performance gaps in the quality of care for common respiratory illnesses. Future directions include examining health inequities, and understanding and addressing the effects of the coronavirus disease 2019 pandemic on care quality.

Design of a Whole-Cell Biosensor Based on Bacillus subtilis Spores and the Green Fluorescent Protein To Monitor Arsenic.

A green fluorescent protein (GFP)-based whole-cell biosensor (WCB-GFP) for monitoring arsenic (As) was developed in Bacillus subtilis. To this end, we designed a reporter gene fusion carrying the gfpmut3a gene under the control of the promoter/operator region of the arsenic operon (Pars::gfpmut3a) in the extrachromosomal plasmid pAD123. This construct was transformed into B. subtilis 168, and the resultant strain was used as a whole-cell biosensor (BsWCB-GFP) for the detection of As. The BsWCB-GFP was specifically activated by inorganic As(III) and As(V), but not by dimethylarsinic acid [DMA(V)], and exhibited high tolerance to the noxious effects of arsenic. Accordingly, after 12 h exposure, B. subtilis cells carrying the Pars::gfpmut3a fusion exhibited 50 and 90% lethal doses (LD50 and LD90) to As(III) of 0.89 mM and As 1.71 mM, respectively. Notably, dormant spores from the BsWCB-GFP were able to report the presence of As(III) in a concentration range from 0.1 to 1,000 µM 4 h after the onset of germination. In summary, the specificity and high sensitivity for As, as well as its ability to proliferate under concentrations of the metal that are considered toxic in water and soil, makes the B. subtilis biosensor developed here a potentially important tool for monitoring environmental samples contaminated with this pollutant. IMPORTANCE Arsenic (As) contamination of groundwater is associated with serious worldwide health risks. Detection of this pollutant at concentrations that are established as permissible for water consumption by WHO is a matter of significant interest. Here, we report the generation of a whole-cell biosensor for As detection in the Gram-positive spore former B. subtilis. This biosensor reports the presence of inorganic As, activating the expression of the green fluorescent protein (GFP) under the control of the promoter/operator of the ars operon. The biosensor can proliferate under concentrations of As(III) that are considered toxic in water and soil and detect this ion at concentrations as low as 0.1 µM. Of note, spores of the Pars-GFP biosensor exhibited the ability to detect As(III) following germination and outgrowth. Therefore, this novel tool has the potential to be directly applied to monitor As contamination in environmental samples.

Protection of the DNA from Selected Species of Five Kingdoms in Nature by Ba(II), Sr(II), and Ca(II) Silica-Carbonates: Implications about Biogenicity and Evolving from Prebiotic Chemistry to Biological Chemistry.

The origin of life on Earth is associated with the Precambrian era, in which the existence of a large diversity of microbial fossils has been demonstrated. Notwithstanding, despite existing evidence of the emergence of life many unsolved questions remain. The first question could be as follows: Which was the inorganic structure that allowed isolation and conservation of the first biomolecules in the existing reduced conditions of the primigenial era? Minerals have been postulated as the ones in charge of protecting theses biomolecules against the external environment. There are calcium, barium, or strontium silica-carbonates, called biomorphs, which we propose as being one of the first inorganic structures in which biomolecules were protected from the external medium. Biomorphs are structures with different biological morphologies that are not formed by cells, but by nanocrystals; some of their morphologies resemble the microfossils found in Precambrian cherts. Even though biomorphs are unknown structures in the geological registry, their similarity with some biological forms, including some Apex fossils, could suggest them as the first "inorganic scaffold" where the first biomolecules became concentrated, conserved, aligned, and duplicated to give rise to the pioneering cell. However, it has not been documented whether biomorphs could have been the primary structures that conserved biomolecules in the Precambrian era. To attain a better understanding on whether biomorphs could have been the inorganic scaffold that existed in the primigenial Earth, the aim of this contribution is to synthesize calcium, barium, and strontium biomorphs in the presence of genomic DNA from organisms of the five kingdoms in conditions emulating the atmosphere of the Precambrian era and that CO2 concentration in conditions emulating current atmospheric conditions. Our results showed, for the first time, the formation of the kerogen signal, which is a marker of biogenicity in fossils, in the biomorphs grown in the presence of DNA. We also found the DNA to be internalized into the structure of biomorphs.

