Magnetically Detected Protein Binding Using Spin-Labeled Slow Off-Rate Modified Aptamers.

Recent developments in aptamer chemistry open up opportunities for new tools for protein biosensing. In this work, we present an approach to use immobilized slow off-rate modified aptamers (SOMAmers) site-specifically labeled with a nitroxide radical via azide-alkyne click chemistry as a means for detecting protein binding. Protein binding induces a change in rotational mobility of the spin label, which is detected via solution-state electron paramagnetic resonance (EPR) spectroscopy. We demonstrate the workflow and test the protocol using the SOMAmer SL5 and its protein target, platelet-derived growth factor B (PDGF-BB). In a complete site scan of the nitroxide over the SOMAmer, we determine the rotational mobility of the spin label in the absence and presence of target protein. Several sites with sufficiently tight affinity and large rotational mobility change upon protein binding are identified. We then model a system where the spin-labeled SOMAmer assay is combined with fluorescence detection via diamond nitrogen-vacancy (NV) center relaxometry. The NV center spin-lattice relaxation time is modulated by the rotational mobility of a proximal spin label and thus responsive to SOMAmer-protein binding. The spin label-mediated assay provides a general approach for transducing protein binding events into magnetically detectable signals.

Assessment of adherence to aspirin for preeclampsia prophylaxis and reasons for nonadherence.

BACKGROUND: Preeclampsia is a hypertensive disease unique to pregnancy and has a significant impact on maternal and neonatal morbidity and mortality. Daily aspirin has been demonstrated to reduce the risk of preeclampsia. The American College of Obstetricians and Gynecologists recommends daily low-dose aspirin, ideally before 16 weeks' gestation, in at-risk patients for preeclampsia risk reduction. This study examined whether patients at-risk for preeclampsia by the American College of Obstetricians and Gynecologists criteria recalled aspirin recommendation and factors associated with treatment adherence. OBJECTIVE: This study examined whether patients at-risk for preeclampsia by the American College of Obstetricians and Gynecologists criteria recalled aspirin recommendation and factors associated with treatment adherence. STUDY DESIGN: This study used an anonymous written survey. Pregnant patients were asked to record self-reported risk factors and to recall recommendation to take aspirin for preeclampsia prophylaxis. Participants were then determined to be high-, moderate-, or low-risk on the basis of the American College of Obstetricians and Gynecologists guidelines. Self-reported adherence to recommendations and factors contributing to the patients' decisions to take or decline aspirin were assessed. Secondary outcomes included demographic characteristics of adherent patients and patients who did not recall aspirin recommendation. RESULTS: A total of 544 surveys were distributed and 500 were returned (91.9% response rate). Of the 104 high-risk pregnancies identified, aspirin was recommended in 60 (57.7%; 95% confidence interval, 0.48-0.67). Of the 269 patients with 2 or more moderate-risk factors, aspirin was recommended for 13 (4.8%; 95% confidence interval, 0.03-0.08). Among the participants who recalled aspirin recommendation, adherence was similar between high-risk (81.7%) and moderate-risk (76.9%) groups (P=.69). Patients with chronic hypertension, a history of preeclampsia or gestational hypertension in a previous pregnancy, and pregestational diabetes mellitus were most likely to report receiving aspirin recommendation (78.8%, 76.5%, 63.8%, and 53.3%, respectively). No high-risk factor was associated with a decreased likelihood of adherence. Nonadherent patients rarely discussed their decision with their medical provider (5.9%). In the 42.3% of high-risk participants who did not recall aspirin recommendation, autoimmune disease, multiple gestation, and kidney disease were the most prevalent risk factors (42.9%, 35.7%, and 25.0%, respectively). CONCLUSION: In the population studied, many at-risk patients, as defined by the American College of Obstetricians and Gynecologists criteria, did not recall recommendations to take aspirin for preeclampsia prophylaxis. This raises concerns for absent or ineffective counseling. Of the patients who recalled aspirin recommendation, most reported adherence, and a history of hypertensive disorders or preeclampsia, autoimmune disease, and pregestational diabetes mellitus were most often associated with adherence. There was no single factor most strongly associated with intentional nonadherence.

