An Efficient and Rapid Method to Monitor the Oxidative Degradation of Protein Pharmaceuticals: Probing Tyrosine Oxidation with Fluorogenic Derivatization.

PubMed

Bommana, Rupesh; Mozziconacci, Olivier; John Wang, Y; Schöneich, Christian

2017-07-01

The loss of potency of protein therapeutics can be linked to the oxidation of specific amino acid residues leading to a great variety of oxidative modifications. The comprehensive identification of these oxidative modifications requires high-resolution mass spectrometry analysis, which requires time and expensive resources. Here, we propose a fluorogenic derivatization method of oxidized Tyr and Phe yielding benzoxazole derivatives, as an orthogonal technique for the rapid screening of protein oxidation. Four model proteins, IgG1, human growth hormone (hGH), insulin and bovine serum albumin (BSA) were exposed to oxidation via peroxyl radicals and metal-catalyzed reactions and efficiently screened by fluorogenic derivatization of Tyr and Phe oxidation products. Complementary LC-MS analysis was done to identify the extent of methionine oxidation in oxidized proteins. The Fluorogenic derivatization technique can easily be adapted to a 96-well plate, in which several protein formulations can be screened in short time. Representatively for hGH, we show that the formation of benzoxazole parallels the oxidation of Met to methionine sulfoxide which enables estimation of Met oxidation by just recording the fluorescence. Our rapid fluorescence based screening allows for the fast comparison of the stability of multiple formulations.

Novel isoprenylated proteins identified by an expression library screen.

PubMed

Biermann, B J; Morehead, T A; Tate, S E; Price, J R; Randall, S K; Crowell, D N

1994-10-14

Isoprenylated proteins are involved in eukaryotic cell growth and signal transduction. The protein determinant for prenylation is a short carboxyl-terminal motif containing a cysteine, to which the isoprenoid is covalently attached via thioether linkage. To date, isoprenylated proteins have almost all been identified by demonstrating the attachment of an isoprenoid to previously known proteins. Thus, many isoprenylated proteins probably remain undiscovered. To identify novel isoprenylated proteins for subsequent biochemical study, colony blots of a Glycine max cDNA expression library were [3H]farnesyl-labeled in vitro. Proteins identified by this screen contained several different carboxyl termini that conform to consensus farnesylation motifs. These proteins included known farnesylated proteins (DnaJ homologs) and several novel proteins, two of which contained six or more tandem repeats of a hexapeptide having the consensus sequence (E/G)(G/P)EK(P/K)K. Thus, plants contain a diverse array of genes encoding farnesylated proteins, and our results indicate that fundamental differences in the identities of farnesylated proteins may exist between plants and other eukaryotes. Expression library screening by direct labeling can be adapted to identify isoprenylated proteins from other organisms, as well as proteins with other post-translational modifications.

Application of the stochastic tunneling method to high throughput database screening

NASA Astrophysics Data System (ADS)

Merlitz, H.; Burghardt, B.; Wenzel, W.

2003-03-01

The stochastic tunneling technique is applied to screen a database of chemical compounds to the active site of dihydrofolate reductase for lead candidates in the receptor-ligand docking problem. Using an atomistic force field we consider the ligand's internal rotational degrees of freedom. It is shown that the natural ligand (methotrexate) scores best among 10 000 randomly chosen compounds. We analyze the top scoring compounds to identify hot-spots of the receptor. We mutate the amino acids that are responsible for the hot-spots of the receptor and verify that its specificity is lost upon modification.

Loss of a Conserved tRNA Anticodon Modification Perturbs Plant Immunity

PubMed Central

López, Ana; Castelló, María José; Gil, María José; Zheng, Bo; Chen, Peng; Vera, Pablo

2015-01-01

tRNA is the most highly modified class of RNA species, and modifications are found in tRNAs from all organisms that have been examined. Despite their vastly different chemical structures and their presence in different tRNAs, occurring in different locations in tRNA, the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s). Recent discoveries have revealed unprecedented complexity in the modification patterns of tRNA, their regulation and function, suggesting that each modified nucleoside in tRNA may have its own specific function. However, in plants, our knowledge on the role of individual tRNA modifications and how they are regulated is very limited. In a genetic screen designed to identify factors regulating disease resistance and activation of defenses in Arabidopsis, we identified SUPPRESSOR OF CSB3 9 (SCS9). Our results reveal SCS9 encodes a tRNA methyltransferase that mediates the 2´-O-ribose methylation of selected tRNA species in the anticodon loop. These SCS9-mediated tRNA modifications enhance during the course of infection with the bacterial pathogen Pseudomonas syringae DC3000, and lack of such tRNA modification, as observed in scs9 mutants, severely compromise plant immunity against the same pathogen without affecting the salicylic acid (SA) signaling pathway which regulates plant immune responses. Our results support a model that gives importance to the control of certain tRNA modifications for mounting an effective immune response in Arabidopsis, and therefore expands the repertoire of molecular components essential for an efficient disease resistance response. PMID:26492405

Advancing epilepsy treatment through personalized genetic zebrafish models.

PubMed

Griffin, A; Krasniak, C; Baraban, S C

2016-01-01

With an increase in the number of disease causing genetic mutations identified from epilepsy cohorts, zebrafish are proving to be an attractive vertebrate model for functional analysis of these allele variants. Not only do zebrafish have conserved gene functions, but larvae harboring mutations in identified human epileptic genes show spontaneous seizure activity and mimic the convulsive behavioral movements observed in humans. With zebrafish being compatible with medium to high-throughput screening, they are also proving to be a unique and powerful system for early preclinical drug screening, including novel target identification, pharmacology, and toxicology. Additionally, with recent advances in genomic engineering technologies, it is now possible to study the precise pathophysiology of patient-specific gene mutations in zebrafish. The following sections highlight how the unique attributes of zebrafish, in combination with genetic modifications, are continuing to transform our understanding of epilepsy and help identify personalized therapeutics for specific patient cohorts. © 2016 Elsevier B.V. All rights reserved.

Coupling bimolecular PARylation biosensors with genetic screens to identify PARylation targets.

PubMed

Krastev, Dragomir B; Pettitt, Stephen J; Campbell, James; Song, Feifei; Tanos, Barbara E; Stoynov, Stoyno S; Ashworth, Alan; Lord, Christopher J

2018-05-22

Poly (ADP-ribose)ylation is a dynamic protein modification that regulates multiple cellular processes. Here, we describe a system for identifying and characterizing PARylation events that exploits the ability of a PBZ (PAR-binding zinc finger) protein domain to bind PAR with high-affinity. By linking PBZ domains to bimolecular fluorescent complementation biosensors, we developed fluorescent PAR biosensors that allow the detection of temporal and spatial PARylation events in live cells. Exploiting transposon-mediated recombination, we integrate the PAR biosensor en masse into thousands of protein coding genes in living cells. Using these PAR-biosensor "tagged" cells in a genetic screen we carry out a large-scale identification of PARylation targets. This identifies CTIF (CBP80/CBP20-dependent translation initiation factor) as a novel PARylation target of the tankyrase enzymes in the centrosomal region of cells, which plays a role in the distribution of the centrosomal satellites.

Prevalence and Patterns of Learning Disabilities in School Children.

PubMed

Padhy, Susanta Kumar; Goel, Sonu; Das, Shyam Sinder; Sarkar, Siddharth; Sharma, Vijaylaxmi; Panigrahi, Mahima

2016-04-01

To assess the prevalence and patterns of learning disabilities (LD) in school going children in a northern city of India. The present cross-sectional study comprised of three-staged screening procedure for assessing learning disabilities of 3rd and 4th grade students studying in government schools. The first stage comprised of the teacher identifying at-risk student. In the second stage, teachers assessed at-risk students using Specific Learning Disability-Screening Questionnaire (SLD-SQ). The third stage comprised of assessment of the screen positive students using Brigance Diagnostic Inventory (BDI) part of NIMHANS Index of Specific Learning Disabilities for identifying the cases of LD. A total of 1211 (33.6%) children out of the total screened (n = 3600) were identified as at-risk by the teachers at the first stage. Of them, 360 were found to screen positive on the second stage using SLD-SQ. The most common deficits were missing out words or sentences while reading, misplacing letters or words while reading or writing, and making frequent mistake in spelling while writing or reading. Of these, 108 children were confirmed to have learning disability on the third stage using BDI, which represented 3.08% of the total population. Learning disability is an important concern in young school aged children. Early identification of such students can help in early institution of intervention and suitable modifications in teaching techniques.

Identification of Spen as a Crucial Factor for Xist Function through Forward Genetic Screening in Haploid Embryonic Stem Cells

PubMed Central

Monfort, Asun; Di Minin, Giulio; Postlmayr, Andreas; Freimann, Remo; Arieti, Fabiana; Thore, Stéphane; Wutz, Anton

2015-01-01

Summary In mammals, the noncoding Xist RNA triggers transcriptional silencing of one of the two X chromosomes in female cells. Here, we report a genetic screen for silencing factors in X chromosome inactivation using haploid mouse embryonic stem cells (ESCs) that carry an engineered selectable reporter system. This system was able to identify several candidate factors that are genetically required for chromosomal repression by Xist. Among the list of candidates, we identify the RNA-binding protein Spen, the homolog of split ends. Independent validation through gene deletion in ESCs confirms that Spen is required for gene repression by Xist. However, Spen is not required for Xist RNA localization and the recruitment of chromatin modifications, including Polycomb protein Ezh2. The identification of Spen opens avenues for further investigation into the gene-silencing pathway of Xist and shows the usefulness of haploid ESCs for genetic screening of epigenetic pathways. PMID:26190100

The m/r SEBT: development of a functional screening tool for dance educators.

PubMed

Wilson, Margaret; Batson, Glenna

2014-12-01

Dance screenings provide direct and indirect data bearing on a dancer's readiness to undertake rigorous physical training. Rarely, however, are dance teachers able to translate results from these screenings into practical technical knowledge. In this article, an example of a preseason assessment tool is presented that translates scientific findings into useful information for dance teachers conducting auditions. Designed as a baseline assessment of the dancer during auditioning, the m/r SEBT tool helps teachers stratify technical levels, identify injury risk, and consequently assist with immediate and appropriate recommendations for supplemental training and//or follow-up with a medical professional. The tool evolved out of more than 3 years of collaborative, multisite research utilizing the Star Excursion Balance Test (SEBT) as a dynamic test of balance. Modifications were made to render the test more dance-specific and to increase balance challenges. Within the 3-year period, more than 100 dancers were tested in four sites, two in the United States and two in the United Kingdom. Despite the relatively large collective sample size, neither the original SEBT nor its modifications (m/r SEBT) held robust face or content validity as balance screens. What did emerge, however, were qualitative criteria that the authors organized into a feasible assessment tool for preseason auditions. While this tool awaits further validation, its current evolution helps serve as a bridge between dance teachers' clinical and practical knowledge.

Consolidated principles for screening based on a systematic review and consensus process.

PubMed

Dobrow, Mark J; Hagens, Victoria; Chafe, Roger; Sullivan, Terrence; Rabeneck, Linda

2018-04-09

In 1968, Wilson and Jungner published 10 principles of screening that often represent the de facto starting point for screening decisions today; 50 years on, are these principles still the right ones? Our objectives were to review published work that presents principles for population-based screening decisions since Wilson and Jungner's seminal publication, and to conduct a Delphi consensus process to assess the review results. We conducted a systematic review and modified Delphi consensus process. We searched multiple databases for articles published in English in 1968 or later that were intended to guide population-based screening decisions, described development and modification of principles, and presented principles as a set or list. Identified sets were compared for basic characteristics (e.g., number, categorization), a citation analysis was conducted, and principles were iteratively synthesized and consolidated into categories to assess evolution. Participants in the consensus process assessed the level of agreement with the importance and interpretability of the consolidated screening principles. We identified 41 sets and 367 unique principles. Each unique principle was coded to 12 consolidated decision principles that were further categorized as disease/condition, test/intervention or program/system principles. Program or system issues were the focus of 3 of Wilson and Jungner's 10 principles, but comprised almost half of all unique principles identified in the review. The 12 consolidated principles were assessed through 2 rounds of the consensus process, leading to specific refinements to improve their relevance and interpretability. No gaps or missing principles were identified. Wilson and Jungner's principles are remarkably enduring, but increasingly reflect a truncated version of contemporary thinking on screening that does not fully capture subsequent focus on program or system principles. Ultimately, this review and consensus process provides a comprehensive and iterative modernization of guidance to inform population-based screening decisions. © 2018 Joule Inc. or its licensors.

Consolidated principles for screening based on a systematic review and consensus process

PubMed Central

Hagens, Victoria; Chafe, Roger; Sullivan, Terrence; Rabeneck, Linda

2018-01-01

BACKGROUND: In 1968, Wilson and Jungner published 10 principles of screening that often represent the de facto starting point for screening decisions today; 50 years on, are these principles still the right ones? Our objectives were to review published work that presents principles for population-based screening decisions since Wilson and Jungner’s seminal publication, and to conduct a Delphi consensus process to assess the review results. METHODS: We conducted a systematic review and modified Delphi consensus process. We searched multiple databases for articles published in English in 1968 or later that were intended to guide population-based screening decisions, described development and modification of principles, and presented principles as a set or list. Identified sets were compared for basic characteristics (e.g., number, categorization), a citation analysis was conducted, and principles were iteratively synthesized and consolidated into categories to assess evolution. Participants in the consensus process assessed the level of agreement with the importance and interpretability of the consolidated screening principles. RESULTS: We identified 41 sets and 367 unique principles. Each unique principle was coded to 12 consolidated decision principles that were further categorized as disease/condition, test/intervention or program/system principles. Program or system issues were the focus of 3 of Wilson and Jungner’s 10 principles, but comprised almost half of all unique principles identified in the review. The 12 consolidated principles were assessed through 2 rounds of the consensus process, leading to specific refinements to improve their relevance and interpretability. No gaps or missing principles were identified. INTERPRETATION: Wilson and Jungner’s principles are remarkably enduring, but increasingly reflect a truncated version of contemporary thinking on screening that does not fully capture subsequent focus on program or system principles. Ultimately, this review and consensus process provides a comprehensive and iterative modernization of guidance to inform population-based screening decisions. PMID:29632037

My First Patient Program to introduce first-year pharmacy students to health promotion and disease prevention.

PubMed

Maffeo, Carrie; Chase, Patricia; Brown, Bonnie; Tuohy, Kevin; Kalsekar, Iftekhar

2009-10-01

To implement and assess the effectiveness of a program to teach pharmacy students the importance of taking personal responsibility for their health. The My First Patient Program was created and lectures were incorporated into an existing first-year course to introduce the concepts of health beliefs, behavior modification, stress management, substance abuse, and nutrition. Each student received a comprehensive health screening and health risk assessment which they used to develop a personal health portfolio and identify strategies to attain and/or maintain their personal health goals. Student learning was assessed through written assignments and student reflections, follow-up surveys, and course evaluations. Students' attainment of health goals and their ability to identify their personal health status illustrated the positive impact of the program. This program serves as a model for colleges and schools of pharmacy and for other health professions in the instruction of health promotion, disease prevention, and behavior modification.

Screening for elevated levels of fear-avoidance beliefs regarding work or physical activities in people receiving outpatient therapy.

PubMed

Hart, Dennis L; Werneke, Mark W; George, Steven Z; Matheson, James W; Wang, Ying-Chih; Cook, Karon F; Mioduski, Jerome E; Choi, Seung W

2009-08-01

Screening people for elevated levels of fear-avoidance beliefs is uncommon, but elevated levels of fear could worsen outcomes. Developing short screening tools might reduce the data collection burden and facilitate screening, which could prompt further testing or management strategy modifications to improve outcomes. The purpose of this study was to develop efficient yet accurate screening methods for identifying elevated levels of fear-avoidance beliefs regarding work or physical activities in people receiving outpatient rehabilitation. A secondary analysis of data collected prospectively from people with a variety of common neuromusculoskeletal diagnoses was conducted. Intake Fear-Avoidance Beliefs Questionnaire (FABQ) data were collected from 17,804 people who had common neuromusculoskeletal conditions and were receiving outpatient rehabilitation in 121 clinics in 26 states (in the United States). Item response theory (IRT) methods were used to analyze the FABQ data, with particular emphasis on differential item functioning among clinically logical groups of subjects, and to identify screening items. The accuracy of screening items for identifying subjects with elevated levels of fear was assessed with receiver operating characteristic analyses. Three items for fear of physical activities and 10 items for fear of work activities represented unidimensional scales with adequate IRT model fit. Differential item functioning was negligible for variables known to affect functional status outcomes: sex, age, symptom acuity, surgical history, pain intensity, condition severity, and impairment. Items that provided maximum information at the median for the FABQ scales were selected as screening items to dichotomize subjects by high versus low levels of fear. The accuracy of the screening items was supported for both scales. This study represents a retrospective analysis, which should be replicated using prospective designs. Future prospective studies should assess the reliability and validity of using one FABQ item to screen people for high levels of fear-avoidance beliefs. The lack of differential item functioning in the FABQ scales in the sample tested in this study suggested that FABQ screening could be useful in routine clinical practice and allowed the development of single-item screening for fear-avoidance beliefs that accurately identified subjects with elevated levels of fear. Because screening was accurate and efficient, single IRT-based FABQ screening items are recommended to facilitate improved evaluation and care of heterogeneous populations of people receiving outpatient rehabilitation.

Multiphoton microscopy guides neurotrophin modification with poly(ethylene glycol) to enhance interstitial diffusion

NASA Astrophysics Data System (ADS)

Stroh, Mark; Zipfel, Warren R.; Williams, Rebecca M.; Ma, Shu Chin; Webb, Watt W.; Saltzman, W. Mark

2004-07-01

Brain-derived neurotrophic factor (BDNF) is a promising therapeutic agent for the treatment of neurodegenerative diseases. However, the limited distribution of this molecule after administration into the brain tissue considerably hampers its efficacy. Here, we show how multiphoton microscopy of fluorescently tagged BDNF in brain-tissue slices provides a useful and rapid screening method for examining the diffusion of large molecules in tissues, and for studying the effects of chemical modifications-for example, conjugating with polyethylene glycol (PEG)-on the diffusion constant. This single variable, obtained by monitoring short-term diffusion in real time, can be effectively used for rational drug design. In this study on fluorescently tagged BDNF and BDNF-PEG, we identify slow diffusion as a major contributing factor to the limited penetration of BDNF, and demonstrate how chemical modification can be used to overcome this barrier.

Piezoresistive cantilever array sensor for consolidated bioprocess monitoring

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Seonghwan Sam; Rahman, Touhidur; Senesac, Larry R

2009-01-01

Cellulolytic microbes occur in diverse natural niches and are being screened for industrial modification and utility. A microbe for Consolidated bioprocessing (CBP) development can rapidly degrade pure cellulose and then ferment the resulting sugars into fuels. To identify and screen for novel microbes for CBP, we have developed a piezoresistive cantilever array sensor which is capable of simultaneous monitoring of glucose and ethanol concentration changes in a phosphate buffer solution. 4-mercaptophenylboronic acid (4-MPBA) and polyethyleneglycol (PEG)-thiol are employed to functionalize each piezoresistive cantilever for glucose and ethanol sensing, respectively. Successful concentration measurements of glucose and ethanol with minimal interferences aremore » obtained with our cantilever array sensor.« less

A screen of chemical modifications identifies position-specific modification by UNA to most potently reduce siRNA off-target effects

PubMed Central

Bramsen, Jesper B.; Pakula, Malgorzata M.; Hansen, Thomas B.; Bus, Claus; Langkjær, Niels; Odadzic, Dalibor; Smicius, Romualdas; Wengel, Suzy L.; Chattopadhyaya, Jyoti; Engels, Joachim W.; Herdewijn, Piet; Wengel, Jesper; Kjems, Jørgen

2010-01-01

Small interfering RNAs (siRNAs) are now established as the preferred tool to inhibit gene function in mammalian cells yet trigger unintended gene silencing due to their inherent miRNA-like behavior. Such off-target effects are primarily mediated by the sequence-specific interaction between the siRNA seed regions (position 2–8 of either siRNA strand counting from the 5′-end) and complementary sequences in the 3′UTR of (off-) targets. It was previously shown that chemical modification of siRNAs can reduce off-targeting but only very few modifications have been tested leaving more to be identified. Here we developed a luciferase reporter-based assay suitable to monitor siRNA off-targeting in a high throughput manner using stable cell lines. We investigated the impact of chemically modifying single nucleotide positions within the siRNA seed on siRNA function and off-targeting using 10 different types of chemical modifications, three different target sequences and three siRNA concentrations. We found several differently modified siRNAs to exercise reduced off-targeting yet incorporation of the strongly destabilizing unlocked nucleic acid (UNA) modification into position 7 of the siRNA most potently reduced off-targeting for all tested sequences. Notably, such position-specific destabilization of siRNA–target interactions did not significantly reduce siRNA potency and is therefore well suited for future siRNA designs especially for applications in vivo where siRNA concentrations, expectedly, will be low. PMID:20453030

Body modification and substance use in adolescents: is there a link?

PubMed

Brooks, Traci L; Woods, Elizabeth R; Knight, John R; Shrier, Lydia A

2003-01-01

To describe the characteristics of body modification among adolescents and to determine whether adolescents who engage in body modification are more likely to screen positive for alcohol and other drug problems than those who do not. Adolescents aged 14 to 18 years presenting to an urban adolescent clinic for routine health care completed a questionnaire about body modification and a substance use assessment battery that included the 17-item Problem Oriented Screening Instrument for Teenagers Alcohol/Drug Use and Abuse Scale (POSIT-ADS). Body modification was defined as piercings (other than one pair of bilateral earlobe piercings in females), tattoos, scarification, and branding. Problem substance use was defined as a POSIT-ADS score > or =1. Data were analyzed using logistic regression to determine whether the presence of body modification was an independent predictor of problem substance use. The 210 participants had a mean (+/- SD) age of 16.0 (+/- 1.4) years and 63% were female. One hundred adolescents (48%) reported at least one body modification; girls were more likely than boys to have body modification (59% vs. 28%, p < or = .0005). Ninety (42%) reported piercings, 22 (10%) tattoos, 9 (4%) scarification, and 1 (< 1%) branding; 21 (10%) had more than one type of body modification. These were in a variety of locations, most commonly the ear and the nose (piercings) or the extremities (tattoos). One-third of the sample (33%) screened positive for problem substance use on the POSIT-ADS questionnaire. Controlling for age, adolescents with body modification had 3.1 times greater odds of problem substance use than those without body modification (95% CI 1.7, 5.8). Body modification was associated with self-reported problem alcohol and other drug use among middle adolescents presenting for primary care. More research is needed to determine the clinical and sociocultural significance of body modification and its relationship to substance use in this population. Copyright Society for Adolescent Medicine, 2003

A voltammetric method for Fe(iii) in blood serum using a screen-printed electrode modified with a Schiff base ionophore.

PubMed

Mittal, Susheel K; Rana, Sonia; Kaur, Navneet; Banks, Craig E

2018-05-23

Herein, a potent electrochemical ionophore (SMS-2) based on a Schiff base has been used for the modification of a screen-printed electrode (SPE). The modified disposable electrode can selectively detect ferric ions in an aqueous medium. Redox behavior of the proposed strip was characterized using cyclic voltammetry (CV) and differential pulse voltammetry (DPV). Incorporation of the ligand in the ink of the SPE enhanced the analytical performance of the electrode, and its surface modification was confirmed by SEM and EDX analysis. Shifting/quenching of the cathodic peak potential of the ionophore after binding with Fe(iii) ions was used to detect and measure the ferric ion concentration. This sensor can identify Fe(iii) in the detection range from 0.625 μM to 7.5 μM. The modified SPE can selectively detect ferric ions in the presence of many other interfering ions and has been successfully used to determine the Fe(iii) content in blood serum samples. The metal-ionophore complex structure was optimized using DFT calculations to study the energetics of the metal-ionophore interactions.

Heterogeneous Antibody-Based Activity Assay for Lysine Specific Demethylase 1 (LSD1) on a Histone Peptide Substrate.

PubMed

Schmitt, Martin L; Ladwein, Kathrin I; Carlino, Luca; Schulz-Fincke, Johannes; Willmann, Dominica; Metzger, Eric; Schilcher, Pierre; Imhof, Axel; Schüle, Roland; Sippl, Wolfgang; Jung, Manfred

2014-07-01

Posttranslational modifications of histone tails are very important for epigenetic gene regulation. The lysine-specific demethylase LSD1 (KDM1A/AOF2) demethylates in vitro predominantly mono- and dimethylated lysine 4 on histone 3 (H3K4) and is a promising target for drug discovery. We report a heterogeneous antibody-based assay, using dissociation-enhanced lanthanide fluorescent immunoassay (DELFIA) for the detection of LSD1 activity. We used a biotinylated histone 3 peptide (amino acids 1-21) with monomethylated lysine 4 (H3K4me) as the substrate for the detection of LSD1 activity with antibody-mediated quantitation of the demethylated product. We have successfully used the assay to measure the potency of reference inhibitors. The advantage of the heterogeneous format is shown with cumarin-based LSD1 inhibitor candidates that we have identified using virtual screening. They had shown good potency in an established LSD1 screening assay. The new heterogeneous assay identified them as false positives, which was verified using mass spectrometry. © 2014 Society for Laboratory Automation and Screening.

A genome-wide map of hyper-edited RNA reveals numerous new sites.

PubMed

Porath, Hagit T; Carmi, Shai; Levanon, Erez Y

2014-08-27

Adenosine-to-inosine editing is one of the most frequent post-transcriptional modifications, manifested as A-to-G mismatches when comparing RNA sequences with their source DNA. Recently, a number of RNA-seq data sets have been screened for the presence of A-to-G editing, and hundreds of thousands of editing sites identified. Here we show that existing screens missed the majority of sites by ignoring reads with excessive ('hyper') editing that do not easily align to the genome. We show that careful alignment and examination of the unmapped reads in RNA-seq studies reveal numerous new sites, usually many more than originally discovered, and in precisely those regions that are most heavily edited. Specifically, we discover 327,096 new editing sites in the heavily studied Illumina Human BodyMap data and more than double the number of detected sites in several published screens. We also identify thousands of new sites in mouse, rat, opossum and fly. Our results establish that hyper-editing events account for the majority of editing sites.

Genome-wide screen for inositol auxotrophy in Saccharomyces cerevisiae implicates lipid metabolism in stress response signaling.

PubMed

Villa-García, Manuel J; Choi, Myung Sun; Hinz, Flora I; Gaspar, María L; Jesch, Stephen A; Henry, Susan A

2011-02-01

Inositol auxotrophy (Ino(-) phenotype) in budding yeast has classically been associated with misregulation of INO1 and other genes involved in lipid metabolism. To identify all non-essential yeast genes that are necessary for growth in the absence of inositol, we carried out a genome-wide phenotypic screening for deletion mutants exhibiting Ino(-) phenotypes under one or more growth conditions. We report the identification of 419 genes, including 385 genes not previously reported, which exhibit this phenotype when deleted. The identified genes are involved in a wide range of cellular processes, but are particularly enriched in those affecting transcription, protein modification, membrane trafficking, diverse stress responses, and lipid metabolism. Among the Ino(-) mutants involved in stress response, many exhibited phenotypes that are strengthened at elevated temperature and/or when choline is present in the medium. The role of inositol in regulation of lipid metabolism and stress response signaling is discussed.

Modification of the rheological properties of screen printing ceramic paints containing gold

NASA Astrophysics Data System (ADS)

Izak, P.; Mastalska-Poplawska, J.; Lis, J.; Stempkowska, A.

2017-01-01

This work presents the results of modification of rheological properties of screen printing paints containing gold. 15 wt% glossy gold paste and 15 wt% glossy liquid gold were used as modifiers containing gold. The study showed that the gold paint for screen printing can be obtained by evaporation of the 15 wt% liquid gold and the golden luster. The compaction process of liquid gold by evaporation is slow and easy to perform in industrial conditions. The second way to adapt the 15 wt% gold ceramic paint for screen printing application depended on adding the aniseed oil and the pine oil. The course of the flow curve of the gold paste without modification indicates that it is shear thinning and shows the desired effect of thixotropy, and even anti-thixotropy, at low shear rates (<50-1 s-1). The introduction of the essential oils eliminates this phenomenon and the paste converts itself from the non-rheostable to the rheostable liquid.

A review of cultural adaptations of screening tools for autism spectrum disorders.

PubMed

Soto, Sandra; Linas, Keri; Jacobstein, Diane; Biel, Matthew; Migdal, Talia; Anthony, Bruno J

2015-08-01

Screening children to determine risk for Autism Spectrum Disorders has become more common, although some question the advisability of such a strategy. The purpose of this systematic review is to identify autism screening tools that have been adapted for use in cultures different from that in which they were developed, evaluate the cultural adaptation process, report on the psychometric properties of the adapted instruments, and describe the implications for further research and clinical practice. A total of 21 articles met criteria for inclusion, reporting on the cultural adaptation of autism screening in 19 countries and in 10 languages. The cultural adaptation process was not always clearly outlined and often did not include the recommended guidelines. Cultural/linguistic modifications to the translated tools tended to increase with the rigor of the adaptation process. Differences between the psychometric properties of the original and adapted versions were common, indicating the need to obtain normative data on populations to increase the utility of the translated tool. © The Author(s) 2014.

Yeast One-Hybrid Gγ Recruitment System for Identification of Protein Lipidation Motifs

PubMed Central

Fukuda, Nobuo; Doi, Motomichi; Honda, Shinya

2013-01-01

Fatty acids and isoprenoids can be covalently attached to a variety of proteins. These lipid modifications regulate protein structure, localization and function. Here, we describe a yeast one-hybrid approach based on the Gγ recruitment system that is useful for identifying sequence motifs those influence lipid modification to recruit proteins to the plasma membrane. Our approach facilitates the isolation of yeast cells expressing lipid-modified proteins via a simple and easy growth selection assay utilizing G-protein signaling that induces diploid formation. In the current study, we selected the N-terminal sequence of Gα subunits as a model case to investigate dual lipid modification, i.e., myristoylation and palmitoylation, a modification that is widely conserved from yeast to higher eukaryotes. Our results suggest that both lipid modifications are required for restoration of G-protein signaling. Although we could not differentiate between myristoylation and palmitoylation, N-terminal position 7 and 8 play some critical role. Moreover, we tested the preference for specific amino-acid residues at position 7 and 8 using library-based screening. This new approach will be useful to explore protein-lipid associations and to determine the corresponding sequence motifs. PMID:23922919

Modifications to the Langley 8-foot transonic pressure tunnel for the laminar flow control experiment

NASA Technical Reports Server (NTRS)

Harris, Charles D.; Brooks, Cuyler W., Jr.

1988-01-01

Modifications to the NASA Langley 8 Foot Transonic Pressure Tunnel in support of the Lamina Flow Control (LFC) Experiment included the installation of a honeymoon and five screens in the settling chamber upstream of the test section 41-long test section liner that extended from the upstream end of the test section contraction region, through the best section, and into the diffuser. The honeycomb and screens were installed as permanent additions to the facility, and the liner was a temporary addition to be removed at the conclusion of the LFC Experiment. These modifications are briefly described.