Dynamics of Mismatch and Alternative Excision-Dependent Repair in Replicating Bacillus subtilis DNA Examined Under Conditions of Neutral Selection.

Spontaneous DNA deamination is a potential source of transition mutations. In Bacillus subtilis, EndoV, a component of the alternative excision repair pathway (AER), counteracts the mutagenicity of base deamination-induced mispairs. Here, we report that the mismatch repair (MMR) system, MutSL, prevents the harmful effects of HNO2, a deaminating agent of Cytosine (C), Adenine (A), and Guanine (G). Using Maximum Depth Sequencing (MDS), which measures mutagenesis under conditions of neutral selection, in B. subtilis strains proficient or deficient in MutSL and/or EndoV, revealed asymmetric and heterogeneous patterns of mutations in both DNA template strands. While the lagging template strand showed a higher frequency of C → T substitutions; G → A mutations, occurred more frequently in the leading template strand in different genetic backgrounds. In summary, our results unveiled a role for MutSL in preventing the deleterious effects of base deamination and uncovered differential patterns of base deamination processing by the AER and MMR systems that are influenced by the sequence context and the replicating DNA strand.

Medications and Adherence to Treatment Guidelines Among Children Hospitalized With Acute COVID-19.

OBJECTIVES: Coronavirus disease 2019 (COVID-19) treatment guidelines rapidly evolved during the pandemic. The December 2020 Infectious Diseases Society of America (IDSA) guideline, endorsed by the Pediatric Infectious Diseases Society, recommended steroids for critical disease, and suggested steroids and remdesivir for severe disease. We evaluated how medications for children hospitalized with COVID-19 changed after guideline publication. METHODS: We performed a multicenter, retrospective cohort study of children aged 30 days to <18 years hospitalized with acute COVID-19 at 42 tertiary care US children's hospitals April 2020 to December 2021. We compared medication use before and after the December 2020 IDSA guideline (pre- and postguideline) stratified by COVID-19 disease severity (mild-moderate, severe, critical) with interrupted time series. RESULTS: Among 18 364 patients who met selection criteria, 80.3% were discharged in the postguideline period. Remdesivir and steroid use increased postguideline relative to the preguideline period, although the trend slowed. Postguideline, among patients with severe disease, 75.4% received steroids and 55.2% remdesivir, and in those with critical disease, 82.4% received steroids and 41.4% remdesivir. Compared with preguideline, enoxaparin use increased overall but decreased among patients with critical disease. Postguideline, tocilizumab use increased and hydroxychloroquine, azithromycin, anakinra, and antibiotic use decreased. Antibiotic use remained high in severe (51.7%) and critical disease (81%). CONCLUSIONS: Although utilization of COVID-19 medications changed after December 2020 IDSA guidelines, there was a decline in uptake and incomplete adherence for children with severe and critical disease. Efforts should enhance reliable delivery of guideline-directed therapies to children hospitalized with COVID-19 and assess their effectiveness.

Inequities in Pain Assessment and Care of Hospitalized Children With Limited English Proficiency.

OBJECTIVES: To examine inequities in pain assessment and management of hospitalized children with limited English proficiency (LEP) as assessed by (1) self-reported pain prevalence and intensity, and (2) nurse-documented pain assessments and analgesia. METHODS: A cross-sectional survey of hospitalized children and parent proxies examined preferred language and pain prevalence, intensity, and etiology; subsequent electronic medical record chart review examined demographics, nurse-documented pain scores, and analgesia prescribed for children aged ≤21 years at a tertiary care children's hospital. The primary outcome was a difference of ≥3 points between self-reported and nurse-documented worst pain scores. Descriptive statistics, Fisher's exact tests, and multivariable logistic regression were used to identify differences in outcomes between children with and without LEP. RESULTS: A total of 155 patients (50% children and 50% parental proxies) were interviewed (96% response rate). Of those, 60% (n = 93) reported pain in the previous 24 hours, most frequently because of acute illnesses. Of patients reporting pain, 65% (n = 60) reported a worst pain score of ≥3 points higher than nurse-documented scores; this discrepancy affected more patients with LEP (82%, n = 27) than English-proficient patients (55%, n = 33) (P = .01) with an adjusted odds ratio of 3.2 (95% confidence interval: 1.13-10.31). Patients with LEP were also less likely than English-proficient patients to receive medications at the time of their worst pain (60% vs 82%, P = .03), particularly opioid analgesia (9% vs 22%, P = .04). CONCLUSIONS: Children with LEP were more likely to self-report pain scores that exceeded nurse-documented scores and received less medications, particularly opiates. This population may be particularly vulnerable to underassessment and inadequate management of pain.