Discovery and Validation of a Six-Marker Serum Protein Signature for the Diagnosis of Active Pulmonary Tuberculosis.

New non-sputum biomarker tests for active tuberculosis (TB) diagnostics are of the highest priority for global TB control. We performed in-depth proteomic analysis using the 4,000-plex SOMAscan assay on 1,470 serum samples from seven countries where TB is endemic. All samples were from patients with symptoms and signs suggestive of active pulmonary TB that were systematically confirmed or ruled out for TB by culture and clinical follow-up. HIV coinfection was present in 34% of samples, and 25% were sputum smear negative. Serum protein biomarkers were identified by stability selection using L1-regularized logistic regression and by Kolmogorov-Smirnov (KS) statistics. A naive Bayes classifier using six host response markers (HR6 model), including SYWC, kallistatin, complement C9, gelsolin, testican-2, and aldolase C, performed well in a training set (area under the sensitivity-specificity curve [AUC] of 0.94) and in a blinded verification set (AUC of 0.92) to distinguish TB and non-TB samples. Differential expression was also highly significant (P < 10-20) for previously described TB markers, such as IP-10, LBP, FCG3B, and TSP4, and for many novel proteins not previously associated with TB. Proteins with the largest median fold changes were SAA (serum amyloid protein A), NPS-PLA2 (secreted phospholipase A2), and CA6 (carbonic anhydrase 6). Target product profiles (TPPs) for a non-sputum biomarker test to diagnose active TB for treatment initiation (TPP#1) and for a community-based triage or referral test (TPP#2) have been published by the WHO. With 90% sensitivity and 80% specificity, the HR6 model fell short of TPP#1 but reached TPP#2 performance criteria. In conclusion, we identified and validated a six-marker signature for active TB that warrants diagnostic development on a patient-near platform.

Potential of High-Affinity, Slow Off-Rate Modified Aptamer Reagents for Mycobacterium tuberculosis Proteins as Tools for Infection Models and Diagnostic Applications.

Direct pathogen detection in blood to diagnose active tuberculosis (TB) has been difficult due to low levels of circulating antigens or due to the lack of specific, high-affinity binding reagents and reliable assays with adequate sensitivity. We sought to determine whether slow off-rate modified aptamer (SOMAmer) reagents with subnanomolar affinity for Mycobacterium tuberculosis proteins (antigens 85A, 85B, 85C, GroES, GroEL2, DnaK, CFP10, KAD, CFP2, RplL, and Tpx) could be useful to diagnose tuberculosis. When incorporated into the multiplexed, array-based proteomic SOMAscan assay, limits of detection reached the subpicomolar range in 40% serum. Binding to native M. tuberculosis proteins was confirmed by using M. tuberculosis culture filtrate proteins and fractions from infected macrophages and via affinity capture assays and subsequent mass spectrometry. Comparison of serum from culture-positive pulmonary TB patients and TB suspects systematically ruled out for TB revealed small but statistically significant (P < 0.0001) differences in the median M. tuberculosis signals and in specific pathogen markers, such as antigen 85B. Samples where many M. tuberculosis aptamers produced high signals were rare exceptions. In concentrated, protein-normalized urine from TB patients and non-TB controls, the CFP10 (EsxB) SOMAmer yielded the most significant differential signals (P < 0.0276), particularly in TB patients with HIV coinfection. In conclusion, direct M. tuberculosis antigen detection proved difficult even with a sensitive method such as SOMAscan, likely due to their very low, subpicomolar abundance. The observed differences between cases and controls had limited diagnostic utility in serum and urine, but further evaluation of M. tuberculosis SOMAmers using other platforms and sample types is warranted.

The salt-sensitive structure and zinc inhibition of Borrelia burgdorferi protease BbHtrA.

