Tag and Snag: A New Platform for Bioactive Natural Product Screening from Mixtures.

Natural products provide an unparalleled diversity of small molecules to fuel drug screening efforts, but deconvoluting the pharmacological activity of natural product mixtures to identify key bioactive compounds remains a vexing and labor-intensive process. Therefore, we have developed a new platform to probe the non-specific pharmacological potential of compounds present in common dietary supplements via shotgun derivatization with isotopically labeled propanoic acid, a live cell affinity assay, which was used to selectively recognize the population of compounds which bind tightly to HeLa cells in culture, and a computational LC-MS data analysis of isotopically labeled compounds from cell lysate. The data analysis showed that hundreds of compounds were successfully derivatized in each extract, and dozens of those compounds showed high affinity for HeLa cells. In total, over a thousand isotopically labeled compounds were screened for cell affinity across three separate experiments, resulting in the identification of several known bioactive compounds with specific protein targets and six previously unreported structures. The new natural products include three tulsinol compounds which were isolated from Ocimum tenuiflorum and three valeraninium alkaloids from Valeriana officinalis. The valeraninium alkaloids constitute a distinct new family of alkaloids from valerian, which may have previously undescribed bioactivity. These results collectively demonstrate the tag and snag workflow's viability as a drug discovery method.

Bioactive Natural Product Discovery via Deuterium Adduct Bioactivity Screening.

The discovery of bioactive natural products lies at the forefront of human medicine. The continued discovery of these molecules is imperative in the fight against infection and disease. While natural products have historically dominated the drug market, discovery in recent years has slowed significantly, partly due to limitations in current discovery methodologies. This work demonstrates a new workflow, deuterium adduct bioactivity screening (DABS), which pairs untargeted isotope labeling with whole cell binding assays for bioactive natural product discovery. DABS was validated and led to the discovery of a new isoprenyl guanidine alkaloid, zillamycin, which showed anti-cancer and anti-microbial activities. DABS thus represents a new workflow to accelerate discovery of natural products with a wide range of bioactive potentials.

Evaluation of the Stability of Diamine-Appended Mg2(dobpdc) Frameworks to Sulfur Dioxide.

Diamine-appended Mg2(dobpdc) (dobpdc4- = 4,4'-dioxidobiphenyl-3,3'-dicarboxylate) metal-organic frameworks are a promising class of CO2 adsorbents, although their stability to SO2─a trace component of industrially relevant exhaust streams─remains largely untested. Here, we investigate the impact of SO2 on the stability and CO2 capture performance of dmpn-Mg2(dobpdc) (dmpn = 2,2-dimethyl-1,3-propanediamine), a candidate material for carbon capture from coal flue gas. Using SO2 breakthrough experiments and CO2 isobar measurements, we find that the material retains 91% of its CO2 capacity after saturation with a wet simulated flue gas containing representative levels of CO2 and SO2, highlighting the robustness of this framework to SO2 under realistic CO2 capture conditions. Initial SO2 cycling experiments suggest dmpn-Mg2(dobpdc) may achieve a stable operating capacity in the presence of SO2 after initial passivation. Evaluation of several other diamine-Mg2(dobpdc) variants reveals that those with primary,primary (1°,1°) diamines, including dmpn-Mg2(dobpdc), are more robust to humid SO2 than those featuring primary,secondary (1°,2°) or primary,tertiary (1°,3°) diamines. Based on the solid-state 15N NMR spectra and density functional theory calculations, we find that under humid conditions, SO2 reacts with the metal-bound primary amine in 1°,2° and 1°,3° diamine-appended Mg2(dobpdc) to form a metal-bound bisulfite species that is charge balanced by a primary ammonium cation, thereby facilitating material degradation. In contrast, humid SO2 reacts with the free end of 1°,1° diamines to form ammonium bisulfite, leaving the metal-diamine bond intact. This structure-property relationship can be used to guide further optimization of these materials for CO2 capture applications.

Probing the Mechanism of Isonitrile Formation by a Non-Heme Iron(II)-Dependent Oxidase/Decarboxylase.