Stress-Associated and Growth-Dependent Mutagenesis Are Divergently Regulated by c-di-AMP Levels in Bacillus subtilis.

A previous proteomic study uncovered a relationship between nutritional stress and fluctuations in levels of diadenylate cyclases (DACs) and other proteins that regulate DAC activity, degrade, or interact with c-di-AMP, suggesting a possible role of this second messenger in B. subtilis stress-associated mutagenesis (SAM). Here, we investigated a possible role of c-di-AMP in SAM and growth-associated mutagenesis (GAM). Our results showed that in growing cells of B. subtilis YB955 (hisC952, metB25 and leuC427), the DACs CdaA and DisA, which play crucial roles in cell wall homeostasis and chromosomal fidelity, respectively, counteracted spontaneous and Mitomycin-C-induced mutagenesis. However, experiments in which hydrogen peroxide was used to induce mutations showed that single deficiencies in DACs caused opposite effects compared to each other. In contrast, in the stationary-phase, DACs promoted mutations in conditions of nutritional stress. These results tracked with intracellular levels of c-di-AMP, which are significantly lower in cdaA- and disA-deficient strains. The restoration of DAC-deficient strains with single functional copies of the cdaA and/or disA returned SAM and GAM levels to those observed in the parental strain. Taken together, these results reveal a role for c-di-AMP in promoting genetic diversity in growth-limiting conditions in B. subtilis. Finally, we postulate that this novel function of c-di-AMP can be exerted through proteins that possess binding domains for this second messenger and play roles in DNA repair, ion transport, transcriptional regulation, as well as oxidative stress protection.

Development and Use of a Calculator to Measure Pediatric Low-Value Care Delivered in US Children's Hospitals.

Importance: The scope of low-value care in children's hospitals is poorly understood. Objective: To develop and apply a calculator of hospital-based pediatric low-value care to estimate prevalence and cost of low-value services. Design, Setting, and Participants: This cross-sectional study developed and applied a calculator of hospital-based pediatric low-value care to estimate the prevalence and cost of low-value services among 1 011 950 encounters reported in 49 US children's hospitals contributing to the Pediatric Health Information System (PHIS) database. To develop the calculator, a multidisciplinary stakeholder group searched existing pediatric low-value care measures and used an iterative process to identify and operationalize relevant hospital-based measures in the PHIS database. Children with an eligible encounter in 2019 were included in the calculator-applied analysis. Two cohorts were analyzed: an emergency department cohort (with encounters resulting in emergency department discharge) and a hospitalized cohort. Exposures: Eligible condition-specific hospital encounters. Main Outcomes and Measures: The proportion and volume of encounters in which low-value services were delivered and their associated standardized costs. Measures were ranked by those outcomes. Results: There were 1 011 950 encounters eligible for 1 or more of 30 calculator-included measures in 2019; encounters were incurred by 816 098 unique patients with a median age of 3 years (IQR, 1-8 years). In the emergency department cohort, low-value services delivered in the greatest percentage of encounters were Group A streptococcal testing among children younger than 3 years with pharyngitis (3679 of 9785 [37.6%]), computed tomography scan for minor head injury (7541 of 42 602 [17.7%]), and bronchodilators for treatment of bronchiolitis (8899 of 55 616 [16.0%]). In the hospitalized cohort, low-value care was most prevalent for broad-spectrum antibiotics in the treatment of community-acquired pneumonia (3406 of 5658 [60.2%]), acid suppression therapy for infants with esophageal reflux (3814 of 7507 of [50.8%]), and blood cultures for uncomplicated community-acquired pneumonia (2277 of 5823 [39.1%]). Measured low-value services generated nearly $17 million in total standardized cost. The costliest services in the emergency department cohort were computed tomography scan for abdominal pain (approximately $1.8 million) and minor head injury (approximately $1.5 million) and chest radiography for asthma (approximately $1.1 million). The costliest services in the hospitalized cohort were receipt of 2 or more concurrent antipsychotics (approximately $2.4 million), and chest radiography for bronchiolitis ($801 680) and asthma ($625 866). Conclusions and Relevance: This cross-sectional analysis found that low-value care for some pediatric services was prevalent and costly. Measuring receipt of low-value services across conditions informs prioritization of deimplementation efforts. Continued use of this calculator may establish trends in low-value care delivery.

