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Abstract Background About one quarter of adults are hypertensive and high blood pressure carries increased risk for heart disease, stroke, kidney disease and death. Increased arterial stiffness is a key factor in the pathogenesis of systolic hypertension and cardiovascular disease. Substantial heritability of blood-pressure (BP) and arterial-stiffness suggests important genetic contributions. Methods In Framingham Heart Study families, we analyzed genome-wide SNP (Affymetrix 100K GeneChip) associations with systolic (SBP) and diastolic (DBP) BP at a single examination in 1971–1975 (n = 1260), at a recent examination in 1998–2001 (n = 1233), and long-term averaged SBP and DBP from 1971–2001 (n = 1327, mean age 52 years, 54% women) and with arterial stiffness measured by arterial tonometry (carotid-femoral and carotid-brachial pulse wave velocity, forward and reflected pressure wave amplitude, and mean arterial pressure; 1998–2001, n = 644). In primary analyses we used generalized estimating equations in models for an additive genetic effect to test associations between SNPs and phenotypes of interest using multivariable-adjusted residuals. A total of 70,987 autosomal SNPs with minor allele frequency ≥ 0.10, genotype call rate ≥ 0.80, and Hardy-Weinberg equilibrium p ≥ 0.001 were analyzed. We also tested for association of 69 SNPs in six renin-angiotensin-aldosterone pathway genes with BP and arterial stiffness phenotypes as part of a candidate gene search. Results In the primary analyses, none of the associations attained genome-wide significance. For the six BP phenotypes, seven SNPs yielded p values < 10-5. The lowest p-values for SBP and DBP respectively were rs10493340 (p = 1.7 × 10-6) and rs1963982 (p = 3.3 × 10-6). For the five tonometry phenotypes, five SNPs had p values < 10-5; lowest p-values were for reflected wave (rs6063312, p = 2.1 × 10-6) and carotid-brachial pulse wave velocity (rs770189, p = 2.5 × 10-6) in MEF2C, a regulator of cardiac morphogenesis. We found only weak association of SNPs in the renin-angiotensin-aldosterone pathway with BP or arterial stiffness. Conclusion These results of genome-wide association testing for blood pressure and arterial stiffness phenotypes in an unselected community-based sample of adults may aid in the identification of the genetic basis of hypertension and arterial disease, help identify high risk individuals, and guide novel therapies for hypertension. Additional studies are needed to replicate any associations identified in these analyses.

Abstract Background Echocardiographic left ventricular (LV) measurements, exercise responses to standardized treadmill test (ETT) and brachial artery (BA) vascular function are heritable traits that are associated with cardiovascular disease risk. We conducted a genome-wide association study (GWAS) in the community-based Framingham Heart Study. Methods We estimated multivariable-adjusted residuals for quantitative echocardiography, ETT and BA function traits. Echocardiography residuals were averaged across 4 examinations and included LV mass, diastolic and systolic dimensions, wall thickness, fractional shortening, left atrial and aortic root size. ETT measures (single exam) included systolic blood pressure and heart rate responses during exercise stage 2, and at 3 minutes post-exercise. BA measures (single exam) included vessel diameter, flow-mediated dilation (FMD), and baseline and hyperemic flow responses. Generalized estimating equations (GEE), family-based association tests (FBAT) and variance-components linkage were used to relate multivariable-adjusted trait residuals to 70,987 SNPs (Human 100K GeneChip, Affymetrix) restricted to autosomal SNPs with minor allele frequency ≥0.10, genotype call rate ≥0.80, and Hardy-Weinberg equilibrium p ≥ 0.001. Results We summarize results from 17 traits in up to 1238 related middle-aged to elderly men and women. Results of all association and linkage analyses are web-posted at http://ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007. We confirmed modest-to-strong heritabilities (estimates 0.30–0.52) for several Echo, ETT and BA function traits. Overall, p < 10-5 in either GEE or FBAT models were observed for 21 SNPs (nine for echocardiography, eleven for ETT and one for BA function). The top SNPs associated were (GEE results): LV diastolic dimension, rs1379659 (SLIT2, p = 1.17*10-7); LV systolic dimension, rs10504543 (KCNB2, p = 5.18*10-6); LV mass, rs10498091 (p = 5.68*10-6); Left atrial size, rs1935881 (FAM5C, p = 6.56*10-6); exercise heart rate, rs6847149 (NOLA1, p = 2.74*10-6); exercise systolic blood pressure, rs2553268 (WRN, p = 6.3*10-6); BA baseline flow, rs3814219 (OBFC1, 9.48*10-7), and FMD, rs4148686 (CFTR, p = 1.13*10-5). Several SNPs are reasonable biological candidates, with some being related to multiple traits suggesting pleiotropy. The peak LOD score was for LV mass (4.38; chromosome 5); the 1.5 LOD support interval included NRG2. Conclusion In hypothesis-generating GWAS of echocardiography, ETT and BA vascular function in a moderate-sized community-based sample, we identified several SNPs that are candidates for replication attempts and we provide a web-based GWAS resource for the research community.

Abstract Background Prior studies reported conflicting findings on the association between metabolic syndrome and inflammatory biomarkers. We tested the cross-sectional associations between metabolic syndrome and nine inflammatory markers. Methods We measured C-reactive protein, CD40 ligand, interleukin-6, intercellular adhesion molecule-1, monocyte chemoattractant protein-1, osteoprotegerin, P-selectin, tumor necrosis factor-alpha, and tumor necrosis factor receptor-2 in 2570 Framingham Offspring Study participants free of diabetes and cardiovascular disease at examination 7. Metabolic syndrome was defined by National Cholesterol Education Program criteria. We performed multivariable linear regressions for each biomarker with metabolic syndrome as the exposure adjusting for age, sex, smoking, aspirin use, and hormone replacement. We subsequently added to the models components of the metabolic syndrome as continuous traits plus lipid lowering and hypertension treatments. We considered P Results Metabolic syndrome was present in 984 (38%) participants and was statistically significantly associated with each biomarker (all P < 0.02) except osteoprotegerin. After adjusting for its component variables, the metabolic syndrome was associated only with P-selectin (1.06 fold higher in metabolic syndrome, 95% CI 1.02, 1.10, p = 0.005). Conclusions Metabolic syndrome was associated with multiple inflammatory biomarkers. However, adjusting for each of its components eliminated the association with most inflammatory markers, except P-selectin. Our results suggest that the relation between metabolic syndrome and inflammation is largely accounted for by its components.

Abstract This paper presents the rationale and methods for a randomized controlled evaluation of web-based training in motivational interviewing, goal setting, and behavioral task assignment. Web-based training may be a practical and cost-effective way to address the need for large-scale mental health training in evidence-based practice; however, there is a dearth of well-controlled outcome studies of these approaches. For the current trial, 168 mental health providers treating post-traumatic stress disorder (PTSD) were assigned to web-based training plus supervision, web-based training, or training-as-usual (control). A novel standardized patient (SP) assessment was developed and implemented for objective measurement of changes in clinical skills, while on-line self-report measures were used for assessing changes in knowledge, perceived self-efficacy, and practice related to cognitive behavioral therapy (CBT) techniques. Eligible participants were all actively involved in mental health treatment of veterans with PTSD. Study methodology illustrates ways of developing training content, recruiting participants, and assessing knowledge, perceived self-efficacy, and competency-based outcomes, and demonstrates the feasibility of conducting prospective studies of training efficacy or effectiveness in large healthcare systems.