Validation of Version 3.0 of the Breast Cancer Genetics Referral Screening Tool (B-RST™).

PubMed

Bellcross, Cecelia; Hermstad, April; Tallo, Christine; Stanislaw, Christine

2018-05-08

Despite increased awareness of hereditary breast and ovarian cancer among clinicians and the public, many BRCA1/2 mutation carriers remain unaware of their risk status. The Breast Cancer Genetics Referral Screening Tool (B-RST™) was created and validated to easily identify individuals at increased risk for hereditary breast and ovarian cancer for referral to cancer genetics services. The purpose of this study was to revise B-RST™ to maximize sensitivity against BRCA1/2 mutation status. We analyzed pedigrees of 277 individuals who had undergone BRCA1/2 testing to determine modifications to the B-RST™ 2.0 algorithm that would maximize sensitivity for mutations, while maintaining simplicity. We used McNemar's chi-square test to compare validation measures between the revised version (3.0) and the 2.0 version. Algorithmic changes made to B-RST™ 2.0 increased the sensitivity against BRCA1/2 mutation analysis from 71.1 to 94.0% (P < 0.0001). While specificity decreased, all screen-positive individuals were appropriate for cancer genetics referral, the primary purpose of the tool. Despite calls for BRCA1/2 population screening, there remains a critical need to identify those most at risk who should receive cancer genetics services. B-RST™ version 3.0 demonstrates high sensitivity for BRCA1/2 mutations, yet remains a simple and quick screening tool for at-risk individuals.

Exploring peptide hormones in plants: identification of four peptide hormone-receptor pairs and two post-translational modification enzymes

PubMed Central

MATSUBAYASHI, Yoshikatsu

2018-01-01

The identification of hormones and their receptors in multicellular organisms is one of the most exciting research areas and has lead to breakthroughs in understanding how their growth and development are regulated. In particular, peptide hormones offer advantages as cell-to-cell signals in that they can be synthesized rapidly and have the greatest diversity in their structure and function. Peptides often undergo post-translational modifications and proteolytic processing to generate small oligopeptide hormones. In plants, such small post-translationally modified peptides constitute the largest group of peptide hormones. We initially explored this type of peptide hormone using bioassay-guided fractionation and later by in silico gene screening coupled with biochemical peptide detection, which led to the identification of four types of novel peptide hormones in plants. We also identified specific receptors for these peptides and transferases required for their post-translational modification. This review summarizes how we discovered these peptide hormone–receptor pairs and post-translational modification enzymes, and how these molecules function in plant growth, development and environmental adaptation. PMID:29434080

Exploring peptide hormones in plants: identification of four peptide hormone-receptor pairs and two post-translational modification enzymes.

PubMed

Matsubayashi, Yoshikatsu

2018-01-01

The identification of hormones and their receptors in multicellular organisms is one of the most exciting research areas and has lead to breakthroughs in understanding how their growth and development are regulated. In particular, peptide hormones offer advantages as cell-to-cell signals in that they can be synthesized rapidly and have the greatest diversity in their structure and function. Peptides often undergo post-translational modifications and proteolytic processing to generate small oligopeptide hormones. In plants, such small post-translationally modified peptides constitute the largest group of peptide hormones. We initially explored this type of peptide hormone using bioassay-guided fractionation and later by in silico gene screening coupled with biochemical peptide detection, which led to the identification of four types of novel peptide hormones in plants. We also identified specific receptors for these peptides and transferases required for their post-translational modification. This review summarizes how we discovered these peptide hormone-receptor pairs and post-translational modification enzymes, and how these molecules function in plant growth, development and environmental adaptation.

Cellular and molecular modifier pathways in tauopathies: the big picture from screening invertebrate models.

PubMed

Hannan, Shabab B; Dräger, Nina M; Rasse, Tobias M; Voigt, Aaron; Jahn, Thomas R

2016-04-01

Abnormal tau accumulations were observed and documented in post-mortem brains of patients affected by Alzheimer's disease (AD) long before the identification of mutations in the Microtubule-associated protein tau (MAPT) gene, encoding the tau protein, in a different neurodegenerative disease called Frontotemporal dementia and Parkinsonism linked to chromosome 17 (FTDP-17). The discovery of mutations in the MAPT gene associated with FTDP-17 highlighted that dysfunctions in tau alone are sufficient to cause neurodegeneration. Invertebrate models have been diligently utilized in investigating tauopathies, contributing to the understanding of cellular and molecular pathways involved in disease etiology. An important discovery came with the demonstration that over-expression of human tau in Drosophila leads to premature mortality and neuronal dysfunction including neurodegeneration, recapitulating some key neuropathological features of the human disease. The simplicity of handling invertebrate models combined with the availability of a diverse range of experimental resources make these models, in particular Drosophila a powerful invertebrate screening tool. Consequently, several large-scale screens have been performed using Drosophila, to identify modifiers of tau toxicity. The screens have revealed not only common cellular and molecular pathways, but in some instances the same modifier has been independently identified in two or more screens suggesting a possible role for these modifiers in regulating tau toxicity. The purpose of this review is to discuss the genetic modifier screens on tauopathies performed in Drosophila and C. elegans models, and to highlight the common cellular and molecular pathways that have emerged from these studies. Here, we summarize results of tau toxicity screens providing mechanistic insights into pathological alterations in tauopathies. Key pathways or modifiers that have been identified are associated with a broad range of processes including, but not limited to, phosphorylation, cytoskeleton organization, axonal transport, regulation of cellular proteostasis, transcription, RNA metabolism, cell cycle regulation, and apoptosis. We discuss the utility and application of invertebrate models in elucidating the cellular and molecular functions of novel and uncharacterized disease modifiers identified in large-scale screens as well as for investigating the function of genes identified as risk factors in genome-wide association studies from human patients in the post-genomic era. In this review, we combined and summarized several large-scale modifier screens performed in invertebrate models to identify modifiers of tau toxicity. A summary of the screens show that diverse cellular processes are implicated in the modification of tau toxicity. Kinases and phosphatases are the most predominant class of modifiers followed by components required for cellular proteostasis and axonal transport and cytoskeleton elements. © 2016 International Society for Neurochemistry.

Application of a screening method in assessing occupational safety and health of computer workstations.

PubMed

Niskanen, Toivo; Lehtelä, Jouni; Länsikallio, Riina

2014-01-01

Employers and workers need concrete guidance to plan and implement changes in the ergonomics of computer workstations. The Näppärä method is a screening tool for identifying problems requiring further assessment and corrective actions. The aim of this study was to assess the work of occupational safety and health (OSH) government inspectors who used Näppärä as part of their OSH enforcement inspections (430 assessments) related to computer work. The modifications in workstation ergonomics involved mainly adjustments to the screen, mouse, keyboard, forearm supports, and chair. One output of the assessment is an index indicating the percentage of compliance items. This method can be considered as exposure assessment and ergonomics intervention used as a benchmark for the level of ergonomics. Future research can examine whether the effectiveness of participatory ergonomics interventions should be investigated with Näppärä.

Discovery of a novel general anesthetic chemotype using high-throughput screening.

PubMed

McKinstry-Wu, Andrew R; Bu, Weiming; Rai, Ganesha; Lea, Wendy A; Weiser, Brian P; Liang, David F; Simeonov, Anton; Jadhav, Ajit; Maloney, David J; Eckenhoff, Roderic G

2015-02-01

The development of novel anesthetics has historically been a process of combined serendipity and empiricism, with most recent new anesthetics developed via modification of existing anesthetic structures. Using a novel high-throughput screen employing the fluorescent anesthetic 1-aminoanthracene and apoferritin as a surrogate for on-pathway anesthetic protein target(s), we screened a 350,000 compound library for competition with 1-aminoanthracene-apoferritin binding. Hit compounds meeting structural criteria had their binding affinities for apoferritin quantified with isothermal titration calorimetry and were tested for γ-aminobutyric acid type A receptor binding using a flunitrazepam binding assay. Chemotypes with a strong presence in the top 700 and exhibiting activity via isothermal titration calorimetry were selected for medicinal chemistry optimization including testing for anesthetic potency and toxicity in an in vivo Xenopus laevis tadpole assay. Compounds with low toxicity and high potency were tested for anesthetic potency in mice. From an initial chemical library of more than 350,000 compounds, we identified 2,600 compounds that potently inhibited 1-aminoanthracene binding to apoferritin. A subset of compounds chosen by structural criteria (700) was successfully reconfirmed using the initial assay. Based on a strong presence in both the initial and secondary screens the 6-phenylpyridazin-3(2H)-one chemotype was assessed for anesthetic activity in tadpoles. Medicinal chemistry efforts identified four compounds with high potency and low toxicity in tadpoles, two were found to be effective novel anesthetics in mice. The authors demonstrate the first use of a high-throughput screen to successfully identify a novel anesthetic chemotype and show mammalian anesthetic activity for members of that chemotype.

Inference of RhoGAP/GTPase regulation using single-cell morphological data from a combinatorial RNAi screen.

PubMed

Nir, Oaz; Bakal, Chris; Perrimon, Norbert; Berger, Bonnie

2010-03-01

Biological networks are highly complex systems, consisting largely of enzymes that act as molecular switches to activate/inhibit downstream targets via post-translational modification. Computational techniques have been developed to perform signaling network inference using some high-throughput data sources, such as those generated from transcriptional and proteomic studies, but comparable methods have not been developed to use high-content morphological data, which are emerging principally from large-scale RNAi screens, to these ends. Here, we describe a systematic computational framework based on a classification model for identifying genetic interactions using high-dimensional single-cell morphological data from genetic screens, apply it to RhoGAP/GTPase regulation in Drosophila, and evaluate its efficacy. Augmented by knowledge of the basic structure of RhoGAP/GTPase signaling, namely, that GAPs act directly upstream of GTPases, we apply our framework for identifying genetic interactions to predict signaling relationships between these proteins. We find that our method makes mediocre predictions using only RhoGAP single-knockdown morphological data, yet achieves vastly improved accuracy by including original data from a double-knockdown RhoGAP genetic screen, which likely reflects the redundant network structure of RhoGAP/GTPase signaling. We consider other possible methods for inference and show that our primary model outperforms the alternatives. This work demonstrates the fundamental fact that high-throughput morphological data can be used in a systematic, successful fashion to identify genetic interactions and, using additional elementary knowledge of network structure, to infer signaling relations.

KpnBI is the prototype of a new family (IE) of bacterial type I restriction-modification system

PubMed Central

Chin, V.; Valinluck, V.; Magaki, S.; Ryu, J.

2004-01-01

KpnBI is a restriction-modification (R-M) system recognized in the GM236 strain of Klebsiella pneumoniae. Here, the KpnBI modification genes were cloned into a plasmid using a modification expression screening method. The modification genes that consist of both hsdM (2631 bp) and hsdS (1344 bp) genes were identified on an 8.2 kb EcoRI chromosomal fragment. These two genes overlap by one base and share the same promoter located upstream of the hsdM gene. Using recently developed plasmid R-M tests and a computer program RM Search, the DNA recognition sequence for the KpnBI enzymes was identified as a new 8 nt sequence containing one degenerate base with a 6 nt spacer, CAAANNNNNNRTCA. From Dam methylation and HindIII sensitivity tests, the methylation loci were predicted to be the italicized third adenine in the 5′ specific region and the adenine opposite the italicized thymine in the 3′ specific region. Combined with previous sequence data for hsdR, we concluded that the KpnBI system is a typical type I R-M system. The deduced amino acid sequences of the three subunits of the KpnBI system show only limited homologies (25 to 33% identity) at best, to the four previously categorized type I families (IA, IB, IC, and ID). Furthermore, their identity scores to other uncharacterized putative genome type I sequences were 53% at maximum. Therefore, we propose that KpnBI is the prototype of a new ‘type IE’ family. PMID:15475385

Akt3 is a privileged first responder in isozyme-specific electrophile response.

PubMed

Long, Marcus J C; Parvez, Saba; Zhao, Yi; Surya, Sanjna L; Wang, Yiran; Zhang, Sheng; Aye, Yimon

2017-03-01

Isozyme-specific post-translational regulation fine tunes signaling events. However, redundancy in sequence or activity renders links between isozyme-specific modifications and downstream functions uncertain. Methods to study this phenomenon are underdeveloped. Here we use a redox-targeting screen to reveal that Akt3 is a first-responding isozyme sensing native electrophilic lipids. Electrophile modification of Akt3 modulated downstream pathway responses in cells and Danio rerio (zebrafish) and markedly differed from Akt2-specific oxidative regulation. Digest MS sequencing identified Akt3 C119 as the privileged cysteine that senses 4-hydroxynonenal. A C119S Akt3 mutant was hypomorphic for all downstream phenotypes shown by wild-type Akt3. This study documents isozyme-specific and chemical redox signal-personalized physiological responses.

Walla Walla River Basin Fish Screen Evaluations; Nursery Bridge Fishway and Garden City/Lowden II Sites, 2005-2006 Progress Report.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chamness, Mickie

2006-06-01

Pacific Northwest National Laboratory (PNNL) evaluated two fish screen facilities in the Walla Walla River basin in 2005 and early 2006. The Garden City/Lowden screen site was evaluated in April and June 2005 to determine whether the fish screens met National Marine Fisheries Service criteria to provide safe passage for juvenile salmonids. Louvers behind the screens at the Nursery Bridge Fishway were modified in fall 2005 in an attempt to minimize high approach velocities. PNNL evaluated the effects of those modifications in March 2006. Results of the Garden City/Lowden evaluations indicate the site performs well at varying river levels andmore » canal flows. Approach velocities did not exceed 0.4 feet per second (fps) at any time. Sweep velocities increased toward the fish ladder in March but not in June. The air-burst mechanism appears to keep large debris off the screens, although it does not prevent algae and periphyton from growing on the screen face, especially near the bottom of the screens. At Nursery Bridge, results indicate all the approach velocities were below 0.4 fps under the moderate river levels and operational conditions encountered on March 7, 2006. Sweep did not consistently increase toward the fish ladder, but the site generally met the criteria for safe passage of juvenile salmonids. Modifications to the louvers seem to allow more control over the amount of water moving through the screens. We will measure approach velocities when river levels are higher to determine whether the louver modifications can help correct excessive approach velocities under a range of river levels and auxiliary water supply flows.« less

Current Screening Procedures for the Usher Syndrome at Residential Schools for the Deaf.

ERIC Educational Resources Information Center

Day, Creagh Walker

1982-01-01

The results indicated that 53 percent of the schools that responded are screening students for Usher syndrome. One-half of the schools with screening programs offered some support services: personal counseling, genetic counseling, curricular modifications, and vocational counseling. (Author)

Nuclear morphology for the detection of alterations in bronchial cells from lung cancer: an attempt to improve sensitivity and specificity.

PubMed

Fafin-Lefevre, Mélanie; Morlais, Fabrice; Guittet, Lydia; Clin, Bénédicte; Launoy, Guy; Galateau-Sallé, Françoise; Plancoulaine, Benoît; Herlin, Paulette; Letourneux, Marc

2011-08-01

To identify which morphologic or densitometric parameters are modified in cell nuclei from bronchopulmonary cancer based on 18 parameters involving shape, intensity, chromatin, texture, and DNA content and develop a bronchopulmonary cancer screening method relying on analysis of sputum sample cell nuclei. A total of 25 sputum samples from controls and 22 bronchial aspiration samples from patients presenting with bronchopulmonary cancer who were professionally exposed to cancer were used. After Feulgen staining, 18 morphologic and DNA content parameters were measured on cell nuclei, via image cytom- etry. A method was developed for analyzing distribution quantiles, compared with simply interpreting mean values, to characterize morphologic modifications in cell nuclei. Distribution analysis of parameters enabled us to distinguish 13 of 18 parameters that demonstrated significant differences between controls and cancer cases. These parameters, used alone, enabled us to distinguish two population types, with both sensitivity and specificity > 70%. Three parameters offered 100% sensitivity and specificity. When mean values offered high sensitivity and specificity, comparable or higher sensitivity and specificity values were observed for at least one of the corresponding quantiles. Analysis of modification in morphologic parameters via distribution analysis proved promising for screening bronchopulmonary cancer from sputum.

Modifications to the Current EPA Endocrine Disruptor Screening Program's Tier 1 Female Pubertal Protocol: A Study on the Effects of the Chlorotriazine Simazine

EPA Science Inventory

Currently the US EPA is implementing a screening program for environmental endocrine disruptors. One of the in vivo assays in the Tier 1 Screen of the Endocrine Disruptors Screening Program (EDSP) is a female pubertal assay. In this study we examined the chlorotriazine simazine, ...

Discovery of a Novel General Anesthetic Chemotype Using High-throughput Screening

PubMed Central

McKinstry-Wu, Andrew R.; Bu, Weiming; Rai, Ganesha; Lea, Wendy A.; Weiser, Brian P.; Liang, David F.; Simeonov, Anton; Jadhav, Ajit; Maloney, David J.; Eckenhoff, Roderic G.

2014-01-01

Background The development of novel anesthetics has historically been a process of combined serendipity and empiricism, with most recent new anesthetics developed via modification of existing anesthetic structures. Methods Using a novel high-throughput screen employing the fluorescent anesthetic 1-aminoanthracene (1-AMA) and apoferritin as a surrogate for on-pathway anesthetic protein target(s), we screened a 350,000 compound library for competition with 1-AMA-apoferritin binding. Hit compounds meeting structural criteria had their binding affinities for apoferritin quantified with isothermal titration calorimetry and were tested for γ-aminobutyric acid type A-receptor binding using a flunitrazepam binding assay. Chemotypes with a strong presence in the top 700 and exhibiting activity via isothermal titration calorimetry were selected for medicinal chemistry optimization including testing for anesthetic potency and toxicity in an in vivo Xenopus laevis tadpole assay. Compounds with low toxicity and high potency were tested for anesthetic potency in mice. Results From an initial chemical library of over 350,000 compounds, we identified 2,600 compounds that potently inhibited 1-AMA binding to apoferritin. A subset of compounds chosen by structural criteria (700) was successfully reconfirmed using the initial assay. Based upon a strong presence in both the initial and secondary screens the 6-phenylpyridazin-3(2H)-one chemotype was assessed for anesthetic activity in tadpoles. Medicinal chemistry efforts identified four compounds with high potency and low toxicity in tadpoles, two were found to be effective novel anesthetics in mice. Conclusions We demonstrate the first use of a high-throughput screen to successfully identify a novel anesthetic chemotype and show mammalian anesthetic activity for members of that chemotype. PMID:25603205

A bacterial genetic selection system for ubiquitylation cascade discovery.

PubMed

Levin-Kravets, Olga; Tanner, Neta; Shohat, Noa; Attali, Ilan; Keren-Kaplan, Tal; Shusterman, Anna; Artzi, Shay; Varvak, Alexander; Reshef, Yael; Shi, Xiaojing; Zucker, Ori; Baram, Tamir; Katina, Corine; Pilzer, Inbar; Ben-Aroya, Shay; Prag, Gali

2016-11-01

About one-third of the eukaryotic proteome undergoes ubiquitylation, but the enzymatic cascades leading to substrate modification are largely unknown. We present a genetic selection tool that utilizes Escherichia coli, which lack deubiquitylases, to identify interactions along ubiquitylation cascades. Coexpression of split antibiotic resistance protein tethered to ubiquitin and ubiquitylation target together with a functional ubiquitylation apparatus results in a covalent assembly of the resistance protein, giving rise to bacterial growth on selective media. We applied the selection system to uncover an E3 ligase from the pathogenic bacteria EHEC and to identify the epsin ENTH domain as an ultraweak ubiquitin-binding domain. The latter was complemented with a structure-function analysis of the ENTH-ubiquitin interface. We also constructed and screened a yeast fusion library, discovering Sem1 as a novel ubiquitylation substrate of Rsp5 E3 ligase. Collectively, our selection system provides a robust high-throughput approach for genetic studies of ubiquitylation cascades and for small-molecule modulator screening.

The Deubiquitinating Enzyme UBPY Is Required for Lysosomal Biogenesis and Productive Autophagy in Drosophila.

PubMed

Jacomin, Anne-Claire; Bescond, Amandine; Soleilhac, Emmanuelle; Gallet, Benoît; Schoehn, Guy; Fauvarque, Marie-Odile; Taillebourg, Emmanuel

2015-01-01

Autophagy is a catabolic process that delivers cytoplasmic components to the lysosomes. Protein modification by ubiquitination is involved in this pathway: it regulates the stability of autophagy regulators such as BECLIN-1 and it also functions as a tag targeting specific substrates to autophagosomes. In order to identify deubiquitinating enzymes (DUBs) involved in autophagy, we have performed a genetic screen in the Drosophila larval fat body. This screen identified Uch-L3, Usp45, Usp12 and Ubpy. In this paper, we show that Ubpy loss of function results in the accumulation of autophagosomes due to a blockade of the autophagy flux. Furthermore, analysis by electron and confocal microscopy of Ubpy-depleted fat body cells revealed altered lysosomal morphology, indicating that Ubpy inactivation affects lysosomal maintenance and/or biogenesis. Lastly, we have shown that shRNA mediated inactivation of UBPY in HeLa cells affects autophagy in a different way: in UBPY-depleted HeLa cells autophagy is deregulated.

The story of protein arginine methylation: characterization, regulation, and function.

PubMed

Peng, Chao; Wong, Catherine Cl

2017-02-01

Arginine methylation is an important post-translational modification (PTM) in cells, which is catalyzed by a group of protein arginine methyltransferases (PRMTs). It plays significant roles in diverse cellular processes and various diseases. Misregulation and aberrant expression of PRMTs can provide potential biomarkers and therapeutic targets for drug discovery. Areas covered: Herein, we review the arginine methylation literature and summarize the methodologies for the characterization of this modification, as well as describe the recent insights into arginine methyltransferases and their biological functions in diseases. Expert commentary: Benefits from the enzyme-based large-scale screening approach, the novel affinity enrichment strategies, arginine methylated protein family is the focus of attention. Although a number of arginine methyltransferases and related substrates are identified, the catalytic mechanism of different types of PRMTs remains unclear and few related demethylases are characterized. Novel functional studies continuously reveal the importance of this modification in the cell cycle and diseases. A deeper understanding of arginine methylated proteins, modification sites, and their mechanisms of regulation is needed to explore their role in life processes, especially their relationship with diseases, thus accelerating the generation of potent, selective, cell-penetrant drug candidates.

Application of mass spectrometry technologies for the discovery of low-molecular weight modulators of enzymes and protein-protein interactions.

PubMed

Zehender, Hartmut; Mayr, Lorenz M

2007-10-01

In recent years, mass spectrometry has gained widespread use as an assay and screening technology in drug discovery because it enables sensitive, label-free detection of low-molecular weight modulators of biomolecules as well as sensitive and accurate detection of high-molecular weight modifications of biomolecules. Electrospray and matrix-assisted laser desorption ionization are the most widely used ionization techniques to identify chemical compounds interfering with enzymatic function, receptor-ligand binding or molecules modulating a protein-protein interaction of interest. Mass spectrometry based techniques are no longer restricted to screening in biochemical assay systems but have now become also applicable to imaging of biomolecules and chemical compounds in cell-based assay systems and even in highly complex tissue sections.

Discovery of novel hedgehog antagonists from cell-based screening: Isosteric modification of p38 bisamides as potent inhibitors of SMO.

PubMed

Yang, Bin; Hird, Alexander W; Russell, Daniel John; Fauber, Benjamin P; Dakin, Les A; Zheng, Xiaolan; Su, Qibin; Godin, Robert; Brassil, Patrick; Devereaux, Erik; Janetka, James W

2012-07-15

Cell-based subset screening of compounds using a Gli transcription factor reporter cell assay and shh stimulated cell differentiation assay identified a series of bisamide compounds as hedgehog pathway inhibitors with good potency. Using a ligand-based optimization strategy, heteroaryl groups were utilized as conformationally restricted amide isosteres replacing one of the amides which significantly increased their potency against SMO and the hedgehog pathway while decreasing activity against p38α kinase. We report herein the identification of advanced lead compounds such as imidazole 11c and 11f encompassing good p38α selectivity, low nanomolar potency in both cell assays, excellent physiochemical properties and in vivo pharmacokinetics. Copyright © 2012 Elsevier Ltd. All rights reserved.

DNA markers in molecular diagnostics for hepatocellular carcinoma

PubMed Central

Su, Ying-Hsiu; Lin, Selena Y; Song, Wei; Jain, Surbhi

2015-01-01

Hepatocellular carcinoma (HCC) is the one of the leading causes of cancer mortality in the world, mainly due to the difficulty of early detection and limited therapeutic options. The implementation of HCC surveillance programs in well-defined, high-risk populations were only able to detect about 40–50% of HCC at curative stages (Barcelona Clinic Liver Cancer stages 0 & 1) due to the low sensitivities of the current screening methods. The advance of sequencing technologies has identified numerous modifications as potential candidate DNA markers for diagnosis/surveillance. Here we aim to provide an overview of the DNA alterations that result in activation of cancer pathways known to potentially drive HCC carcinogenesis and to summarize performance characteristics of each DNA marker in the periphery (blood or urine) for HCC screening. PMID:25098554

Uncovering the Protein Lysine and Arginine Methylation Network in Arabidopsis Chloroplasts

PubMed Central

Mininno, Morgane; Brugière, Sabine; Gilgen, Annabelle; Ma, Sheng; Mazzoleni, Meryl; Gigarel, Océane; Martin-Laffon, Jacqueline; Ferro, Myriam; Ravanel, Stéphane

2014-01-01

Post-translational modification of proteins by the addition of methyl groups to the side chains of Lys and Arg residues is proposed to play important roles in many cellular processes. In plants, identification of non-histone methylproteins at a cellular or subcellular scale is still missing. To gain insights into the extent of this modification in chloroplasts we used a bioinformatics approach to identify protein methyltransferases targeted to plastids and set up a workflow to specifically identify Lys and Arg methylated proteins from proteomic data used to produce the Arabidopsis chloroplast proteome. With this approach we could identify 31 high-confidence Lys and Arg methylation sites from 23 chloroplastic proteins, of which only two were previously known to be methylated. These methylproteins are split between the stroma, thylakoids and envelope sub-compartments. They belong to essential metabolic processes, including photosynthesis, and to the chloroplast biogenesis and maintenance machinery (translation, protein import, division). Also, the in silico identification of nine protein methyltransferases that are known or predicted to be targeted to plastids provided a foundation to build the enzymes/substrates relationships that govern methylation in chloroplasts. Thereby, using in vitro methylation assays with chloroplast stroma as a source of methyltransferases we confirmed the methylation sites of two targets, plastid ribosomal protein L11 and the β-subunit of ATP synthase. Furthermore, a biochemical screening of recombinant chloroplastic protein Lys methyltransferases allowed us to identify the enzymes involved in the modification of these substrates. The present study provides a useful resource to build the methyltransferases/methylproteins network and to elucidate the role of protein methylation in chloroplast biology. PMID:24748391

The Potential of Clear Sky Carbon Dioxide Satellite Retrievals

NASA Astrophysics Data System (ADS)

Nelson, R.; O'Dell, C.

2013-12-01

It has been shown that neglecting scattering and absorption by aerosols and thin clouds can lead to significant errors in retrievals of the column-averaged dry-air mole fraction of carbon dioxide (XCO2) from space-based measurements of near-infrared reflected sunlight. These clear sky retrievals, which assume no aerosol effects, are desirable because of their high computational efficiency relative to common full physics retrievals. Further, clear sky retrievals may be able to make higher quality measurements relative to the full physics approach because they may introduce fewer potential biases under certain circumstances. These biases can appear when we try to retrieve clouds and aerosols in the full physics methods when there are none actually present. Recent work has shown that intelligent pre-screening can remove soundings with large light-path modifications over ocean surfaces. In this work, we test the hypothesis that intelligent pre-screening of soundings may be successfully used over land surfaces as well as oceans, which would allow clear sky retrievals to be applicable over all surfaces. We also test the hypothesis that major light path modification effects associated with aerosols can be identified based on spectral tests at 0.76, 1.6, and 2 microns. This presentation summarizes our study of both simulated data and satellite observations from the GOSAT instrument in order to assess the effectiveness of using a clear sky retrieval algorithm coupled with intelligent pre-screening to accurately measure carbon dioxide from space-borne instruments.

Homogeneous screening assay for human tankyrase.

PubMed

Narwal, Mohit; Fallarero, Adyary; Vuorela, Pia; Lehtiö, Lari

2012-06-01

Tankyrase, a member of human PARP protein superfamily, catalyzes a covalent post-translational modification of substrate proteins. This modification, poly(ADP-ribos)ylation, leads to changes in protein interactions and modifies downstream signaling events. Tankyrase 1 is a potential drug target due to its functions in telomere homeostasis and in Wnt signaling. We describe here optimization and application of an activity-based homogenous assay for tankyrase inhibitors in a high-throughput screening format. The method measures the consumption of substrate by the chemical conversion of the remaining NAD(+) into a stable fluorescent condensation product. Conditions were optimized to measure the enzymatic auto-modification of a recombinant catalytic fragment of tankyrase 1. The fluorescence assay is inexpensive, operationally easy and performs well according to the statistical analysis (Z'= 0.7). A validatory screen with a natural product library confirmed suitability of the assay for finding new tankyrase inhibitors. Flavone was the most potent (IC(50)=325 nM) hit from the natural compounds. A flavone derivative, apigenin, and isopropyl gallate showed potency on the micromolar range, but displayed over 30-fold selectivity for tankyrase over the studied isoenzymes PARP1 and PARP2. The assay is robust and will be useful for screening new tankyrase inhibitors.

High-throughput Screening Identifies Aclacinomycin as a Radiosensitizer of EGFR-Mutant Non-Small Cell Lung Cancer1

PubMed Central

Bennett, Daniel C; Charest, Jonathan; Sebolt, Katrina; Lehrman, Mark; Rehemtulla, Alnawaz; Contessa, Joseph N

2013-01-01

The endoplasmic reticulum (ER) provides a specialized environment for the folding and modification of trans-membrane proteins, including receptor tyrosine kinases (RTKs), which are vital for the growth and survival of malignancies. To identify compounds which disrupt the function of the ER and thus could potentially impair cancer cell survival signaling, we adapted a set of glycosylation-sensitive luciferase reporters for the development and optimization of a cell-based high-throughput screen (HTS). Secondary screens for false-positive luciferase activation and tertiary lectin-based and biochemical analyses were also devised for compound triage. Through a pilot screen of 2802 compounds from the National Cancer Institute (NCI) chemical libraries, we identified aclacinomycin (Acm) as a compound that preferentially affects ER function. We report that Acm reduces plasma membrane expression of glycoproteins including epidermal growth factor receptor (EGFR) and Met but does not inhibit N-linked glycosylation or generalized protein translation. Fluorescence microscopy co-localization experiments were also performed and demonstrated Acm accumulation in the ER in further support of the overall HTS design. The consequences of Acm treatment on cell survival were analyzed through clonogenic survival analysis. Consistent with the reduction of EGFR levels, pretreatment with Acm sensitizes the EGFR-mutant non-small cell lung cancer (NSCLC) cell lines HCC827 and HCC2935 to ionizing radiation and did not affect the sensitivity of the RTK-independent and KRAS-mutant A549 NSCLC cell line. Thus, Acm and similar compounds targeting the ER may represent a novel approach for radiosensitizing tumor cells dependent on RTK function. PMID:23730419

Assessment of critical minerals: Updated application of an early-warning screening methodology

USGS Publications Warehouse

McCullough, Erin A.; Nassar, Nedal

2017-01-01

Increasing reliance on non-renewable mineral resources reinforces the need for identifying potential supply constraints before they occur. The US National Science and Technology Council recently released a report that outlines a methodology for screening potentially critical minerals based on three indicators: supply risk (R), production growth (G), and market dynamics (M). This early-warning screening was initially applied to 78 minerals across the years 1996 to 2013 and identified a subset of minerals as “potentially critical” based on the geometric average of these indicators—designated as criticality potential (C). In this study, the screening methodology has been updated to include data for 2014, as well as to incorporate revisions and modifications to the data, where applicable. Overall, C declined in 2014 for the majority of minerals examined largely due to decreases in production concentration and price volatility. However, the results vary considerably across minerals, with some minerals, such as gallium, recording increases for all three indicators. In addition to assessing magnitudinal changes, this analysis also examines the significance of the change relative to historical variation for each mineral. For example, although mined nickel’s R declined modestly in 2014 in comparison to that of other minerals, it was by far the largest annual change recorded for mined nickel across all years examined and is attributable to Indonesia’s ban on the export of unprocessed minerals. Based on the 2014 results, 20 minerals with the highest C values have been identified for further study including the rare earths, gallium, germanium, rhodium, tantalum, and tungsten.