Factors Associated With COVID-19 Disease Severity in US Children and Adolescents.

BACKGROUND: Little is known about the clinical factors associated with COVID-19 disease severity in children and adolescents. METHODS: We conducted a retrospective cohort study across 45 US children's hospitals between April 2020 to September 2020 of pediatric patients discharged with a primary diagnosis of COVID-19. We assessed factors associated with hospitalization and factors associated with clinical severity (eg, admission to inpatient floor, admission to intensive care unit [ICU], admission to ICU with mechanical ventilation, shock, death) among those hospitalized. RESULTS: Among 19,976 COVID-19 encounters, 15,913 (79.7%) patients were discharged from the emergency department (ED) and 4063 (20.3%) were hospitalized. The clinical severity distribution among those hospitalized was moderate (3222, 79.3%), severe (431, 11.3%), and very severe (380, 9.4%). Factors associated with hospitalization vs discharge from the ED included private payor insurance (adjusted odds ratio [aOR],1.16; 95% CI, 1.1-1.3), obesity/type 2 diabetes mellitus (type 2 DM) (aOR, 10.4; 95% CI, 8.9-13.3), asthma (aOR, 1.4; 95% CI, 1.3-1.6), cardiovascular disease, (aOR, 5.0; 95% CI, 4.3- 5.8), immunocompromised condition (aOR, 5.9; 95% CI, 5.0-6.7), pulmonary disease (aOR, 5.3; 95% CI, 3.4-8.2), and neurologic disease (aOR, 3.2; 95% CI, 2.7-5.8). Among children and adolescents hospitalized with COVID-19, greater disease severity was associated with Black or other non-White race; age greater than 4 years; and obesity/type 2 DM, cardiovascular, neuromuscular, and pulmonary conditions. CONCLUSIONS: Among children and adolescents presenting to US children's hospital EDs with COVID-19, 20% were hospitalized; of these, 21% received care in the ICU. Older children and adolescents had a lower risk for hospitalization but more severe illness when hospitalized. There were differences in disease severity by race and ethnicity and the presence of selected comorbidities. These factors should be taken into consideration when prioritizing mitigation and vaccination strategies.

Non-B DNA-Forming Motifs Promote Mfd-Dependent Stationary-Phase Mutagenesis in Bacillus subtilis.

Transcription-induced mutagenic mechanisms limit genetic changes to times when expression happens and to coding DNA. It has been hypothesized that intrinsic sequences that have the potential to form alternate DNA structures, such as non-B DNA structures, influence these mechanisms. Non-B DNA structures are promoted by transcription and induce genome instability in eukaryotic cells, but their impact in bacterial genomes is less known. Here, we investigated if G4 DNA- and hairpin-forming motifs influence stationary-phase mutagenesis in Bacillus subtilis. We developed a system to measure the influence of non-B DNA on B. subtilis stationary-phase mutagenesis by deleting the wild-type argF at its chromosomal position and introducing IPTG-inducible argF alleles differing in their ability to form hairpin and G4 DNA structures into an ectopic locus. Using this system, we found that sequences predicted to form non-B DNA structures promoted mutagenesis in B. subtilis stationary-phase cells; such a response did not occur in growing conditions. We also found that the transcription-coupled repair factor Mfd promoted mutagenesis at these predicted structures. In summary, we showed that non-B DNA-forming motifs promote genetic instability, particularly in coding regions in stressed cells; therefore, non-B DNA structures may have a spatial and temporal mutagenic effect in bacteria. This study provides insights into mechanisms that prevent or promote mutagenesis and advances our understanding of processes underlying bacterial evolution.