HtrA serine proteases are highly conserved and essential ATP-independent proteases with chaperone activity. Bacteria express a variable number of HtrA homologues that contribute to the virulence and pathogenicity of bacterial pathogens. Lyme disease spirochetes possess a single HtrA protease homologue, Borrelia burgdorferi HtrA (BbHtrA). Previous studies established that, like the human orthologue HtrA1, BbHtrA is proteolytically active against numerous extracellular proteins in vitro. In this study, we utilized size exclusion chromatography and blue native polyacrylamide gel electrophoresis (BN-PAGE) to demonstrate BbHtrA oligomeric structures that were substrate independent and salt sensitive. Examination of the influence of transition metals on the activity of BbHtrA revealed that this protease is inhibited by Zn(2+) > Cu(2+) > Mn(2+). Extending this analysis to two other HtrA proteases, E. coli DegP and HtrA1, revealed that all three HtrA proteases were reversibly inhibited by ZnCl2 at all micro molar concentrations examined. Commercial inhibitors for HtrA proteases are not available and physiologic HtrA inhibitors are unknown. Our observation of conserved zinc inhibition of HtrA proteases will facilitate structural and functional studies of additional members of this important class of proteases.

Evaluation of Borrelia burgdorferi BbHtrA Protease as a Vaccine Candidate for Lyme Borreliosis in Mice.

Borrelia burgdorferi synthesizes an HtrA protease (BbHtrA) which is a surface-exposed, conserved protein within Lyme disease spirochetes with activity toward CheX and BmpD of Borrelia spp, as well as aggrecan, fibronectin and proteoglycans found in skin, joints and neural tissues of vertebrates. An antibody response against BbHtrA is observed in Lyme disease patients and in experimentally infected laboratory mice and rabbits. Given the surface location of BbHtrA on B. burgdorferi and its ability to elicit an antibody response in infected hosts, we explored recombinant BbHtrA as a potential vaccine candidate in a mouse model of tick-transmitted Lyme disease. We immunized mice with two forms of BbHtrA: the proteolytically active native form and BbHtrA ablated of activity by a serine to alanine mutation at amino acid 226 (BbHtrA(S226A)). Although inoculation with either BbHtrA or BbHtrA(S226A) produced high-titer antibody responses in C3H/HeJ mice, neither antigen was successful in protecting mice from B. burgdorferi challenge. These results indicate that the search for novel vaccine candidates against Lyme borreliosis remains a challenge.

A multi-scale approach reveals that NF-κB cRel enforces a B-cell decision to divide.

Understanding the functions of multi-cellular organs in terms of the molecular networks within each cell is an important step in the quest to predict phenotype from genotype. B-lymphocyte population dynamics, which are predictive of immune response and vaccine effectiveness, are determined by individual cells undergoing division or death seemingly stochastically. Based on tracking single-cell time-lapse trajectories of hundreds of B cells, single-cell transcriptome, and immunofluorescence analyses, we constructed an agent-based multi-modular computational model to simulate lymphocyte population dynamics in terms of the molecular networks that control NF-κB signaling, the cell cycle, and apoptosis. Combining modeling and experimentation, we found that NF-κB cRel enforces the execution of a cellular decision between mutually exclusive fates by promoting survival in growing cells. But as cRel deficiency causes growing B cells to die at similar rates to non-growing cells, our analysis reveals that the phenomenological decision model of wild-type cells is rooted in a biased race of cell fates. We show that a multi-scale modeling approach allows for the prediction of dynamic organ-level physiology in terms of intra-cellular molecular networks.

Investigation of dry powder inhaler (DPI) resistance and aerosol dispersion timing on emitted aerosol aerodynamic particle sizing by multistage cascade impactor when sampled volume is reduced from compendial value of 4 L.