Abstract Background Animal studies suggest that local adipocyte-mediated activity of the renin-angiotensin-aldosterone system (RAAS) contributes to circulating levels, and may promote the development of obesity-related hypertension in rodents. Methods We examined relations of systemic RAAS activity, as assessed by circulating plasma renin activity (PRA), serum aldosterone level, and aldosterone:renin ratio (ARR), with specific regional adiposity measures in a large, community-based sample. Third Generation Framingham Heart Study participants underwent multidetector computed tomography assessment of SAT and VAT volumes during Exam 1 (2002 and 2005). PRA and serum aldosterone were measured after approximately 10 minutes of supine rest; results were log-transformed for analysis. Correlation coefficients between log-transformed RAAS measures and adiposity measurements were calculated, adjusted for age and sex. Partial correlations between log-transformed RAAS measures and adiposity measurements were also calculated, adjusted for standard CVD risk factors. Results Overall, 992 women and 897 men were analyzed (mean age 40 years; 7% hypertension; 3% diabetes). No associations were observed with SAT (renin r = 0.04, p = 0.1; aldosterone r = -0.01, p = 0.6) or VAT (renin r = 0.03, p = 0.2; aldosterone r = -0.03, p = 0.2). Similar results were observed for ARR, in sex-stratified analyses, and for BMI and waist circumference. Non-significant partial correlations were also observed in models adjusted for standard cardiovascular risk factors. Conclusions Regional adiposity measures were not associated with circulating measures of RAAS activity in this large population-based study. Further studies are required to determine whether adipocyte-derived RAAS components contribute to systemic RAAS activity in humans.

Abstract Background Chronic medical diseases require regular and longitudinal care and self-management for effective treatment. When chronic diseases include substance use disorders, care and treatment of both the medical and addiction disorders may affect access to care and the ability to focus on both conditions. The objective of this paper is to evaluate the association between the presence of chronic medical disease and recent addiction treatment utilization among adults with substance dependence. Methods Cross-sectional secondary data analysis of self-reported baseline data from alcohol and/or drug-dependent adults enrolled in a randomized clinical trial of a disease management program for substance dependence in primary care. The main independent variable was chronic medical disease status, categorized using the Katz Comorbidity Score as none, single condition of lower severity, or higher severity (multiple conditions or single higher severity condition), based on comorbidity scores determined from self-report. Asthma was also examined in secondary analyses. The primary outcome was any self-reported addiction treatment utilization (excluding detoxification) in the 3 months prior to study entry, including receipt of any addiction-focused counseling or addiction medication from any healthcare provider. Logistic regression models were adjusted for sociodemographics, type of substance dependence, recruitment site, current smoking, and recent anxiety severity. Results Of 563 subjects, 184 (33%) reported any chronic disease (20% low severity; 13% higher severity) and 111 (20%) reported asthma; 157 (28%) reported any addiction treatment utilization in the past 3 months. In multivariate regression analyses, no significant effect was detected for chronic disease on addiction treatment utilization (adjusted odds ratio [AOR] 0.88 lower severity vs. none, 95% confidence interval (CI): 0.60, 1.28; AOR 1.29 higher severity vs. none, 95% CI: 0.89, 1.88) nor for asthma. Conclusions In this cohort of alcohol and drug dependent persons, there was no significant effect of chronic medical disease on recent addiction treatment utilization. Chronic disease may not hinder or facilitate connection to addiction treatment.

Abstract Background Genome-wide association (GWA) studies that use population-based association approaches may identify spurious associations in the presence of population admixture. In this paper, we propose a novel three-stage approach that is computationally efficient and robust to population admixture and more powerful than the family-based association test (FBAT) for GWA studies with family data. We propose a three-stage approach for GWA studies with family data. The first stage is to perform linear regression ignoring phenotypic correlations among family members. SNPs with a first stage p-value below a liberal cut-off (e.g. 0.1) are then analyzed in the second stage that employs a linear mixed effects (LME) model that accounts for within family correlations. Next, SNPs that reach genome-wide significance (e.g. 10-6 for 34,625 genotyped SNPs in this paper) are analyzed in the third stage using FBAT, with correction of multiple testing only for SNPs that enter the third stage. Simulations are performed to evaluate type I error and power of the proposed method compared to LME adjusting for 10 principal components (PC) of the genotype data. We also apply the three-stage approach to the GWA analyses of uric acid in Framingham Heart Study's SNP Health Association Resource (SHARe) project. Results Our simulations show that whether or not population admixture is present, the three-stage approach has no inflated type I error. In terms of power, using LME adjusting PC is only slightly more powerful than the three-stage approach. When applied to the GWA analyses of uric acid in the SHARe project of FHS, the three-stage approach successfully identified and confirmed three SNPs previously reported as genome-wide significant signals. Conclusions For GWA analyses of quantitative traits with family data, our three-stage approach provides another appealing solution to population admixture, in addition to LME adjusting for genetic PC.

Abstract Background The highly conserved macromolecular synthesis operon (MMSO) contains both dnaG (primase) and sigA (primary sigma factor). However, in previously evaluated gram-positive species, the MMSO is divergent upstream of dnaG. The MMSO of Bacillus subtilis contains three open reading frames (ORFs) that are differentially regulated by multiple promoters. In conjunction with studies to determine the expression profile of dnaG, the MMSO of Staphylococus epidermidis was characterized. Results The ORFs of S. epidermidis were compared to the previously described MMSO of B. subtilis and two additional ORFs in S. epidermidis, serp1129 and serp1130, were identified. The largest transcript, 4.8 kb in length, was expressed only in exponential growth and encompassed all four ORFs (serp1130, serp1129, dnaG, and sigA). A separate transcript (1.5 kb) comprising serp1130 and serp1129 was expressed in early exponential growth. Two smaller transcripts 1.3 and 1.2 kb in size were detected with a sigA probe in both exponential and post-exponential phases of growth. Western blot analysis correlated with the transcriptional profile and demonstrated that Serp1129 was detected only in the exponential phase of growth. Computational analysis identified that Serp1130 contained a CBS motif whereas Serp1129 contained an ATP/GTP binding motif. Functional studies of Serp1129 demonstrated that it was capable of binding both ATP and GTP. Comparisons with a sigB:dhfr mutant revealed that the 1.3 kb sigA transcript was regulated by a σB-dependent promoter. Conclusions These studies demonstrated that the S. epidermidis 1457 MMSO contains two ORFs (serp1129 and serp1130) not described within the B. subtilis MMSO and at least three promoters, one of which is σβ-dependent. The transcriptional regulation of sigA by σB provides evidence that the staphylococcal σB-dependent response is controlled at both the transcriptional and post-transcriptional level. The conservation of serp1129 across multiple gram-positive organisms and its capability to bind ATP and GTP support the need for further investigation of its role in bacterial growth.

Abstract Background The Framingham Heart Study (FHS) recently obtained initial results from the first genome-wide association scan for renal traits. The study of 70,987 single nucleotide polymorphisms (SNPs) in 1,010 FHS participants provides a list of SNPs showing the strongest associations with renal traits which need to be verified in independent study samples. Methods Sixteen SNPs were selected for replication based on the most promising associations with chronic kidney disease (CKD), estimated glomerular filtration rate (eGFR), and serum cystatin C in FHS. These SNPs were genotyped in 15,747 participants of the Atherosclerosis in Communities (ARIC) Study and evaluated for association using multivariable adjusted regression analyses. Primary outcomes in ARIC were CKD and eGFR. Secondary prospective analyses were conducted for association with kidney disease progression using multivariable adjusted Cox proportional hazards regression. The definition of the outcomes, all covariates, and the use of an additive genetic model was consistent with the original analyses in FHS. Results The intronic SNP rs6495446 in the gene MTHFS was significantly associated with CKD among white ARIC participants at visit 4: the odds ratio per each C allele was 1.24 (95% CI 1.09–1.41, p = 0.001). Borderline significant associations of rs6495446 were observed with CKD at study visit 1 (p = 0.024), eGFR at study visits 1 (p = 0.073) and 4 (lower mean eGFR per C allele by 0.6 ml/min/1.73 m2, p = 0.043) and kidney disease progression (hazard ratio 1.13 per each C allele, 95% CI 1.00–1.26, p = 0.041). Another SNP, rs3779748 in EYA1, was significantly associated with CKD at ARIC visit 1 (odds ratio per each T allele 1.22, p = 0.01), but only with eGFR and cystatin C in FHS. Conclusion This genome-wide association study provides unbiased information implicating MTHFS as a candidate gene for kidney disease. Our findings highlight the importance of replication to identify common SNPs associated with renal traits.