Barriers to Recruitment and Adherence in a Randomized Controlled Diet and Exercise Weight Loss Intervention Among Minority Breast Cancer Survivors.

PubMed

Aycinena, A Corina; Valdovinos, Cristina; Crew, Katherine D; Tsai, Wei Yann; Mata, Jennie M; Sandoval, Rossy; Hershman, Dawn; Greenlee, Heather

2017-02-01

Minority recruitment to cancer trials is low and there are limited data on minority adherence to lifestyle modification interventions. We examined factors related to recruitment and adherence to a pilot weight loss intervention among Hispanic and black breast cancer survivors. Participants completed a detailed screening interview to assess barriers to enrollment. An index was created to assess adherence at 6 months. 112 potentially eligible women were identified; 66 consented and completed a screening interview. After screening, 9 were ineligible; 15 opted to not enroll; and 42 were randomized. Among eligible women, earlier stage at diagnosis, treatment type, and negative beliefs related to exercise and diet after diagnosis were negatively associated with study enrollment (P < 0.05). Self-reported barriers to adherence included fatigue, family responsibilities, illness, work, transportation, and negative perceptions of exercise and diet. Results from this study emphasize the need to adapt recruitment and adherence strategies to address these factors.

Immobilized OBOC combinatorial bead array to facilitate multiplicative screening.

PubMed

Xiao, Wenwu; Bononi, Fernanda C; Townsend, Jared; Li, Yuanpei; Liu, Ruiwu; Lam, Kit S

2013-07-01

One-bead-one-compound (OBOC) combinatorial library screening has been broadly utilized for the last two decades to identify small molecules, peptides or peptidomimetics targeting variable screening probes such as cell surface receptors, bacteria, protein kinases, phosphatases, proteases etc. In previous screening methods, library beads were suspended in solution and screened against one single probe. Only the positive beads were tracked and isolated for additional screens and finally selected for chemical decoding. During this process, the remaining negative beads were not tracked and discarded. Here we report a novel bead immobilization method such that a bead library array can be conveniently prepared and screened in its entirety, sequentially many times with a series of distinct probes. This method not only allows us to increase the screening efficiency but also permits us to determine the binding profile of each and every library bead against a large number of target receptors. As proof of concept, we serially screened a random OBOC disulfide containing cyclic heptapeptide library with three water soluble dyes as model probes: malachite green, bromocresol purple and indigo carmine. This multiplicative screening approach resulted in a rapid determination of the binding profile of each and every bead respective to each of the three dyes. Beads that interacted with malachite green only, bromocresol purple only, or both indigo carmine and bromocresol purple were isolated, and their peptide sequences were determined with microsequencer. Ultimately, the novel OBOC multiplicative screening approach could play a key role in the enhancement of existing on-bead assays such as whole cell binding, bacteria binding, protein binding, posttranslational modifications etc. with increased efficiency, capacity, and specificity.

Evaluating Sense Codon Reassignment with a Simple Fluorescence Screen.

PubMed

Biddle, Wil; Schmitt, Margaret A; Fisk, John D

2015-12-22

Understanding the interactions that drive the fidelity of the genetic code and the limits to which modifications can be made without breaking the translational system has practical implications for understanding the molecular mechanisms of evolution as well as expanding the set of encodable amino acids, particularly those with chemistries not provided by Nature. Because 61 sense codons encode 20 amino acids, reassigning the meaning of sense codons provides an avenue for biosynthetic modification of proteins, furthering both fundamental and applied biochemical research. We developed a simple screen that exploits the absolute requirement for fluorescence of an active site tyrosine in green fluorescent protein (GFP) to probe the pliability of the degeneracy of the genetic code. Our screen monitors the restoration of the fluorophore of GFP by incorporation of a tyrosine in response to a sense codon typically assigned another meaning in the genetic code. We evaluated sense codon reassignment at four of the 21 sense codons read through wobble interactions in Escherichia coli using the Methanocaldococcus jannaschii orthogonal tRNA/aminoacyl tRNA synthetase pair originally developed and commonly used for amber stop codon suppression. By changing only the anticodon of the orthogonal tRNA, we achieved sense codon reassignment efficiencies between 1% (Phe UUU) and 6% (Lys AAG). Each of the orthogonal tRNAs preferentially decoded the codon traditionally read via a wobble interaction in E. coli with the exception of the orthogonal tRNA with an AUG anticodon, which incorporated tyrosine in response to both the His CAU and His CAC codons with approximately equal frequencies. We applied our screen in a high-throughput manner to evaluate a 10(9)-member combined tRNA/aminoacyl tRNA synthetase library to identify improved sense codon reassigning variants for the Lys AAG codon. A single rapid screen with the ability to broadly evaluate reassignable codons will facilitate identification and improvement of the combinations of sense codons and orthogonal pairs that display efficient reassignment.

Improving Alcohol Screening for College Students: Screening for Alcohol Misuse amongst College Students with a Simple Modification to the CAGE Questionnaire

ERIC Educational Resources Information Center

Taylor, Purcell; El-Sabawi, Taleed; Cangin, Causenge

2016-01-01

Objective: To improve the CAGE (Cut down, Annoyed, Guilty, Eye opener) questionnaire's predictive accuracy in screening college students. Participants: The sample consisted of 219 midwestern university students who self-administered a confidential survey. Methods: Exploratory factor analysis, confirmatory factor analysis, receiver operating…

Engineering of a DNA Polymerase for Direct m6 A Sequencing.

PubMed

Aschenbrenner, Joos; Werner, Stephan; Marchand, Virginie; Adam, Martina; Motorin, Yuri; Helm, Mark; Marx, Andreas

2018-01-08

Methods for the detection of RNA modifications are of fundamental importance for advancing epitranscriptomics. N 6 -methyladenosine (m 6 A) is the most abundant RNA modification in mammalian mRNA and is involved in the regulation of gene expression. Current detection techniques are laborious and rely on antibody-based enrichment of m 6 A-containing RNA prior to sequencing, since m 6 A modifications are generally "erased" during reverse transcription (RT). To overcome the drawbacks associated with indirect detection, we aimed to generate novel DNA polymerase variants for direct m 6 A sequencing. Therefore, we developed a screen to evolve an RT-active KlenTaq DNA polymerase variant that sets a mark for N 6 -methylation. We identified a mutant that exhibits increased misincorporation opposite m 6 A compared to unmodified A. Application of the generated DNA polymerase in next-generation sequencing allowed the identification of m 6 A sites directly from the sequencing data of untreated RNA samples. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Clinical analysis of PMS2: mutation detection and avoidance of pseudogenes.

PubMed

Vaughn, Cecily P; Robles, Jorge; Swensen, Jeffrey J; Miller, Christine E; Lyon, Elaine; Mao, Rong; Bayrak-Toydemir, Pinar; Samowitz, Wade S

2010-05-01

Germline mutation detection in PMS2, one of four mismatch repair genes associated with Lynch syndrome, is greatly complicated by the presence of numerous pseudogenes. We used a modification of a long-range PCR method to evaluate PMS2 in 145 clinical samples. This modification avoids potential interference from the pseudogene PMS2CL by utilizing a long-range product spanning exons 11-15, with the forward primer anchored in exon 10, an exon not shared by PMS2CL. Large deletions were identified by MLPA. Pathogenic PMS2 mutations were identified in 22 of 59 patients whose tumors showed isolated loss of PMS2 by immunohistochemistry (IHC), the IHC profile most commonly associated with a germline PMS2 mutation. Three additional patients with pathogenic mutations were identified from 53 samples without IHC data. Thirty-seven percent of the identified mutations were large deletions encompassing one or more exons. In 27 patients whose tumors showed absence of either another protein or combination of proteins, no pathogenic mutations were identified. We conclude that modified long-range PCR can be used to preferentially amplify the PMS2 gene and avoid pseudogene interference, thus providing a clinically useful germline analysis of PMS2. Our data also support the use of IHC screening to direct germline testing of PMS2. (c) 2010 Wiley-Liss, Inc.

Adjustment of Trehalose Metabolism in Wine Saccharomyces cerevisiae Strains To Modify Ethanol Yields

PubMed Central

Rossouw, D.; Heyns, E. H.; Setati, M. E.; Bosch, S.

2013-01-01

The ability of Saccharomyces cerevisiae to efficiently produce high levels of ethanol through glycolysis has been the focus of much scientific and industrial activity. Despite the accumulated knowledge regarding glycolysis, the modification of flux through this pathway to modify ethanol yields has proved difficult. Here, we report on the systematic screening of 66 strains with deletion mutations of genes encoding enzymes involved in central carbohydrate metabolism for altered ethanol yields. Five of these strains showing the most prominent changes in carbon flux were selected for further investigation. The genes were representative of trehalose biosynthesis (TPS1, encoding trehalose-6-phosphate synthase), central glycolysis (TDH3, encoding glyceraldehyde-3-phosphate dehydrogenase), the oxidative pentose phosphate pathway (ZWF1, encoding glucose-6-phosphate dehydrogenase), and the tricarboxylic acid (TCA) cycle (ACO1 and ACO2, encoding aconitase isoforms 1 and 2). Two strains exhibited lower ethanol yields than the wild type (tps1Δ and tdh3Δ), while the remaining three showed higher ethanol yields. To validate these findings in an industrial yeast strain, the TPS1 gene was selected as a good candidate for genetic modification to alter flux to ethanol during alcoholic fermentation in wine. Using low-strength promoters active at different stages of fermentation, the expression of the TPS1 gene was slightly upregulated, resulting in a decrease in ethanol production and an increase in trehalose biosynthesis during fermentation. Thus, the mutant screening approach was successful in terms of identifying target genes for genetic modification in commercial yeast strains with the aim of producing lower-ethanol wines. PMID:23793638

Developmental origins of novel gut morphology in frogs

PubMed Central

Bloom, Stephanie; Ledon-Rettig, Cris; Infante, Carlos; Everly, Anne; Hanken, James; Nascone-Yoder, Nanette

2013-01-01

SUMMARY Phenotypic variation is a prerequisite for evolution by natural selection, yet the processes that give rise to the novel morphologies upon which selection acts are poorly understood. We employed a chemical genetic screen to identify developmental changes capable of generating ecologically relevant morphological variation as observed among extant species. Specifically, we assayed for exogenously applied small molecules capable of transforming the ancestral larval foregut of the herbivorous Xenopus laevis to resemble the derived larval foregut of the carnivorous Lepidobatrachus laevis. Appropriately, the small molecules that demonstrate this capacity modulate conserved morphogenetic pathways involved in gut development, including downregulation of retinoic acid (RA) signaling. Identical manipulation of RA signaling in a species that is more closely related to Lepidobatrachus, Ceratophrys cranwelli, yielded even more similar transformations, corroborating the relevance of RA signaling variation in interspecific morphological change. Finally, we were able to recover the ancestral gut phenotype in Lepidobatrachus by performing a reverse chemical manipulation to upregulate RA signaling, providing strong evidence that modifications to this specific pathway promoted the emergence of a lineage-specific phenotypic novelty. Interestingly, our screen also revealed pathways that have not yet been implicated in early gut morphogenesis, such as thyroid hormone signaling. In general, the chemical genetic screen may be a valuable tool for identifying developmental mechanisms that underlie ecologically and evolutionarily relevant phenotypic variation. PMID:23607305

Predictive QSAR modeling workflow, model applicability domains, and virtual screening.

PubMed

Tropsha, Alexander; Golbraikh, Alexander

2007-01-01

Quantitative Structure Activity Relationship (QSAR) modeling has been traditionally applied as an evaluative approach, i.e., with the focus on developing retrospective and explanatory models of existing data. Model extrapolation was considered if only in hypothetical sense in terms of potential modifications of known biologically active chemicals that could improve compounds' activity. This critical review re-examines the strategy and the output of the modern QSAR modeling approaches. We provide examples and arguments suggesting that current methodologies may afford robust and validated models capable of accurate prediction of compound properties for molecules not included in the training sets. We discuss a data-analytical modeling workflow developed in our laboratory that incorporates modules for combinatorial QSAR model development (i.e., using all possible binary combinations of available descriptor sets and statistical data modeling techniques), rigorous model validation, and virtual screening of available chemical databases to identify novel biologically active compounds. Our approach places particular emphasis on model validation as well as the need to define model applicability domains in the chemistry space. We present examples of studies where the application of rigorously validated QSAR models to virtual screening identified computational hits that were confirmed by subsequent experimental investigations. The emerging focus of QSAR modeling on target property forecasting brings it forward as predictive, as opposed to evaluative, modeling approach.

Two-track virtual screening approach to identify both competitive and allosteric inhibitors of human small C-terminal domain phosphatase 1

NASA Astrophysics Data System (ADS)

Park, Hwangseo; Lee, Hye Seon; Ku, Bonsu; Lee, Sang-Rae; Kim, Seung Jun

2017-08-01

Despite a wealth of persuasive evidence for the involvement of human small C-terminal domain phosphatase 1 (Scp1) in the impairment of neuronal differentiation and in Huntington's disease, small-molecule inhibitors of Scp1 have been rarely reported so far. This study aims to the discovery of both competitive and allosteric Scp1 inhibitors through the two-track virtual screening procedure. By virtue of the improvement of the scoring function by implementing a new molecular solvation energy term and by reoptimizing the atomic charges for the active-site Mg2+ ion cluster, we have been able to identify three allosteric and five competitive Scp1 inhibitors with low-micromolar inhibitory activity. Consistent with the results of kinetic studies on the inhibitory mechanisms, the allosteric inhibitors appear to be accommodated in the peripheral binding pocket through the hydrophobic interactions with the nonpolar residues whereas the competitive ones bind tightly in the active site with a direct coordination to the central Mg2+ ion. Some structural modifications to improve the biochemical potency of the newly identified inhibitors are proposed based on the binding modes estimated with docking simulations.

Screening for Drug Abuse Among College Students: Modification of the Michigan Alcoholism Screening Test

ERIC Educational Resources Information Center

Cannell, M. Barry; Favazza, Armando R.

1978-01-01

Modified version of the Michigan Alcoholism Screening Test was anonymously given to 245 college students on two Midwestern university campuses. Cutoff score for suspected drug abuse was set at five points. The percent of students scoring five or more points was 25 and 22 from campuses A and B respectively. (Author)

Pollution reduction technology program for small jet aircraft engines, phase 1

NASA Technical Reports Server (NTRS)

Bruce, T. W.; Davis, F. G.; Kuhn, T. E.; Mongia, H. C.

1977-01-01

A series of combustor pressure rig screening tests was conducted on three combustor concepts applied to the TFE731-2 turbofan engine combustion system for the purpose of evaluating their relative emissions reduction potential consistent with prescribed performance, durability, and envelope contraints. The three concepts and their modifications represented increasing potential for reducing emission levels with the penalty of increased hardware complexity and operational risk. Concept 1 entailed advanced modifications to the present production TFE731-2 combustion system. Concept 2 was based on the incorporation of an axial air-assisted airblast fuel injection system. Concept 3 was a staged premix/prevaporizing combustion system. Significant emissions reductions were achieved in all three concepts, consistent with acceptable combustion system performance. Concepts 2 and 3 were identified as having the greatest achievable emissions reduction potential, and were selected to undergo refinement to prepare for ultimate incorporation within an engine.

Global profiling of alternative RNA splicing events provides insights into molecular differences between various types of hepatocellular carcinoma.

PubMed

Tremblay, Marie-Pier; Armero, Victoria E S; Allaire, Andréa; Boudreault, Simon; Martenon-Brodeur, Camille; Durand, Mathieu; Lapointe, Elvy; Thibault, Philippe; Tremblay-Létourneau, Maude; Perreault, Jean-Pierre; Scott, Michelle S; Bisaillon, Martin

2016-08-26

Dysregulations in alternative splicing (AS) patterns have been associated with many human diseases including cancer. In the present study, alterations to the global RNA splicing landscape of cellular genes were investigated in a large-scale screen from 377 liver tissue samples using high-throughput RNA sequencing data. Our study identifies modifications in the AS patterns of transcripts encoded by more than 2500 genes such as tumor suppressor genes, transcription factors, and kinases. These findings provide insights into the molecular differences between various types of hepatocellular carcinoma (HCC). Our analysis allowed the identification of 761 unique transcripts for which AS is misregulated in HBV-associated HCC, while 68 are unique to HCV-associated HCC, 54 to HBV&HCV-associated HCC, and 299 to virus-free HCC. Moreover, we demonstrate that the expression pattern of the RNA splicing factor hnRNPC in HCC tissues significantly correlates with patient survival. We also show that the expression of the HBx protein from HBV leads to modifications in the AS profiles of cellular genes. Finally, using RNA interference and a reverse transcription-PCR screening platform, we examined the implications of cellular proteins involved in the splicing of transcripts involved in apoptosis and demonstrate the potential contribution of these proteins in AS control. This study provides the first comprehensive portrait of global changes in the RNA splicing signatures that occur in hepatocellular carcinoma. Moreover, these data allowed us to identify unique signatures of genes for which AS is misregulated in the different types of HCC.

Engineering of global regulators and cell surface properties toward enhancing stress tolerance in Saccharomyces cerevisiae.

PubMed

Kuroda, Kouichi; Ueda, Mitsuyoshi

2017-12-01

Microbial cell factories are subject to various stresses, leading to the reductions of metabolic activity and bioproduction efficiency. Therefore, the development of stress-tolerant microorganisms is important for improving bio-production efficiency. Recently, modifications of cell surface properties and master regulators have been shown to be effective approaches for enhancing stress tolerance. The cell surface is an attractive target owing to its interactions with the environment and its role in transmitting environmental information. Cell surface engineering in yeast has enabled the convenient modification of cell surface properties. Displaying random peptide libraries and subsequent screening can successfully improve stress tolerance. Furthermore, master regulators including transcription factors are also promising target to be engineered because stress tolerance is determined by many cooperative factors and modification of master regulators can simultaneously affect the expression of multiple downstream genes. The key single amino acid mutations in transcription factors have been identified by analyzing tolerant yeasts that were isolated by adaptive evolution under stress conditions. This enabled the reconstruction of stress-tolerant yeast without burdening cells by introducing the identified mutations. Therefore, for the construction of stress-tolerant yeast from any strains, these two approaches are promising alternatives to conventional overexpression and deletion of stress-related genes. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

MSBIS: A Multi-Step Biomedical Informatics Screening Approach for Identifying Medications that Mitigate the Risks of Metoclopramide-Induced Tardive Dyskinesia.

PubMed

Xu, Dong; Ham, Alexandrea G; Tivis, Rickey D; Caylor, Matthew L; Tao, Aoxiang; Flynn, Steve T; Economen, Peter J; Dang, Hung K; Johnson, Royal W; Culbertson, Vaughn L

2017-12-01

In 2009 the U.S. Food and Drug Administration (FDA) placed a black box warning on metoclopramide (MCP) due to the increased risks and prevalence of tardive dyskinesia (TD). In this study, we developed a multi-step biomedical informatics screening (MSBIS) approach leveraging publicly available bioactivity and drug safety data to identify concomitant drugs that mitigate the risks of MCP-induced TD. MSBIS includes (1) TargetSearch (http://dxulab.org/software) bioinformatics scoring for drug anticholinergic activity using CHEMBL bioactivity data; (2) unadjusted odds ratio (UOR) scoring for indications of TD-mitigating effects using the FDA Adverse Event Reporting System (FAERS); (3) adjusted odds ratio (AOR) re-scoring by removing the effect of cofounding factors (age, gender, reporting year); (4) logistic regression (LR) coefficient scoring for confirming the best TD-mitigating drug candidates. Drugs with increasing TD protective potential and statistical significance were obtained at each screening step. Fentanyl is identified as the most promising drug against MCP-induced TD (coefficient: -2.68; p-value<0.01). The discovery is supported by clinical reports that patients fully recovered from MCP-induced TD after fentanyl-induced general anesthesia. Loperamide is identified as a potent mitigating drug against a broader range of drug-induced movement disorders through pharmacokinetic modifications. Using drug-induced TD as an example, we demonstrated that MSBIS is an efficient in silico tool for unknown drug-drug interaction detection, drug repurposing, and combination therapy design. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

High Throughput Screening for Compounds That Alter Muscle Cell Glycosylation Identifies New Role for N-Glycans in Regulating Sarcolemmal Protein Abundance and Laminin Binding*

PubMed Central

Cabrera, Paula V.; Pang, Mabel; Marshall, Jamie L.; Kung, Raymond; Nelson, Stanley F.; Stalnaker, Stephanie H.; Wells, Lance; Crosbie-Watson, Rachelle H.; Baum, Linda G.

2012-01-01

Duchenne muscular dystrophy is an X-linked disorder characterized by loss of dystrophin, a cytoskeletal protein that connects the actin cytoskeleton in skeletal muscle cells to extracellular matrix. Dystrophin binds to the cytoplasmic domain of the transmembrane glycoprotein β-dystroglycan (β-DG), which associates with cell surface α-dystroglycan (α-DG) that binds laminin in the extracellular matrix. β-DG can also associate with utrophin, and this differential association correlates with specific glycosylation changes on α-DG. Genetic modification of α-DG glycosylation can promote utrophin binding and rescue dystrophic phenotypes in mouse dystrophy models. We used high throughput screening with the plant lectin Wisteria floribunda agglutinin (WFA) to identify compounds that altered muscle cell surface glycosylation, with the goal of finding compounds that increase abundance of α-DG and associated sarcolemmal glycoproteins, increase utrophin usage, and increase laminin binding. We identified one compound, lobeline, from the Prestwick library of Food and Drug Administration-approved compounds that fulfilled these criteria, increasing WFA binding to C2C12 cells and to primary muscle cells from wild type and mdx mice. WFA binding and enhancement by lobeline required complex N-glycans but not O-mannose glycans that bind laminin. However, inhibiting complex N-glycan processing reduced laminin binding to muscle cell glycoproteins, although O-mannosylation was intact. Glycan analysis demonstrated a general increase in N-glycans on lobeline-treated cells rather than specific alterations in cell surface glycosylation, consistent with increased abundance of multiple sarcolemmal glycoproteins. This demonstrates the feasibility of high throughput screening with plant lectins to identify compounds that alter muscle cell glycosylation and identifies a novel role for N-glycans in regulating muscle cell function. PMID:22570487

Screen printing technology applied to silicon solar cell fabrication

NASA Technical Reports Server (NTRS)

Thornhill, J. W.; Sipperly, W. E.

1980-01-01

The process for producing space qualified solar cells in both the conventional and wraparound configuration using screen printing techniques was investigated. Process modifications were chosen that could be easily automated or mechanized. Work was accomplished to optimize the tradeoffs associated with gridline spacing, gridline definition and junction depth. An extensive search for possible front contact metallization was completed. The back surface field structures along with the screen printed back contacts were optimized to produce open circuit voltages of at least an average of 600 millivolts. After all intended modifications on the process sequence were accomplished, the cells were exhaustively tested. Electrical tests at AMO and 28 C were made before and after boiling water immersion, thermal shock, and storage under conditions of high temperature and high humidity.

The Evolution of the Snellen E to the Blackbird. (Blackbird Preschool Vision Screening Program).

ERIC Educational Resources Information Center

Sato-Viacrucis, Kiyo

Comparison of a variety of vision screening methods used with preschool children led to modification of the standard Snellen E test called the Blackbird Vision Screening System. An instructional story using an "E-bird" was developed to teach children the various possible positions of the E. The visual confusion caused by the chart was…

Real-Time Optical Image Processing Techniques

DTIC Science & Technology

1988-10-31

pursued through the analysis, design, and fabrication of pulse frequency modulated halftone screens and the modification of micro-chan- nel spatial...required for non-linear operation. Real-time nonlinear processing was performed using the halftone screen and MSLM. The experiments showed the effectiveness...pulse frequency modulation has been pursued through the analysis, design, and fabrication of pulse frequency modulated halftone screens and the

A combined study of heat and mass transfer in an infant incubator with an overhead screen.

PubMed

Ginalski, Maciej K; Nowak, Andrzej J; Wrobel, Luiz C

2007-06-01

The main objective of this study is to investigate the major physical processes taking place inside an infant incubator, before and after modifications have been made to its interior chamber. The modification involves the addition of an overhead screen to decrease radiation heat losses from the infant placed inside the incubator. The present study investigates the effect of these modifications on the convective heat flux from the infant's body to the surrounding environment inside the incubator. A combined analysis of airflow and heat transfer due to conduction, convection, radiation and evaporation has been performed, in order to calculate the temperature and velocity fields inside the incubator before and after the design modification. Due to the geometrical complexity of the model, computer-aided design (CAD) applications were used to generate a computer-based model. All numerical calculations have been performed using the commercial computational fluid dynamics (CFD) package FLUENT, together with in-house routines used for managing purposes and user-defined functions (UDFs) which extend the basic solver capabilities. Numerical calculations have been performed for three different air inlet temperatures: 32, 34 and 36 degrees C. The study shows a decrease of the radiative and convective heat losses when the overhead screen is present. The results obtained were numerically verified as well as compared with results available in the literature from investigations of dry heat losses from infant manikins.

Crystal Nucleation Using Surface-Energy-Modified Glass Substrates.

PubMed

Nordquist, Kyle A; Schaab, Kevin M; Sha, Jierui; Bond, Andrew H

2017-08-02

Systematic surface energy modifications to glass substrates can induce nucleation and improve crystallization outcomes for small molecule active pharmaceutical ingredients (APIs) and proteins. A comparatively broad probe for function is presented in which various APIs, proteins, organic solvents, aqueous media, surface energy motifs, crystallization methods, form factors, and flat and convex surface energy modifications were examined. Replicate studies ( n ≥ 6) have demonstrated an average reduction in crystallization onset times of 52(4)% (alternatively 52 ± 4%) for acetylsalicylic acid from 91% isopropyl alcohol using two very different techniques: bulk cooling to 0 °C using flat surface energy modifications or microdomain cooling to 4 °C from the interior of a glass capillary having convex surface energy modifications that were immersed in the solution. For thaumatin and bovine pancreatic trypsin, a 32(2)% reduction in crystallization onset times was demonstrated in vapor diffusion experiments ( n ≥ 15). Nucleation site arrays have been engineered onto form factors frequently used in crystallization screening, including microscope slides, vials, and 96- and 384-well high-throughput screening plates. Nucleation using surface energy modifications on the vessels that contain the solutes to be crystallized adds a layer of useful variables to crystallization studies without requiring significant changes to workflows or instrumentation.

Attitudes and beliefs of sports medicine providers to sickle cell trait screening of student athletes.

PubMed

Acharya, Kruti; Benjamin, Holly J; Clayton, Ellen W; Ross, Lainie F

2011-11-01

To describe the attitudes of members of the American Medical Society for Sports Medicine (AMSSM) toward the new National Collegiate Athletic Association (NCAA) policy to require all Division I student athletes be screened for sickle cell trait (SCT), have prior evidence of testing, or sign a waiver. Cross-sectional survey of members of the AMSSM electronic mailing list was conducted. Descriptive, McNemar, and χ2 statistics were performed. Internet survey. Of the 1765 AMSSM e-mail list members, 370 returned partial or completed surveys. Dependent variables included familiarity with the NCAA policy, support of universal or targeted screening programs, preferences regarding screening methodologies, and athletic restrictions or modifications for student athletes identified with SCT. Respondents' gender, race/ethnicity, and involvement as an NCAA team physician were independent variables. Of the respondents, 76% were men, 85% were whites, and 53% served as NCAA Division I team physicians. Ninety percent were aware of the policy. There was greater support for targeted (76%, 267 of 353) compared with universal (39%, 137 of 353; P < 0.01) screening, with targeting based on race/ethnicity and sport. Respondents supported targeted screening of varsity and freshman athletes in all NCAA divisions, but most (88%) also supported waivers. Respondents favored using existing medical records (73%) or Sickledex screening (71%) methodologies despite concerns about inaccuracies (16% for each methodology). Most respondents agreed that there is discrimination in athletic participation and obtaining insurance. There is lack of consensus within the AMSSM regarding the current NCAA SCT screening policy. Implementation must take into consideration potential discrimination.

Phage display for the discovery of hydroxyapatite-associated peptides.

PubMed

Jin, Hyo-Eon; Chung, Woo-Jae; Lee, Seung-Wuk

2013-01-01

In nature, proteins play a critical role in the biomineralization process. Understanding how different peptide or protein sequences selectively interact with the target crystal is of great importance. Identifying such protein structures is one of the critical steps in verifying the molecular mechanisms of biomineralization. One of the promising ways to obtain such information for a particular crystal surface is to screen combinatorial peptide libraries in a high-throughput manner. Among the many combinatorial library screening procedures, phage display is a powerful method to isolate such proteins and peptides. In this chapter, we will describe our established methods to perform phage display with inorganic crystal surfaces. Specifically, we will use hydroxyapatite as a model system for discovery of apatite-associated proteins in bone or tooth biomineralization studies. This model approach can be generalized to other desired crystal surfaces using the same experimental design principles with a little modification of the procedures. © 2013 Elsevier Inc. All rights reserved.

DNA-Damage Response RNA-Binding Proteins (DDRBPs): Perspectives from a New Class of Proteins and Their RNA Targets.

PubMed

Dutertre, Martin; Vagner, Stéphan

2017-10-27

Upon DNA damage, cells trigger an early DNA-damage response (DDR) involving DNA repair and cell cycle checkpoints, and late responses involving gene expression regulation that determine cell fate. Screens for genes involved in the DDR have found many RNA-binding proteins (RBPs), while screens for novel RBPs have identified DDR proteins. An increasing number of RBPs are involved in early and/or late DDR. We propose to call this new class of actors of the DDR, which contain an RNA-binding activity, DNA-damage response RNA-binding proteins (DDRBPs). We then discuss how DDRBPs contribute not only to gene expression regulation in the late DDR but also to early DDR signaling, DNA repair, and chromatin modifications at DNA-damage sites through interactions with both long and short noncoding RNAs. Copyright © 2016 Elsevier Ltd. All rights reserved.