The COVID-19 Pandemic and Changes in Healthcare Utilization for Pediatric Respiratory and Nonrespiratory Illnesses in the United States.

The impact of COVID-19 public health interventions on pediatric illnesses nationwide is unknown. We performed a multicenter, cross-sectional study of encounters at 44 children's hospitals in the United States to assess changes in healthcare utilization during the pandemic. The COVID-19 pandemic was associated with substantial reductions in encounters for respiratory diseases; these large reductions were consistent across illness subgroups. Although encounters for nonrespiratory diseases decreased as well, reductions were more modest and varied by age. Encounters for respiratory diseases among adolescents declined to a lesser degree and returned to previous levels faster compared with those of younger children. Further study is needed to determine the contributions of decreased illness and changes in care-seeking behavior to this observed reduction.

Femur absorptiometry changes determined by X-ray image segmentation in mice under experimental diabetes and ovariectomy.

AIM: The aim of the present work was to determine if both ovariectomy (OVX) and type 2 diabetes mellitus (T2DM) can change X-ray absorptiometry until reach the osteoporosis condition. RESULTS: The segmentation allowed us to quantitatively determine the X-ray absorption in the femurs of mice subjected to OVX, T2DM and both pathologies together. CONCLUSIONS: The test subjects suffering from the mentioned pathologies separately or together, did not reach the osteoporosis condition when they were 30 weeks old.

Mfd Affects Global Transcription and the Physiology of Stressed Bacillus subtilis Cells.

For several decades, Mfd has been studied as the bacterial transcription-coupled repair factor. However, recent observations indicate that this factor influences cell functions beyond DNA repair. Our lab recently described a role for Mfd in disulfide stress that was independent of its function in nucleotide excision repair and base excision repair. Because reports showed that Mfd influenced transcription of single genes, we investigated the global differences in transcription in wild-type and mfd mutant growth-limited cells in the presence and absence of diamide. Surprisingly, we found 1,997 genes differentially expressed in Mfd- cells in the absence of diamide. Using gene knockouts, we investigated the effect of genetic interactions between Mfd and the genes in its regulon on the response to disulfide stress. Interestingly, we found that Mfd interactions were complex and identified additive, epistatic, and suppressor effects in the response to disulfide stress. Pathway enrichment analysis of our RNASeq assay indicated that major biological functions, including translation, endospore formation, pyrimidine metabolism, and motility, were affected by the loss of Mfd. Further, our RNASeq findings correlated with phenotypic changes in growth in minimal media, motility, and sensitivity to antibiotics that target the cell envelope, transcription, and DNA replication. Our results suggest that Mfd has profound effects on the modulation of the transcriptome and on bacterial physiology, particularly in cells experiencing nutritional and oxidative stress.

Transcriptional coupling and repair of 8-OxoG activate a RecA-dependent checkpoint that controls the onset of sporulation in Bacillus subtilis.

During sporulation Bacillus subtilis Mfd couples transcription to nucleotide excision repair (NER) to eliminate DNA distorting lesions. Here, we report a significant decline in sporulation following Mfd disruption, which was manifested in the absence of external DNA-damage suggesting that spontaneous lesions activate the function of Mfd for an efficient sporogenesis. Accordingly, a dramatic decline in sporulation efficiency took place in a B. subtilis strain lacking Mfd and the repair/prevention guanine oxidized (GO) system (hereafter, the ∆GO system), composed by YtkD, MutM and MutY. Furthermore, the simultaneous absence of Mfd and the GO system, (i) sensitized sporulating cells to H2O2, and (ii) elicited spontaneous and oxygen radical-induced rifampin-resistance (Rifr) mutagenesis. Epifluorescence (EF), confocal and transmission electron (TEM) microscopy analyses, showed a decreased ability of ∆GO ∆mfd strain to sporulate and to develop the typical morphologies of sporulating cells. Remarkably, disruption of sda, sirA and disA partially, restored the sporulation efficiency of the strain deficient for Mfd and the ∆GO system; complete restoration occurred in the RecA- background. Overall, our results unveil a novel Mfd mechanism of transcription-coupled-repair (TCR) elicited by 8-OxoG which converges in the activation of a RecA-dependent checkpoint event that control the onset of sporulation in B. subtilis.