Compendial methods determining dry powder inhaler (DPI)-emitted aerosol aerodynamic particle size distribution (APSD) collect a 4-L air sample containing the aerosol bolus, where the flow, which propagates through the cascade impactor (CI) measurement system from the vacuum source, is used to actuate the inhaler. A previous article described outcomes with two CIs (Andersen eight-stage cascade impactor (ACI) and Next-Generation Pharmaceutical Impactor (NGI)) when the air sample volume was ≤4 L with moderate-resistance DPIs. This article extends that work, examining the hypothesis that DPI flow resistance may be a factor in determining outcomes. APSD measurements were made using the same CI systems with inhalers representing low and high flow resistance extremes (Cyclohaler® and HandiHaler® DPIs, respectively). The ratio of sample volume to internal dead space (normalized volume (V*)) was varied from 0.25 to 1.98 (NGI) and from 0.43 to 3.46 (ACI). Inhaler resistance was a contributing factor to the rate of bolus transfer; the higher resistance DPI completing bolus relocation to the NGI pre-separator via the inlet when V* was as small as 0.25, whereas only ca. 50% of the bolus mass was collected at this condition with the Cyclohaler® DPI. Size fractionation of the bolus from either DPI was completed within the ACI at smaller values of V* than within the NGI. Bolus transfer from the Cyclohaler® capsule and from the HandiHaler® to the ACI system were unaffected by the different flow rise time observed in the two different flow controller systems, and the effects the ACI-based on APSD measurements were marginal.

Assessment of new culture method for detection of Borrelia species from serum of lyme disease patients.

A novel method of culturing spirochetes from the serum of U.S. Lyme disease patients was recently reported by Sapi and colleagues to have 94% sensitivity and 100% specificity for Borrelia species as assessed by microscopy and DNA sequence analysis of the pyrG gene (E. Sapi, N. Pabbati, A. Datar, E. M. Davies, A. Rattelle, and B. A. Kuo, Int. J. Med. Sci. 10:362-376, 2013). The majority of the spirochetes described were related by pyrG sequences to species of Borrelia previously undetected in North American patients without a reported history of travel to Europe or Asia. To better understand these unexpected findings, we determined pyrG sequences of the laboratory reference strains used by the investigators for method development and testing of culture medium. Eighty percent (41/51) of the reported patient-derived pyrG sequences were identical to one of the laboratory strains, and an additional 12% (6/51) differed by only a single nucleotide across a 603-bp region of the pyrG gene. Thus, false positivity due to laboratory contamination of patient samples cannot be ruled out, and further validation of the proposed novel culture method is required.

Borrelia burgdorferi†BbHtrA degrades host ECM proteins and stimulates release of inflammatory cytokines in vitro.

The Lyme disease spirochaete, Borrelia burgdorferi, causes damage to diverse host tissues and induces inflammation but the mechanisms of injury are poorly understood. We recently reported that a surface-exposed B. burgdorferi protease, which is expressed during human disease and is conserved within the major Lyme disease spirochaete species, degrades the extracellular matrix proteoglycan, aggrecan. Here we demonstrate that BbHtrA also degrades fibronectin and numerous proteoglycans found in skin, joints and neural tissues. BbHtrA degradation of fibronectin released known pro-inflammatory fibronectin fragments FnIII(13-14) and Fnf-29, which may amplify the inflammatory processes triggered by the presence of the bacteria. When this hypothesis was tested directly by exposing chondrocytes to BbHtrA in vitro, inflammatory cytokines (sICAM-1 and IL-6) and chemokines (CXCL1, CCL1, CCL2 and CCL5) that are hallmarks of Lyme disease were induced. These results provide the first evidence that, by utilizing BbHtrA, B. burgdorferi may actively participate in its dissemination and in the tissue damage and inflammation observed in Lyme disease.

Lyme disease spirochaetes possess an aggrecan-binding protease with aggrecanase activity.