A novel high-throughput screening format to identify inhibitors of secreted acid sphingomyelinase.

PubMed

Mintzer, Robert J; Appell, Kenneth C; Cole, Andrew; Johns, Anthony; Pagila, Rene; Polokoff, Mark A; Tabas, Ira; Snider, R Michael; Meurer-Ogden, Janet A

2005-04-01

Secreted extracellular acid sphingomyelinase (sASM) activity has been suggested to promote atherosclerosis by enhancing subendothelial aggregation and retention of low-density lipoprotein (LDL) with resultant foam cell formation. Compounds that inhibit sASM activity, at neutral pH, may prevent lipid retention and thus would be expected to be anti-atherosclerotic. With the goal of identifying novel compounds that inhibit sASM at pH 7.4, a high-throughput screen was performed. Initial screening was run using a modification of a proven system that measures the hydrolysis of radiolabeled sphingomyelin presented in detergent micelles in a 96-well format. Separation of the radiolabeled aqueous phosphorylcholine reaction product from uncleaved sphingomyelin lipid substrate was achieved by chloroform/methanol extraction. During the screening campaign, a novel extraction procedure was developed to eliminate the use of the hazardous organic reagents. This new procedure exploited the ability of uncleaved, radiolabeled lipid substrate to interact with hydrophobic phenyl-sepharose beads. A comparison of the organic-based and the bead-based extraction sASM screening assays revealed Z' factor values ranging from 0.7 to 0.95 for both formats. In addition, both assay formats led to the identification of sub- to low micromolar inhibitors of sASM at pH 7.4 with similar IC(50) values. Subsequent studies demonstrated that both methods were also adaptable to run in a 384-well format. In contrast to the results observed at neutral pH, however, only the organic extraction assay was capable of accurately measuring sASM activity at its pH optimum of 5.0. The advantages and disadvantages of both sASM assay formats are discussed.

Assessing emotional well-being of children in a Honduran orphanage: feasibility of two screening tools.

PubMed

Debiasi, Laura B; Reynolds, Annette; Buckner, Ellen B

2012-01-01

The World Health Organization (WHO) has determined mental health in children to be a priority area for evidence-based interventions. Effective and efficient screening methods are needed to assess emotional well-being of children from diverse cultures. This descriptive study examined two tools for feasibility, sensitivity, cultural appropriateness, and cost/time effectiveness. Emotional well-being was conceptualized using the Roy Adaptation Model as part of the self-concept adaptive mode. Emotional indicators were measured from Human Figure Drawings. Anxiety was measured using a modification of the Revised Children's Manifest Anxiety Survey (RCMAS). The sample included 11 girls who were 7 to 12 years of age and recruited from a girls' orphanage in Honduras. Results indicated the Human Figure Drawings identified more children possibly at risk than the RCMAS. Human Figure Drawings were found to be a time/cost-effective, sensitive, and culturally appropriate means for measuring emotional well-being in the setting. This study contributes to nursing knowledge by demonstrating feasibility of the screening tools for measuring emotional well-being of children in varied cultures.

Real Time Detection of Protein Trafficking with High Throughput Flow Cytometry (HTFC) and Fluorogen Activating Protein (FAP) Base Biosensor

PubMed Central

Wu, Yang; Tapia, Phillip H.; Jarvik, Jonathan; Waggoner, Alan S.; Sklar, Larry A.

2014-01-01

We combined fluorogen activating protein (FAP) technology with high-throughput flow cytometry to detect real-time protein trafficking to and from the plasma membrane in living cells. The hybrid platform allows drug discovery for trafficking receptors, such as G-protein coupled receptors, receptor tyrosine kinases and ion channels, that were previously not suitable for high throughput screening by flow cytometry.. The system has been validated using the β2-adrenergic receptor (β2AR) system and extended to other GPCRs. When a chemical library containing ~1,200 off-patent drugs was screened against cells expressing FAP tagged β2AR, all known β2AR active ligands in the library were successfully identified, together with a few compounds that were later confirmed to regulate receptor internalization in a non-traditional manner. The unexpected discovery of new ligands by this approach indicates the potential of using this protocol for GPCR de-orphanization. In addition, screens of multiplexed targets promise improved efficiency with minor protocol modification. PMID:24510772

Single-Cell Quantification of Cytosine Modifications by Hyperspectral Dark-Field Imaging.

PubMed

Wang, Xiaolei; Cui, Yi; Irudayaraj, Joseph

2015-12-22

Epigenetic modifications on DNA, especially on cytosine, play a critical role in regulating gene expression and genome stability. It is known that the levels of different cytosine derivatives are highly dynamic and are regulated by a variety of factors that act on the chromatin. Here we report an optical methodology based on hyperspectral dark-field imaging (HSDFI) using plasmonic nanoprobes to quantify the recently identified cytosine modifications on DNA in single cells. Gold (Au) and silver (Ag) nanoparticles (NPs) functionalized with specific antibodies were used as contrast-generating agents due to their strong local surface plasmon resonance (LSPR) properties. With this powerful platform we have revealed the spatial distribution and quantity of 5-carboxylcytosine (5caC) at the different stages in cell cycle and demonstrated that 5caC was a stably inherited epigenetic mark. We have also shown that the regional density of 5caC on a single chromosome can be mapped due to the spectral sensitivity of the nanoprobes in relation to the interparticle distance. Notably, HSDFI enables an efficient removal of the scattering noises from nonspecifically aggregated nanoprobes, to improve accuracy in the quantification of different cytosine modifications in single cells. Further, by separating the LSPR fingerprints of AuNPs and AgNPs, multiplex detection of two cytosine modifications was also performed. Our results demonstrate HSDFI as a versatile platform for spatial and spectroscopic characterization of plasmonic nanoprobe-labeled nuclear targets at the single-cell level for quantitative epigenetic screening.

From screening to postpartum follow-up – the determinants and barriers for gestational diabetes mellitus (GDM) services, a systematic review

PubMed Central

2014-01-01

Background Gestational diabetes mellitus (GDM) – a transitory form of diabetes first recognised during pregnancy complicates between < 1% and 28% of all pregnancies. GDM has important short and long-term health consequences for both the mother and her offspring. To prevent adverse pregnancy outcomes and to prevent or delay future onset of type 2 diabetes in mother and offspring, timely detection, optimum treatment, and preventive postpartum care and follow-up is necessary. However the area remains grossly under-prioritised. Methods To investigate determinants and barriers to GDM care from initial screening and diagnosis to prenatal treatment and postpartum follow-up, a PubMed database search to identify quantitative and qualitative studies on the subject was done in September 2012. Fifty-eight relevant studies were reviewed. Results Adherence to prevailing GDM screening guidelines and compliance to screening tests seems sub-optimal at best and arbitrary at worst, with no clear or consistent correlation to health care provider, health system or client characteristics. Studies indicate that most women express commitment and motivation for behaviour change to protect the health of their unborn baby, but compliance to recommended treatment and advice is fraught with challenges, and precious little is known about health system or societal factors that hinder compliance and what can be done to improve it. A number of barriers related to health care provider/system and client characteristics have been identified by qualitative studies. Immediately following a GDM pregnancy many women, when properly informed, desire and intend to maintain healthy lifestyles to prevent future diabetes, but find the effort challenging. Adherence to recommended postpartum screening and continued lifestyle modifications seems even lower. Here too, health care provider, health system and client related determinants and barriers were identified. Studies reveal that sense of self-efficacy and social support are key determinants. Conclusions The paper identifies and discusses determinants and barriers for GDM care, fully recognising that these are highly dependent on the context. PMID:24450389

Label-free screening of foodborne Salmonella using surface plasmon resonance imaging

USDA-ARS?s Scientific Manuscript database

Since 15 pathogens cause approximately 95% of the foodborne infections, it is desirable to develop rapid and simultaneous screening methods for these major pathogens. In this study, we developed an immunoassay for Salmonella based on surface plasmon resonance imaging (SPRi). The sensor surface modif...

Sleeping Beauty transposon mutagenesis identifies genes that cooperate with mutant Smad4 in gastric cancer development

PubMed Central

Takeda, Haruna; Rust, Alistair G.; Ward, Jerrold M.; Yew, Christopher Chin Kuan; Jenkins, Nancy A.; Copeland, Neal G.

2016-01-01

Mutations in SMAD4 predispose to the development of gastrointestinal cancer, which is the third leading cause of cancer-related deaths. To identify genes driving gastric cancer (GC) development, we performed a Sleeping Beauty (SB) transposon mutagenesis screen in the stomach of Smad4+/− mutant mice. This screen identified 59 candidate GC trunk drivers and a much larger number of candidate GC progression genes. Strikingly, 22 SB-identified trunk drivers are known or candidate cancer genes, whereas four SB-identified trunk drivers, including PTEN, SMAD4, RNF43, and NF1, are known human GC trunk drivers. Similar to human GC, pathway analyses identified WNT, TGF-β, and PI3K-PTEN signaling, ubiquitin-mediated proteolysis, adherens junctions, and RNA degradation in addition to genes involved in chromatin modification and organization as highly deregulated pathways in GC. Comparative oncogenomic filtering of the complete list of SB-identified genes showed that they are highly enriched for genes mutated in human GC and identified many candidate human GC genes. Finally, by comparing our complete list of SB-identified genes against the list of mutated genes identified in five large-scale human GC sequencing studies, we identified LDL receptor-related protein 1B (LRP1B) as a previously unidentified human candidate GC tumor suppressor gene. In LRP1B, 129 mutations were found in 462 human GC samples sequenced, and LRP1B is one of the top 10 most deleted genes identified in a panel of 3,312 human cancers. SB mutagenesis has, thus, helped to catalog the cooperative molecular mechanisms driving SMAD4-induced GC growth and discover genes with potential clinical importance in human GC. PMID:27006499

Sleeping Beauty transposon mutagenesis identifies genes that cooperate with mutant Smad4 in gastric cancer development.

PubMed

Takeda, Haruna; Rust, Alistair G; Ward, Jerrold M; Yew, Christopher Chin Kuan; Jenkins, Nancy A; Copeland, Neal G

2016-04-05

Mutations in SMAD4 predispose to the development of gastrointestinal cancer, which is the third leading cause of cancer-related deaths. To identify genes driving gastric cancer (GC) development, we performed a Sleeping Beauty (SB) transposon mutagenesis screen in the stomach of Smad4(+/-) mutant mice. This screen identified 59 candidate GC trunk drivers and a much larger number of candidate GC progression genes. Strikingly, 22 SB-identified trunk drivers are known or candidate cancer genes, whereas four SB-identified trunk drivers, including PTEN, SMAD4, RNF43, and NF1, are known human GC trunk drivers. Similar to human GC, pathway analyses identified WNT, TGF-β, and PI3K-PTEN signaling, ubiquitin-mediated proteolysis, adherens junctions, and RNA degradation in addition to genes involved in chromatin modification and organization as highly deregulated pathways in GC. Comparative oncogenomic filtering of the complete list of SB-identified genes showed that they are highly enriched for genes mutated in human GC and identified many candidate human GC genes. Finally, by comparing our complete list of SB-identified genes against the list of mutated genes identified in five large-scale human GC sequencing studies, we identified LDL receptor-related protein 1B (LRP1B) as a previously unidentified human candidate GC tumor suppressor gene. In LRP1B, 129 mutations were found in 462 human GC samples sequenced, and LRP1B is one of the top 10 most deleted genes identified in a panel of 3,312 human cancers. SB mutagenesis has, thus, helped to catalog the cooperative molecular mechanisms driving SMAD4-induced GC growth and discover genes with potential clinical importance in human GC.

A Target-Based Whole Cell Screen Approach To Identify Potential Inhibitors of Mycobacterium tuberculosis Signal Peptidase

PubMed Central

2016-01-01

The general secretion (Sec) pathway is a conserved essential pathway in bacteria and is the primary route of protein export across the cytoplasmic membrane. During protein export, the signal peptidase LepB catalyzes the cleavage of the signal peptide and subsequent release of mature proteins into the extracellular space. We developed a target-based whole cell assay to screen for potential inhibitors of LepB, the sole signal peptidase in Mycobacterium tuberculosis, using a strain engineered to underexpress LepB (LepB-UE). We screened 72,000 compounds against both the Lep-UE and wild-type (wt) strains. We identified the phenylhydrazone (PHY) series as having higher activity against the LepB-UE strain. We conducted a limited structure–activity relationship determination around a representative PHY compound with differential activity (MICs of 3.0 μM against the LepB-UE strain and 18 μM against the wt); several analogues were less potent against the LepB overexpressing strain. A number of chemical modifications around the hydrazone moiety resulted in improved potency. Inhibition of LepB activity was observed for a number of compounds in a biochemical assay using cell membrane fraction derived from M. tuberculosis. Compounds did not increase cell permeability, dissipate membrane potential, or inhibit an unrelated mycobacterial enzyme, suggesting a specific mode of action related to the LepB secretory mechanism. PMID:27642770

Developmental origins of a novel gut morphology in frogs.

PubMed

Bloom, Stephanie; Ledon-Rettig, Cris; Infante, Carlos; Everly, Anne; Hanken, James; Nascone-Yoder, Nanette

2013-05-01

Phenotypic variation is a prerequisite for evolution by natural selection, yet the processes that give rise to the novel morphologies upon which selection acts are poorly understood. We employed a chemical genetic screen to identify developmental changes capable of generating ecologically relevant morphological variation as observed among extant species. Specifically, we assayed for exogenously applied small molecules capable of transforming the ancestral larval foregut of the herbivorous Xenopus laevis to resemble the derived larval foregut of the carnivorous Lepidobatrachus laevis. Appropriately, the small molecules that demonstrate this capacity modulate conserved morphogenetic pathways involved in gut development, including downregulation of retinoic acid (RA) signaling. Identical manipulation of RA signaling in a species that is more closely related to Lepidobatrachus, Ceratophrys cranwelli, yielded even more similar transformations, corroborating the relevance of RA signaling variation in interspecific morphological change. Finally, we were able to recover the ancestral gut phenotype in Lepidobatrachus by performing a reverse chemical manipulation to upregulate RA signaling, providing strong evidence that modifications to this specific pathway promoted the emergence of a lineage-specific phenotypic novelty. Interestingly, our screen also revealed pathways that have not yet been implicated in early gut morphogenesis, such as thyroid hormone signaling. In general, the chemical genetic screen may be a valuable tool for identifying developmental mechanisms that underlie ecologically and evolutionarily relevant phenotypic variation. © 2013 Wiley Periodicals, Inc.

Using genome-wide CRISPR library screening with library resistant DCK to find new sources of Ara-C drug resistance in AML.

PubMed

Kurata, Morito; Rathe, Susan K; Bailey, Natashay J; Aumann, Natalie K; Jones, Justine M; Veldhuijzen, G Willemijn; Moriarity, Branden S; Largaespada, David A

2016-11-03

Acute myeloid leukemia (AML) can display de novo or acquired resistance to cytosine arabinoside (Ara-C), a primary component of induction chemotherapy. To identify genes capable of independently imposing Ara-C resistance, we applied a genome-wide CRISPR library to human U937 cells and exposed to them to Ara-C. Interestingly, all drug resistant clones contained guide RNAs for DCK. To avoid DCK gene modification, gRNA resistant DCK cDNA was created by the introduction of silent mutations. The CRISPR screening was repeated using the gRNA resistant DCK, and loss of SLC29A was identified as also being capable of conveying Ara-C drug resistance. To determine if loss of Dck results in increased sensitivity to other drugs, we conducted a screen of 446 FDA approved drugs using two Dck-defective BXH-2 derived murine AML cell lines and their Ara-C sensitive parental lines. Both cell lines showed an increase in sensitivity to prednisolone. Guide RNA resistant cDNA rescue was a legitimate strategy and multiple DCK or SLC29A deficient human cell clones were established with one clone becoming prednisolone sensitive. Dck-defective leukemic cells may become prednisolone sensitive indicating prednisolone may be an effective adjuvant therapy in some cases of DCK-negative AML.

Artificial specific binders directly recovered from chemically modified nucleic acid libraries.

PubMed

Kasahara, Yuuya; Kuwahara, Masayasu

2012-01-01

Specific binders comprised of nucleic acids, that is, RNA/DNA aptamers, are attractive functional biopolymers owing to their potential broad application in medicine, food hygiene, environmental analysis, and biological research. Despite the large number of reports on selection of natural DNA/RNA aptamers, there are not many examples of direct screening of chemically modified nucleic acid aptamers. This is because of (i) the inferior efficiency and accuracy of polymerase reactions involving transcription/reverse-transcription of modified nucleotides compared with those of natural nucleotides, (ii) technical difficulties and additional time and effort required when using modified nucleic acid libraries, and (iii) ambiguous efficacies of chemical modifications in binding properties until recently; in contrast, the effects of chemical modifications on biostability are well studied using various nucleotide analogs. Although reports on the direct screening of a modified nucleic acid library remain in the minority, chemical modifications would be essential when further functional expansion of nucleic acid aptamers, in particular for medical and biological uses, is considered. This paper focuses on enzymatic production of chemically modified nucleic acids and their application to random screenings. In addition, recent advances and possible future research are also described.

New antibody and immunoassay pretreatment strategy to screen polychlorinated biphenyls in Korean transformer oil.

PubMed

Terakado, Shingo; Ohmura, Naoya; Park, Seok-Un; Lee, Seung-Min; Glass, Thomas R

2013-01-01

Development and modifications are described that expand the application of an immunoassay from the detection of Kanechlors (Japanese technical PCBs mixtures) to the detection of Aroclors (U. S. technical PCB mixtures, used in Korea) in contaminated Korean transformer oil. The first necessary modification was the development of a new antibody with a reactivity profile favorable for Aroclors. The second modification was the addition of a second column to the solid-phase extraction method to reduce assay interference caused by the Korean oil matrix. The matrix interference is suspected to be caused by the presence of synthetic oils (or similar materials) present as contaminants. The modified assay was validated by comparison to high-resolution gas chromatography/high-resolution mass spectrometry analysis, and was shown to be tolerant of up to 10% of several common synthetic insulating oils. Finally the screening performance of the modified assay was evaluated using 500 used transformer oil samples of Korean origin, and was shown to have good performance in terms of false positive and false negative rates. This report provides evidence for the first establishment of immunoassay screening for Aroclor based PCB contamination in Korean transformer oil.

IRAS: High-Throughput Identification of Novel Alternative Splicing Regulators.

PubMed

Zheng, S

2016-01-01

Alternative splicing is a fundamental regulatory process of gene expression. Defects in alternative splicing can lead to various diseases, and modification of disease-causing splicing events presents great therapeutic promise. Splicing outcome is commonly affected by extracellular stimuli and signaling cascades that converge on RNA-binding splicing regulators. These trans-acting factors recognize cis-elements in pre-mRNA transcripts to affect spliceosome assembly and splice site choices. Identification of these splicing regulators and/or upstream modulators has been difficult and traditionally done by piecemeal. High-throughput screening strategies to find multiple regulators of exon splicing have great potential to accelerate the discovery process, but typically confront low sensitivity and low specificity of screening assays. Here we describe a unique screening strategy, IRAS (identifying regulators of alternative splicing), using a pair of dual-output minigene reporters to allow for sensitive detection of exon splicing changes. Each dual-output reporter produces green fluorescent protein (GFP) and red fluorescent protein (RFP) fluorescent signals to assay the two spliced isoforms exclusively. The two complementary minigene reporters alter GFP/RFP output ratios in the opposite direction in response to splicing change. Applying IRAS in cell-based high-throughput screens allows sensitive and specific identification of splicing regulators and modulators for any alternative exons of interest. In comparison to previous high-throughput screening methods, IRAS substantially enhances the specificity of the screening assay. This strategy significantly eliminates false positives without sacrificing sensitive identification of true regulators of splicing. © 2016 Elsevier Inc. All rights reserved.

Recent modifications and calibration of the Langley low-turbulence pressure tunnel

NASA Technical Reports Server (NTRS)

Mcghee, R. J.; Beasley, W. D.; Foster, J. M.

1984-01-01

Modifications to the Langley Low-Turbulence Pressure Tunnel are presented and a calibration of the mean flow parameters in the test section is provided. Also included are the operational capability of the tunnel and typical test results for both single-element and multi-element airfoils. Modifications to the facility consisted of the following: replacement of the original cooling coils and antiturbulence screens and addition of a tunnel-shell heating system, a two dimensional model-support and force-balance system, a sidewall boundary layer control system, a remote-controlled survey apparatus, and a new data acquisition system. A calibration of the mean flow parameters in the test section was conducted over the complete operational range of the tunnel. The calibration included dynamic-pressure measurements, Mach number distributions, flow-angularity measurements, boundary-layer characteristics, and total-pressure profiles. In addition, test-section turbulence measurements made after the tunnel modifications have been included with these calibration data to show a comparison of existing turbulence levels with data obtained for the facility in 1941 with the original screen installation.

The Succinated Proteome of FH-Mutant Tumours

PubMed Central

Yang, Ming; Ternette, Nicola; Su, Huizhong; Dabiri, Raliat; Kessler, Benedikt M.; Adam, Julie; Teh, Bin Tean; Pollard, Patrick J.

2014-01-01

Inherited mutations in the Krebs cycle enzyme fumarate hydratase (FH) predispose to hereditary leiomyomatosis and renal cell cancer (HLRCC). Loss of FH activity in HLRCC tumours causes accumulation of the Krebs cycle intermediate fumarate to high levels, which may act as an oncometabolite through various, but not necessarily mutually exclusive, mechanisms. One such mechanism, succination, is an irreversible non-enzymatic modification of cysteine residues by fumarate, to form S-(2-succino)cysteine (2SC). Previous studies have demonstrated that succination of proteins including glyceraldehyde 3-phosphate dehydrogenase (GAPDH), kelch-like ECH-associated protein 1 (KEAP1) and mitochondrial aconitase (ACO2) can have profound effects on cellular metabolism. Furthermore, immunostaining for 2SC is a sensitive and specific biomarker for HLRCC tumours. Here, we performed a proteomic screen on an FH-mutant tumour and two HLRCC-derived cancer cell lines and identified 60 proteins where one or more cysteine residues were succinated; 10 of which were succinated at cysteine residues either predicted, or experimentally proven, to be functionally significant. Bioinformatic enrichment analyses identified most succinated targets to be involved in redox signaling. To our knowledge, this is the first proteomic-based succination screen performed in human tumours and cancer-derived cells and has identified novel 2SC targets that may be relevant to the pathogenesis of HLRCC. PMID:25105836

Gene Deletions in Mycobacterium bovis BCG Stimulate Increased CD8+ T Cell Responses

PubMed Central

Panas, Michael W.; Sixsmith, Jaimie D.; White, KeriAnn; Korioth-Schmitz, Birgit; Shields, Shana T.; Moy, Brian T.; Lee, Sunhee; Schmitz, Joern E.; Jacobs, William R.; Porcelli, Steven A.; Haynes, Barton F.; Letvin, Norman L.

2014-01-01

Mycobacteria, the etiological agents of tuberculosis and leprosy, have coevolved with mammals for millions of years and have numerous ways of suppressing their host's immune response. It has been suggested that mycobacteria may contain genes that reduce the host's ability to elicit CD8+ T cell responses. We screened 3,290 mutant Mycobacterium bovis bacillus Calmette Guerin (BCG) strains to identify genes that decrease major histocompatibility complex (MHC) class I presentation of mycobacterium-encoded epitope peptides. Through our analysis, we identified 16 mutant BCG strains that generated increased transgene product-specific CD8+ T cell responses. The genes disrupted in these mutant strains had disparate predicted functions. Reconstruction of strains via targeted deletion of genes identified in the screen recapitulated the enhanced immunogenicity phenotype of the original mutant strains. When we introduced the simian immunodeficiency virus (SIV) gag gene into several of these novel BCG strains, we observed enhanced SIV Gag-specific CD8+ T cell responses in vivo. This study demonstrates that mycobacteria carry numerous genes that act to dampen CD8+ T cell responses and suggests that genetic modification of these genes may generate a novel group of recombinant BCG strains capable of serving as more effective and immunogenic vaccine vectors. PMID:25287928

Gene deletions in Mycobacterium bovis BCG stimulate increased CD8+ T cell responses.

PubMed

Panas, Michael W; Sixsmith, Jaimie D; White, KeriAnn; Korioth-Schmitz, Birgit; Shields, Shana T; Moy, Brian T; Lee, Sunhee; Schmitz, Joern E; Jacobs, William R; Porcelli, Steven A; Haynes, Barton F; Letvin, Norman L; Gillard, Geoffrey O

2014-12-01

Mycobacteria, the etiological agents of tuberculosis and leprosy, have coevolved with mammals for millions of years and have numerous ways of suppressing their host's immune response. It has been suggested that mycobacteria may contain genes that reduce the host's ability to elicit CD8(+) T cell responses. We screened 3,290 mutant Mycobacterium bovis bacillus Calmette Guerin (BCG) strains to identify genes that decrease major histocompatibility complex (MHC) class I presentation of mycobacterium-encoded epitope peptides. Through our analysis, we identified 16 mutant BCG strains that generated increased transgene product-specific CD8(+) T cell responses. The genes disrupted in these mutant strains had disparate predicted functions. Reconstruction of strains via targeted deletion of genes identified in the screen recapitulated the enhanced immunogenicity phenotype of the original mutant strains. When we introduced the simian immunodeficiency virus (SIV) gag gene into several of these novel BCG strains, we observed enhanced SIV Gag-specific CD8(+) T cell responses in vivo. This study demonstrates that mycobacteria carry numerous genes that act to dampen CD8(+) T cell responses and suggests that genetic modification of these genes may generate a novel group of recombinant BCG strains capable of serving as more effective and immunogenic vaccine vectors. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Copper-catalyzed azide-alkyne cycloaddition (click chemistry)-based Detection of Global Pathogen-host AMPylation on Self-assembled Human Protein Microarrays*

PubMed Central

Yu, Xiaobo; Woolery, Andrew R.; Luong, Phi; Hao, Yi Heng; Grammel, Markus; Westcott, Nathan; Park, Jin; Wang, Jie; Bian, Xiaofang; Demirkan, Gokhan; Hang, Howard C.; Orth, Kim; LaBaer, Joshua

2014-01-01

AMPylation (adenylylation) is a recently discovered mechanism employed by infectious bacteria to regulate host cell signaling. However, despite significant effort, only a few host targets have been identified, limiting our understanding of how these pathogens exploit this mechanism to control host cells. Accordingly, we developed a novel nonradioactive AMPylation screening platform using high-density cell-free protein microarrays displaying human proteins produced by human translational machinery. We screened 10,000 unique human proteins with Vibrio parahaemolyticus VopS and Histophilus somni IbpAFic2, and identified many new AMPylation substrates. Two of these, Rac2, and Rac3, were confirmed in vivo as bona fide substrates during infection with Vibrio parahaemolyticus. We also mapped the site of AMPylation of a non-GTPase substrate, LyGDI, to threonine 51, in a region regulated by Src kinase, and demonstrated that AMPylation prevented its phosphorylation by Src. Our results greatly expanded the repertoire of potential host substrates for bacterial AMPylators, determined their recognition motif, and revealed the first pathogen-host interaction AMPylation network. This approach can be extended to identify novel substrates of AMPylators with different domains or in different species and readily adapted for other post-translational modifications. PMID:25073739

TRIM25 Enhances the Antiviral Action of Zinc-Finger Antiviral Protein (ZAP)

PubMed Central

Lau, Zerlina; Cheung, Pamela; Schneider, William M.; Bozzacco, Leonia; Buehler, Eugen; Takaoka, Akinori; Rice, Charles M.; Felsenfeld, Dan P.; MacDonald, Margaret R.

2017-01-01

The host factor and interferon (IFN)-stimulated gene (ISG) product, zinc-finger antiviral protein (ZAP), inhibits a number of diverse viruses by usurping and intersecting with multiple cellular pathways. To elucidate its antiviral mechanism, we perform a loss-of-function genome-wide RNAi screen to identify cellular cofactors required for ZAP antiviral activity against the prototype alphavirus, Sindbis virus (SINV). In order to exclude off-target effects, we carry out stringent confirmatory assays to verify the top hits. Important ZAP-liaising partners identified include proteins involved in membrane ion permeability, type I IFN signaling, and post-translational protein modification. The factor contributing most to the antiviral function of ZAP is TRIM25, an E3 ubiquitin and ISG15 ligase. We demonstrate here that TRIM25 interacts with ZAP through the SPRY domain, and TRIM25 mutants lacking the RING or coiled coil domain fail to stimulate ZAP’s antiviral activity, suggesting that both TRIM25 ligase activity and its ability to form oligomers are critical for its cofactor function. TRIM25 increases the modification of both the short and long ZAP isoforms by K48- and K63-linked polyubiquitin, although ubiquitination of ZAP does not directly affect its antiviral activity. However, TRIM25 is critical for ZAP’s ability to inhibit translation of the incoming SINV genome. Taken together, these data uncover TRIM25 as a bona fide ZAP cofactor that leads to increased ZAP modification enhancing its translational inhibition activity. PMID:28060952

TRIM25 Enhances the Antiviral Action of Zinc-Finger Antiviral Protein (ZAP).

PubMed

Li, Melody M H; Lau, Zerlina; Cheung, Pamela; Aguilar, Eduardo G; Schneider, William M; Bozzacco, Leonia; Molina, Henrik; Buehler, Eugen; Takaoka, Akinori; Rice, Charles M; Felsenfeld, Dan P; MacDonald, Margaret R

2017-01-01

The host factor and interferon (IFN)-stimulated gene (ISG) product, zinc-finger antiviral protein (ZAP), inhibits a number of diverse viruses by usurping and intersecting with multiple cellular pathways. To elucidate its antiviral mechanism, we perform a loss-of-function genome-wide RNAi screen to identify cellular cofactors required for ZAP antiviral activity against the prototype alphavirus, Sindbis virus (SINV). In order to exclude off-target effects, we carry out stringent confirmatory assays to verify the top hits. Important ZAP-liaising partners identified include proteins involved in membrane ion permeability, type I IFN signaling, and post-translational protein modification. The factor contributing most to the antiviral function of ZAP is TRIM25, an E3 ubiquitin and ISG15 ligase. We demonstrate here that TRIM25 interacts with ZAP through the SPRY domain, and TRIM25 mutants lacking the RING or coiled coil domain fail to stimulate ZAP's antiviral activity, suggesting that both TRIM25 ligase activity and its ability to form oligomers are critical for its cofactor function. TRIM25 increases the modification of both the short and long ZAP isoforms by K48- and K63-linked polyubiquitin, although ubiquitination of ZAP does not directly affect its antiviral activity. However, TRIM25 is critical for ZAP's ability to inhibit translation of the incoming SINV genome. Taken together, these data uncover TRIM25 as a bona fide ZAP cofactor that leads to increased ZAP modification enhancing its translational inhibition activity.

Laser-scanning techniques for rapid ballistics identification

NASA Technical Reports Server (NTRS)

Woodburgy, R. C.; Nakich, R. B.