The isonitrile moiety is an electron-rich functionality that decorates various bioactive natural products isolated from diverse kingdoms of life. Isonitrile biosynthesis was restricted for over a decade to isonitrile synthases, a family of enzymes catalyzing a condensation reaction between l-Trp/l-Tyr and ribulose-5-phosphate. The discovery of ScoE, a non-heme iron(II) and α-ketoglutarate-dependent dioxygenase, demonstrated an alternative pathway employed by nature for isonitrile installation. Biochemical, crystallographic, and computational investigations of ScoE have previously been reported, yet the isonitrile formation mechanism remains obscure. In the present work, we employed in vitro biochemistry, chemical synthesis, spectroscopy techniques, and computational simulations that enabled us to propose a plausible molecular mechanism for isonitrile formation. Our findings demonstrate that the ScoE reaction initiates with C5 hydroxylation of (R)-3-((carboxymethyl)amino)butanoic acid to generate 1, which undergoes dehydration, presumably mediated by Tyr96 to synthesize 2 in a trans configuration. (R)-3-isocyanobutanoic acid is finally generated through radical-based decarboxylation of 2, instead of the common hydroxylation pathway employed by this enzyme superfamily.

Biosynthesis of triacsin featuring an N-hydroxytriazene pharmacophore.

Triacsins are an intriguing class of specialized metabolites possessing a conserved N-hydroxytriazene moiety not found in any other known natural products. Triacsins are notable as potent acyl-CoA synthetase inhibitors in lipid metabolism, yet their biosynthesis has remained elusive. Through extensive mutagenesis and biochemical studies, we here report all enzymes required to construct and install the N-hydroxytriazene pharmacophore of triacsins. Two distinct ATP-dependent enzymes were revealed to catalyze the two consecutive N-N bond formation reactions, including a glycine-utilizing, hydrazine-forming enzyme (Tri28) and a nitrite-utilizing, N-nitrosating enzyme (Tri17). This study paves the way for future mechanistic interrogation and biocatalytic application of enzymes for N-N bond formation.

Adaptation of Mycobacterium tuberculosis to Biofilm Growth Is Genetically Linked to Drug Tolerance.

Mycobacterium tuberculosis spontaneously grows at the air-medium interface, forming pellicle biofilms, which harbor more drug-tolerant persisters than planktonic cultures. The underlying basis for increased persisters in M. tuberculosis biofilms is unknown. Using a transposon sequencing (Tn-seq) approach, we show here that multiple genes that are necessary for fitness of M. tuberculosis cells within biofilms, but not in planktonic cultures, are also implicated in tolerance of bacilli to a diverse set of stressors and antibiotics. Thus, development of M. tuberculosis biofilms appears to be associated with an enrichment of population, in which challenging growth conditions within biofilm architecture select for cells that maintain intrinsic tolerance to exogenous stresses, including antibiotic exposure. We further observed that the intrinsic drug tolerance of constituent cells of a biofilm determines the frequency of persisters. These findings together allow us to propose that the selection of elite cells during biofilm development promotes the frequency of persisters. Furthermore, probing the possibility that the population enrichment is an outcome of unique environment within biofilms, we demonstrate biofilm-specific induction in the synthesis of isonitrile lipopeptide (INLP). Mutation analysis indicates that INLP is necessary for the architecture development of M. tuberculosis biofilms. In summary, this study offers an insight into persistence of M. tuberculosis biofilms under antibiotic exposure, while identifying INLP as a potential biomarker for further investigation of this phenomenon.

Naringenin-responsive riboswitch-based fluorescent biosensor module for Escherichia coli co-cultures.