Abstract Background High-throughput genotyping generates vast amounts of data for analysis; results can be difficult to summarize succinctly. A single project may involve genotyping many genes with multiple variants per gene and analyzing each variant in relation to numerous phenotypes, using several genetic models and population subgroups. Hundreds of statistical tests may be performed for a single SNP, thereby complicating interpretation of results and inhibiting identification of patterns of association. Results To facilitate visual display and summary of large numbers of association tests of genetic loci with multiple phenotypes, we developed a Phenotype-Genotype Association (PGA) grid display. A database-backed web server was used to create PGA grids from phenotypic and genotypic data (sample sizes, means and standard errors, P-value for association). HTML pages were generated using Tcl scripts on an AOLserver platform, using an Oracle database, and the ArsDigita Community System web toolkit. The grids are interactive and permit display of summary data for individual cells by a mouse click (i.e. least squares means for a given SNP and phenotype, specified genetic model and study sample). PGA grids can be used to visually summarize results of individual SNP associations, gene-environment associations, or haplotype associations. Conclusion The PGA grid, which permits interactive exploration of large numbers of association test results, can serve as an easily adapted common and useful display format for large-scale genetic studies. Doing so would reduce the problem of publication bias, and would simplify the task of summarizing large-scale association studies.

Background: Empathy is critical for optimal patient experience with health-care providers. Verbal empathy is routinely taught to medical students, but nonverbal empathy, including touch, less so. Our objective was to determine whether instruction encouraging empathic touch and eye gaze at exit can impact behaviors and change patient-perceived empathy. Materials: A randomized, controlled, double-blinded trial of 34 first-year medical students was conducted during standardized patient (SP) interviews. A video either encouraging empathic touch and eye gaze at exit or demonstrating proper hand hygiene (control) was shown. Encounter videos were analyzed for touch and eye gaze at exit. The Jefferson Scale of Patient Perceptions of Physician Empathy was used to measure correlations. Intervention students were surveyed regarding patient touch. Results: Of this, 23.5% of intervention students touched the SP versus zero controls; 88.2% of intervention students demonstrated eye gaze at exit. Eye gaze at exit positively impacted patient-perceived empathy (correlation = 0.48, P > .001). Survey responses revealed specific barriers to touch. Conclusion: Medical students may increase perceived empathy using eye gaze at exit. Instruction on empathic touch and sustained eye gaze at exit at the medical school level may be useful in promoting empathic nonverbal communication. Medical educators should consider providing specific instructions on how to appropriately touch patients during history-taking. This is one of the few studies to explore touch with patients and the first ever to report the positive correlation of a health provider’s sustained eye gaze at exit with the patient’s perceived empathy. Further studies are needed to explore barriers to empathic touch.

Francisella tularensis is one of the most virulent bacterial pathogens known and causes the disease tularemia, which can be fatal if untreated. This zoonotic and intracellular pathogen is exposed to diverse environmental and host stress factors that require an appropriate response to survive. However, the stress tolerance mechanisms used by F. tularensis to persist are not fully understood. To address this aspect, we evaluated the highly conserved u niversal s tress p rotein (Usp) that is encoded by a single-copy gene in F. tularensis , unlike the majority of other bacterial pathogens that produce several to many Usp homologs. We determined that the F. tularensis Usp transcript is unusually stable with a half-life of over 30 minutes, and that usp transcript and protein levels remained abundant when exposed to low pH, nutrient deprivation, hydrogen peroxide, and paraquat. Of these and other stress conditions evaluated, the F. tularensis Δ usp mutant only exhibited reduced survival relative to the wild type during stationary phase and exposure to paraquat, a highly toxic compound that generates superoxide anions and other free radicals. Comparison of transcript levels in untreated and paraquat-treated F. tularensis wild type and Δ usp indicated that Usp contributes to enhanced expression of antioxidant defense genes, oxyR and katG . In summary, the high abundance and stability of Usp provide prompt protection during extended periods of growth arrest and free radical exposure, promoting F. tularensis persistence. We propose that F. tularensis Usp contributes to an adaptive response that prolongs viability and increases the longevity of this zoonotic pathogen in the environment., Importance: Francisella tularensis is classified as a Tier 1 select agent due to the low infectious dose, ease of transmission, and potential use as a bioweapon. To better understand the stress defense mechanisms that contribute to the ability of this highly virulent pathogen to persist, we evaluated the conserved F. tularensis u niversal s tress p rotein (Usp). We show that F. tularensis Usp is unusually stable and remains abundant, regardless of the stress conditions tested, differing from other bacterial Usp homologs. We also determined that F. tularensis Usp enhances the expression of several critical antioxidant defense genes and increases survival during paraquat exposure and growth arrest. Determining the factors that promote F. tularensis persistence in the environment is needed to prevent tularemia transmission., Competing Interests: The authors declare no conflict of interest.

Objective: To investigate the disposition of enrofloxacin and its active metabolite, ciprofloxacin, in plasma, pulmonary epithelial lining fluid (PELF), peritoneal fluid, and CSF in horses following IV administration of enrofloxacin at doses of 5 mg/kg and 7.5 mg/kg of body weight., Methods: 6 healthy, mature mares were randomly assigned to receive a single dose of enrofloxacin at either 5 mg/kg or 7.5 mg/kg in a crossover design with a washout period of 10 days. Concentrations of enrofloxacin and ciprofloxacin were determined in plasma, PELF, peritoneal fluid, and CSF., Results: Both doses of enrofloxacin were generally well tolerated. One horse developed focal, self-limiting limb edema. The median maximum concentration extrapolated to time 0 and area under the plasma concentration-versus-time curve from time 0 to the last quantifiable time point (24 hours) for enrofloxacin in plasma were significantly greater when horses were given enrofloxacin at 7.5 mg/kg. Similarly, the median elimination rate constant, half-life of the terminal phase, peak serum concentration (Cmax), area under the plasma concentration-versus-time curve from time 0 to the last quantifiable time point (24 hours), area under the plasma concentration-versus-time curve extrapolated to infinity, and mean residence time for ciprofloxacin in plasma were significantly greater following administration of enrofloxacin at 7.5 mg/kg. There were no significant differences between doses in any of the measured pharmacokinetic variables in PELF., Conclusions: There was no apparent pharmacokinetic advantage of enrofloxacin at the 7.5-mg/kg dose for susceptible isolates; however, this dose achieved higher concentrations and prolonged persistence in fluid matrices. Further studies are required to evaluate repeated administration at this dose for tolerability and clinical efficacy., Clinical Relevance: Despite the wide use of enrofloxacin in horses, pharmacokinetic data is limited. This study provides pharmacokinetic data that can be used in a clinical setting.