1974-01-01

Two different laser-scanning methods may be utilized. In each case scanned cylindrical bullet surface is displayed ""unwrapped'' on oscilloscope screen. Bullets are compared by photographing each display and superimposing negatives of two images. With some modifications bullets can be scanned and compared by superimposing images on screen of dual-beam oscilloscope.

Should Screening for Depression among Children and Adolescents Be Demedicalized?

ERIC Educational Resources Information Center

Horwitz, Allan V.; Wakefield, Jerome C.

2009-01-01

The criteria for diagnosing depressive disorders fails to place the symptoms of intense sadness in the context of major losses in life, and separating normal sadness from depressive disorder among adolescents is especially difficult. Suggested modifications to the screening of suicidal ideation among adolescents are also presented.

E-mail to Promote Colorectal Cancer Screening Within Social Networks: Acceptability and Content

PubMed Central

CUTRONA, SARAH L.; WAGNER, JOANN; ROBLIN, DOUGLAS W.; GAGLIO, BRIDGET; WILLIAMS, ANDREW; TORRES-STONE, ROSALIE; MAZOR, KATHLEEN M.

2016-01-01

Effective techniques to encourage colorectal cancer (CRC) screening in underscreened populations have included social support interventions and email reminders from physicians. Personalized email messages to promote CRC screening within social networks could be even more effective, but have not been studied. We interviewed 387 email users, aged 42-73 years in Massachusetts, Hawaii, and Georgia. Participants were asked to edit a sample message in which the sender shares a recent colonoscopy experience and urges the recipient to discuss CRC screening with a doctor. For those reporting willingness to send this message, changes to the message and suggested subject lines were recorded. Edited text was analyzed for content and concordance with original message. The majority of participants (74.4%) were willing to email a modifiable message. Of those willing, 63.5% edited the message. Common edits included deletion (17.7%) or modification (17.4%) of a negatively framed sentence on colon cancer risks and addition or modification of personalizing words (15.6%). Few edits changed the meaning of the message (5.6%) and even fewer introduced factual inaccuracies (1.7%). Modifiable email messages offer a way for screened individuals to promote CRC screening to social network members. Accuracy and impact of such messages should be further studied. PMID:25839968

A parametrisation of modified gravity on nonlinear cosmological scales

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lombriser, Lucas, E-mail: llo@roe.ac.uk

2016-11-01

Viable modifications of gravity on cosmological scales predominantly rely on screening mechanisms to recover Einstein's Theory of General Relativity in the Solar System, where it has been well tested. A parametrisation of the effects of such modifications in the spherical collapse model is presented here for the use of modelling the modified nonlinear cosmological structure. The formalism allows an embedding of the different screening mechanisms operating in scalar-tensor theories through large values of the gravitational potential or its first or second derivatives as well as of linear suppression effects or more general transitions between modified and Einstein gravity limits. Eachmore » screening or suppression mechanism is parametrised by a time, mass, and environment dependent screening scale, an effective modified gravitational coupling in the fully unscreened limit that can be matched to linear theory, the exponent of a power-law radial profile of the screened coupling, determined by derivatives, symmetries, and potentials in the scalar field equation, and an interpolation rate between the screened and unscreened limits. Along with generalised perturbative methods, the parametrisation may be used to formulate a nonlinear extension to the linear parametrised post-Friedmannian framework to enable generalised tests of gravity with the wealth of observations from the nonlinear cosmological regime.« less

Theory-based modifications of an advanced notification letter improves screening for bowel cancer in men: A randomised controlled trial.

PubMed

Zajac, Ian T; Duncan, Amy C; Flight, Ingrid; Wittert, Gary A; Cole, Stephen R; Young, Graeme P; Wilson, Carlene J; Turnbull, Deborah A

2016-09-01

Male participation in screening for bowel cancer is sub-optimal. Theory-based interventions provide a means of improving screening uptake. To test the efficacy of modifying consumer invitation material in line with continuum and stage theories of health behaviour on screening participation. N = 9216 Australian men aged 50-74 years were randomised to one of four trial arms in a 2 × 2 factorial design randomised controlled trial. Participants received either standard invitation material (control group), or combinations of modified advance-notification and invitation letters. A subsample completed baseline and endpoint behavioural surveys. Participants who received the modified advance notification letter were 12% more likely to screen than those who received the standard version (RR = 1.12, χ(2)(1) = 10.38, p = 0.001). The modified invitation letter did not impact screening uptake (RR = 0.97, χ(2)(1) = 0.63, p = 0.424). No significant changes in psychological variables due to the intervention were observed. Modifications to advance notification letters in line with health behaviour theories significantly improves screening uptake in men. Australian New Zealand Clinical Trials Registry: ACTRN12612001122842 https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=362688. Copyright © 2016 Elsevier Ltd. All rights reserved.

Unlocking the Bottleneck in Forward Genetics Using Whole-Genome Sequencing and Identity by Descent to Isolate Causative Mutations

PubMed Central

Siggs, Owen M.; Miosge, Lisa A.; Roots, Carla M.; Enders, Anselm; Bertram, Edward M.; Crockford, Tanya L.; Whittle, Belinda; Potter, Paul K.; Simon, Michelle M.; Mallon, Ann-Marie; Brown, Steve D. M.; Beutler, Bruce; Goodnow, Christopher C.; Lunter, Gerton; Cornall, Richard J.

2013-01-01

Forward genetics screens with N-ethyl-N-nitrosourea (ENU) provide a powerful way to illuminate gene function and generate mouse models of human disease; however, the identification of causative mutations remains a limiting step. Current strategies depend on conventional mapping, so the propagation of affected mice requires non-lethal screens; accurate tracking of phenotypes through pedigrees is complex and uncertain; out-crossing can introduce unexpected modifiers; and Sanger sequencing of candidate genes is inefficient. Here we show how these problems can be efficiently overcome using whole-genome sequencing (WGS) to detect the ENU mutations and then identify regions that are identical by descent (IBD) in multiple affected mice. In this strategy, we use a modification of the Lander-Green algorithm to isolate causative recessive and dominant mutations, even at low coverage, on a pure strain background. Analysis of the IBD regions also allows us to calculate the ENU mutation rate (1.54 mutations per Mb) and to model future strategies for genetic screens in mice. The introduction of this approach will accelerate the discovery of causal variants, permit broader and more informative lethal screens to be used, reduce animal costs, and herald a new era for ENU mutagenesis. PMID:23382690

An adaptive, comprehensive monitoring strategy for chemicals of emerging concern (CECs) in California's Aquatic Ecosystems.

PubMed

Maruya, Keith A; Schlenk, Daniel; Anderson, Paul D; Denslow, Nancy D; Drewes, Jörg E; Olivieri, Adam W; Scott, Geoffrey I; Snyder, Shane A

2014-01-01

A scientific advisory panel was convened by the State of California to recommend monitoring for chemicals of emerging concern (CECs) in aquatic systems that receive discharge of municipal wastewater treatment plant (WWTP) effluent and stormwater runoff. The panel developed a risk-based screening framework that considered environmental sources and fate of CECs observed in receiving waters across the State. Using existing occurrence and risk threshold data in water, sediment, and biological tissue, the panel applied the framework to identify a priority list of CECs for initial monitoring in three representative receiving water scenarios. The initial screening list of 16 CECs identified by the panel included consumer and commercial chemicals, flame retardants, pesticides, pharmaceuticals and personal care products, and natural hormones. The panel designed an iterative, phased strategy with interpretive guidelines that direct and update management actions commensurate with potential risk identified using the risk-based framework and monitoring data. Because of the ever-changing nature of chemical use, technology, and management practices, the panel offered recommendations to improve CEC monitoring, including development of bioanalytical screening methods whose responses integrate exposure to complex mixtures and that can be linked to higher-order effects; development or refinement of models that predict the input, fate, and effects of future chemicals; and filling of key data gaps on CEC occurrence and toxicity. Finally, the panel stressed the need for adaptive management, allowing for future review of, and if warranted, modifications to the strategy to incorporate the latest science available to the water resources community. © 2013 SETAC.

Cost-Effective Fabrication of Wettability Gradient Copper Surface by Screen Printing and its Application to Condensation Heat Transfer

NASA Astrophysics Data System (ADS)

Leu, Tzong-Shyng; Huang, Hung-Ming; Huang, Ding-Jun

2016-06-01

In this paper, wettability gradient pattern is applied to condensation heat transfer on a copper tube surface. For this application, the vital issue is how to fabricate gradient patterns on a curve tube surface to accelerate the droplet collection efficiently. For this purpose, novel fabrication processes are developed to form wettability gradient patterns on a curve copper tube surface by using roller screen printing surface modification techniques. The roller screen printing surface modification techniques can easily realize wettability gradient surfaces with superhydrophobicity and superhydrophilicity on a copper tube surface. Experimental results show the droplet nucleation sites, movement and coalescence toward the collection areas can be effectively controlled which can assist in removing the condensation water from the surface. The effectiveness of droplet collection is appropriate for being applied to condensation heat transfer in the foreseeable future.

Modifications of the IBM personal computer synchronous communications support programs for use with the Multics

USGS Publications Warehouse

Kork, John O.

1983-01-01

Version 1.00 of the Asynchronous Communications Support supplied with the IBM Personal Computer must be modified to be used for communications with Multics. Version 2.00 can be used as supplied, but error checking and screen printing capabilities can be added by using modifications very similar to those required for Version 1.00. This paper describes and lists required programs on Multics and appropriate modifications to both Versions 1.00 and 2.00 of the programs supplied by IBM.

Obesity in the Workplace: Impact, Outcomes, and Recommendations.

PubMed

Yarborough, Charles M; Brethauer, Stacy; Burton, Wayne N; Fabius, Raymond J; Hymel, Pamela; Kothari, Shanu; Kushner, Robert F; Morton, John Magaña; Mueller, Kathryn; Pronk, Nicolaas P; Roslin, Mitchell S; Sarwer, David B; Svazas, Brian; Harris, Jeffrey S; Ash, Garrett I; Stark, Jamie T; Dreger, Marianne; Ording, Julie

2018-01-01

To conduct a comprehensive literature review to develop recommendations for managing obesity among workers to improve health outcomes and to explore the impact of obesity on health costs to determine whether a case can be made for surgical interventions and insurance coverage. We searched PubMed from 2011 to 2016, and CINAHL, Scopus, and Cochrane Registry of Clinical Trials for interventions addressing obesity in the workplace. A total of 1419 articles were screened, resulting in 275 articles being included. Several areas were identified that require more research and investigation. Our findings support the use of both lifestyle modification and bariatric surgery to assist appropriate patients in losing weight.

Late-stage optimization of a tercyclic class of S1P3-sparing, S1P1 receptor agonists.

PubMed

Horan, Joshua C; Kuzmich, Daniel; Liu, Pingrong; DiSalvo, Darren; Lord, John; Mao, Can; Hopkins, Tamara D; Yu, Hui; Harcken, Christian; Betageri, Raj; Hill-Drzewi, Melissa; Patenaude, Lori; Patel, Monica; Fletcher, Kimberly; Terenzzio, Donna; Linehan, Brian; Xia, Heather; Patel, Mita; Studwell, Debbie; Miller, Craig; Hickey, Eugene; Levin, Jeremy I; Smith, Dustin; Kemper, Raymond A; Modis, Louise K; Bannen, Lynne C; Chan, Diva S; Mac, Morrison B; Ng, Stephanie; Wang, Yong; Xu, Wei; Lemieux, René M

2016-01-15

Poor solubility and cationic amphiphilic drug-likeness were liabilities identified for a lead series of S1P3-sparing, S1P1 agonists originally developed from a high-throughput screening campaign. This work describes the subsequent optimization of these leads by balancing potency, selectivity, solubility and overall molecular charge. Focused SAR studies revealed favorable structural modifications that, when combined, produced compounds with overall balanced profiles. The low brain exposure observed in rat suggests that these compounds would be best suited for the potential treatment of peripheral autoimmune disorders. Copyright © 2015 Elsevier Ltd. All rights reserved.

Material-Efficient Microfluidic Platform for Exploratory Studies of Visible-Light Photoredox Catalysis.

PubMed

Coley, Connor W; Abolhasani, Milad; Lin, Hongkun; Jensen, Klavs F

2017-08-07

We present an automated microfluidic platform for in-flow studies of visible-light photoredox catalysis in liquid or gas-liquid reactions at the 15 μL scale. An oscillatory flow strategy enables a flexible residence time while preserving the mixing and heat transfer advantages of flow systems. The adjustable photon flux made possible with the platform is characterized using actinometry. Case studies of oxidative hydroxylation of phenylboronic acids and dimerization of thiophenol demonstrate the capabilities and advantages of the system. Reaction conditions identified through droplet screening translate directly to continuous synthesis with minor platform modifications. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of anisotropic thermal transport on the resistive plasma response to resonant magnetic perturbation field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bai, Xue; Liu, Yueqiang; Gao, Zhe

Plasma response to the resonant magnetic perturbation (RMP) field is numerically investigated by an extended toroidal fluid model, which includes anisotropic thermal transport physics parallel and perpendicular to the total magnetic field. The thermal transport is found to be effective in eliminating the toroidal average curvature induced plasma screening (the so called Glasser-Green-Johnson, GGJ screening) at slow toroidal flow regime, whilst having minor effect on modifying the conventional plasma screening regimes at faster flow. Furthermore, this physics effect of interaction between thermal transport and GGJ screening is attributed to the modification of the radial structure of the shielding current, resultedmore » from the plasma response to the applied field. The modification of the plasma response (shielding current, response field, plasma displacement and the perturbed velocity) also has direct consequence on the toroidal torques produced by RMP. These modelling results show that thermal transport reduces the resonant electromagnetic torque as well as the torque associated with the Reynolds stress, but enhances the neoclassical toroidal viscous torque at slow plasma flow.« less

Effect of anisotropic thermal transport on the resistive plasma response to resonant magnetic perturbation field

DOE PAGES

Bai, Xue; Liu, Yueqiang; Gao, Zhe

2017-09-21

Plasma response to the resonant magnetic perturbation (RMP) field is numerically investigated by an extended toroidal fluid model, which includes anisotropic thermal transport physics parallel and perpendicular to the total magnetic field. The thermal transport is found to be effective in eliminating the toroidal average curvature induced plasma screening (the so called Glasser-Green-Johnson, GGJ screening) at slow toroidal flow regime, whilst having minor effect on modifying the conventional plasma screening regimes at faster flow. Furthermore, this physics effect of interaction between thermal transport and GGJ screening is attributed to the modification of the radial structure of the shielding current, resultedmore » from the plasma response to the applied field. The modification of the plasma response (shielding current, response field, plasma displacement and the perturbed velocity) also has direct consequence on the toroidal torques produced by RMP. These modelling results show that thermal transport reduces the resonant electromagnetic torque as well as the torque associated with the Reynolds stress, but enhances the neoclassical toroidal viscous torque at slow plasma flow.« less

Effect of anisotropic thermal transport on the resistive plasma response to resonant magnetic perturbation field

NASA Astrophysics Data System (ADS)

Bai, Xue; Liu, Yueqiang; Gao, Zhe

2017-10-01

Plasma response to the resonant magnetic perturbation (RMP) field is numerically investigated by an extended toroidal fluid model, which includes anisotropic thermal transport physics parallel and perpendicular to the total magnetic field. The thermal transport is found to be effective in eliminating the toroidal average curvature induced plasma screening (the so called Glasser-Green-Johnson, GGJ screening) in a slow toroidal flow regime, whilst having minor effect on modifying the conventional plasma screening regimes at faster flow. This physics effect of interaction between thermal transport and GGJ screening is attributed to the modification of the radial structure of the shielding current, which resulted from the plasma response to the applied field. The modification of the plasma response (shielding current, response field, plasma displacement, and the perturbed velocity) also has direct consequence on the toroidal torques produced by RMP. Modelling results show that thermal transport reduces the resonant electromagnetic torque as well as the torque associated with the Reynolds stress, but enhances the neoclassical toroidal viscous torque at slow plasma flow.

Adapting the Australian system: is an organized screening program feasible in Malaysia?--an overview of cervical cancer screening in both countries.

PubMed

Rashid, Rima Ma; Dahlui, Maznah; Mohamed, Majdah; Gertig, Dorota

2013-01-01

Cervical cancer is the third most common form of cancer that strikes Malaysian women. The National Cancer Registry in 2006 and 2007 reported that the age standardized incidence (ASR) of cervical cancer was 12.2 and 7.8 per 100,000 women, respectively. The cumulative risk of developing cervical cancer for a Malaysian woman is 0.9 for 74 years. Among all ethnic groups, the Chinese experienced the highest incidence rate in 2006, followed by Indians and Malays. The percentage cervical cancer detected at stage I and II was 55% (stage I: 21.0%, stage II: 34.0%, stage III: 26.0% and stage IV: 19.0%). Data from Ministry of Health Malaysia (2006) showed a 58.9% estimated coverage of pap smear screening conducted among those aged 30-49 years. Only a small percentage of women aged 50-59 and 50-65 years old were screened, 14% and 13.8% coverage, respectively. Incidence of cervical cancer was highest (71.6%) among those in the 60-65 age group (MOH, 2003). Currently, there is no organized population-based screening program available for the whole of Malaysia. A pilot project was initiated in 2006, to move from opportunistic cervical screening of women who attend antenatal and postnatal visits to a population based approach to be able to monitor the women through the screening pathway and encourage women at highest risk to be screened. The project was modelled on the screening program in Australia with some modifications to suit the Malaysian setting. Substantial challenges have been identified, particularly in relation to information systems for call and recall of women, as well as laboratory reporting and quality assurance. A cost-effective locally-specific approach to organized screening, that will provide the infrastructure for increasing participation in the cervical cancer screening program, is urgently required.

Screening of anionic-modified polymers in terms of stability, disintegration, and swelling behavior.

PubMed

Laffleur, Flavia; Ijaz, Muhammad; Menzel, Claudia

2017-11-01

This study aimed to screen the stability, disintegration, and swelling behavior of chemically modified anionic polymers. Investigated polymers were well-known and widely used staples of the pharmaceutical and medical field, namely, alginate (AL), carboxymethyl cellulose (CMC), polycarbophil (PC), and hyaluronic acid (HA). On the basis of amide bond formation between the carboxylic acid moieties of anionic polymers and the primary amino group of the modification ligand cysteine (CYS), the modified polymers were obtained. Unmodified polymers served as controls throughout all studies. With the Ellman's assay, modification degrees were determined of synthesized polymeric excipients. Stability assay in terms of erosion study at physiological conditions were performed. Moreover, water uptake of compressed polymeric discs were evaluated and further disintegration studies according to the USP were carried out to define the potential ranking. Results ranking figured out PCCYS > CMCCYS > HACYS > ALCYS in terms of water uptake capacity compared to respective controls. Cell viability assays on Caco-2 cell line as well as on RPMI 2650 (ATTC CCL30) proved modification not being harmful to those. Due to the results of this study, an intense screening of prominent anionic polymer derivate was performed in order to help the pharmaceutical research for the best choice of polymeric excipients for developments of controlled drug release systems.

Development of a comprehensive list of criteria for evaluating consumer education materials on colorectal cancer screening

PubMed Central

2013-01-01

Background Appropriate patient information materials may support the consumer’s decision to attend or not to attend colorectal cancer (CRC) screening tests (fecal occult blood test and screening colonoscopy). The aim of this study was to develop a list of criteria to assess whether written health information materials on CRC screening provide balanced, unbiased, quantified, understandable, and evidence-based health information (EBHI) about CRC and CRC screening. Methods The list of criteria was developed based on recommendations and assessment tools for health information in the following steps: (1) Systematic literature search in 13 electronic databases (search period: 2000–2010) and completed by an Internet search (2) Extraction of identified criteria (3) Grouping of criteria into categories and domains (4) Compilation of a manual of adequate answers derived from systematic reviews and S3 guidelines (5) Review by external experts (6) Modification (7) Final discussion with external experts. Results Thirty-one publications on health information tools and recommendations were identified. The final list of criteria includes a total of 230 single criteria in three generic domains (formal issues, presentation and understandability, and neutrality and balance) and one CRC-specific domain. A multi-dimensional rating approach was used whenever appropriate (e.g., rating for the presence, correctness, presentation and level of evidence of information). Free text input was allowed to ensure the transparency of assessment. The answer manual proved to be essential to the rating process. Quantitative analyses can be made depending on the level and dimensions of criteria. Conclusions This comprehensive list of criteria clearly has a wider range of evaluation than previous assessment tools. It is not intended as a final quality assessment tool, but as a first step toward thorough evaluation of specific information materials for their adherence to EBHI requirements. This criteria list may also be used to revise leaflets and to develop evidence-based health information on CRC screening. After adjustment for different procedure-specific criteria, the list of criteria can also be applied to other cancer screening procedures. PMID:24028691

Activity-based assay for human mono-ADP-ribosyltransferases ARTD7/PARP15 and ARTD10/PARP10 aimed at screening and profiling inhibitors.

PubMed

Venkannagari, Harikanth; Fallarero, Adyary; Feijs, Karla L H; Lüscher, Bernhard; Lehtiö, Lari

2013-05-13

Poly(ADP-ribose) polymerases (PARPs) or diphtheria toxin like ADP-ribosyl transferases (ARTDs) are enzymes that catalyze the covalent modification of proteins by attachment of ADP-ribose units to the target amino acid residues or to the growing chain of ADP-ribose. A subclass of the ARTD superfamily consists of mono-ADP-ribosyl transferases that are thought to modify themselves and other substrate proteins by covalently adding only a single ADP-ribose moiety to the target. Many of the ARTD enzymes are either established or potential drug targets and a functional activity assay for them will be a valuable tool to identify selective inhibitors for each enzyme. Existing assays are not directly applicable for screening of inhibitors due to the different nature of the reaction and different target molecules. We modified and applied a fluorescence-based assay previously described for PARP1/ARTD1 and tankyrase/ARTD5 for screening of PARP10/ARTD10 and PARP15/ARTD7 inhibitors. The assay measures the amount of NAD(+) present after chemically converting it to a fluorescent analog. We demonstrate that by using an excess of a recombinant acceptor protein the performance of the activity-based assay is excellent for screening of compound libraries. The assay is homogenous and cost effective, making it possible to test relatively large compound libraries. This method can be used to screen inhibitors of mono-ARTDs and profile inhibitors of the enzyme class. The assay was optimized for ARTD10 and ARTD7, but it can be directly applied to other mono-ARTDs of the ARTD superfamily. Profiling of known ARTD inhibitors against ARTD10 and ARTD7 in a validatory screening identified the best inhibitors with submicromolar potencies. Only few of the tested ARTD inhibitors were potent, implicating that there is a need to screen new compound scaffolds. This is needed to create small molecules that could serve as biological probes and potential starting points for drug discovery projects against mono-ARTDs. Copyright © 2013 Elsevier B.V. All rights reserved.

Identification of Eight Synthetic Cannabinoids, Including 5F-AKB48 in Seized Herbal Products Using DART-TOF-MS and LC-QTOF-MS as Nontargeted Screening Methods.

PubMed

Moore, Katherine N; Garvin, Demetra; Thomas, Brian F; Grabenauer, Megan

2017-09-01

Synthetic cannabinoids are sprayed onto plant material and smoked for their marijuana-like effects. Clandestine manufacturers modify synthetic cannabinoid structures by creating closely related analogs. Forensic laboratories are tasked with detection of these analog compounds, but targeted analytical methods are often thwarted by the structural modifications. Here, direct analysis in real time coupled to accurate mass time-of-flight mass spectrometry (DART-TOF-MS) in combination with liquid chromatography quadruple time-of-flight mass spectrometry (LC-QTOF-MS) are presented as a screening and nontargeted confirmation method, respectively. Methanol extracts of herbal material were run using both methods. Spectral data from four different herbal products were evaluated by comparing fragmentation pattern, accurate mass and retention time to available reference standards. JWH-018, JWH-019, AM2201, JWH-122, 5F-AKB48, AKB48-N-(4-pentenyl) analog, UR144, and XLR11 were identified in the products. Results demonstrate that DART-TOF-MS affords a useful approach for rapid screening of herbal products for the presence and identification of synthetic cannabinoids. © 2017 American Academy of Forensic Sciences.

The development of an observational screening tool to assess safe, effective and appropriate walking aid use in people with multiple sclerosis.

PubMed

Eitzen, Abby; Finlayson, Marcia; Carolan-Laing, Leanne; Nacionales, Arthur Junn; Walker, Christie; O'Connor, Josephine; Asano, Miho; Coote, Susan

2017-08-01

The purpose of this study was to identify potential items for an observational screening tool to assess safe, effective and appropriate walking aid use among people with multiple sclerosis (MS). Such a tool is needed because of the association between fall risk and mobility aid use in this population. Four individuals with MS were videotaped using a one or two straight canes, crutches or a rollator in different settings. Seventeen health care professionals from Canada, Ireland and the United States were recruited, and viewed the videos, and were then interviewed about the use of the devices by the individuals in the videos. Interview questions addressed safety, effectiveness and appropriateness of the device in the setting. Data were analyzed qualitatively. Coding consistency across raters was evaluated and confirmed. Nineteen codes were identified as possible items for the screening tool. The most frequent issues raised regardless of setting and device were "device used for duration/abandoned", "appropriate device", "balance and stability", "device technique", "environmental modification" and "hands free." With the identification of a number of potential tool items, researchers can now move forward with the development of the tool. This will involve consultation with both healthcare professionals and people with MS. Implications for rehabilitation Falls among people with multiple sclerosis are associated with mobility device use and use of multiple devices is associated with greater falls risk. The ability to assess for safe, effective and efficient use of walking aids is therefore important, no tools currently exist for this purpose. The codes arising from this study will be used to develop a screening tool for safe, effective and efficient walking aid use with the aim of reducing falls risk.

Matrix metalloproteinase proteomics: substrates, targets, and therapy.

PubMed

Morrison, Charlotte J; Butler, Georgina S; Rodríguez, David; Overall, Christopher M

2009-10-01

Proteomics encompasses powerful techniques termed 'degradomics' for unbiased high-throughput protease substrate discovery screens that have been applied to an important family of extracellular proteases, the matrix metalloproteinases (MMPs). Together with the data generated from genetic deletion and transgenic mouse models and genomic profiling, these screens can uncover the diverse range of MMP functions, reveal which MMPs and MMP-mediated pathways exacerbate pathology, and which are involved in protection and the resolution of disease. This information can be used to identify and validate candidate drug targets and antitargets, and is critical for the development of new inhibitors of MMP function. Such inhibitors may target either the MMP directly in a specific manner or pathways upstream and downstream of MMP activity that are mediating deleterious effects in disease. Since MMPs do not operate alone but are part of the 'protease web', it is necessary to use system-wide approaches to understand MMP proteolysis in vivo, to discover new biological roles and their potential for therapeutic modification.

Inhibiting AMPylation: a novel screen to identify the first small molecule inhibitors of protein AMPylation.

PubMed

Lewallen, Daniel M; Sreelatha, Anju; Dharmarajan, Venkatasubramanian; Madoux, Franck; Chase, Peter; Griffin, Patrick R; Orth, Kim; Hodder, Peter; Thompson, Paul R

2014-02-21

Enzymatic transfer of the AMP portion of ATP to substrate proteins has recently been described as an essential mechanism of bacterial infection for several pathogens. The first AMPylator to be discovered, VopS from Vibrio parahemolyticus, catalyzes the transfer of AMP onto the host GTPases Cdc42 and Rac1. Modification of these proteins disrupts downstream signaling events, contributing to cell rounding and apoptosis, and recent studies have suggested that blocking AMPylation may be an effective route to stop infection. To date, however, no small molecule inhibitors have been discovered for any of the AMPylators. Therefore, we developed a fluorescence-polarization-based high-throughput screening assay and used it to discover the first inhibitors of protein AMPylation. Herein we report the discovery of the first small molecule VopS inhibitors (e.g., calmidazolium, GW7647, and MK886) with Ki's ranging from 6 to 50 μM and upward of 30-fold selectivity versus HYPE, the only known human AMPylator.

Inhibiting AMPylation: A novel screen to identify the first small molecule inhibitors of protein AMPylation‡

PubMed Central

Lewallen, Daniel M.; Sreelatha, Anju; Dharmarajan, Venkatasubramanian; Madoux, Franck; Chase, Peter; Griffin, Patrick R.; Orth, Kim; Hodder, Peter; Thompson, Paul R.

2014-01-01

Enzymatic transfer of the AMP portion of ATP to substrate proteins has recently been described as an essential mechanism of bacterial infection for several pathogens. The first AMPylator to be discovered, VopS from Vibrio parahaemolyticus, catalyzes the transfer of AMP on to the host GTPases Cdc42 and Rac1. Modification of these proteins disrupts downstream signaling events, contributing to cell rounding and apoptosis, and recent studies have suggested that blocking AMPylation may be an effective route to stop infection. To date, however, no small molecule inhibitors have been discovered for any of the AMPylators. Therefore, we developed a fluorescence-polarization based high-throughput-screening assay and used it to discover the first inhibitors of protein AMPylation. Herein we report the discovery of the first small molecule VopS inhibitors (e.g. calmidazolium, GW7647 and MK886) with Kis ranging from 6–50 µM and upwards of 30-fold selectivity versus HYPE, the only known human AMPylator. PMID:24274060

Quantification of free cysteines in membrane and soluble proteins using a fluorescent dye and thermal unfolding.

PubMed

Branigan, Emma; Pliotas, Christos; Hagelueken, Gregor; Naismith, James H

2013-11-01

Cysteine is an extremely useful site for selective attachment of labels to proteins for many applications, including the study of protein structure in solution by electron paramagnetic resonance (EPR), fluorescence spectroscopy and medical imaging. The demand for quantitative data for these applications means that it is important to determine the extent of the cysteine labeling. The efficiency of labeling is sensitive to the 3D context of cysteine within the protein. Where the label or modification is not directly measurable by optical or magnetic spectroscopy, for example, in cysteine modification to dehydroalanine, assessing labeling efficiency is difficult. We describe a simple assay for determining the efficiency of modification of cysteine residues, which is based on an approach previously used to determine membrane protein stability. The assay involves a reaction between the thermally unfolded protein and a thiol-specific coumarin fluorophore that is only fluorescent upon conjugation with thiols. Monitoring fluorescence during thermal denaturation of the protein in the presence of the dye identifies the temperature at which the maximum fluorescence occurs; this temperature differs among proteins. Comparison of the fluorescence intensity at the identified temperature between modified, unmodified (positive control) and cysteine-less protein (negative control) allows for the quantification of free cysteine. We have quantified both site-directed spin labeling and dehydroalanine formation. The method relies on a commonly available fluorescence 96-well plate reader, which rapidly screens numerous samples within 1.5 h and uses <100 μg of material. The approach is robust for both soluble and detergent-solubilized membrane proteins.

Synergistic effects between analogs of DNA and RNA improve the potency of siRNA-mediated gene silencing

PubMed Central

Deleavey, Glen F.; Watts, Jonathan K.; Alain, Tommy; Robert, Francis; Kalota, Anna; Aishwarya, Veenu; Pelletier, Jerry; Gewirtz, Alan M.; Sonenberg, Nahum; Damha, Masad J.