Connective tissues are the most common area of colonization for the Lyme disease spirochaete Borrelia burgdorferi. Colonization is aided by the interaction between numerous bacterial adhesins with components of the extracellular matrix (ECM). Here we describe a novel interaction between B. burgdorferi and the major ECM proteoglycan found in joints, aggrecan. Using affinity chromatography and mass spectrometry we identify two borrelial aggrecan-binding proteins: the known ECM ligand Bgp (BB0588) and an uncharacterized protease BbHtrA (BB0104). Proteinase K studies demonstrate that BbHtrA is surface exposed. Immunoblots using sera from patients with both early and late Lyme disease establish that BbHtrA is expressed during human disease, immunogenic, and conserved in the three major Lyme disease spirochaete species. Consequences of the interaction between aggrecan and BbHtrA were examined by proteolysis assays. BbHtrA cleaves aggrecan at a site known to destroy aggrecan function and which has been previously observed in the synovial fluid of patients with Lyme arthritis. These data demonstrate that B. burgdorferi possess aggrecan-binding proteins which may provide the organism with additional capability to colonize connective tissues. Moreover, our studies provide the first evidence that B. burgdorferi possess proteolytic activity which may contribute to the pathogenesis of Lyme arthritis.

Adapting the Abbreviated Impactor Measurement (AIM) concept to make appropriate inhaler aerosol measurements to compare with clinical data: a scoping study with the "Alberta" idealized throat (AIT) inlet.

BACKGROUND: The Abbreviated Impactor Measurement (AIM) concept simplifies determination of aerodynamic size metrics for inhaler quality control testing. A similar approach is needed to compare in vitro particle size distribution metrics with human respiratory tract (HRT) deposition. METHODS: An abbreviated impactor based on the Andersen eight-stage cascade impactor (ACI) was developed having two size-fractionating stages with cut-points at 4.7 and 1.1 µm aerodynamic diameter at 28.3 L/min, to distinguish between coarse (CPM), fine (FPM), and extra-fine (EPM) mass fractions likely to deposit in the oropharynx, airways of the lungs, or be exhaled, respectively. In vitro data were determined for pressurized metered dose inhaler (pMDI)-delivered salbutamol (100 µg/actuation ex valve) with an "Alberta" idealized adult upper airway (throat) inlet (AIM-pHRT). Corresponding benchmark data for a full resolution Andersen eight-stage cascade impactor with "Alberta" idealized throat (ACI-AIT) and ACI-Ph.Eur./USP inlet were obtained with the same product. RESULTS: Mass recoveries (µg/actuation; mean ± SD) were equivalent at 100.5 ± 0.7; 97.2 ± 4.9 and 101.5 ± 9.5 for the AIM-pHRT, ACI-AIT, and ACI-Ph.Eur./USP induction port, respectively [one-way analysis of variance (ANOVA), p=0.64]. Corresponding values of CPM were 59.2 ± 4.2; 58.4 ± 2.4, and 65.6 ± 5.8; the AIT captured larger particles more efficiently than the Ph.Eur./USP induction port, so that less large particle mass was apparent in the upper stages of the ACI-AIT (p ≤ 0.037). Equivalent values of FPM were similar regardless of inlet/abbreviation at 41.3 ± 4.2; 38.7 ± 3.0, and 35.9 ± 3.8 (p=0.054), and EPM measures (1.7 ± 0.3; 2.0 ± 0.5; 2.1 ± 0.3) were also comparable (p=0.32). CONCLUSIONS: The AIT inlet significantly increased the capture of the coarse fraction compared with that collected by the Ph.Eur./USP induction port. Measures obtained using the AIM-pHRT apparatus were comparable with those obtained with the ACI-AIT.

Mutation in the factor VII hepatocyte nuclear factor 4α-binding site contributes to factor VII deficiency.