Introduction: Clinical trials provide meaningful data regarding the safety and efficacy of novel therapies but there is often a lag between the time of new drug approval and information on posttreatment clinical outcomes in real-world practice. This study evaluated clinical outcomes in a large real-world population of patients with relapsed and/or refractory large B-cell lymphoma (r/r LBCL) treated with chemoimmunotherapy or novel therapies in second or later lines of therapy (2L+)., Materials and Methods: Data from the Lymphoma Epidemiology of Outcomes (LEO) Consortium of Real-World Evidence (CReWE) cohort (1/1/2015-2/15/2023) were analyzed. Patients' demographic and clinical characteristics were described and response rates, duration of response, progression-free survival, and overall survival were evaluated. Multivariable Cox proportional hazards regression models were used to assess associations between patient clinical characteristics and outcomes., Results: The 2L+ cohort included patients treated with chemoimmunotherapy (N = 593), lenalidomide-based therapy (n = 60), polatuzumab vedotin-based therapy (N = 116), tafasitamab-based therapy (N = 55), and loncastuximab tesirine (N = 42). Most patients who received prior chimeric antigen receptor T-cell therapy (CAR-T) were refractory to the treatment. Across all patients, overall response rates were <50%, with one-quarter achieving complete response and median duration of response and overall survival were short (<6 and <10 months, respectively) among patients treated with chemoimmunotherapy or novel therapies. The prognosis was worse for patients who had previously received CAR-T. Primary refractory status, high-risk disease, and failing 3 or more lines of therapy were significantly associated with worse outcomes., Conclusion: Patients with r/r LBCL have unfavorable outcomes and need more effective treatment alternatives., Competing Interests: Disclosure LJN has received honoraria for participating in the advisory boards of AbbVie, AstraZeneca, BMS, Genentech, Genmab, Gilead/Kite, Incyte, Ipsen, Janssen, Merck, Novartis, Regeneron, and Takeda; and research support from BMS, Caribou Biosciences, Genentech, Genmab, Gilead/Kite, IGM Biosciences, Janssen, Merck, Novartis, and Takeda. YW has received research funding (to his institution) from AbbVie, Eli Lilly, Genentech, Genmab, Incyte, InnoCare, LOXO Oncology, MorphoSys, and Novartis; compensation (to his institution) for serving on the advisory boards of AstraZeneca, BeiGene, Eli Lilly, Genmab, Incyte, InnoCare, Jansen, Kite, LOXO Oncology, and TG Therapeutics; compensation (to his institution) for providing consultancy services to AbbVie and Innocare; and honoraria (to his institution) from Kite. TMH is on the Data Monitoring Committees of Eli Lilly & Company and Seagen; and has received research funding (to his institution) from Genentech/Roche, Genmab, and Sorrento. DC has received honoraria from Beigene and Ono, and research funding from BMS, Genmab, Ipsen, Morphosys, and Ono. BSK has served as a consultant for ADC Therapeutics, Celgene/BMS, and Genentech/Roche. BKL has received compensation from Genentech/Roche and MEI Inc. for Data Safety Monitoring Board participation, and for participating in the advisory board of Genentech/Roche; and has received research funding from AstraZenenca, Genentech/Roche, and Genmab. JLK has received honoraria for providing consultancy services to or compensation for participating in the advisory boards of AbbVie and Beigene; and research support from Viracta Therapeutics. JBC has served as an advisor to ADCT, AstraZeneca, Beigene, Janssen, Kite/Gilead, and Loxo/Lilly; and has received research funding from AstraZeneca, BMS/Celgene, Genentech, Loxo/Lilly, Novartis, and Takeda. PM has served as a consultant for AbbVie, AstraZeneca, Beigene, Daiichi Sankyo, Epizyme, Genentech, Janssen, and Merck. ISL is a current employee of the University of Miami; has received honoraria from Adaptive; has served in a consulting or advisory role for Lymphoma Research Foundation; has received research funding from the National Cancer Institute; and has received compensation for teaching from Kyowa Kirin. CC has served as consultant for and has received honoraria from AbbVie, BMS, Genentech, and Mashup Media; has received research funding from Genentech, Genmab, and Gilead; and has had leadership roles in Follicular Lymphoma Cures Foundation and American Society of Hematology. SA has received research funding (to his instituition) from AstraZeneca, Beigene, Genentech, Genmab, and Regeneron; has served on the Speakers Bureau for Genentech and Total CME; and has acted as a consultant/advisor for Abbvie, ADC Therapeutics, Beigene, Fate Therapeutics, Genentech, and Seattle Genetics. MAL has received compensation from Genmab and GNE. MJM has received research funding from BMS, Genmab, and Roche/Genentech; is on the advisory board of AstraZeneca; and has received compensation (to his institution) for providing consultancy services to BMS. LH, CG, RR, and MSD are employees of Analysis Group Inc., which provided paid consultancy services to Genmab, the study sponsor. AM, TW, MJ, and AK are current employees of Genmab and hold stock options. AW and RK are current employees of AbbVie and hold stock options. CRF has served as a consultant for AbbVie, Bayer, BeiGene, Celgene, Denovo Biopharma, Foresight Diagnostics, Genentech/Roche, Genmab, Gilead, Karyopharm, N-Power Medicine, Pharmacyclics/Janssen, SeaGen, and Spectrum; holds stock or stock options for Foresight Diagnostics and N-Power Medicine; and has received research funding from 4D, AbbVie, Acerta, Adaptimmune, Allogene, Amgen, Bayer, BostonGene, Celgene, Cellectis EMD, Gilead, Genentech/Roche, Guardant, Iovance, Janssen Pharmaceutical, Kite, Morphosys, Nektar, Novartis, Pfizer, Pharmacyclics, Sanofi, Takeda, TG Therapeutics, Xencor, and Ziopharm as well as Burroughs Wellcome Fund, Cancer Prevention and Research Institute of Texas RR190079: CPRIT Scholar in Cancer Research; Eastern Cooperative Oncology Group, National Cancer Institute, and V Foundation. All the other authors declared that they have no conflicts of interest to declare., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Objective: There are limited data on the reproductive health of women with vasculitis. This study used a prospective, international vasculitis pregnancy registry to survey women during and after pregnancy., Methods: The Vasculitis Pregnancy Registry (VPREG) is imbedded within the Vasculitis Patient-Powered Research Network, an international online research infrastructure. Any pregnant woman with a diagnosis of vasculitis can self-enroll. After enrollment, women are invited to complete online surveys at study entry, once per trimester, and postpartum. Descriptive statistics are reported here., Results: Between 2015 and 2022, 147 women with 149 pregnancies enrolled in VPREG from 16 countries. Data on 78 pregnancies with known outcomes were included in this analysis. During pregnancy, women on average experienced low levels of pain related to vasculitis (scale 0-10, median 2 [IQR 1-5]) and preserved feelings of wellness (scale 0-10, median 3 [IQR 1-5]). Thirty-six percent of women reported their vasculitis was active during pregnancy. Of the 14 women requiring hospitalization during pregnancy outside of delivery, 4 cited active vasculitis as the indication. Most women (54/73, 74%) were prescribed medications for vasculitis during pregnancy. Seventy-six (97%) pregnancies resulted in live births, with 64% delivering vaginally and 21% experiencing a preterm delivery., Conclusion: These results demonstrate that most women with vasculitis can experience pregnancies that result in live births delivered at term. During pregnancy, a minority of women reported flares of vasculitis or the need for hospitalization due to vasculitis. These data are useful to rheumatologists and patients to inform and facilitate discussions about reproductive health and vasculitis., (Copyright © 2024 by the Journal of Rheumatology.)

Recombinant Francisella tularensis universal stress protein with a C-terminal histidine-tag (rUsp/His6) was expressed in Escherichia coli. Endogenous F. tularensis Usp has a predicted molecular mass of 30 kDa, but rUsp/His6 had an apparent molecular weight of 33 kDa based on Western blot analyses. To determine the source of the higher molecular weight for rUsp/His6, post translational modifications were examined. Tryptic peptides of purified rUsp/His6 were subjected to liquid chromatography tandem mass spectrometry (LC-MS/MS) and fragmentation spectra were searched for acetylated lysines and polyaminated glutamines. Of the 24 lysines in rUsp/His6, 10 were acetylated (K63, K68, K72, K129, K175, K201, K208, K212, K233, and K238) and three of the four glutamines had putrescine, spermidine and spermine adducts (Q55, Q60 and Q267). The level of post-translational modification was substoichiometric, eliminating the possibility that these modifications were the sole contributor to the 3 kDa extra mass of rUsp/His6. LC-MS/MS revealed that stop codon readthrough had occurred resulting in the unexpected addition of 20 extra amino acids at the C-terminus of rUsp/His6, after the histidine tag. Further, the finding of polyaminated glutamines in rUsp/His6 indicated that E. coli is capable of transglutaminase activity., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Girardo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Bacterial and mammalian cells are rich in putrescine, spermidine, and spermine. Polyamines are required for optimum fitness, but the biological function of these small aliphatic compounds has only been partially revealed. Known functions of polyamines include interaction with nucleic acids that alters gene expression and with proteins that modulate activity. Although polyamines can be incorporated into proteins, very few naturally occurring polyaminated proteins have been identified, which is due in part to the difficulty in detecting these adducts. In the current study, bovine albumin and the recombinant universal stress protein from Francisella tularensis were used as models for mass spectrometry analysis of polyaminated proteins. The proteins were covalently bound to putrescine, spermidine, or spermine by the action of carbodiimide or microbial transglutaminase. Tryptic peptides, subjected to liquid chromatography tandem mass spectrometry (LC-MS/MS), were identified using Protein Prospector software. We describe the search parameters for identifying polyaminated peptides and show MS/MS spectra for adducts with putrescine, spermidine, and spermine. Manual evaluation led us to recognize signature ions for polyamine adducts on aspartate, glutamate, and glutamine, as well as neutral loss from putrescine, spermidine, and spermine during the fragmentation process. Mechanisms for the formation of signature ions and neutral loss are presented. Manual evaluation identified a false-positive adduct that had formed during trypsinolysis and resulted in peptide sequence rearrangement. Another false positive initially appeared to be a 71 kDa putrescine adduct on a cysteine residue. However, it was an acrylamide adduct on cysteine for a sample extracted from a polyacrylamide gel. The information presented in this report provides guidance and serves as a model for identifying naturally occurring polyaminated proteins., Competing Interests: The authors declare that they have no conflicts of interest., (Copyright © 2024 Lawrence M. Schopfer et al.)