2010-01-01

We report that combining a DNA analog (2′F-ANA) with rigid RNA analogs [2′F-RNA and/or locked nucleic acid (LNA)] in siRNA duplexes can produce gene silencing agents with enhanced potency. The favored conformations of these two analogs are different, and combining them in a 1–1 pattern led to reduced affinity, whereas alternating short continuous regions of individual modifications increased affinity relative to an RNA:RNA duplex. Thus, the binding affinity at key regions of the siRNA duplex could be tuned by changing the pattern of incorporation of DNA-like and RNA-like nucleotides. These heavily or fully modified duplexes are active against a range of mRNA targets. Effective patterns of modification were chosen based on screens using two sequences targeting firefly luciferase. We then applied the most effective duplex designs to the knockdown of the eIF4E binding proteins 4E-BP1 and 4E-BP2. We identified modified duplexes with potency comparable to native siRNA. Modified duplexes showed dramatically enhanced stability to serum nucleases, and were characterized by circular dichroism and thermal denaturation studies. Chemical modification significantly reduced the immunostimulatory properties of these siRNAs in human peripheral blood mononuclear cells. PMID:20413581

The uncharacterized transcription factor YdhM is the regulator of the nemA gene, encoding N-ethylmaleimide reductase.

PubMed

Umezawa, Yoshimasa; Shimada, Tomohiro; Kori, Ayako; Yamada, Kayoko; Ishihama, Akira

2008-09-01

N-ethylmaleimide (NEM) has been used as a specific reagent of Cys modification in proteins and thus is toxic for cell growth. On the Escherichia coli genome, the nemA gene coding for NEM reductase is located downstream of the gene encoding an as-yet-uncharacterized transcription factor, YdhM. Disruption of the ydhM gene results in reduction of nemA expression even in the induced state, indicating that the two genes form a single operon. After in vitro genomic SELEX screening, one of the target recognition sequences for YdhM was identified within the promoter region for this ydhM-nemA operon. Both YdhM binding in vitro to the ydhM promoter region and transcription repression in vivo of the ydhM-nemA operon by YdhM were markedly reduced by the addition of NEM. Taken together, we propose that YdhM is the repressor for the nemA gene, thus hereafter designated NemR. The repressor function of NemR was inactivated by the addition of not only NEM but also other Cys modification reagents, implying that Cys modification of NemR renders it inactive. This is an addition to the mode of controlling activity of transcription factors by alkylation with chemical agents.

Validation of a Nutritional Screening Tool for Ambulatory Use in Pediatrics.

PubMed

Rub, Gal; Marderfeld, Luba; Poraz, Irit; Hartman, Corina; Amsel, Shlomo; Rosenbaum, Israel; Pergamentzev-Karpol, Shiri; Monsonego-Ornan, Efrat; Shamir, Raanan

2016-05-01

To evaluate the use of Screening Tool for the Assessment of Malnutrition in Pediatrics (STAMP) in a primary health care clinic in the community and to assess the impact of its use on medical staff's awareness of nutritional status. STAMP scoring system was tested as is and with modifications in the ambulatory setting. Nutritional risk according to STAMP was compared with a detailed nutritional assessment performed by a registered dietitian. Recording of nutrition-related data and anthropometric measurements in medical files were compared prior and post implementation. Sixty children were included (31 girls, 52%), ages between 1 and 6 years, mean age 2.8 ± 1.5 (mean ± SD). STAMP scores yielded a fair agreement between STAMP and the dietitian's nutritional assessment: κ = 0.47 (95% confidence interval [CI] 0.24-0.7), sensitivity of 47.62% (95% CI 28.34-67.63). Modified STAMP yielded more substantial agreement: κ = 0.57 (95% CI 0.35-0.79), sensitivity of 76.19% (95% CI 54.91-89.37), specificity of 82.05% (95% CI 67.33-91.02). The use of STAMP resulted in an increase in recording of appetite, dietary intake, and anthropometric measurements. Modification of the STAMP improved nutritional risk evaluation in community setting. The use of STAMP in a primary health care clinic raised clinician's awareness to nutritional status. Further work will identify whether this could be translated into lower malnutrition rates and better child care.

Familial Hypercholesterolemia: A Systematic Review of Guidelines on Genetic Testing and Patient Management.

PubMed

Migliara, Giuseppe; Baccolini, Valentina; Rosso, Annalisa; D'Andrea, Elvira; Massimi, Azzurra; Villari, Paolo; De Vito, Corrado

2017-01-01

Familial hypercholesterolemia (FH) is an autosomal-dominant hereditary disorder of lipid metabolism that causes lifelong exposure to increased LDL levels resulting in premature coronary heart disease and, if untreated, death. Recent studies have shown its prevalence to be higher than previously considered, which has important implications for the mortality and morbidity of associated cardiovascular disease (CVD). Several clinical tools are used worldwide to help physicians diagnose FH, but nevertheless most patients remain undetected. This systematic review of guidelines aims to assess the role of genetic testing in the screening, diagnosis, and management of patients affected by heterozygous or homozygous FH and to identify related health-care pathways. We performed a systematic review of the literature; inclusion criteria were English or Italian guidelines focusing on genetic testing. The guidelines were included and evaluated for their content and development process using the Appraisal of Guidelines for Research and Evaluation II instrument. Ten guidelines were considered eligible, and all were judged to be of good quality, with slight differences among them. The most common indications for performing genetic tests were high levels of cholesterol, or physical findings consistent with lipid disorder, in the subject or in the family history. Subsequent screening of family members was indicated when a mutation had been identified in the index patient. Regarding patient management, the various guidelines agreed that intensive treatment with lipid-lowering medications should begin as quickly as possible and that lifestyle modifications should be an integral part of the therapy. Since the early detection of affected patients is beneficial for effective prevention of CVD, genetic testing is particularly useful for identifying family members via cascade screening and for distinguishing between heterozygous and homozygous individuals, the latter of which require more extreme therapeutic intervention.

The effect of acetaminophen on ubiquitin homeostasis in Saccharomyces cerevisiae

PubMed Central

Huseinovic, Angelina; van Leeuwen, Jolanda S.; van Welsem, Tibor; Stulemeijer, Iris; van Leeuwen, Fred; Vermeulen, Nico P. E.; Kooter, Jan M.; Vos, J. Chris

2017-01-01

Acetaminophen (APAP), although considered a safe drug, is one of the major causes of acute liver failure by overdose, and therapeutic chronic use can cause serious health problems. Although the reactive APAP metabolite N-acetyl-p-benzoquinoneimine (NAPQI) is clearly linked to liver toxicity, toxicity of APAP is also found without drug metabolism of APAP to NAPQI. To get more insight into mechanisms of APAP toxicity, a genome-wide screen in Saccharomyces cerevisiae for APAP-resistant deletion strains was performed. In this screen we identified genes related to the DNA damage response. Next, we investigated the link between genotype and APAP-induced toxicity or resistance by performing a more detailed screen with a library containing mutants of 1522 genes related to nuclear processes, like DNA repair and chromatin remodelling. We identified 233 strains that had an altered growth rate relative to wild type, of which 107 showed increased resistance to APAP and 126 showed increased sensitivity. Gene Ontology analysis identified ubiquitin homeostasis, regulation of transcription of RNA polymerase II genes, and the mitochondria-to-nucleus signalling pathway to be associated with APAP resistance, while histone exchange and modification, and vesicular transport were connected to APAP sensitivity. Indeed, we observed a link between ubiquitin levels and APAP resistance, whereby ubiquitin deficiency conferred resistance to APAP toxicity while ubiquitin overexpression resulted in sensitivity. The toxicity profile of various chemicals, APAP, and its positional isomer AMAP on a series of deletion strains with ubiquitin deficiency showed a unique resistance pattern for APAP. Furthermore, exposure to APAP increased the level of free ubiquitin and influenced the ubiquitination of proteins. Together, these results uncover a role for ubiquitin homeostasis in APAP-induced toxicity. PMID:28291796

Clinical utility of magnetic resonance imaging radiographs for suspected organic syndromes in adult psychiatry.

PubMed

Erhart, Stephen M; Young, Alexander S; Marder, Stephen R; Mintz, Jim

2005-08-01

In psychiatric practice, adult patients are most commonly referred for magnetic resonance imaging (MRI) to screen for suspected organic medical diseases of the central nervous system that can mimic psychiatric syndromes. We identified the most common signs and symptoms prompting MRIs to establish the predictive value of these signs and symptoms for clinically pertinent organic syndromes. This study was a retrospective chart review of psychiatric patients at the Veterans Affairs Greater Los Angeles Health Care Center (Los Angeles, Calif.) who were referred for MRI of the brain between 1996 and 2002. Patients referred for evaluation of dementia were excluded. The specific indications leading clinicians to obtain MRI were identified and grouped. In order to offset the uncertain significance of many MRI findings, for this study, the predictive value of each indication was calculated based on the percentage of patients in whom clinical management changed in response to MRI findings rather than on the percentage with any abnormal MRI results. Of 253 patients who had MRIs, 38 (15%) incurred some degree of treatment modification as a result of MRI findings, including 6 patients in whom MRI identified a medical condition that became the focus of treatment. Six indications appeared most likely to prompt clinicians to obtain MRIs. Because pertinent results were associated with each of these indications, statistical evaluation did not reveal significant differences in their predictive values (chi(2) = 4.32, df = 5, p = .505). Unlike prior studies showing no value to screening radioimaging, this study shows MRI can be a useful screening test among patients suspected of having organic psychiatric disorders and that the common indications for MRI employed at one institution were predictive.

The effect of acetaminophen on ubiquitin homeostasis in Saccharomyces cerevisiae.

PubMed

Huseinovic, Angelina; van Leeuwen, Jolanda S; van Welsem, Tibor; Stulemeijer, Iris; van Leeuwen, Fred; Vermeulen, Nico P E; Kooter, Jan M; Vos, J Chris

2017-01-01

Acetaminophen (APAP), although considered a safe drug, is one of the major causes of acute liver failure by overdose, and therapeutic chronic use can cause serious health problems. Although the reactive APAP metabolite N-acetyl-p-benzoquinoneimine (NAPQI) is clearly linked to liver toxicity, toxicity of APAP is also found without drug metabolism of APAP to NAPQI. To get more insight into mechanisms of APAP toxicity, a genome-wide screen in Saccharomyces cerevisiae for APAP-resistant deletion strains was performed. In this screen we identified genes related to the DNA damage response. Next, we investigated the link between genotype and APAP-induced toxicity or resistance by performing a more detailed screen with a library containing mutants of 1522 genes related to nuclear processes, like DNA repair and chromatin remodelling. We identified 233 strains that had an altered growth rate relative to wild type, of which 107 showed increased resistance to APAP and 126 showed increased sensitivity. Gene Ontology analysis identified ubiquitin homeostasis, regulation of transcription of RNA polymerase II genes, and the mitochondria-to-nucleus signalling pathway to be associated with APAP resistance, while histone exchange and modification, and vesicular transport were connected to APAP sensitivity. Indeed, we observed a link between ubiquitin levels and APAP resistance, whereby ubiquitin deficiency conferred resistance to APAP toxicity while ubiquitin overexpression resulted in sensitivity. The toxicity profile of various chemicals, APAP, and its positional isomer AMAP on a series of deletion strains with ubiquitin deficiency showed a unique resistance pattern for APAP. Furthermore, exposure to APAP increased the level of free ubiquitin and influenced the ubiquitination of proteins. Together, these results uncover a role for ubiquitin homeostasis in APAP-induced toxicity.

Drug discovery with an RBM20 dependent titin splice reporter identifies cardenolides as lead structures to improve cardiac filling.

PubMed

Liss, Martin; Radke, Michael H; Eckhard, Jamina; Neuenschwander, Martin; Dauksaite, Vita; von Kries, Jens-Peter; Gotthardt, Michael

2018-01-01

Diastolic dysfunction is increasingly prevalent in our ageing society and an important contributor to heart failure. The giant protein titin could serve as a therapeutic target, as its elastic properties are a main determinant of cardiac filling in diastole. This study aimed to develop a high throughput pharmacological screen to identify small molecules that affect titin isoform expression through differential inclusion of exons encoding the elastic PEVK domains. We used a dual luciferase splice reporter assay that builds on the titin splice factor RBM20 to screen ~34,000 small molecules and identified several compounds that inhibit the exclusion of PEVK exons. These compounds belong to the class of cardenolides and affect RBM20 dependent titin exon exclusion but did not affect RBFOX1 mediated splicing of FMNL3. We provide evidence that cardenolides do not bind to the RNA interacting domain of RBM20, but reduce RBM20 protein levels and alter transcription of select splicing factors that interact with RBM20. Cardenolides affect titin isoform expression. Understanding their mode of action and harnessing the splice effects through chemical modifications that suppress the effects on ion homeostasis and more selectively affect cardiac splicing has the potential to improve cardiac filling and thus help patients with diastolic heart failure, for which currently no targeted therapy exists.

Screen-Printed Electrodes Modified with “Green” Metals for Electrochemical Stripping Analysis of Toxic Elements

PubMed Central

Economou, Anastasios

2018-01-01

This work reviews the field of screen-printed electrodes (SPEs) modified with “green” metals for electrochemical stripping analysis of toxic elements. Electrochemical stripping analysis has been established as a useful trace analysis technique offering many advantages compared to competing optical techniques. Although mercury has been the preferred electrode material for stripping analysis, the toxicity of mercury and the associated legal requirements in its use and disposal have prompted research towards the development of “green” metals as alternative electrode materials. When combined with the screen-printing technology, such environment-friendly metals can lead to disposable sensors for trace metal analysis with excellent operational characteristics. This review focuses on SPEs modified with Au, Bi, Sb, and Sn for stripping analysis of toxic elements. Different modification approaches (electroplating, bulk modification, use of metal precursors, microengineering techniques) are considered and representative applications are described. A developing related field, namely biosensing based on stripping analysis of metallic nanoprobe labels, is also briefly mentioned. PMID:29596391

Screen-Printed Electrodes Modified with "Green" Metals for Electrochemical Stripping Analysis of Toxic Elements.

PubMed

Economou, Anastasios

2018-03-29

This work reviews the field of screen-printed electrodes (SPEs) modified with "green" metals for electrochemical stripping analysis of toxic elements. Electrochemical stripping analysis has been established as a useful trace analysis technique offering many advantages compared to competing optical techniques. Although mercury has been the preferred electrode material for stripping analysis, the toxicity of mercury and the associated legal requirements in its use and disposal have prompted research towards the development of "green" metals as alternative electrode materials. When combined with the screen-printing technology, such environment-friendly metals can lead to disposable sensors for trace metal analysis with excellent operational characteristics. This review focuses on SPEs modified with Au, Bi, Sb, and Sn for stripping analysis of toxic elements. Different modification approaches (electroplating, bulk modification, use of metal precursors, microengineering techniques) are considered and representative applications are described. A developing related field, namely biosensing based on stripping analysis of metallic nanoprobe labels, is also briefly mentioned.

Evaluation of an existing screening tool for psoriatic arthritis in people with psoriasis and the development of a new instrument: the Psoriasis Epidemiology Screening Tool (PEST) questionnaire.

PubMed

Ibrahim, G H; Buch, M H; Lawson, C; Waxman, R; Helliwell, P S

2009-01-01

To evaluate an existing tool (the Swedish modification of the Psoriasis Assessment Questionnaire) and to develop a new instrument to screen for psoriatic arthritis in people with psoriasis. The starting point was a community-based survey of people with psoriasis using questionnaires developed from the literature. Selected respondents were examined and additional known cases of psoriatic arthritis were included in the analysis. The new instrument was developed using univariate statistics and a logistic regression model, comparing people with and without psoriatic arthritis. The instruments were compared using receiver operating curve (ROC) curve analysis. 168 questionnaires were returned (response rate 27%) and 93 people attended for examination (55% of questionnaire respondents). Of these 93, twelve were newly diagnosed with psoriatic arthritis during this study. These 12 were supplemented by 21 people with known psoriatic arthritis. Just 5 questions were found to be significant predictors of psoriatic arthritis in this population. Figures for sensitivity and specificity were 0.92 and 0.78 respectively, an improvement on the Alenius tool (sensitivity and specificity, 0.63 and 0.72 respectively). A new screening tool for identifying people with psoriatic arthritis has been developed. Five simple questions demonstrated good sensitivity and specificity in this population but further validation is required.

MRI screening for breast cancer in women at high risk; is the Australian breast MRI screening access program addressing the needs of women at high risk of breast cancer?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schenberg, Tess; Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, Victoria; Mitchell, Gillian

Breast magnetic resonance imaging (MRI) screening of women under 50 years old at high familial risk of breast cancer was given interim funding by Medicare in 2009 on the basis that a review would be undertaken. An updated literature review has been undertaken by the Medical Services Advisory Committee but there has been no assessment of the quality of the screening or other screening outcomes. This review examines the evidence basis of breast MRI screening and how this fits within an Australian context with the purpose of informing future modifications to the provision of Medicare-funded breast MRI screening in Australia.more » Issues discussed will include selection of high-risk women, the options for MRI screening frequency and measuring the outcomes of screening.« less

Electron-phonon mediated heat flow in disordered graphene

NASA Astrophysics Data System (ADS)

Chen, Wei; Clerk, Aashish A.

2012-09-01

We calculate the heat flux and electron-phonon thermal conductance in a disordered graphene sheet, going beyond a Fermi’s golden rule approach to fully account for the modification of the electron-phonon interaction by disorder. Using the Keldysh technique combined with standard impurity averaging methods in the regime kFl≫1 (where kF is the Fermi wave vector and l is the mean free path), we consider both scalar potential (i.e., deformation potential) and vector-potential couplings between electrons and phonons. We also consider the effects of electronic screening at the Thomas-Fermi level. We find that the temperature dependence of the heat flux and thermal conductance is sensitive to the presence of disorder and screening, and reflects the underlying chiral nature of electrons in graphene and the corresponding modification of their diffusive behavior. In the case of weak screening, disorder enhances the low-temperature heat flux over the clean system (changing the associated power law from T4 to T3), and the deformation potential dominates. For strong screening, both the deformation potential and vector-potential couplings make comparable contributions, and the low-temperature heat flux obeys a T5 power law.

Interleukin 1 β-induced SMAD2/3 linker modifications are TAK1 dependent and delay TGFβ signaling in primary human mesenchymal stem cells.

PubMed

van den Akker, Guus G; van Beuningen, Henk M; Vitters, Elly L; Koenders, Marije I; van de Loo, Fons A; van Lent, Peter L; Blaney Davidson, Esmeralda N; van der Kraan, Peter M

2017-12-01

Chondrogenic differentiation of mesenchymal stem cells (MSC) requires transforming growth factor beta (TGFβ) signaling. TGFβ binds to the type I receptor activin-like kinase (ALK)5 and results in C-terminal SMAD2/3 phosphorylation (pSMAD2/3C). In turn pSMAD2/3C translocates to the nucleus and regulates target gene expression. Inflammatory mediators are known to exert an inhibitory effect on MSC differentiation. In this study we investigated the effect of interleukin 1 β (IL1β) on SMAD2/3 signaling dynamics and post-translational modifications. Co-stimulation of MSC with TGFβ and IL1β did not affect peak pSMAD2C levels at 1h post-stimulation. Surprisingly, SMAD3 transcriptional activity, as determined by the CAGA 12 -luciferase reporter construct, was enhanced by co-stimulation of TGFβ and IL1β compared to TGFβ alone. Furthermore, IL1β stimulation induced CAGA 12 -luciferase activity in a SMAD dependent way. As SMAD function can be modulated independent of canonical TGFβ signaling through the SMAD linker domain, we studied SMAD2 linker phosphorylation at specific threonine and serine residues. SMAD2 linker threonine and serine modifications were observed within 1h following TGFβ, IL1β or TGFβ and IL1β stimulation. Upon co-stimulation linker modified SMAD2 accumulated in the cytoplasm and SMAD2/3 target gene transcription (ID1, JUNB) at 2-4h was inhibited. A detailed time course analysis of IL1β-induced SMAD2 linker modifications revealed a distinct temperospatial pattern compared to TGFβ. Co-stimulation with both factors resulted in a similar kinetic profile as TGFβ alone. Nevertheless, IL1β did subtly alter TGFβ-induced pSMAD2C levels between 8 and 24h post-stimulation, which was reflected by TGFβ target gene expression (PAI1, JUNB). Direct evidence for the importance of SMAD3 linker modifications for the effect of IL1β on TGFβ signaling was obtained by over-expression of SMAD3 or a SMAD3 linker phospho-mutant. Finally, an inhibitor screening was performed to identify kinases involved in SMAD2/3 linker modifications. We identified TAK1 kinase activity as crucial for IL1β-induced SMAD2 linker modifications and CAGA 12 -luciferase activity. TGFβ and IL1β signaling interact at the SMAD2/3 level in human primary MSC. Down-stream TGFβ target genes were repressed by IL1β independent of C-terminal SMAD2 phosphorylation. We demonstrate that SMAD2/3 linker modifications are required for this interplay and identified TAK1 as a crucial mediator of IL1β-induced TGFβ signal modulation. Copyright © 2017 Elsevier Inc. All rights reserved.

The Three-item ALERT-B Questionnaire Provides a Validated Screening Tool to Detect Chronic Gastrointestinal Symptoms after Pelvic Radiotherapy in Cancer Survivors.

PubMed

Taylor, S; Byrne, A; Adams, R; Turner, J; Hanna, L; Staffurth, J; Farnell, D; Sivell, S; Nelson, A; Green, J

2016-10-01

Although pelvic radiotherapy is an effective treatment for various malignancies, around half of patients develop significant gastrointestinal problems. These symptoms often remain undetected, despite the existence of effective treatments. This study developed and refined a simple screening tool to detect common gastrointestinal symptoms in outpatient clinics. These symptoms have a significant effect on quality of life. This tool will increase detection rates and so enable access to specialist gastroenterologists, which will in turn lead to improved symptom control and quality of life after treatment. A literature review and expert consensus meeting identified four items for the ALERT-B (Assessment of Late Effects of RadioTherapy - Bowel) screening tool. ALERT-B was face tested for its usability and acceptability using cognitive interviews with 12 patients experiencing late gastrointestinal symptoms after pelvic radiotherapy. Thematic analysis and probe category were used to analyse interview transcripts. Interview data were presented to a group of experts to agree on the final content and format of the tool. ALERT-B was assessed for reliability and tested for validity against the Gastrointestinal Symptom Rating Scale in a clinical study (EAGLE). Overall, the tool was found to be acceptable in terms of wording, response format and completion time. Participant-reported experiences, including lifestyle modifications and the psychological effect of the symptoms, led to further modifications of the tool. The refined tool includes three questions covering rectal bleeding, incontinence, nocturnal bowel movements and impact on quality of life, including mood, relationships and socialising. ALERT-B was successfully validated against the Gastrointestinal Symptom Rating Scale in the EAGLE study with the tool shown broadly to be internally consistent (Cronbach's α = 0.61 and all item-subscale correlation [Spearman] coefficients are > 0.6). The ALERT-B screening tool can be used in clinical practice to improve post-treatment supportive care by triggering the clinical assessment of patients suitable for referral to a gastroenterologist. Copyright © 2016 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

Reader interactome of epigenetic histone marks in birds.

PubMed

Bluhm, Alina; Casas-Vila, Nuria; Scheibe, Marion; Butter, Falk

2016-02-01

Lysine methylation is part of the posttranscriptional histone code employed to recruit modification specific readers to chromatin. Unbiased, quantitative mass spectrometry approaches combined with peptide pull-downs have been used to study histone methylation-dependent binders in mammalian cells. Here, we extend the study to birds by investigating the interaction partners for H3K4me3, H3K9me3, H3K27me3 and H3K36me3 in chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) using label-free quantitative proteomics. In general, we find very strong overlap in interaction partners for the trimethyl marks in birds compared to mammals, underscoring the known conserved function of these modifications. In agreement with their epigenetic role, we find binding of PHF2 and members of the TFIID, SAGA, SET1 and NURF complex to the activation mark H3K4me3. Our data furthermore supports the existence of a LID complex in vertebrates recruited to the H3K4me3 mark. The repressive marks are bound by the HP1 proteins and the EED subunit of the PRC2 complex as well as by WIZ. Like reported in the previous mammalian screens, we found ZNF462, ZNF828 and POGZ enriched at H3K9me3. However, we noted some unexpected differences. N-PAC (also known as GLYR1), an H3K36me3 interactor in mammals, is reproducible not enriched at this modification in our screen in birds. This initial finding suggests that despite strong conservation of the histone tail sequence, a few species-specific differences in epigenetic readers may have evolved between birds and mammals. All MS data have been deposited in the ProteomeXchange with identifier PXD002282 (http://proteomecentral.proteomexchange.org/dataset/PXD002282). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemical Modification of the Multi-Target Neuroprotective Compound Fisetin

PubMed Central

Chiruta, Chandramouli; Schubert, David; Dargusch, Richard; Maher, Pamela

2012-01-01

Many factors are implicated in age-related CNS disorders making it unlikely that modulating only a single factor will provide effective treatment. Perhaps a better approach is to identify small molecules that have multiple biological activities relevant to the maintenance of brain function. Recently, we identified an orally active, neuroprotective and cognition-enhancing molecule, the flavonoid fisetin, that is effective in several animal models of CNS disorders. Fisetin has direct antioxidant activity and can also increase the intracellular levels of glutathione (GSH), the major endogenous antioxidant. In addition, fisetin has both neurotrophic and anti-inflammatory activity. However, its relatively high EC50 in cell based assays, low lipophilicity, high tPSA and poor bioavailability suggest that there is room for medicinal chemical improvement. Here we describe a multi-tiered approach to screening that has allowed us to identify fisetin derivatives with significantly enhanced activity in an in vitro neuroprotection model while at the same time maintaining other key activities. PMID:22192055

Robust functional statistics applied to Probability Density Function shape screening of sEMG data.

PubMed

Boudaoud, S; Rix, H; Al Harrach, M; Marin, F

2014-01-01

Recent studies pointed out possible shape modifications of the Probability Density Function (PDF) of surface electromyographical (sEMG) data according to several contexts like fatigue and muscle force increase. Following this idea, criteria have been proposed to monitor these shape modifications mainly using High Order Statistics (HOS) parameters like skewness and kurtosis. In experimental conditions, these parameters are confronted with small sample size in the estimation process. This small sample size induces errors in the estimated HOS parameters restraining real-time and precise sEMG PDF shape monitoring. Recently, a functional formalism, the Core Shape Model (CSM), has been used to analyse shape modifications of PDF curves. In this work, taking inspiration from CSM method, robust functional statistics are proposed to emulate both skewness and kurtosis behaviors. These functional statistics combine both kernel density estimation and PDF shape distances to evaluate shape modifications even in presence of small sample size. Then, the proposed statistics are tested, using Monte Carlo simulations, on both normal and Log-normal PDFs that mimic observed sEMG PDF shape behavior during muscle contraction. According to the obtained results, the functional statistics seem to be more robust than HOS parameters to small sample size effect and more accurate in sEMG PDF shape screening applications.

Zebrafish embryos as a screen for DNA methylation modifications after compound exposure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bouwmeester, Manon C.; Ruiter, Sander; Lommelaars, Tobias

Modified epigenetic programming early in life is proposed to underlie the development of an adverse adult phenotype, known as the Developmental Origins of Health and Disease (DOHaD) concept. Several environmental contaminants have been implicated as modifying factors of the developing epigenome. This underlines the need to investigate this newly recognized toxicological risk and systematically screen for the epigenome modifying potential of compounds. In this study, we examined the applicability of the zebrafish embryo as a screening model for DNA methylation modifications. Embryos were exposed from 0 to 72 h post fertilization (hpf) to bisphenol-A (BPA), diethylstilbestrol, 17α-ethynylestradiol, nickel, cadmium, tributyltin,more » arsenite, perfluoroctanoic acid, valproic acid, flusilazole, 5-azacytidine (5AC) in subtoxic concentrations. Both global and site-specific methylation was examined. Global methylation was only affected by 5AC. Genome wide locus-specific analysis was performed for BPA exposed embryos using Digital Restriction Enzyme Analysis of Methylation (DREAM), which showed minimal wide scale effects on the genome, whereas potential informative markers were not confirmed by pyrosequencing. Site-specific methylation was examined in the promoter regions of three selected genes vasa, vtg1 and cyp19a2, of which vasa (ddx4) was the most responsive. This analysis distinguished estrogenic compounds from metals by direction and sensitivity of the effect compared to embryotoxicity. In conclusion, the zebrafish embryo is a potential screening tool to examine DNA methylation modifications after xenobiotic exposure. The next step is to examine the adult phenotype of exposed embryos and to analyze molecular mechanisms that potentially link epigenetic effects and altered phenotypes, to support the DOHaD hypothesis. - Highlights: • Compound induced effects on DNA methylation in zebrafish embryos • Global methylation not an informative biomarker • Minimal genome wide site specific changes as detected with DREAM • Compound/class specific effects suggested by pyrosequence of specific targets • Zebrafish embryo may be a screening model for epigenetic effects.« less

Discovery of host-targeted covalent inhibitors of dengue virus

PubMed Central

de Wispelaere, Mélissanne; Carocci, Margot; Liang, Yanke; Liu, Qingsong; Sun, Eileen; Vetter, Michael L.; Wang, Jinhua; Gray, Nathanael S.; Yang, Priscilla L.

2017-01-01

We report here on an approach targeting the host reactive cysteinome to identify inhibitors of host factors required for the infectious cycle of Flaviviruses and other viruses. We used two parallel cellular phenotypic screens to identify a series of covalent inhibitors, exemplified by QL-XII-47, that are active against dengue virus. We show that the compounds effectively block viral protein expression and that this inhibition is associated with repression of downstream processes of the infectious cycle, and thus significantly contributes to the potent antiviral activity of these compounds. We demonstrate that QL-XII-47’s antiviral activity requires selective, covalent modification of a host target by showing that the compound's antiviral activity is recapitulated when cells are preincubated with QL-XII-47 and then washed prior to viral infection and by showing that QL-XII-47R, a non-reactive analog, lacks antiviral activity at concentrations more than 20-fold higher than QL-XII-47's IC90. QL-XII-47’s inhibition of Zika virus, West Nile virus, hepatitis C virus, and poliovirus further suggests that it acts via a target mediating inhibition of these other medically relevant viruses. These results demonstrate the utility of screens targeting the host reactive cysteinome for rapid identification of compounds with potent antiviral activity. PMID:28034743

An RNA Interference Screen Identifies the Deubiquitinase STAMBPL1 as a Critical Regulator of Human T-Cell Leukemia Virus Type 1 Tax Nuclear Export and NF-κB Activation

PubMed Central

Lavorgna, Alfonso

2012-01-01

The human T-cell leukemia virus type 1 (HTLV-1) Tax oncoprotein actively shuttles between the nucleus, where it interacts with transcriptional and splicing regulatory proteins, and the cytoplasm, where it activates NF-κB. Posttranslational modifications of Tax such as ubiquitination regulate its subcellular localization and hence its function; however, the regulation of Tax trafficking and NF-κB activation by host factors is poorly understood. By screening a deubiquitinating (DUB) enzyme small interfering RNA (siRNA) library, we identified the metalloprotease STAM-binding protein-like 1 (STAMBPL1) as a positive regulator of Tax-mediated NF-κB activation. Overexpression of wild-type STAMBPL1, but not a catalytically inactive mutant, enhanced Tax-mediated NF-κB activation, whereas silencing of STAMBPL1 with siRNA impaired Tax activation of both the canonical and noncanonical NF-κB signaling pathways. STAMBPL1 regulated Tax-induced NF-κB signaling indirectly by controlling Tax nuclear/cytoplasmic transport and was required for DNA damage-induced Tax nuclear export. Together, these results reveal that the deubiquitinase STAMBPL1 is a key regulator of Tax trafficking and function. PMID:22258247

Ingestible roasted barley for contrast-enhanced photoacoustic imaging in animal and human subjects.