Severe coagulant factor VII (FVII) deficiency in postpubertal dizygotic twin males results from two point mutations in the FVII gene, a promoter region T→C transition at -60 and a His-to-Arg substitution at amino acid 348; both mutations prevent persistence of plasma functional FVII. This report documents longitudinal laboratory measurements from infancy to adulthood of FVII coagulant activity (FVII:C) in the twin FVII-deficient patients; it also details specific biochemical analyses of the -60 T→C mutation. The results revealed FVII:C levels of less than 1% in infancy that remain severely decreased through puberty and into adulthood. In-vitro analyses utilizing hepatocyte nuclear factor 4α (HNF4α) co-transfection and a chromatin immunoprecipitation assay indicate that the -60 T→C mutation severely diminishes functional interaction between the FVII promoter and transcription factor HNF4α. The importance of interaction between the FVII gene and HNF4α in normal FVII expression provides an in-vivo illustration of the regulated expression of an autosomal gene encoding a coagulation protein. The constancy of FVII:C and peripubertal patient symptomatology reported here illustrates androgen-independent expression in contrast to expression with an analogous mutation in the promoter region of the gene encoding coagulation FIX.

In vivo CD8+ T-cell suppression of siv viremia is not mediated by CTL clearance of productively infected cells.

The CD8+ T-cell is a key mediator of antiviral immunity, potentially contributing to control of pathogenic lentiviral infection through both innate and adaptive mechanisms. We studied viral dynamics during antiretroviral treatment of simian immunodeficiency virus (SIV) infected rhesus macaques following CD8+ T-cell depletion to test the importance of adaptive cytotoxic effects in clearance of cells productively infected with SIV. As previously described, plasma viral load (VL) increased following CD8+ T-cell depletion and was proportional to the magnitude of CD8+ T-cell depletion in the GALT, confirming a direct relationship between CD8+ T-cell loss and viral replication. Surprisingly, first phase plasma virus decay following administration of antiretroviral drugs was not slower in CD8+ T-cell depleted animals compared with controls indicating that the short lifespan of the average productively infected cell is not a reflection of cytotoxic T-lymphocyte (CTL) killing. Our findings support a dominant role for non-cytotoxic effects of CD8+ T-cells on control of pathogenic lentiviral infection and suggest that cytotoxic effects, if present, are limited to early, pre-productive stages of the viral life cycle. These observations have important implications for future strategies to augment immune control of HIV.

Asymptomatic factor VII deficiency in African Americans.

African Americans with factor VII (FVII) deficiency, as defined by clinical laboratory values, are frequently asymptomatic. To date the genotypes underlying this FVII defect in asymptomatic African Americans have not been established. We show in 3 unrelated African-American patients that the defect is due to a G to A nucleotide change resulting in an arginine to glutamine mutation in Factor VII amino acid 304. This defect results in low FVII coagulant activity levels using rabbit brain thromboplastin but not using human thromboplastin. This report may aid transfusion and hematology specialists evaluate patient results and prevent unnecessary transfusions to treat patients with abnormal laboratory values.

Why is work intensity associated with heavy alcohol use among adolescents?

PURPOSE: To examine and explain the relationship between work intensity (number of hours worked per week) and heavy alcohol use among adolescents. METHODS: Analyses were conducted with two waves of in-home interview data provided by a representative sample of adolescents who participated in the National Longitudinal Study of Adolescent Health. Multinomial logistic regression analyses were conducted to determine whether a higher level of work intensity at Wave 1 predicted a higher level of past-year heavy drinking approximately 1 year later at Wave 2, and the degree to which the relationship between work intensity and heavy drinking persisted after adjusting for demographic characteristics, alcohol use before Wave 1, and psychosocial risk and protective factors in family, school, and peer-individual domains. RESULTS: Higher levels of work intensity at Wave 1 (11-20 or more than 20 hours/week) were predictive of heavy drinking at Wave 2. However, these effects were substantially attenuated after adjusting for demographic characteristics and prior alcohol use. Risk and protective factors such as school commitment, friends' drinking, and delinquency also partially explained the effects of work intensity and background variables on heavy drinking, suggesting that these factors may act as confounders and/or mediators. CONCLUSIONS: This study suggests that working more than 10 h/week increases the likelihood of heavy alcohol use among adolescents, and that the effect of work intensity is largely, but not completely attributable to demographic characteristics (e.g., age, race/ethnicity, personal income), prior alcohol use, and family, school, and peer-individual factors.