Objective: To evaluate the relative prevalence of 8 rheumatic and musculoskeletal diseases (RMDs) across racial and ethnic groups within the National Patient-Centered Clinical Research Network (PCORnet)., Methods: Electronic health records from participating PCORnet institutions and systems from January 1, 2013, to December 31, 2018, were used to identify adult patients with ≥ 2 diagnosis codes for rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), osteoporosis (OP), granulomatosis with polyangiitis (GPA), microscopic polyangiitis (MPA), eosinophilic granulomatosis with polyangiitis (EGPA), giant cell arteritis (GCA), and Takayasu arteritis (TAK). Among those with race and ethnicity data available, we compared prevalence of RMDs by race and ethnicity., Results: Data from 28,059,546 patients were available for analysis. RA was more common in patients who were American Indian or Alaska Native vs White, with a prevalence of 11.57 vs 10.11/1000 (odds ratio [OR] 1.15, 95% CI 1.09-1.22). SLE was more common in patients who were Black or African American (6.73/1000), American Indian or Alaska Native (3.82/1000), and Asian (3.39/1000) vs White (2.80/1000; OR 2.43, 95% CI 2.39-2.46; OR 1.39, 95% CI 1.25-1.53; OR 1.26, 95% CI 1.21-1.31, respectively). SLE was more common in patients who were Hispanic vs non-Hispanic (prevalence 3.93 vs 3.45/1000, OR 1.14, 95% CI 1.12-1.16). TAK was more common in patients who were Asian vs White (prevalence 0.05 vs 0.04/1000, OR 1.43, 95% CI 1.00-2.03). OP, RA, and the vasculitides were all more common in patients who were White vs Black or African American., Conclusion: These data provide important information on the prevalence of RMDs by race and ethnicity in the United States. PCORnet can be used as a reliable data source to study RMDs within a large representative population., (Copyright © 2023 by the Journal of Rheumatology.)

Introduction: Surgical site infections are common postoperative complications. Some operating rooms have open-floor drainage systems for fluid disposal during endourologic cases, although nonendoscopy cases are not always allowed in these rooms. We hypothesized that operating rooms with open-floor drainage systems would not materially affect risk of surgical site infections for patients undergoing open and laparoscopic procedures., Methods: Patients who had surgical site infections from 2016 through 2020 were identified from data of the National Surgical Quality Improvement Program. Patients without surgical incisions, with open wounds, and with surgical site infections at surgery were excluded. The primary outcome was surgical site infection occurrence within 30 days of surgery. Multilevel multivariable logistic regression was used to estimate the observed-to-expected surgical site infection ratio for each operating room (2 with and 23 without open-floor drainage systems)., Results: We identified 8,419 surgical cases, of which 802 (9.5%) were performed in operating rooms with open-floor drainage systems; 166 patients (2.0%) had surgical site infections. Of the surgical site infections, 7 (4.2%) occurred in operating rooms with open-floor drainage systems. Surgical specialty, American Society of Anesthesiologists physical status, higher case acuity, dyspnea, immunosuppression, longer surgical duration, and wound classification were associated with surgical site infections ( P < .05 for all). The observed-to-expected ratios of surgical site infections occurring in the 2 operating rooms with open-floor drainage systems were 0.85 and 1.15. The odds ratio of surgical site infections for urologic cases performed in room with vs without open-floor drainage systems was 1.30 ( P = .65)., Conclusions: Urology operating room designs often include open-floor drainage systems for water-based cases. These drainage systems were not associated with an increased risk of surgical site infections.

Understanding the contributions of mitochondrial genetics to disease pathogenesis is facilitated by a new and unique model-the mitochondrial-nuclear exchange mouse. Here we report the rationale for their development, the methods used to create them, and a brief summary of how MNX mice have been used to understand the contributions of mitochondrial DNA in multiple diseases, focusing on cancer metastasis. Polymorphisms in mtDNA which distinguish mouse strains exert intrinsic and extrinsic effects on metastasis efficiency by altering epigenetic marks in the nuclear genome, changing production of reactive oxygen species, altering the microbiota, and influencing immune responses to cancer cells. Although the focus of this report is cancer metastasis, MNX mice have proven to be valuable in studying mitochondrial contributions to other diseases as well., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Francisella tularensis is a highly infectious zoonotic pathogen with as few as 10 organisms causing tularemia, a disease that is fatal if untreated. Although F. tularensis subspecies tularensis (type A) and subspecies holarctica (type B) share over 99.5% average nucleotide identity, notable differences exist in genomic organization and pathogenicity. The type A clade has been further divided into subtypes A.I and A.II, with A.I strains being recognized as some of the most virulent bacterial pathogens known. In this study, we report on major disparities that exist between the F. tularensis subpopulations in arginine catabolism and subsequent polyamine biosynthesis. The genes involved in these pathways include the speHEA and aguAB operons, along with metK . In the hypervirulent F. tularensis A.I clade, such as the A.I prototype strain SCHU S4, these genes were found to be intact and highly transcribed. In contrast, both subtype A.II and type B strains have a truncated speA gene, while the type B clade also has a disrupted aguA and truncated aguB . Ablation of the chromosomal speE gene that encodes a spermidine synthase reduced subtype A.I SCHU S4 growth rate, whereas the growth rate of type B LVS was enhanced. These results demonstrate that spermine synthase SpeE promotes faster replication in the F. tularensis A.I clade, whereas type B strains do not rely on this enzyme for in vitro fitness. Our ongoing studies on amino acid and polyamine flux within hypervirulent A.I strains should provide a better understanding of the factors that contribute to F. tularensis pathogenicity., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Yue, Puniya, Helikar, Girardo, Hinrichs and Larson.)

Francisella tularensis can cause the zoonotic disease tularemia and is partitioned into subspecies due to differences in chromosomal organization and virulence. The subspecies holarctica (type B) is generally considered more clonal than the other subpopulations with moderate virulence compared to the hypervirulent A.I clade. We performed whole genome sequencing (WGS) on six type B strains isolated from the blood of patients with tularemia within a one-year period from the same United States region, to better understand the associated pathogenicity. The WGS data were compared to the prototype strain for this subspecies, specifically FSC200, which was isolated from a patient with tularemia in Europe. These findings revealed 520-528 single nucleotide polymorphisms (SNPs) between the six United States type B strains compared to FSC200, with slightly higher A+T content in the latter strain. In contrast, comparisons between the six type B isolates showed that five of the six type B isolates had only 4-22 SNPs, while one of the strains had 47-53 SNPs. Analysis of SNPs in the core genome for the six United States type B isolates and the FSC200 strain gave similar results, suggesting that some of these mutations may have been nonsynonymous, resulting in altered protein function and pathogenicity.

The highly infectious and zoonotic pathogen Francisella tularensis is the etiologic agent of tularemia, a potentially fatal disease if untreated. Despite the high average nucleotide identity, which is >99.2% for the virulent subspecies and >98% for all four subspecies, including the opportunistic microbe Francisella tularensis subsp. novicida , there are considerable differences in genetic organization. These chromosomal disparities contribute to the substantial differences in virulence observed between the various F. tularensis subspecies and subtypes. The methods currently available to genotype F. tularensis cannot conclusively identify the associated subpopulation without using time-consuming testing or complex scoring matrices. To address this need, we developed both single and multiplex quantitative real-time PCR (qPCR) assays that can accurately detect and identify the hypervirulent F. tularensis subsp. tularensis subtype A.I, the virulent F. tularensis subsp. tularensis subtype A.II, F. tularensis subsp. holarctica (also referred to as type B), and F. tularensis subsp. mediasiatica , as well as opportunistic F. tularensis subsp. novicida from each other and near neighbors, such as Francisella philomiragia , Francisella persica , and Francisella -like endosymbionts found in ticks. These fluorescence-based singleplex and non-matrix scoring multiplex qPCR assays utilize a hydrolysis probe, providing sensitive and specific F. tularensis subspecies and subtype identification in a rapid manner. Furthermore, sequencing of the amplified F. tularensis targets provides clade confirmation and informative strain-specific details. Application of these qPCR- and sequencing-based detection assays will provide an improved capability for molecular typing and clinical diagnostics, as well as facilitate the accurate identification and differentiation of F. tularensis subpopulations during epidemiological investigations of tularemia source outbreaks., (Copyright © 2020 Larson et al.)