PubMed

Wang, Depeng; Lee, Dong Hyeun; Huang, Haoyuan; Vu, Tri; Lim, Rachel Su Ann; Nyayapathi, Nikhila; Chitgupi, Upendra; Liu, Maggie; Geng, Jumin; Xia, Jun; Lovell, Jonathan F

2018-08-01

Photoacoustic computed tomography (PACT) is an emerging imaging modality. While many contrast agents have been developed for PACT, these typically cannot immediately be used in humans due to the lengthy regulatory process. We screened two hundred types of ingestible foodstuff samples for photoacoustic contrast with 1064 nm pulse laser excitation, and identified roasted barley as a promising candidate. Twenty brands of roasted barley were further screened to identify the one with the strongest contrast, presumably based on complex chemical modifications incurred during the roasting process. Individual roasted barley particles could be detected through 3.5 cm of chicken-breast tissue and through the whole hand of healthy human volunteers. With PACT, but not ultrasound imaging, a single grain of roasted barley was detected in a field of hundreds of non-roasted particles. Upon oral administration, roasted barley enabled imaging of the gut and peristalsis in mice. Prepared roasted barley tea could be detected through 2.5 cm chicken breast tissue. When barley tea was administered to humans, photoacoustic imaging visualized swallowing dynamics in healthy volunteers. Thus, roasted barley represents an edible foodstuff that should be considered for photoacoustic contrast imaging of swallowing and gut processes, with immediate potential for clinical translation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Benefits, Harms, and Costs of Osteoporosis Screening in Male Veterans

DTIC Science & Technology

2016-10-01

of many was modest, and some were negatively associated with screening (diabetes, stroke, kidney disease ). Co-morbidities had a modest...was estimated using baseline creatinine values and calculated with the Modification of Diet in Renal Disease equation. Subjects were followed to...those with diabetes, incident fractures were associated with presence of cardiovascular disease (20.8% vs 12.4%, P < 0.0001) and chronic kidney

Elevation of cellular O-GlcNAcylation level by a potent and selective O-GlcNAcase inhibitor based on tetrahydroimidazopyridine scaffold.

PubMed

Li, Tiehai; Li, Zhonghua; Li, Jing; Wang, Jiajia; Guo, Lina; Wang, Peng George; Zhao, Wei

2012-11-15

Protein O-GlcNAc glycosylation is a ubiquitous post-translational modification in metazoans. O-GlcNAcase (OGA), which is responsible for removing O-GlcNAc from serine or threonine residues, plays a key role in O-GlcNAc metabolism. Potent and selective O-GlcNAcase (OGA) inhibitors are useful tools for investigating the role of this modification in a broad range of cellular processes, and may also serve as drug candidates for treatment of neurodegenerative diseases. Biological screening of the gluco-configured tetrahydroimidazopyridine derivatives identified a compound as a potent and competitive inhibitor of human O-GlcNAcase (OGA) with a K(i) of 5.9 μM, and it also displayed 28-fold selectivity for human OGA over human lysosomal β-hexosaminidase A (Hex A, K(i)=163 μM). In addition, cell-based assay revealed that this compound was cell-permeant and effectively induced cellular hyper-O-GlcNAcylation at 10 μM concentration. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

Zebrafish embryos as a screen for DNA methylation modifications after compound exposure.

PubMed

Bouwmeester, Manon C; Ruiter, Sander; Lommelaars, Tobias; Sippel, Josefine; Hodemaekers, Hennie M; van den Brandhof, Evert-Jan; Pennings, Jeroen L A; Kamstra, Jorke H; Jelinek, Jaroslav; Issa, Jean-Pierre J; Legler, Juliette; van der Ven, Leo T M

2016-01-15

Modified epigenetic programming early in life is proposed to underlie the development of an adverse adult phenotype, known as the Developmental Origins of Health and Disease (DOHaD) concept. Several environmental contaminants have been implicated as modifying factors of the developing epigenome. This underlines the need to investigate this newly recognized toxicological risk and systematically screen for the epigenome modifying potential of compounds. In this study, we examined the applicability of the zebrafish embryo as a screening model for DNA methylation modifications. Embryos were exposed from 0 to 72 h post fertilization (hpf) to bisphenol-A (BPA), diethylstilbestrol, 17α-ethynylestradiol, nickel, cadmium, tributyltin, arsenite, perfluoroctanoic acid, valproic acid, flusilazole, 5-azacytidine (5AC) in subtoxic concentrations. Both global and site-specific methylation was examined. Global methylation was only affected by 5AC. Genome wide locus-specific analysis was performed for BPA exposed embryos using Digital Restriction Enzyme Analysis of Methylation (DREAM), which showed minimal wide scale effects on the genome, whereas potential informative markers were not confirmed by pyrosequencing. Site-specific methylation was examined in the promoter regions of three selected genes vasa, vtg1 and cyp19a2, of which vasa (ddx4) was the most responsive. This analysis distinguished estrogenic compounds from metals by direction and sensitivity of the effect compared to embryotoxicity. In conclusion, the zebrafish embryo is a potential screening tool to examine DNA methylation modifications after xenobiotic exposure. The next step is to examine the adult phenotype of exposed embryos and to analyze molecular mechanisms that potentially link epigenetic effects and altered phenotypes, to support the DOHaD hypothesis. Copyright © 2015 Elsevier Inc. All rights reserved.

A comprehensive screen for volatile organic compounds in biological fluids.

PubMed

Sharp, M E

2001-10-01

A headspace gas chromatographic (GC) screen for common volatile organic compounds in biological fluids is reported. Common GC phases, DB-1 and DB-WAX, with split injection provide separation and identification of more than 40 compounds in a single 20-min run. In addition, this method easily accommodates quantitation. The screen detects commonly encountered volatile compounds at levels below 4 mg%. A control mixture, providing qualitative and semiquantitative information, is described. For comparison, elution of the volatiles on a specialty phase, DB-624, is reported. This method is an expansion and modification of a screen that had been used for more than 20 years. During its first year of use, the expanded screen has proven to be advantageous in routine forensic casework.

Identification and classification of genes required for tolerance to high-sucrose stress revealed by genome-wide screening of Saccharomyces cerevisiae.

PubMed

Ando, Akira; Tanaka, Fumiko; Murata, Yoshinori; Takagi, Hiroshi; Shima, Jun

2006-03-01

Yeasts used in bread making are exposed to high concentrations of sucrose during sweet dough fermentation. Despite its importance, tolerance to high-sucrose stress is poorly understood at the gene level. To clarify the genes required for tolerance to high-sucrose stress, genome-wide screening was undertaken using the complete deletion strain collection of diploid Saccharomyces cerevisiae. The screening identified 273 deletions that yielded high sucrose sensitivity, approximately 20 of which were previously uncharacterized. These 273 deleted genes were classified based on their cellular function and localization of their gene products. Cross-sensitivity of the high-sucrose-sensitive mutants to high concentrations of NaCl and sorbitol was studied. Among the 273 sucrose-sensitive deletion mutants, 269 showed cross-sensitivities to sorbitol or NaCl, and four (i.e. ade5,7, ade6, ade8, and pde2) were specifically sensitive to high sucrose. The general stress response pathways via high-osmolarity glycerol and stress response element pathways and the function of the invertase in the ade mutants were similar to those in the wild-type strain. In the presence of high-sucrose stress, intracellular contents of ATP in ade mutants were at least twofold lower than that of the wild-type cells, suggesting that depletion of ATP is a factor in sensitivity to high-sucrose stress. The genes identified in this study might be important for tolerance to high-sucrose stress, and therefore should be target genes in future research into molecular modification for breeding of yeast tolerant to high-sucrose stress.

Agents that Stabilize Mutated von Hippel Lindau Protein Result in Differential Post-Translational Modification and Subcellular Localization

PubMed Central

Ding, Zhiyong; German, Peter; Bai, Shanshan; Feng, Zhehui; Gao, Meng; Si, Wendy; Sobieski, Mary M.; Stephan, Clifford C.; Mills, Gordon B.; Jonasch, Eric

2014-01-01

Background von Hippel Lindau (VHL) disease is an autosomal dominant inherited disorder that results in multiple organ systems being affected. Treatment is mainly surgical, however, effective systemic therapies are needed. We developed and tested a cell-based screening tool to identify compounds that stabilize or upregulate full-length, point mutated VHL. Methods The 786-0 cell line was infected with full-length W117A mutated VHL linked to a C-terminal Venus fluorescent protein. This VHL-W117A-Venus line was used to screen the Prestwick drug library and was tested against the known proteasome inhibitors MG132 and bortezomib. Western blot validation and evaluation of downstream functional readouts, including HIF and GLUT1 levels, were performed. Results Bortezomib, MG132, and the Prestwick compounds 8-azaguanine, thiostrepton and thioguanosine were found to reliably upregulate VHL-W117A-Venus in 786-0 cells. 8-azaguanine was found to downregulate HIF2α levels, and was augmented by the presence of VHL W117A. VHL p30 band intensities varied as a function of compound used, suggesting alternate post-translational processing. In addition, nuclear-cytoplasmic localization of pVHL varied amongst the different compounds. Conclusion 786-0 cells containing VHL-W117A-Venus can be successfully used to identify compounds that upregulate VHL levels, and that have a differential effect on pVHL intracellular localization and posttranslational processing. Further screening efforts will broaden the number of pharmacophores available to develop therapeutic agents that will upregulate and refunctionalize mutated VHL. PMID:22357874

Finding Horndeski theories with Einstein gravity limits

DOE Office of Scientific and Technical Information (OSTI.GOV)

McManus, Ryan; Lombriser, Lucas; Peñarrubia, Jorge, E-mail: ryanm@roe.ac.uk, E-mail: llo@roe.ac.uk, E-mail: jorpega@roe.ac.uk

The Horndeski action is the most general scalar-tensor theory with at most second-order derivatives in the equations of motion, thus evading Ostrogradsky instabilities and making it of interest when modifying gravity at large scales. To pass local tests of gravity, these modifications predominantly rely on nonlinear screening mechanisms that recover Einstein's Theory of General Relativity in regions of high density. We derive a set of conditions on the four free functions of the Horndeski action that examine whether a specific model embedded in the action possesses an Einstein gravity limit or not. For this purpose, we develop a new andmore » surprisingly simple scaling method that identifies dominant terms in the equations of motion by considering formal limits of the couplings that enter through the new terms in the modified action. This enables us to find regimes where nonlinear terms dominate and Einstein's field equations are recovered to leading order. Together with an efficient approximation of the scalar field profile, one can then further evaluate whether these limits can be attributed to a genuine screening effect. For illustration, we apply the analysis to both a cubic galileon and a chameleon model as well as to Brans-Dicke theory. Finally, we emphasise that the scaling method also provides a natural approach for performing post-Newtonian expansions in screened regimes.« less

Development of high temperature silicone adhesive formulations for thermal protection system applications

NASA Technical Reports Server (NTRS)

Hockridge, R. R.

1973-01-01

Trade-off studies and screening evaluations were made of commercial polymers and silicone foam sheet stock. A low modulus, low density 0.26 gm/cc modification was developed of the GE-RESD PD-200 system based upon GE RTV-560 silicone polymer. The bond system modification was initially characterized for mechanical and thermal properties, evaluated for application methods, and its capability demonstrated as a strain arrestor bond system.

Associations among family history of cancer, cancer screening and lifestyle behaviors: a population-based study.

PubMed

Bostean, Georgiana; Crespi, Catherine M; McCarthy, William J

2013-08-01

Some cancers are largely preventable through modification of certain behavioral risk factors and preventive screening, even among those with a family history of cancer. This study examined the associations between (1) family cancer history and cancer screening, (2) family history and cancer preventive lifestyle behaviors, and (3) cancer screening and lifestyle behaviors. Data were from the 2009 California Health Interview Survey (n = 12,603). Outcomes included screening for breast cancer (BC) and colorectal cancer (CRC) and six cancer preventive lifestyle behaviors, based on World Cancer Research Fund recommendations. Multivariate logistic regression analyses, stratified by gender and race-ethnicity, examined associations. Predicted probabilities of cancer screening by family cancer history, race-ethnicity, and sex were computed. Family history of site-specific cancer-CRC for men and women, and BC for women-was associated with higher probability of cancer screening for most groups, especially for CRC, but was largely unrelated to other lifestyle behaviors. In the few cases in which family history was significantly associated with lifestyle-for example, physical activity among White and Latino males, smoking among White and Asian females-individuals with a family history had lower odds of adherence to recommendations than those with no family history. Greater overall adherence to lifestyle recommendations was associated with higher odds of up-to-date CRC screening among White and Asian males, and lower odds among Asian females (no significant association with BC screening); this relationship did not vary by family cancer history. The fact that family history of cancer is not associated with better lifestyle behaviors may reflect shared behavioral risks within families, or the lack of knowledge about how certain lifestyle behaviors impact personal cancer risk. Findings can inform interventions aimed at lifestyle behavioral modification for individuals at increased cancer risk due to family history.

Effect of Combined Patient Decision Aid and Patient Navigation vs Usual Care for Colorectal Cancer Screening in a Vulnerable Patient Population: A Randomized Clinical Trial.

PubMed

Reuland, Daniel S; Brenner, Alison T; Hoffman, Richard; McWilliams, Andrew; Rhyne, Robert L; Getrich, Christina; Tapp, Hazel; Weaver, Mark A; Callan, Danelle; Cubillos, Laura; Urquieta de Hernandez, Brisa; Pignone, Michael P

2017-07-01

Colorectal cancer (CRC) screening is underused, especially among vulnerable populations. Decision aids and patient navigation are potentially complementary interventions for improving CRC screening rates, but their combined effect on screening completion is unknown. To determine the combined effect of a CRC screening decision aid and patient navigation compared with usual care on CRC screening completion. In this randomized clinical trial, data were collected from January 2014 to March 2016 at 2 community health center practices, 1 in North Carolina and 1 in New Mexico, serving vulnerable populations. Patients ages 50 to 75 years who had average CRC risk, spoke English or Spanish, were not current with recommended CRC screening, and were attending primary care visits were recruited and randomized 1:1 to intervention or control arms. Intervention participants viewed a CRC screening decision aid in English or Spanish immediately before their clinician encounter. The decision aid promoted screening and presented colonoscopy and fecal occult blood testing as screening options. After the clinician encounter, intervention patients received support for screening completion from a bilingual patient navigator. Control participants viewed a food safety video before the encounter and otherwise received usual care. The primary outcome was CRC screening completion within 6 months of the index study visit assessed by blinded medical record review. Characteristics of the 265 participants were as follows: their mean age was 58 years; 173 (65%) were female, 164 (62%) were Latino; 40 (15%) were white non-Latino; 61 (23%) were black or of mixed race; 191 (78%) had a household income of less than $20 000; 101 (38%) had low literacy; 75 (28%) were on Medicaid; and 91 (34%) were uninsured. Intervention participants were more likely to complete CRC screening within 6 months (68% vs 27%); adjusted-difference, 40 percentage points (95% CI, 29-51 percentage points). The intervention was more effective in women than in men (50 vs 21 percentage point increase, interaction P = .02). No effect modification was observed across other subgroups. A patient decision aid plus patient navigation increased the rate of CRC screening completion in compared with usual care invulnerable primary care patients. clinicaltrials.gov Identifier: NCT02054598.

Molecular Toolkit for Gene Expression Control and Genome Modification in Rhodococcus opacus PD630

DOE PAGES

DeLorenzo, Drew M.; Rottinghaus, Austin G.; Henson, William R.; ...

2018-01-24

Rhodococcus opacus PD630 is a non-model, gram-positive bacterium that possesses desirable traits for lignocellulosic biomass conversion. In particular, it has a relatively rapid growth rate, exhibits genetic tractability, produces high quantities of lipids, and can tolerate and consume toxic, lignin-derived aromatic compounds. Despite these unique, industrially relevant characteristics, R. opacus has been underutilized due to a lack of reliable genetic parts and engineering tools. In this work, we developed a molecular toolbox for reliable gene expression control and genome modification in R. opacus. To facilitate predictable gene expression, a constitutive promoter library spanning ~45-fold in output was constructed. To improvemore » the characterization of available plasmids, the copy numbers of four heterologous and nine endogenous plasmids were determined using quantitative PCR. The molecular toolbox was further expanded by screening a previously unreported antibiotic resistance marker (HygR) and constructing a curable plasmid backbone for temporary gene expression (pB264). Furthermore, a system for genome modification was devised, and three neutral integration sites were identified using a novel combination of transcriptomic data, genomic architecture, and growth rate analysis. Finally, the first reported system for targeted, tunable gene repression in Rhodococcus was developed by utilizing CRISPR interference (CRISPRi). Overall, this work greatly expands the ability to manipulate and engineer R. opacus, making it a viable new chassis for bioproduction from renewable feedstocks.« less

Molecular Toolkit for Gene Expression Control and Genome Modification in Rhodococcus opacus PD630

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeLorenzo, Drew M.; Rottinghaus, Austin G.; Henson, William R.

Rhodococcus opacus PD630 is a non-model, gram-positive bacterium that possesses desirable traits for lignocellulosic biomass conversion. In particular, it has a relatively rapid growth rate, exhibits genetic tractability, produces high quantities of lipids, and can tolerate and consume toxic, lignin-derived aromatic compounds. Despite these unique, industrially relevant characteristics, R. opacus has been underutilized due to a lack of reliable genetic parts and engineering tools. In this work, we developed a molecular toolbox for reliable gene expression control and genome modification in R. opacus. To facilitate predictable gene expression, a constitutive promoter library spanning ~45-fold in output was constructed. To improvemore » the characterization of available plasmids, the copy numbers of four heterologous and nine endogenous plasmids were determined using quantitative PCR. The molecular toolbox was further expanded by screening a previously unreported antibiotic resistance marker (HygR) and constructing a curable plasmid backbone for temporary gene expression (pB264). Furthermore, a system for genome modification was devised, and three neutral integration sites were identified using a novel combination of transcriptomic data, genomic architecture, and growth rate analysis. Finally, the first reported system for targeted, tunable gene repression in Rhodococcus was developed by utilizing CRISPR interference (CRISPRi). Overall, this work greatly expands the ability to manipulate and engineer R. opacus, making it a viable new chassis for bioproduction from renewable feedstocks.« less

Discovery Orbiter Major Modifications

NASA Image and Video Library

2003-08-27

In the Vehicle Assembly Building, Jim Landy, NDE specialist, sets up a flight crew lockers for flash thermography. He is screening the lockers for hidden damage underneath dings and dents that might occur during handling.

Screening for abuse and mental health problems among illiterate runaway adolescents in an Indian metropolis.

PubMed

Bhat, Deepti Pagare; Singh, Meghachandra; Meena, Gajendra Singh

2012-11-01

To evaluate the prevalence of physical and sexual abuse, and their relation to mental health problems among the illiterate/semiliterate runaway adolescents in New Delhi, India. Cross sectional. New Delhi, India. Runaway adolescent boys (n=119) aged 11 to 18 years at an observation home. Study subjects were screened for physical and sexual abuse using the Child Maltreatment History Self Report and Finkelhor's sexual abuse scale. Mental health problems were identified using the Achenbach's Youth Self-Report scale. As the participants were illiterate or semiliterate with Hindi being their primary language, the screening tools were appropriately translated, read out to them and their responses recorded. A total of 72 (62%) boys experienced domestic violence, 70 (59%) had engaged in substance abuse and 103 (87%) boys had been employed as child labourers. Physical abuse was reported by 86 (72%) and sexual abuse by 42 (35%). Mental health problems were recognised in 83 (70%) boys, which included internalising syndromes (59%) and externalising syndromes (34%). Multivariate analysis demonstrated that physical abuse was an independent predictor of internalising syndromes (OR: 3.3; 95% CI 1.2 to 9.1; p<0.01), while substance abuse and sexual abuse were independent predictors of externalising syndromes. Our study demonstrates that childhood abuse and mental health disorders are widely prevalent among the runaway adolescents evaluated at an observation home in New Delhi. Appropriate modification of the standardised self-report screening tools may allow the identification of mental health disorders in this vulnerable illiterate/semiliterate population.

Global Profiling of Huntingtin-associated protein E (HYPE)-Mediated AMPylation through a Chemical Proteomic Approach.

PubMed

Broncel, Malgorzata; Serwa, Remigiusz A; Bunney, Tom D; Katan, Matilda; Tate, Edward W

2016-02-01

AMPylation of mammalian small GTPases by bacterial virulence factors can be a key step in bacterial infection of host cells, and constitutes a potential drug target. This posttranslational modification also exists in eukaryotes, and AMP transferase activity was recently assigned to HYPE Filamentation induced by cyclic AMP domain containing protein (FICD) protein, which is conserved from Caenorhabditis elegans to humans. In contrast to bacterial AMP transferases, only a small number of HYPE substrates have been identified by immunoprecipitation and mass spectrometry approaches, and the full range of targets is yet to be determined in mammalian cells. We describe here the first example of global chemoproteomic screening and substrate validation for HYPE-mediated AMPylation in mammalian cell lysate. Through quantitative mass-spectrometry-based proteomics coupled with novel chemoproteomic tools providing MS/MS evidence of AMP modification, we identified a total of 25 AMPylated proteins, including the previously validated substrate endoplasmic reticulum (ER) chaperone BiP (HSPA5), and also novel substrates involved in pathways of gene expression, ATP biosynthesis, and maintenance of the cytoskeleton. This dataset represents the largest library of AMPylated human proteins reported to date and a foundation for substrate-specific investigations that can ultimately decipher the complex biological networks involved in eukaryotic AMPylation. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Rhodotorula taiwanensis MD1149 produces hypoacetylated PEFA compounds with increased surface activity compared to Rhodotorula babjevae MD1169.

PubMed

Lyman, Mathew; Rubinfeld, Bonnee; Leif, Roald; Mulcahy, Heather; Dugan, Lawrence; Souza, Brian

2018-01-01

Biosurfactants have several desirable characteristics in the industrial sector: detergency, antimicrobial effects, skin hydration, and emulsibility. Several yeast glycolipids are currently being utilized in these capacities: sophorolipids, ustilagic acid, and mannosylerythritol lipids (MELs). An emerging class of glycolipids, termed polyol esters of fatty acids (PEFA), have recently been reported for Rhodotorula babjevae, a basidiomycetous yeast species that secretes hyperacetylated congeners of PEFA (typically with 3-6 acetylation modifications). While screening Rhodotorula species for surfactant production, we identified a new environmental isolate identified as Rhodotorula taiwanensis MD1149 that dropped the surface tension of the liquid medium, indicating that it produced a potent biosurfactant. Acid depolymerization of the purified biosurfactants, followed by gas chromatography-mass spectrometry (GC-MS) analysis revealed that the biosurfactants were composed of PEFA compounds composed mainly of mannitol and arabitol esters of 3-hydroxy fatty acid, 3-methoxy fatty acid, and fatty acids with a single double bond; chain lengths were mainly C16 and C18. Liquid chromatography-mass spectrometry (LC-MS) confirmed the predicted accurate mass of these compounds. Interestingly, PEFA compounds produced by Rhodotorula taiwanensis MD1149 were more surface active due to their hypoacetylation profile (0-4 acetylation modifications) compared to Rhodotorula babjevae MD1169. These disparate surface active properties, based on acetylation, change the hydrophilic-lipophilic balance (HLB) of these compounds, and their potential utility within industrial applications.

Improved Production of a Heterologous Amylase in Saccharomyces cerevisiae by Inverse Metabolic Engineering

PubMed Central

Liu, Zihe; Liu, Lifang; Österlund, Tobias; Hou, Jin; Huang, Mingtao; Fagerberg, Linn; Petranovic, Dina; Uhlén, Mathias

2014-01-01

The increasing demand for industrial enzymes and biopharmaceutical proteins relies on robust production hosts with high protein yield and productivity. Being one of the best-studied model organisms and capable of performing posttranslational modifications, the yeast Saccharomyces cerevisiae is widely used as a cell factory for recombinant protein production. However, many recombinant proteins are produced at only 1% (or less) of the theoretical capacity due to the complexity of the secretory pathway, which has not been fully exploited. In this study, we applied the concept of inverse metabolic engineering to identify novel targets for improving protein secretion. Screening that combined UV-random mutagenesis and selection for growth on starch was performed to find mutant strains producing heterologous amylase 5-fold above the level produced by the reference strain. Genomic mutations that could be associated with higher amylase secretion were identified through whole-genome sequencing. Several single-point mutations, including an S196I point mutation in the VTA1 gene coding for a protein involved in vacuolar sorting, were evaluated by introducing these to the starting strain. By applying this modification alone, the amylase secretion could be improved by 35%. As a complement to the identification of genomic variants, transcriptome analysis was also performed in order to understand on a global level the transcriptional changes associated with the improved amylase production caused by UV mutagenesis. PMID:24973076

The combined effects of noncontingent reinforcement and punishment on the reduction of rumination.

PubMed

DeRosa, Nicole M; Roane, Henry S; Bishop, Jamie R; Silkowski, Erica L

2016-09-01

The current study extends the literature on the assessment and treatment of rumination through the evaluation of a combined reinforcement- and punishment-based intervention. The study included a single participant with a history of rumination maintained by automatic reinforcement, as identified via a functional analysis. Both noncontingent reinforcement (NCR) with preferred edible items and punishment, in the form of a facial screen, were implemented separately to evaluate their independent effects on the occurrence of rumination. The final treatment package included both NCR and punishment procedures. Implementation of the combined treatment resulted in a 96.5% reduction in rumination relative to baseline. Procedural modifications and integrity errors also were evaluated. © 2016 Society for the Experimental Analysis of Behavior.

Profiling Changes in Histone Post-translational Modifications by Top-Down Mass Spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Mowei; Wu, Si; Stenoien, David L.

Top-down mass spectrometry is a valuable tool for charactering post-translational modifications on histones for understanding of gene control and expression. In this protocol, we describe a top-down workflow using liquid chromatography coupled to mass spectrometry for fast global profiling of changes in histone proteoforms between a wild-type and a mutant of a fungal species. The proteoforms exhibiting different abundances can be subjected to further targeted studies by other mass spectrometric or biochemical assays. This method can be generally adapted for preliminary screening for changes in histone modifications between samples such as wild-type vs. mutant, and control vs. disease.

Evaluation and revision of checklists for screening facilities and municipal governmental programs for gastric cancer and colorectal cancer screening in Japan.

PubMed

Higashi, Takahiro; Machii, Ryoko; Aoki, Ayako; Hamashima, Chisato; Saito, Hiroshi

2010-11-01

To evaluate the appropriateness of current checklists created by a governmental committee to assess screening programs run by municipal governments and service provider facilities for gastric and colorectal cancer, and to accumulate expert opinions to provide insights aimed at the next revision. We convened an expert panel that consisted of physicians nominated by regional offices of the Japanese Society for Gastrointestinal Cancer Screening and radiology technicians nominated by the technician chapter of the society. The panel rated the appropriateness of each checklist item on a scale of 1-9 (1, extremely inappropriate; 9, extremely appropriate) twice, between which they had a face-to-face discussion meeting. During the process they were allowed to propose modifications and additions to the items. In the first round of rating, the panelists rated all 57 and 56 checklists items for gastric and colorectal cancer, respectively, as appropriate based on an acceptance rule determined a priori. During the process of the face-to-face discussion, however, the panel proposed modifications to 23 (40%) and 22 (39%) items, respectively, and the addition of 27 new items each. After integrating overlapping items and rating again for appropriateness, 66 and 64 items, respectively, were accepted as the revised checklist set. The expert panel considered current checklists for colorectal and gastric cancer-screening programs and facilities to be suitable. Their proposals for a new set of checklist items will help further improve the checklists.

Low Cost Aromatic Acetylene and Oligomeric Benzils and Their Conversion to Acetylene Terminated Quinoxalines

DTIC Science & Technology

1982-07-01

palladium acetate and the appropriate phosphine . This procedure is known to be effective for bromoarenes. In the early screen- ing runs, 4...Delaware), he indicated that he also had screened many phosphines , and the likelihood of success was very small. Dr. Heck reported that the palladium...any simple modification of the palla- dium phosphine catalyst system will effect the desired reaction. 5 III. PREPARATION OF OLIGOMERIC BENZILS AND

Forward Genetics Defines Xylt1 as a Key, Conserved Regulator of Early Chondrocyte Maturation and Skeletal Length

PubMed Central

Mis, Emily K.; Liem, Karel F.; Kong, Yong; Schwartz, Nancy B.; Domowicz, Miriam; Weatherbee, Scott D.

2014-01-01

The long bones of the vertebrate body are built by the initial formation of a cartilage template that is later replaced by mineralized bone. The proliferation and maturation of the skeletal precursor cells (chondrocytes) within the cartilage template and their replacement by bone is a highly coordinated process which, if misregulated, can lead to a number of defects including dwarfism and other skeletal deformities. This is exemplified by the fact that abnormal bone development is one of the most common types of human birth defects. Yet, many of the factors that initiate and regulate chondrocyte maturation are not known. We identified a recessive dwarf mouse mutant (pug) from an N-ethyl-N-nitrosourea (ENU) mutagenesis screen. pug mutant skeletal elements are patterned normally during development, but display a ~20% length reduction compared to wild-type embryos. We show that the pug mutation does not lead to changes in chondrocyte proliferation but instead promotes premature maturation and early ossification, which ultimately leads to disproportionate dwarfism. Using sequence capture and high-throughput sequencing, we identified a missense mutation in the Xylosyltransferase 1 (Xylt1) gene in pug mutants. Xylosyltransferases catalyze the initial step in glycosaminoglycan (GAG) chain addition to proteoglycan core proteins, and these modifications are essential for normal proteoglycan function. We show that the pug mutation disrupts Xylt1 activity and subcellular localization, leading to a reduction in GAG chains in pug mutants. The pug mutant serves as a novel model for mammalian dwarfism and identifies a key role for proteoglycan modification in the initiation of chondrocyte maturation. PMID:24161523

Mapping of ribosomal 23S ribosomal RNA modifications in Clostridium sporogenes.