Novel Biochemical Properties and Physiological Role of the Flavin Mononucleotide Oxidoreductase YhdA from Bacillus subtilis.

Cr(VI) is mutagenic and teratogenic and considered an environmental pollutant of increasing concern. The use of microbial enzymes that convert this ion into its less toxic reduced insoluble form, Cr(III), represents a valuable bioremediation strategy. In this study, we examined the Bacillus subtilis YhdA enzyme, which belongs to the family of NADPH-dependent flavin mononucleotide oxide reductases and possesses azo-reductase activity as a factor that upon overexpression confers protection on B. subtilis from the cytotoxic effects promoted by Cr(VI) and counteracts the mutagenic effects of the reactive oxygen species (ROS)-promoted lesion 8-OxoG. Further, our in vitro assays unveiled catalytic and biochemical properties of biotechnological relevance in YhdA; a pure recombinant His10-YhdA protein efficiently catalyzed the reduction of Cr(VI) employing NADPH as a cofactor. The activity of the pure oxidoreductase YhdA was optimal at 30°C and at pH 7.5 and displayed Km and Vmax values of 7.26 mM and 26.8 µmol·min-1·mg-1 for Cr(VI), respectively. Therefore, YhdA can be used for efficient bioremediation of Cr(VI) and counteracts the cytotoxic and genotoxic effects of oxygen radicals induced by intracellular factors and those generated during reduction of hexavalent chromium.IMPORTANCE Here, we report that the bacterial flavin mononucleotide/NADPH-dependent oxidoreductase YhdA, widely distributed among Gram-positive bacilli, conferred protection to cells from the cytotoxic effects of Cr(VI) and prevented the hypermutagenesis exhibited by a MutT/MutM/MutY-deficient strain. Additionally, a purified recombinant His10-YhdA protein displayed a strong NADPH-dependent chromate reductase activity. Therefore, we postulate that in bacterial cells, YhdA counteracts the cytotoxic and genotoxic effects of intracellular and extracellular inducers of oxygen radicals, including those caused by hexavalent chromium.

The Bacillus Subtilis K-State Promotes Stationary-Phase Mutagenesis via Oxidative Damage.

Bacterial cells develop mutations in the absence of cellular division through a process known as stationary-phase or stress-induced mutagenesis. This phenomenon has been studied in a few bacterial models, including Escherichia coli and Bacillus subtilis; however, the underlying mechanisms between these systems differ. For instance, RecA is not required for stationary-phase mutagenesis in B. subtilis like it is in E. coli. In B. subtilis, RecA is essential to the process of genetic transformation in the subpopulation of cells that become naturally competent in conditions of stress. Interestingly, the transcriptional regulator ComK, which controls the development of competence, does influence the accumulation of mutations in stationary phase in B. subtilis. Since recombination is not involved in this process even though ComK is, we investigated if the development of a subpopulation (K-cells) could be involved in stationary-phase mutagenesis. Using genetic knockout strains and a point-mutation reversion system, we investigated the effects of ComK, ComEA (a protein involved in DNA transport during transformation), and oxidative damage on stationary-phase mutagenesis. We found that stationary-phase revertants were more likely to have undergone the development of competence than the background of non-revertant cells, mutations accumulated independently of DNA uptake, and the presence of exogenous oxidants potentiated mutagenesis in K-cells. Therefore, the development of the K-state creates conditions favorable to an increase in the genetic diversity of the population not only through exogenous DNA uptake but also through stationary-phase mutagenesis.