Embryo transfer surgery is an essential step in the process of generating gene-modified mice, regardless of whether the embryos were modified by DNA, RNA CRISPR components, or embryonic stem cells, or whether they were microinjected or electroporated. Transfer is also a necessary step for assisted reproductive techniques such as rederivation and reanimation by in vitro fertilization. The manipulated embryos must be returned to the reproductive tract of a pseudopregnant recipient female mouse, wherein the transplanted embryos develop to term. Embryos may be transferred to either the oviduct or uterine horn, depending upon the developmental status of the embryos and the stage of the recipient. This chapter will describe the process of transferring embryos surgically to a recipient female.

Generating a transgenic or gene-modified mouse requires the introduction of exogenous reagents into an early-stage embryo. The mouse one-cell embryo or zygote possesses two pronuclei, representing the genetic contribution of the sperm and oocyte. Traditional transgenic mice are generated by injecting a DNA solution containing a purified transgene construct into the male pronucleus, generally the larger of the two pronuclei. Similarly, gene-editing reagents such as ZFNs, TALENs, and CRISPR RNAs are introduced into zygotes in the same manner, making this technique applicable to a wide variety of projects. This chapter presents the procedures for pronuclear microinjection.

The ability to delete the function of an endogenous gene in the mouse was made possible by the development of embryonic stem (ES) cells, pluripotent cells that retain the ability to develop into all tissues of a developing embryo. The ability to genetically modify these cells followed, allowing targeted mutation of ES cells in vitro and the deletion of specific gene function. However, regardless of the simplicity or complexity of the genetic modification, all ES cells require injection into host embryos to establish pregnancies and result in chimeric mice. Blastocysts are commonly used as the host embryos for this purpose, as it is relatively easy to inject cells into the blastocoel cavity of the developing embryo. This chapter describes the procedure for injection of ES cells into blastocyst stage embryos for the generation of knockout mice.

The CRISPR/Cas9 system has enjoyed enormous success and has now become the standard method of generating gene-modified mouse models. The tools for predicting the activity of CRISPR reagents in the mouse embryo are currently limited and not particularly accurate in predicting if a given reagent will be active. Given the time and cost of generating genetically modified mice, it is highly desirable to use CRISPR reagents that are known to be active in the mouse embryo. In this chapter, we provide a detailed procedure for empirically testing the activity of CRISPR reagents via electroporation into cultured preimplantation mouse embryos. This platform has proven to be rapid, efficient, and applicable to a variety of mouse strains, and can be used for assessing on- and off-target activity through a variety of molecular assays.

Vaccination is the most effective intervention to prevent influenza and control the spread of the virus. Alternatives are needed to the traditional egg-based vaccine strategy for a more rapid response to new outbreaks. Two different hemagglutinin (HA) fragments (rHA1 1-326 and rHA1 53-269 ) derived from influenza A virus subtype H1N1 were expressed in Escherichia coli and characterized by immunoblot, gel filtration, hemagglutination, and competitive binding assays. rHA1 1-326 included neutralizing epitopes and the trimerization domain, whereas rHA1 53-269 included only the head of HA with the neutralizing epitopes. Mice were immunized with rHA1 1-326 or rHA1 53-269 , and sera were tested for the presence of neutralizing antibodies. Mice were then challenged with H1N1 and infection severity was monitored. rHA1 1-326 trimerized, whereas rHA1 53-269 was unable to form oligomers. Both rHA1 1-326 and rHA1 53-269 elicited the production of neutralizing antibodies, but only oligomerized rHA1 1-326 protected against live virus challenges in mice. This study demonstrated that bacterially expressed HA was capable of folding properly and eliciting the production of neutralizing antibodies, and that HA oligomerization contributed to protection against viral challenge. Therefore, prokaryotic-derived vaccine platforms can provide antigenic and structural requirements for viral protection, as well as allow for the rapid and cost-effective incorporation of multiple antigens for broader protection.

CCN5/WISP-2 is an anti-invasive molecule and prevents breast cancer (BC) progression. However, it is not well understood how CCN5 prevents invasive phenotypes of BC cells. CCN5 protein expression is detected in estrogen receptor-α (ER-α) -positive normal breast epithelial cells as well as BC cells, which are weakly invasive and rarely metastasize depending on the functional status of ER-α. A unique molecular relation between CCN5 and ER-α has been established as the components of the same signaling pathway that coordinate some essential signals associated with the proliferation as well as delaying the disease progression from a non-invasive to invasive phenotypes. Given the importance of this connection, we determined the role of CCN5 in regulation of ER-α in different cellular settings and their functional relationship. In a genetically engineered mouse model, induced expression of CCN5 in the mammary ductal epithelial cells by doxycycline promotes ER-α expression. Similarly, CCN5 regulates ER-α expression and activity in normal and neoplastic breast cells, as documented in various in vitro settings such as mouse mammary gland culture, human mammary epithelial cell and different BC cell cultures in the presence or absence of human recombinant CCN5 (hrCCN5) protein. Mechanistically, at least in the BC cells, CCN5 is sufficient to induce ER-α expression at the transcription level via interacting with integrins-α6β1 and suppressing Akt followed by activation of FOXO3a. Moreover, in vitro and in vivo functional assays indicate that CCN5 treatment promotes response to tamoxifen in triple-negative BC (TNBC) cells possibly via restoring ER-α. Collectively, these studies implicates that the combination treatments of CCN5 (via activation of CCN5 or hrCCN5 treatment) and tamoxifen as potential therapies for TNBC.

DNA replication is an essential and conserved process in all domains of life and may serve as a target for the development of new antimicrobials. However, such developments are hindered by subtle mechanistic differences and limited understanding of DNA replication in pathogenic microorganisms. Clostridium difficile is the main cause of healthcare-associated diarrhoea and its DNA replication machinery is virtually uncharacterized. We identify and characterize the mechanistic details of the putative replicative helicase (CD3657), helicase-loader ATPase (CD3654) and primase (CD1454) of C. difficile, and reconstitute helicase and primase activities in vitro We demonstrate a direct and ATP-dependent interaction between the helicase loader and the helicase. Furthermore, we find that helicase activity is dependent on the presence of primase in vitro The inherent trinucleotide specificity of primase is determined by a single lysine residue and is similar to the primase of the extreme thermophile Aquifex aeolicus. However, the presence of helicase allows more efficient de novo synthesis of RNA primers from non-preferred trinucleotides. Thus, loader-helicase-primase interactions, which crucially mediate helicase loading and activation during DNA replication in all organisms, differ critically in C. difficile from that of the well-studied Gram-positive Bacillus subtilis model., (© 2016 The Authors.)