The ability to design and construct combinatorial synthetic metabolic pathways has far exceeded our capacity for efficient screening and selection of the resulting microbial strains. The need for high-throughput rapid screening techniques is of upmost importance for the future of synthetic biology and metabolic engineering. Here we describe the development of an RNA riboswitch-based biosensor module with dual fluorescent reporters, and demonstrate a high-throughput flow cytometry-based screening method for identification of naringenin over producing Escherichia coli strains in co-culture. Our efforts helped identify a number of key operating parameters that affect biosensor performance, including the selection of promoter and linker elements within the sensor-actuator domain, and the effect of host strain, fermentation time, and growth medium on sensor dynamic range. The resulting biosensor demonstrates a high correlation between specific fluorescence of the biosensor strain and naringenin titer produced by the second member of the synthetic co-culture system. This technique represents a novel application for synthetic microbial co-cultures and can be expanded from naringenin to any metabolite if a suitable riboswitch is identified. The co-culture technique presented here can be applied to a variety of target metabolites in combination with the SELEX approach for aptamer design. Due to the compartmentalization of the two genetic constructs responsible for production and detection into separate cells and application as independent modules of a synthetic microbial co-culture we have subsequently reduced the need for re-optimization of the producer module when the biosensor is replaced or removed. Biotechnol. Bioeng. 2017;114: 2235-2244. © 2017 Wiley Periodicals, Inc.

Assessing psychological well-being: self-report instruments for the NIH Toolbox.

OBJECTIVE: Psychological well-being (PWB) has a significant relationship with physical and mental health. As a part of the NIH Toolbox for the Assessment of Neurological and Behavioral Function, we developed self-report item banks and short forms to assess PWB. STUDY DESIGN AND SETTING: Expert feedback and literature review informed the selection of PWB concepts and the development of item pools for positive affect, life satisfaction, and meaning and purpose. Items were tested with a community-dwelling US Internet panel sample of adults aged 18 and above (N = 552). Classical and item response theory (IRT) approaches were used to evaluate unidimensionality, fit of items to the overall measure, and calibrations of those items, including differential item function (DIF). RESULTS: IRT-calibrated item banks were produced for positive affect (34 items), life satisfaction (16 items), and meaning and purpose (18 items). Their psychometric properties were supported based on the results of factor analysis, fit statistics, and DIF evaluation. All banks measured the concepts precisely (reliability ≥0.90) for more than 98% of participants. CONCLUSION: These adult scales and item banks for PWB provide the flexibility, efficiency, and precision necessary to promote future epidemiological, observational, and intervention research on the relationship of PWB with physical and mental health.

Emotion assessment using the NIH Toolbox.

One of the goals of the NIH Toolbox for Assessment of Neurological and Behavioral Function was to identify or develop brief measures of emotion for use in prospective epidemiologic and clinical research. Emotional health has significant links to physical health and exerts a powerful effect on perceptions of life quality. Based on an extensive literature review and expert input, the Emotion team identified 4 central subdomains: Negative Affect, Psychological Well-Being, Stress and Self-Efficacy, and Social Relationships. A subsequent psychometric review identified several existing self-report and proxy measures of these subdomains with measurement characteristics that met the NIH Toolbox criteria. In cases where adequate measures did not exist, robust item banks were developed to assess concepts of interest. A population-weighted sample was recruited by an online survey panel to provide initial item calibration and measure validation data. Participants aged 8 to 85 years completed self-report measures whereas parents/guardians responded for children aged 3 to 12 years. Data were analyzed using a combination of classic test theory and item response theory methods, yielding efficient measures of emotional health concepts. An overview of the development of the NIH Toolbox Emotion battery is presented along with preliminary results. Norming activities led to further refinement of the battery, thus enhancing the robustness of emotional health measurement for researchers using the NIH Toolbox.

Norming plans for the NIH Toolbox.

OBJECTIVE: The NIH Toolbox for Assessment of Neurological and Behavioral Function (NIH Toolbox) is a comprehensive battery of brief assessment tools. The purpose of this article is to describe plans to establish normative reference values for the NIH Toolbox measures. METHODS: A large sample will be obtained from the US population for the purpose of calculating normative values. The sample will be stratified by age (ages 3-85 years), sex, and language preference (English or Spanish) and have a total sample size of at least 4,205. The sample will include a minimum of 25-100 individuals in each targeted demographic and language subgroup. RESULTS: Norming methods will include poststratification adjustment calculated using iterative proportional fitting, also known as raking, so that the weighted sample will have the same distribution on key demographic variables as the US population described in the 2010 Census. CONCLUSIONS: As with any set of norms, users should be mindful of the reference population and make conclusions consistent with the limitations of normative sampling, since it is not a probability-based sample. However, the NIH Toolbox norming study has been designed to minimize bias and maximize representativeness and precision of estimates. The availability of a "toolbox" of normed measures will be an important foundation for addressing critical research questions in neurologic and behavioral health.