DNA-dependent RNA primase is essential for de novo primer synthesis during DNA replication in all living organisms. Bacterial DnaG primase is an attractive target for inhibition because it is essential, low in copy number and structurally distinct from eukaryotic and archaeal primases. DnaG primase is sensitive to known inhibitors including suramin and doxorubicin. Recently, tilorone was discovered by high throughput screening to be an inhibitor of Bacillus anthracis primase DnaG but it failed to reduce the growth of B. anthracis in vitro. In this study we determined that tilorone also inhibited DnaG primase from Staphylococcus aureus. C2-Symmetric fluorenone-based compounds, similar to tilorone chemical structure were synthesized and tested to identify potential lead compounds that inhibit bacterial growth in B. anthracis, MRSA and Burkholderia thailandensis. These compounds were evaluated by determining the minimum inhibitory concentration (MIC) against several different bacterial species which demonstrated 17.5 and 16 μg/ml MIC profiles. Importantly, some of the fluorenone-based compounds with a long carbon chain showed a relatively low MIC against B. anthracis, S. aureus, MRSA, Francisella tularensis, and B. thailandensis, suggesting it may be a promising lead compound., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

The kinetic chromogenic endotoxin assay measures the release of p-nitroaniline from the chromogenic peptide substrate Ac-IEAR-pNA. As part of our project to purify large quantities of human butyrylcholinesterase (HuBChE), we evaluated pure HuBChE for endotoxin levels. We found that HuBChE contributed up to 90% of the yellow p-nitroaniline product in a standard endotoxin assay through the catalytic hydrolysis of Ac-IEAR-pNA with a rate constant of 0.016 min(-1) and a Km of 2.9 mM in potassium phosphate buffer pH 7.0 at 24 °C. Thus, endotoxin concentrations for native BChE are artificially high in the kinetic chromogenic assay. Destruction of HuBChE catalytic activity by boiling yields endotoxin concentrations that more accurately reflect the endotoxin concentration in purified HuBChE preparations., (Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.)

The taxonomic status of the bacterium Wolbachia persica is described, and based on the evidence presented, transfer of this species to the genus Francisella as Francisella persica comb. nov. is proposed. This reclassification is supported by data generated from genomic comparisons of W. persica ATCC VR-331T ( = FSC845T = DSM 101678T) to other near neighbours, including Francisella tularensis subsp. novicida. The full-length 16S rRNA gene sequence of strain ATCC VR-331T had 98.5 % nucleotide identity to the cognate gene in F. tularensis, with the highest similarity to subspecies novicida. Phylogenetic trees of full-length 16S rRNA gene, gyrA and recA sequences from species of the genera Wolbachia (class Alphaproteobacteria) and Francisella (class Gammaproteobacteria) indicated that W. persica ATCC VR-331T was most closely related to members of the genus Francisella and not Wolbachia. Local collinear blocks within the chromosome of strain ATCC VR-331T had considerable similarity with F. tularensis subsp. novicida, but not with any Wolbachia strain. The genomes of strain ATCC VR-331T and F. tularensis subsp. novicida Utah 112T ( = ATCC 15482T) contained an average nucleotide identity mean of 88.72 % and median of 89.18 %. Importantly, the genome of strain ATCC VR-331T contained one Francisella Pathogenicity Island, similar to F. tularensis subsp. novicida, as well as the Francisella-specific gene fopA1 and F. tularensis-specific genes fopA2 and lpnA (also referred to as tul4). In contrast to the obligate intracellular genus Wolbachia, strain ATCC VR-331T and facultative intracellular Francisella can replicate in specialized cell-free media. Collectively, these results demonstrate that Wolbachia persica should be reclassified in the genus Francisella as Francisella persica comb. nov. The type strain of Francisella persica comb. nov. is ATCC VR-331T ( = FSC845T = DSM 101678T). An emended description of the family Francisellaceae is also provided.

Introduction: Menaquinone is used for transporting electrons and is essential for the aerobic and anaerobic respiratory systems of all pathogens and prokaryotes. Many Gram-positive bacteria use only menaquinone in the electron transport system. Thus, menaquinone biosynthesis is a potential target for the development of inhibitors against bacteria including drug-resistant pathogens., Results: After modeling, synthesis and in vitro testing, we determined that 7-methoxy-2-naphthol-based inhibitors targeted the MenA enzyme of the menaquinone biosynthesis pathway. The developmental compounds 1 and 2 were active against Mycobacterium tuberculosis and methicillin-resistant Staphylococcus aureus with a minimal inhibitory concentration of 3-5 μg/ml., Conclusion: Nontraditional bicyclic inhibitors, compounds 1 and 2 could serve as lead compounds for the development of an antimicrobial agent, with activities against M. tuberculosis and methicillin-resistant S. aureus.

Although Francisella tularensis is considered a monomorphic intracellular pathogen, molecular genotyping and virulence studies have demonstrated important differences within the tularensis subspecies (type A). To evaluate genetic variation within type A strains, sequencing and assembly of a new subtype A.II genome was achieved for comparison to other completed F. tularensis type A genomes. In contrast with the F. tularensis A.I strains (SCHU S4, FSC198, NE061598, and TI0902), substantial genomic variation was observed between the newly sequenced F. tularensis A.II strain (WY-00W4114) and the only other publically available A.II strain (WY96-3418). Genome differences between WY-00W4114 and WY96-3418 included three major chromosomal translocations, 1580 indels, and 286 nucleotide substitutions of which 159 were observed in predicted open reading frames and 127 were located in intergenic regions. The majority of WY-00W4114 nucleotide deletions occurred in intergenic regions, whereas most of the insertions and substitutions occurred in predicted genes. Of the nucleotide substitutions, 48 (30%) were synonymous and 111 (70%) were nonsynonymous. WY-00W4114 and WY96-3418 nucleotide polymorphisms were predominantly G/C to A/T allelic mutations, with WY-00W4114 having more A+T enrichment. In addition, the A.II genomes contained a considerably higher number of intact genes and longer repetitive sequences, including transposon remnants than the A.I genomes. Together these findings support the premise that F. tularensis A.II may have a fitness advantage compared to the A.I subtype due to the higher abundance of functional genes and repeated chromosomal sequences. A better understanding of the selective forces driving F. tularensis genetic diversity and plasticity is needed.

Tularemia in the United States was examined by reviewing 106 Francisella tularensis isolates, mostly from Nebraska, collected during 1998-2012: 48% of Nebraska cases were cat-associated; 7/8 human cases were caused by subtype A.I. A vaccine is needed to reduce feline-associated tularemia, and cat owners should protect against bites/scratches and limit their pet's outdoor access.

Human BChE (butyrylcholinesterase) protects against the toxicity of organophosphorus nerve agents and pesticides. BChE purified from human plasma is limited and pathogen carry-over is a concern. Unlike the native BChE tetrameric complex with a residence time of days, rBChE (recombinant BChE) is produced predominantly as dimers and monomers that are cleared from the circulation within minutes. Assembly into tetramers requires incorporation of proline-rich peptides, a process that was thought to occur intracellularly. Our goal was to determine whether polyproline added to rBChE under cell-free conditions would promote tetramerization. Secreted rBChE was purified by procainamide affinity chromatography, and synthetic polyprolines (8-mer to 300-mer) were tested to determine their effect on tetramer assembly. These studies demonstrated that 90-98% of purified rBChE (65 μM) could be assembled into tetramers when incubated with synthetic 17-mer or 50-mer polyproline peptides (100 μM) for 1.5 h at 25°C. However, rBChE tetramerization was inefficient with smaller 8-mer polyproline peptides and larger 300-mer polyproline proteins. Collectively, these studies demonstrated that the eukaryotic cellular machinery is not required for assembly of active BChE into tetramers and that this process can occur in vitro with purified rBChE in the presence of peptides containing 15-50 consecutive proline residues.

Estrogens play pivotal roles in development and function of many organ systems, including the reproductive system. We have generated estrogen receptor 1 (Esr1)-knockout rats using zinc finger nuclease (ZFN) genome targeting. mRNAs encoding ZFNs targeted to exon 3 of Esr1 were microinjected into single-cell rat embryos and transferred to pseudopregnant recipients. Of 17 live births, 5 had biallelic and 1 had monoallelic Esr1 mutations. A founder with monoallelic mutations was backcrossed to a wild-type rat. Offspring possessed only wild-type Esr1 alleles or wild-type alleles and Esr1 alleles containing either 482 bp (Δ482) or 223 bp (Δ223) deletions, indicating mosaicism in the founder. These heterozygous mutants were bred for colony expansion, generation of homozygous mutants, and phenotypic characterization. The Δ482 Esr1 allele yielded altered transcript processing, including the absence of exon 3, aberrant splicing of exon 2 and 4, and a frameshift that generated premature stop codons located immediately after the codon for Thr157. ESR1 protein was not detected in homozygous Δ482 mutant uteri. ESR1 disruption affected sexually dimorphic postnatal growth patterns and serum levels of gonadotropins and sex steroid hormones. Both male and female Esr1-null rats were infertile. Esr1-null males had small testes with distended and dysplastic seminiferous tubules, whereas Esr1-null females possessed large polycystic ovaries, thread-like uteri, and poorly developed mammary glands. In addition, uteri of Esr1-null rats did not effectively respond to 17β-estradiol treatment, further demonstrating that the Δ482 Esr1 mutation created a null allele. This rat model provides a new experimental tool for investigating the pathophysiology of estrogen action.

Purpose: A comprehensive strategy was developed and validated for the identification of pathogens from closely related near neighbors using both chromosomal and protein biomarkers, with emphasis on distinguishing Yersinia pestis from the ancestral bacterium Yersinia pseudotuberculosis., Experimental Design: Computational analysis was used to discover chromosomal targets unique to Y. pestis. Locus identifier YPO1670 was selected for further validation and PCR was used to confirm that this biomarker was exclusively present in Y. pestis strains, while absent in other Yersinia species. RT-PCR and Western blot analyses were utilized to evaluate YPO1670 expression and MRM MS was performed to identify the YPO1670 protein within cell lysates., Results: The described study validated that YPO1670 was exclusive to Y. pestis. PCR confirmed the locus to be unique to Y. pestis. The associated transcript and protein were produced throughout growth with the highest abundance occurring in stationary phase and MRM MS conclusively identified the YPO1670 protein in cell extracts., Conclusions and Clinical Relevance: These findings validated YPO1670 as a reliable candidate biomarker for Y. pestis and that a dual DNA and protein targeting approach is feasible for the development of next-generation assays to accurately differentiate pathogens from near neighbors., (© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Bacillus subtilis has two replicative DNA polymerases. PolC is a processive high-fidelity replicative polymerase, while the error-prone DnaEBs extends RNA primers before hand-off to PolC at the lagging strand. We show that DnaEBs interacts with the replicative helicase DnaC and primase DnaG in a ternary complex. We characterize their activities and analyse the functional significance of their interactions using primase, helicase and primer extension assays, and a 'stripped down' reconstituted coupled assay to investigate the coordinated displacement of the parental duplex DNA at a replication fork, synthesis of RNA primers along the lagging strand and hand-off to DnaEBs. The DnaG-DnaEBs hand-off takes place after de novo polymerization of only two ribonucleotides by DnaG, and does not require other replication proteins. Furthermore, the fidelity of DnaEBs is improved by DnaC and DnaG, likely via allosteric effects induced by direct protein-protein interactions that lower the efficiency of nucleotide mis-incorporations and/or the efficiency of extension of mis-aligned primers in the catalytic site of DnaEBs. We conclude that de novo RNA primer synthesis by DnaG and initial primer extension by DnaEBs are carried out by a lagging strand-specific subcomplex comprising DnaG, DnaEBs and DnaC, which stimulates chromosomal replication with enhanced fidelity.

Premise of the Study: Polyploidization is a key factor involved in the diversification of plants. Although polyploids are commonly found, there remains controversy on the mechanisms that lead to their successful establishment. One major problem that has been identified is that newly formed polyploids lack mates of the appropriate ploidy level and may experience severely reduced fertility due to nonproductive intercytotype crosses. Niche differentiation has been proposed as a primary mechanism that can alleviate this reproductive disadvantage and facilitate polyploid establishment. Here we test whether the establishment of tetraploid cytotypes of Heuchera cylindrica (Saxifragaceae) is consistent with climatic niche differentiation. •, Methods: We use a combination of field surveys, flow cytometry and species distribution models to: (1) examine the distribution of diploid and tetraploid cytotypes; and (2) determine whether tetraploid Heuchera cylindrica occupy climates that differ from those of its diploid progenitors. •, Key Results: The geographic distributions of diploid and tetraploid cytotypes are largely allopatric as an extensive survey of 636 plants from 43 locations failed to detect any populations with both cytotypes. Although diploids and tetraploids occur in different geographic areas, polyploid Heuchera cylindrica occur almost exclusively in environments that are predicted to be suitable to diploid populations. •, Conclusions: Climatic niche differentiation does not explain the geographic distribution of tetraploid Heuchera cylindrica. We propose instead that tetraploid lineages were able to establish by taking advantage of glacial retreat and expanding into previously unoccupied sites.

We investigated the use of whole-genome mapping and pulsed-field gel electrophoresis (PFGE) with isolates from an outbreak of Salmonella enterica serotype Saintpaul. PFGE and whole-genome mapping were concordant with 22 of 23 isolates. Whole-genome mapping is a viable alternative tool for the epidemiological analysis of Salmonella food-borne disease investigations.

Tularemia is a potentially fatal disease that is caused by the highly infectious and zoonotic pathogen Francisella tularensis. Despite the monomorphic nature of sequenced F. tularensis genomes, there is a significant degree of plasticity in the organization of genetic elements. The observed variability in these genomes is due primarily to the transposition of direct repeats and insertion sequence (IS) elements. Since current methods used to genotype F. tularensis are time-consuming and require extensive laboratory resources, IS elements were investigated as a means to subtype this organism. The unique spatial location of specific IS elements provided the basis for the development of a differential IS amplification (DISA) assay to detect and distinguish the more virulent F. tularensis subsp. tularensis (subtypes A.I and A.II) and subsp. holarctica (type B) strains from F. tularensis subsp. novicida and other near neighbors, including Francisella philomiragia and Francisella-like endosymbionts found in ticks. Amplicon sizes and sequences derived from DISA showed heterogeneity within members of the subtype A.I and A.II isolates but not the type B strains. These differences were due to a 312-bp fragment derived from the IS element ISFtu1. Analysis of wild-type F. tularensis isolates by DISA correlated with pulsed-field gel electrophoresis genotyping utilizing two different restriction endonucleases and provided rapid results with minimal sample processing. The applicability of this molecular typing assay for environmental studies was demonstrated by the accurate identification and differentiation of tick-borne F. tularensis. The described approach to IS targeting and amplification provides new capability for epidemiological investigations and characterizations of tularemia source outbreaks.

Bacterial primase is stimulated by replicative helicase to produce RNA primers that are essential for DNA replication. To identify mechanisms regulating primase activity, we characterized primase initiation specificity and interactions with the replicative helicase for gram-positive Firmicutes (Staphylococcus, Bacillus and Geobacillus) and gram-negative Proteobacteria (Escherichia, Yersinia and Pseudomonas). Contributions of the primase zinc-binding domain, RNA polymerase domain and helicase-binding domain on de novo primer synthesis were determined using mutated, truncated, chimeric and wild-type primases. Key residues in the β4 strand of the primase zinc-binding domain defined class-associated trinucleotide recognition and substitution of these amino acids transferred specificity across classes. A change in template recognition provided functional evidence for interaction in trans between the zinc-binding domain and RNA polymerase domain of two separate primases. Helicase binding to the primase C-terminal helicase-binding domain modulated RNA primer length in a species-specific manner and productive interactions paralleled genetic relatedness. Results demonstrated that primase template specificity is conserved within a bacterial class, whereas the primase-helicase interaction has co-evolved within each species.

During DNA replication the helicase (DnaB) recruits the primase (DnaG) in the replisome to initiate the polymerization of new DNA strands. DnaB is attached to the tau subunit of the clamp-loader that loads the beta clamp and interconnects the core polymerases on the leading and lagging strands. The tau-DnaB-DnaG ternary complex is at the heart of the replisome and its function is likely to be modulated by a complex network of allosteric interactions. Using a stable ternary complex comprising the primase and helicase from Geobacillus stearothermophilus and the tau subunit of the clamp-loader from Bacillus subtilis we show that changes in the DnaB-tau interaction can stimulate allosterically primer synthesis by DnaG in vitro. The A550V tau mutant stimulates the primase activity more efficiently than the native protein. Truncation of the last 18 C-terminal residues of tau elicits a DnaG-stimulatory effect in vitro that appears to be suppressed in the native tau protein. Thus changes in the tau-DnaB interaction allosterically affect primer synthesis. Although these C-terminal residues of tau are not involved directly in the interaction with DnaB, they may act as a functional gateway for regulation of primer synthesis by tau-interacting components of the replisome through the tau-DnaB-DnaG pathway.