Assessing social support, companionship, and distress: National Institute of Health (NIH) Toolbox Adult Social Relationship Scales.

OBJECTIVE: The quality of our daily social interactions-including perceptions of support, feelings of loneliness, and distress stemming from negative social exchanges-influence physical health and well-being. Despite the importance of social relationships, brief yet precise unidimensional scales that assess key aspects of social relationship quality are lacking. As part of the National Institute of Health (NIH) Toolbox for the Assessment of Neurological and Behavioral Function, we developed brief self-report scales designed to assess aspects of social support, companionship, and social distress across age cohorts. This article details the development and psychometric testing of the adult NIH Toolbox Social Relationship scales. METHODS: Social relationship concepts were selected, and item sets were developed and revised based on expert feedback and literature review. Items were then tested across a community-dwelling U.S. Internet panel sample of adults aged 18 and above (N = 692) using traditional (classic) psychometric methods and item response theory approaches to identify items for inclusion in 5-8 item unidimensional scales. Finally, concurrent validity of the newly developed scales was evaluated with respect to their interrelationships with classic social relationship validation instruments. RESULTS: Results provide support for the internal reliability and concurrent validity of resulting self-report scales assessing Emotional Support, Instrumental Support, Friendship, Loneliness, Perceived Rejection, and Perceived Hostility. CONCLUSION: These brief social relationship scales provide the pragmatic utility and enhanced precision needed to promote future epidemiological and social neuroscience research on the impact of social relationships on physical and emotional health outcomes.

Assessment of self-reported negative affect in the NIH Toolbox.

We report on the selection of self-report measures for inclusion in the NIH Toolbox that are suitable for assessing the full range of negative affect including sadness, fear, and anger. The Toolbox is intended to serve as a "core battery" of assessment tools for cognition, sensation, motor function, and emotional health that will help to overcome the lack of consistency in measures used across epidemiological, observational, and intervention studies. A secondary goal of the NIH Toolbox is the identification of measures that are flexible, efficient, and precise, an agenda best fulfilled by the use of item banks calibrated with models from item response theory (IRT) and suitable for adaptive testing. Results from a sample of 1763 respondents supported use of the adult and pediatric item banks for emotional distress from the Patient-Reported Outcomes Measurement Information System (PROMIS(®)) as a starting point for capturing the full range of negative affect in healthy individuals. Content coverage for the adult Toolbox was also enhanced by the development of a scale for somatic arousal using items from the Mood and Anxiety Symptom Questionnaire (MASQ) and scales for hostility and physical aggression using items from the Buss-Perry Aggression Questionnaire (BPAQ).

Neighborhoods as a developmental context: a multilevel analysis of neighborhood effects on Head Start families and children.

Neighborhoods have been recognized in theory and research as an important context for child development. This study used data from the Head Start Family and Child Experiences Survey (FACES) and Census 2000 to assess the underlying factor structure and impact of neighborhood factors on child cognitive and behavioral outcomes, including the critical family and social factors that may mediate and/or moderate these relationships. Factor analyses found five factors described Head Start neighborhoods. After controlling for family and child factors, multilevel analyses found significant direct effects of neighborhood factors on Head Start children's cognitive and behavioral outcomes. There were no mediation effects found for family or social variables between neighborhood factors and child outcomes. A large number of moderation effects were found although there was not a clear pattern to the results. Future research, policy, and practice implications are discussed.

Teachers' education, classroom quality, and young children's academic skills: results from seven studies of preschool programs.

In an effort to provide high-quality preschool education, policymakers are increasingly requiring public preschool teachers to have at least a Bachelor's degree, preferably in early childhood education. Seven major studies of early care and education were used to predict classroom quality and children's academic outcomes from the educational attainment and major of teachers of 4-year-olds. The findings indicate largely null or contradictory associations, indicating that policies focused solely on increasing teachers' education will not suffice for improving classroom quality or maximizing children's academic gains. Instead, raising the effectiveness of early childhood education likely will require a broad range of professional development activities and supports targeted toward teachers' interactions with children.