PubMed

Kirpekar, Finn; Hansen, Lykke H; Mundus, Julie; Tryggedsson, Stine; Teixeira Dos Santos, Patrícia; Ntokou, Eleni; Vester, Birte

2018-06-27

All organisms contain RNA modifications in their ribosomal RNA (rRNA), but the importance, positions and exact function of these are still not fully elucidated. Various functions such as stabilising structures, controlling ribosome assembly and facilitating interactions have been suggested and in some cases substantiated. Bacterial rRNA contains much fewer modifications than eukaryotic rRNA. The rRNA modification patterns in bacteria differ from each other, but too few organisms have been mapped to draw general conclusions. This study maps 23S ribosomal RNA modifications in Clostridium sporogenes that can be characterised as a non-toxin producing Clostridium botulinum. Clostridia are able to sporulate and thereby survive harsh conditions, and are in general considered to be resilient to antibiotics. Selected regions of the 23S rRNA were investigated by mass spectrometry and by primer extension analysis to pinpoint modified sites and the nature of the modifications. Apparently, C. sporogenes 23S rRNA contains few modifications compared to other investigated bacteria. No modifications were identified in domain II and III of 23S rRNA. Three modifications were identified in domain IV, all of which have also been found in other organisms. Two unusual modifications were identified in domain V, methylated dihydrouridine at position U2449 and dihydrouridine at position U2500 (Escherichia coli numbering), in addition to four previously known modified positions. The enzymes responsible for the modifications were searched for in the C. sporogenes genome using BLAST with characterised enzymes as query. The search identified genes potentially coding for RNA modifying enzymes responsible for most of the found modifications.

Evaluation of Proteomic Search Engines for the Analysis of Histone Modifications

PubMed Central

2015-01-01

Identification of histone post-translational modifications (PTMs) is challenging for proteomics search engines. Including many histone PTMs in one search increases the number of candidate peptides dramatically, leading to low search speed and fewer identified spectra. To evaluate database search engines on identifying histone PTMs, we present a method in which one kind of modification is searched each time, for example, unmodified, individually modified, and multimodified, each search result is filtered with false discovery rate less than 1%, and the identifications of multiple search engines are combined to obtain confident results. We apply this method for eight search engines on histone data sets. We find that two search engines, pFind and Mascot, identify most of the confident results at a reasonable speed, so we recommend using them to identify histone modifications. During the evaluation, we also find some important aspects for the analysis of histone modifications. Our evaluation of different search engines on identifying histone modifications will hopefully help those who are hoping to enter the histone proteomics field. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD001118. PMID:25167464

Evaluation of proteomic search engines for the analysis of histone modifications.

PubMed

Yuan, Zuo-Fei; Lin, Shu; Molden, Rosalynn C; Garcia, Benjamin A

2014-10-03

Identification of histone post-translational modifications (PTMs) is challenging for proteomics search engines. Including many histone PTMs in one search increases the number of candidate peptides dramatically, leading to low search speed and fewer identified spectra. To evaluate database search engines on identifying histone PTMs, we present a method in which one kind of modification is searched each time, for example, unmodified, individually modified, and multimodified, each search result is filtered with false discovery rate less than 1%, and the identifications of multiple search engines are combined to obtain confident results. We apply this method for eight search engines on histone data sets. We find that two search engines, pFind and Mascot, identify most of the confident results at a reasonable speed, so we recommend using them to identify histone modifications. During the evaluation, we also find some important aspects for the analysis of histone modifications. Our evaluation of different search engines on identifying histone modifications will hopefully help those who are hoping to enter the histone proteomics field. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD001118.

Hierarchical virtual screening of the dual MMP-2/HDAC-6 inhibitors from natural products based on pharmacophore models and molecular docking.

PubMed

Wang, Yijun; Yang, Limei; Hou, Jiaying; Zou, Qing; Gao, Qi; Yao, Wenhui; Yao, Qizheng; Zhang, Ji

2018-02-12

The dual-target inhibitors tend to improve the response rate in treating tumors, comparing with the single-target inhibitors. Matrix metalloproteinase-2 (MMP-2) and histone deacetylase-6 (HDAC-6) are attractive targets for cancer therapy. In this study, the hierarchical virtual screening of dual MMP-2/HDAC-6 inhibitors from natural products is investigated. The pharmacophore model of MMP-2 inhibitors is built based on ligands, but the pharmacophore model of HDAC-6 inhibitors is built based on the experimental crystal structures of multiple receptor-ligand complexes. The reliability of these two pharmacophore models is validated subsequently. The hierarchical virtual screening, combining these two different pharmacophore models of MMP-2 and HDAC-6 inhibitors with molecular docking, is carried out to identify the dual MMP-2/HDAC-6 inhibitors from a database of natural products. The four potential dual MMP-2/HDAC-6 inhibitors of natural products, STOCK1 N-46177, STOCK1 N-52245, STOCK1 N-55477, and STOCK1 N-69706, are found. The studies of binding modes show that the screened four natural products can simultaneously well bind with the MMP-2 and HDAC-6 active sites by different kinds of interactions, to inhibit the MMP-2 and HDAC-6 activities. In addition, the ADMET properties of screened four natural products are assessed. These found dual MMP-2/HDAC-6 inhibitors of natural products could serve as the lead compounds for designing the new dual MMP-2/HDAC-6 inhibitors having higher biological activities by carrying out structural modifications and optimizations in the future studies.

Multiple receptor-ligand based pharmacophore modeling and molecular docking to screen the selective inhibitors of matrix metalloproteinase-9 from natural products.

PubMed

Gao, Qi; Wang, Yijun; Hou, Jiaying; Yao, Qizheng; Zhang, Ji

2017-07-01

Matrix metalloproteinase-9 (MMP-9) is an attractive target for cancer therapy. In this study, the pharmacophore model of MMP-9 inhibitors is built based on the experimental binding structures of multiple receptor-ligand complexes. It is found that the pharmacophore model consists of six chemical features, including two hydrogen bond acceptors, one hydrogen bond donor, one ring aromatic regions, and two hydrophobic (HY) features. Among them, the two HY features are especially important because they can enter the S1' pocket of MMP-9 which determines the selectivity of MMP-9 inhibitors. The reliability of pharmacophore model is validated based on the two different decoy sets and relevant experimental data. The virtual screening, combining pharmacophore model with molecular docking, is performed to identify the selective MMP-9 inhibitors from a database of natural products. The four novel MMP-9 inhibitors of natural products, NP-000686, NP-001752, NP-014331, and NP-015905, are found; one of them, NP-000686, is used to perform the experiment of in vitro bioassay inhibiting MMP-9, and the IC 50 value was estimated to be only 13.4 µM, showing the strongly inhibitory activity of NP-000686 against MMP-9, which suggests that our screening results should be reliable. The binding modes of screened inhibitors with MMP-9 active sites were discussed. In addition, the ADMET properties and physicochemical properties of screened four compounds were assessed. The found MMP-9 inhibitors of natural products could serve as the lead compounds for designing the new MMP-9 inhibitors by carrying out structural modifications in the future.

Survey of prenatal counselling practices regarding aneuploidy risk modification, invasive diagnostic procedure risks, and procedure eligibility criteria in Canadian centres.

PubMed

Hull, Danna; Davies, Gregory; Armour, Christine M

2012-07-01

To explore prenatal practices related to aneuploidy screening, risk modification, and invasive diagnostic procedures across Canadian centres. We conducted a survey of members of the Canadian Association of Genetic Counsellors, the Canadian College of Medical Genetics, and the Canadian Society of Maternal Fetal Medicine, who provide direct counselling or management of prenatal patients in Canada. Eighty-two of 157 respondents indicated that their centre's definition of advanced maternal age was ≥ 35 years, with 33/157 respondents reporting an advanced maternal age definition of ≥ 40 years. The majority of respondents reported that prenatal serum screening for aneuploidy is provincially funded in their province or territory (121/147). The majority of respondents who reported that prenatal screening is not provincially funded (17/147) were from Quebec (14/17). Thirty-nine of 123 respondents reported that their centre defines increased nuchal translucency as ≥ 3.0 mm, whereas 49/123 reported a definition of ≥ 3.5 mm. Sixty-four of 150 respondents reported that the aneuploidy risk provided by serum screening is modified by a soft marker likelihood ratio, whereas 46/150 respondents reported that both age-related and serum screening risks are modified. Fifty-nine of 124 respondents reported that their centre will modify aneuploidy risk after a normal ultrasound; the most commonly cited negative likelihood ratio was 0.5. The most commonly reported procedure-related risk for chorionic villus sampling was 1/100 (123/147) and for amniocentesis was 1/200 (73/142). This study demonstrates inconsistencies in prenatal practices and access to screening programs across Canada. The information gained from this study will inform policy advisors developing prenatal practice guidelines at both the provincial and national levels.

CRISPR/Cas9: An inexpensive, efficient loss of function tool to screen human disease genes in Xenopus.

PubMed

Bhattacharya, Dipankan; Marfo, Chris A; Li, Davis; Lane, Maura; Khokha, Mustafa K

2015-12-15

Congenital malformations are the major cause of infant mortality in the US and Europe. Due to rapid advances in human genomics, we can now efficiently identify sequence variants that may cause disease in these patients. However, establishing disease causality remains a challenge. Additionally, in the case of congenital heart disease, many of the identified candidate genes are either novel to embryonic development or have no known function. Therefore, there is a pressing need to develop inexpensive and efficient technologies to screen these candidate genes for disease phenocopy in model systems and to perform functional studies to uncover their role in development. For this purpose, we sought to test F0 CRISPR based gene editing as a loss of function strategy for disease phenocopy in the frog model organism, Xenopus tropicalis. We demonstrate that the CRISPR/Cas9 system can efficiently modify both alleles in the F0 generation within a few hours post fertilization, recapitulating even early disease phenotypes that are highly similar to knockdowns from morpholino oligos (MOs) in nearly all cases tested. We find that injecting Cas9 protein is dramatically more efficacious and less toxic than cas9 mRNA. We conclude that CRISPR based F0 gene modification in X. tropicalis is efficient and cost effective and readily recapitulates disease and MO phenotypes. Copyright © 2015 Elsevier Inc. All rights reserved.

NOVEL METHODS FOR TARGET PROTEIN IDENTIFICATION USING IMMUNOPRECIPITATION - LC/MS/MS

EPA Science Inventory

Proteomics provides a powerful approach to screen and analyze responses to environmental exposures which induce alterations in protein expression, phosphorylation. ubiquitinylation, oxidation. and modulation of general proteome function. Post-translational modifications (PTM) of ...

Selected approaches for rational drug design and high throughput screening to identify anti-cancer molecules.

PubMed

Hedvat, Michael; Emdad, Luni; Das, Swadesh K; Kim, Keetae; Dasgupta, Santanu; Thomas, Shibu; Hu, Bin; Zhu, Shan; Dash, Rupesh; Quinn, Bridget A; Oyesanya, Regina A; Kegelman, Timothy P; Sokhi, Upneet K; Sarkar, Siddik; Erdogan, Eda; Menezes, Mitchell E; Bhoopathi, Praveen; Wang, Xiang-Yang; Pomper, Martin G; Wei, Jun; Wu, Bainan; Stebbins, John L; Diaz, Paul W; Reed, John C; Pellecchia, Maurizio; Sarkar, Devanand; Fisher, Paul B

2012-11-01

Structure-based modeling combined with rational drug design, and high throughput screening approaches offer significant potential for identifying and developing lead compounds with therapeutic potential. The present review focuses on these two approaches using explicit examples based on specific derivatives of Gossypol generated through rational design and applications of a cancer-specificpromoter derived from Progression Elevated Gene-3. The Gossypol derivative Sabutoclax (BI-97C1) displays potent anti-tumor activity against a diverse spectrum of human tumors. The model of the docked structure of Gossypol bound to Bcl-XL provided a virtual structure-activity-relationship where appropriate modifications were predicted on a rational basis. These structure-based studies led to the isolation of Sabutoclax, an optically pure isomer of Apogossypol displaying superior efficacy and reduced toxicity. These studies illustrate the power of combining structure-based modeling with rational design to predict appropriate derivatives of lead compounds to be empirically tested and evaluated for bioactivity. Another approach to cancer drug discovery utilizes a cancer-specific promoter as readouts of the transformed state. The promoter region of Progression Elevated Gene-3 is such a promoter with cancer-specific activity. The specificity of this promoter has been exploited as a means of constructing cancer terminator viruses that selectively kill cancer cells and as a systemic imaging modality that specifically visualizes in vivo cancer growth with no background from normal tissues. Screening of small molecule inhibitors that suppress the Progression Elevated Gene-3-promoter may provide relevant lead compounds for cancer therapy that can be combined with further structure-based approaches leading to the development of novel compounds for cancer therapy.

RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia

PubMed Central

Zuber, Johannes; Shi, Junwei; Wang, Eric; Rappaport, Amy R.; Herrmann, Harald; Sison, Edward A.; Magoon, Daniel; Qi, Jun; Blatt, Katharina; Wunderlich, Mark; Taylor, Meredith J.; Johns, Christopher; Chicas, Agustin; Mulloy, James C.; Kogan, Scott C.; Brown, Patrick; Valent, Peter; Bradner, James E.; Lowe, Scott W.; Vakoc, Christopher R.

2012-01-01

Epigenetic pathways can regulate gene expression by controlling and interpreting chromatin modifications. Cancer cells are characterized by altered epigenetic landscapes, and commonly exploit the chromatin regulatory machinery to enforce oncogenic gene expression programs1. Although chromatin alterations are, in principle, reversible and often amenable to drug intervention, the promise of targeting such pathways therapeutically has been limited by an incomplete understanding of cancer-specific dependencies on epigenetic regulators. Here we describe a non-biased approach to probe epigenetic vulnerabilities in acute myeloid leukaemia (AML), an aggressive haematopoietic malignancy that is often associated with aberrant chromatin states2. By screening a custom library of small hairpin RNAs (shRNAs) targeting known chromatin regulators in a genetically defined AML mouse model, we identify the protein bromodomain-containing 4 (Brd4) as being critically required for disease maintenance. Suppression of Brd4 using shRNAs or the small-molecule inhibitor JQ1 led to robust antileukaemic effects in vitro and in vivo, accompanied by terminal myeloid differentiation and elimination of leukaemia stem cells. Similar sensitivities were observed in a variety of human AML cell lines and primary patient samples, revealing that JQ1 has broad activity in diverse AML subtypes. The effects of Brd4 suppression are, at least in part, due to its role in sustaining Myc expression to promote aberrant self-renewal, which implicates JQ1 as a pharmacological means to suppress MYC in cancer. Our results establish small-molecule inhibition of Brd4 as a promising therapeutic strategy in AML and, potentially, other cancers, and highlight the utility of RNA interference (RNAi) screening for revealing epigenetic vulnerabilities that can be exploited for direct pharmacological intervention. PMID:21814200

Knowledge, attitudes towards and acceptability of genetic modification in Germany.

PubMed

Christoph, Inken B; Bruhn, Maike; Roosen, Jutta

2008-07-01

Genetic modification remains a controversial issue. The aim of this study is to analyse the attitudes towards genetic modification, the knowledge about it and its acceptability in different application areas among German consumers. Results are based on a survey from spring 2005. An exploratory factor analysis is conducted to identify the attitudes towards genetic modification. The identified factors are used in a cluster analysis that identified a cluster of supporters, of opponents and a group of indifferent consumers. Respondents' knowledge of genetics and biotechnology differs among the found clusters without revealing a clear relationship between knowledge and support of genetic modification. The acceptability of genetic modification varies by application area and cluster, and genetically modified non-food products are more widely accepted than food products. The perception of personal health risks has high explanatory power for attitudes and acceptability.

Chromatin immunoprecipitation (ChIP) method for non-model fruit flies (Diptera: Tephritidae) and evidence of histone modifications.

PubMed

Nagalingam, Kumaran; Lorenc, Michał T; Manoli, Sahana; Cameron, Stephen L; Clarke, Anthony R; Dudley, Kevin J

2018-01-01

Interactions between DNA and proteins located in the cell nucleus play an important role in controlling physiological processes by specifying, augmenting and regulating context-specific transcription events. Chromatin immunoprecipitation (ChIP) is a widely used methodology to study DNA-protein interactions and has been successfully used in various cell types for over three decades. More recently, by combining ChIP with genomic screening technologies and Next Generation Sequencing (e.g. ChIP-seq), it has become possible to profile DNA-protein interactions (including covalent histone modifications) across entire genomes. However, the applicability of ChIP-chip and ChIP-seq has rarely been extended to non-model species because of a number of technical challenges. Here we report a method that can be used to identify genome wide covalent histone modifications in a group of non-model fruit fly species (Diptera: Tephritidae). The method was developed by testing and refining protocols that have been used in model organisms, including Drosophila melanogaster. We demonstrate that this method is suitable for a group of economically important pest fruit fly species, viz., Bactrocera dorsalis, Ceratitis capitata, Zeugodacus cucurbitae and Bactrocera tryoni. We also report an example ChIP-seq dataset for B. tryoni, providing evidence for histone modifications in the genome of a tephritid fruit fly for the first time. Since tephritids are major agricultural pests globally, this methodology will be a valuable resource to study taxa-specific evolutionary questions and to assist with pest management. It also provides a basis for researchers working with other non-model species to undertake genome wide DNA-protein interaction studies.

Stress urinary incontinence is highly prevalent in recreationally active women attending gyms or exercise classes.

PubMed

McKenzie, Sally; Watson, Taryn; Thompson, Judith; Briffa, Kathy

2016-08-01

The purpose of this study was to determine the prevalence of stress urinary incontinence (SUI) in recreationally active women attending gyms or exercise classes. Data were collected on the frequency and severity of incontinence and the prevalence of SUI risk factors; screening for PFM dysfunction in a fitness appraisal; symptom modification strategies; knowledge of pelvic floor muscle (PFM) exercises and the Pelvic Floor First (PFF) initiative. Three hundred and sixty-one women aged 18-83 who attended exercise classes or gyms in Western Australia were surveyed. Nearly half (49.3 %) of participants reported SUI, the majority of whom slight or moderate leakage. Ninety-six per cent reported at least one SUI risk factor, with the mean being 2.7 (SD = 1.4). Almost all women surveyed had heard of PFM exercises (97.2 %), but only 15.2 % of participants were screened for PFM dysfunction in a fitness appraisal. Forty-three per cent reported that a fitness instructor cued PFM activation during a workout. Less than 1 in 10 (9.7 %) of the women surveyed had heard about the PFF initiative. Urinary incontinence is common in women attending gyms or exercise classes, but is rarely screened for. More education is required to encourage fitness leaders to screen exercise participants and to provide PFM-'friendly" modifications.

School-Based Screening to Identify At-Risk Students Not Already Known to School Professionals: The Columbia Suicide Screen

PubMed Central

Wilcox, Holly C.; Schonfeld, Irvin Sam; Davies, Mark; Hicks, Roger C.; Turner, J. Blake; Shaffer, David

2009-01-01

Objectives. We sought to determine the degree of overlap between students identified through school-based suicide screening and those thought to be at risk by school administrative and clinical professionals. Methods. Students from 7 high schools in the New York metropolitan area completed the Columbia Suicide Screen; 489 of the 1729 students screened had positive results. The clinical status of 641 students (73% of those who had screened positive and 23% of those who had screened negative) was assessed with modules from the Diagnostic Interview Schedule for Children. School professionals nominated by their principal and unaware of students' screening and diagnostic status were asked to indicate whether they were concerned about the emotional well-being of each participating student. Results. Approximately 34% of students with significant mental health problems were identified only through screening, 13.0% were identified only by school professionals, 34.9% were identified both through screening and by school professionals, and 18.3% were identified neither through screening nor by school professionals. The corresponding percentages among students without mental health problems were 9.1%, 24.0%, 5.5%, and 61.3%. Conclusions. School-based screening can identify suicidal and emotionally troubled students not recognized by school professionals. PMID:19059865

Combinatorial chemoenzymatic synthesis and high-throughput screening of sialosides.

PubMed

Chokhawala, Harshal A; Huang, Shengshu; Lau, Kam; Yu, Hai; Cheng, Jiansong; Thon, Vireak; Hurtado-Ziola, Nancy; Guerrero, Juan A; Varki, Ajit; Chen, Xi

2008-09-19

Although the vital roles of structures containing sialic acid in biomolecular recognition are well documented, limited information is available on how sialic acid structural modifications, sialyl linkages, and the underlying glycan structures affect the binding or the activity of sialic acid-recognizing proteins and related downstream biological processes. A novel combinatorial chemoenzymatic method has been developed for the highly efficient synthesis of biotinylated sialosides containing different sialic acid structures and different underlying glycans in 96-well plates from biotinylated sialyltransferase acceptors and sialic acid precursors. By transferring the reaction mixtures to NeutrAvidin-coated plates and assaying for the yields of enzymatic reactions using lectins recognizing sialyltransferase acceptors but not the sialylated products, the biotinylated sialoside products can be directly used, without purification, for high-throughput screening to quickly identify the ligand specificity of sialic acid-binding proteins. For a proof-of-principle experiment, 72 biotinylated alpha2,6-linked sialosides were synthesized in 96-well plates from 4 biotinylated sialyltransferase acceptors and 18 sialic acid precursors using a one-pot three-enzyme system. High-throughput screening assays performed in NeutrAvidin-coated microtiter plates show that whereas Sambucus nigra Lectin binds to alpha2,6-linked sialosides with high promiscuity, human Siglec-2 (CD22) is highly selective for a number of sialic acid structures and the underlying glycans in its sialoside ligands.

How Compliance Measures, Behavior Modification, and Continuous Quality Improvement Led to Routine HIV Screening in an Emergency Department in Brooklyn, New York.

PubMed

Isaac, Jermel Kyri; Sanchez, Travis H; Brown, Emily H; Thompson, Gina; Sanchez, Christina; Fils-Aime, Stephany; Maria, Jose

2016-01-01

New York State adopted a new HIV testing law in 2010 requiring medical providers to offer an HIV test to all eligible patients aged 13-64 years during emergency room or ambulatory care visits. Since then, Wyckoff Heights Medical Center (WHMC) in Brooklyn, New York, began implementing routine HIV screening organization-wide using a compliance, behavior-modification, and continuous quality-improvement process. WHMC first implemented HIV screening in the emergency department (ED) and evaluated progress with the following monthly indicators: HIV tests offered, HIV tests accepted, HIV tests ordered (starting in December 2013), HIV tests administered, positive HIV tests, and linkage to HIV care. Compliance with the delivery of HIV testing was determined by the proportion of patients who, after accepting a test, received one. During August 2013 through July 2014, of 57,852 eligible patients seen in the WHMC ED, a total of 31,423 (54.3%) were offered an HIV test. Of those, 8,229 (26.2%) patients accepted a test. Of those, 6,114 (74.3%) underwent a test. A total of 26 of the 6,114 patients tested (0.4%) had a positive test, and 24 of the 26 HIV-positive patients were linked to HIV medical care. By July 2014, the monthly proportion of patients offered a test was 62%; the proportion of those offered a test who had a test ordered was 98%, and the proportion of those with a test ordered who were tested was 81%. Testing compliance increased substantially at the WHMC ED, from 77% in December 2013 to >98% in July 2014. Using compliance-monitoring, behavior-modification, and continuous quality-improvement processes produced substantial increases in offers and HIV test completion. WHMC is replicating this approach across departments, and other hospitals implementing routine HIV screening programs should consider this approach as well.

Implementation of COTs Hardware in Non-Critical Space Applications: A Brief Tutorial

NASA Technical Reports Server (NTRS)

Yoder, Geoffrey L.

2004-01-01

Approaches used for manned applications include limited items such as CD-players evaluated for safety to high criticality applications where the COTs hardware is evaluated on a case-by-case basis for the application and commensurate screening and qualification testing. COTS hardware is successfully implemented in both the International Space Station and Space Shuttle but requires evaluation and modifications for the application. Screening and qualification of COTs hardware used in critical applications may need to be more extensive and stringent than traditional military screening. Evaluation for: a) Suitability for the application; b) Safety; c) Reliability and maintainability; and d) Workmanship.

High-throughput screening of small molecules in miniaturized mammalian cell-based assays involving post-translational modifications.

PubMed

Stockwell, B R; Haggarty, S J; Schreiber, S L

1999-02-01

Fully adapting a forward genetic approach to mammalian systems requires efficient methods to alter systematically gene products without prior knowledge of gene sequences, while allowing for the subsequent characterization of these alterations. Ideally, these methods would also allow function to be altered in a temporally controlled manner. We report the development of a miniaturized cell-based assay format that enables a genetic-like approach to understanding cellular pathways in mammalian systems using small molecules, rather than mutations, as the source of gene-product alterations. This whole-cell immunodetection assay can sensitively detect changes in specific cellular macromolecules in high-density arrays of mammalian cells. Furthermore, it is compatible with screening large numbers of small molecules in nanoliter to microliter culture volumes. We refer to this assay format as a 'cytoblot', and demonstrate the use of cytoblotting to monitor biosynthetic processes such as DNA synthesis, and post-translational processes such as acetylation and phosphorylation. Finally, we demonstrate the applicability of these assays to natural-product screening through the identification of marine sponge extracts exhibiting genotype-specific inhibition of 5-bromodeoxyuridine incorporation and suppression of the anti-proliferative effect of rapamycin. We show that cytoblots can be used for high-throughput screening of small molecules in cell-based assays. Together with small-molecule libraries, the cytoblot assay can be used to perform chemical genetic screens analogous to those used in classical genetics and thus should be applicable to understanding a wide variety of cellular processes, especially those involving post-transitional modifications.

Sequence tagging reveals unexpected modifications in toxicoproteomics

PubMed Central

Dasari, Surendra; Chambers, Matthew C.; Codreanu, Simona G.; Liebler, Daniel C.; Collins, Ben C.; Pennington, Stephen R.; Gallagher, William M.; Tabb, David L.

2010-01-01

Toxicoproteomic samples are rich in posttranslational modifications (PTMs) of proteins. Identifying these modifications via standard database searching can incur significant performance penalties. Here we describe the latest developments in TagRecon, an algorithm that leverages inferred sequence tags to identify modified peptides in toxicoproteomic data sets. TagRecon identifies known modifications more effectively than the MyriMatch database search engine. TagRecon outperformed state of the art software in recognizing unanticipated modifications from LTQ, Orbitrap, and QTOF data sets. We developed user-friendly software for detecting persistent mass shifts from samples. We follow a three-step strategy for detecting unanticipated PTMs in samples. First, we identify the proteins present in the sample with a standard database search. Next, identified proteins are interrogated for unexpected PTMs with a sequence tag-based search. Finally, additional evidence is gathered for the detected mass shifts with a refinement search. Application of this technology on toxicoproteomic data sets revealed unintended cross-reactions between proteins and sample processing reagents. Twenty five proteins in rat liver showed signs of oxidative stress when exposed to potentially toxic drugs. These results demonstrate the value of mining toxicoproteomic data sets for modifications. PMID:21214251

Computationally identified novel agonists for GPRC6A

PubMed Central

Ye, Ruisong; Hwang, Dong-Jin; Miller, Duane D.; Smith, Jeremy C.; Baudry, Jerome; Quarles, L. Darryl

2018-01-01

New insights into G protein coupled receptor regulation of glucose metabolism by β-cells, skeletal muscle and liver hepatocytes identify GPRC6A as a potential therapeutic target for treating type 2 diabetes mellitus (T2D). Activating GPRC6A with a small molecule drug represents a potential paradigm-shifting opportunity to make significant strides in regulating glucose homeostasis by simultaneously correcting multiple metabolic derangements that underlie T2D, including abnormalities in β-cell proliferation and insulin secretion and peripheral insulin resistance. Using a computational, structure-based high-throughput screening approach, we identified novel tri-phenyl compounds predicted to bind to the venus fly trap (VFT) and 7-transmembrane (7-TM) domains of GPRC6A. Experimental testing found that these compounds dose-dependently stimulated GPRC6A signaling in a heterologous cell expression system. Additional chemical modifications and functional analysis identified one tri-phenyl lead compound, DJ-V-159 that demonstrated the greatest potency in stimulating insulin secretion in β-cells and lowering serum glucose in wild-type mice. Collectively, these studies show that GPRC6A is a “druggable” target for developing chemical probes to treat T2DM. PMID:29684031

Global Reprogramming of Host SUMOylation during Influenza Virus Infection

PubMed Central

Domingues, Patricia; Golebiowski, Filip; Tatham, Michael H.; Lopes, Antonio M.; Taggart, Aislynn; Hay, Ronald T.; Hale, Benjamin G.

2015-01-01

Summary Dynamic nuclear SUMO modifications play essential roles in orchestrating cellular responses to proteotoxic stress, DNA damage, and DNA virus infection. Here, we describe a non-canonical host SUMOylation response to the nuclear-replicating RNA pathogen, influenza virus, and identify viral RNA polymerase activity as a major contributor to SUMO proteome remodeling. Using quantitative proteomics to compare stress-induced SUMOylation responses, we reveal that influenza virus infection triggers unique re-targeting of SUMO to 63 host proteins involved in transcription, mRNA processing, RNA quality control, and DNA damage repair. This is paralleled by widespread host deSUMOylation. Depletion screening identified ten virus-induced SUMO targets as potential antiviral factors, including C18orf25 and the SMC5/6 and PAF1 complexes. Mechanistic studies further uncovered a role for SUMOylation of the PAF1 complex component, parafibromin (CDC73), in potentiating antiviral gene expression. Our global characterization of influenza virus-triggered SUMO redistribution provides a proteomic resource to understand host nuclear SUMOylation responses to infection. PMID:26549460

Co-factors Required for TLR7- and TLR9- dependent Innate Immune Responses

PubMed Central

Chiang, Chih-yuan; Engel, Alex; Opaluch, Amanda M.; Ramos, Irene; Maestre, Ana M.; Secundino, Ismael; De Jesus, Paul D.; Nguyen, Quy T.; Welch, Genevieve; Bonamy, Ghislain M.C.; Miraglia, Loren J.; Orth, Anthony P.; Nizet, Victor; Fernandez-Sesma, Ana; Zhou, Yingyao; Barton, Gregory M.; Chanda, Sumit K.

2012-01-01

SUMMARY Pathogens commonly utilize endocytic pathways to gain cellular access. The endosomal pattern recognition receptors TLR7 and TLR9 detect pathogen-encoded nucleic acids to initiate MyD88-dependent pro-inflammatory responses to microbial infection. Using genome-wide RNAi screening and integrative systems-based analysis we identify 190 co-factors required for TLR7- and TLR9-directed signaling responses. A set of co-factors were cross-profiled for their activities downstream of several immunoreceptors, and then functionally mapped based on the known architecture of NF-κB signaling pathways. Protein complexes and pathways involved in ubiquitin-protein ligase activities, sphingolipid metabolism, chromatin modifications, and ancient stress responses were found to modulate innate recognition of endosomal nucleic acids. Additionally, hepatocyte growth factor-regulated tyrosine kinase substrate (HRS) was characterized as necessary for ubiquitin-dependent TLR9 targeting to the endolysosome. Proteins and pathways identified here should prove useful in delineating strategies to manipulate innate responses for treatment of autoimmune disorders and microbial infection. PMID:22423970

A community pharmacy-based cardiovascular risk screening service implemented in Iran

PubMed Central

Hakimzadeh, Negar; Najafi, Sheyda; Javadi, Mohammad R.; Hadjibabaie, Molouk

2017-01-01

Background: Cardiovascular disease is a major health concern around the world. Objective: To assess the outcomes and feasibility of a pharmacy-based cardiovascular screening in an urban referral community pharmacy in Iran. Methods: A cross sectional study was conducted in a referral community pharmacy. Subjects aged between 30-75 years without previous diagnose of cardiovascular disease or diabetes were screened. Measurement of all major cardiovascular risk factors, exercise habits, medical conditions, medications, and family history were investigated. Framingham risk score was calculated and high risk individuals were given a clinical summary sheet signed by a clinical pharmacist and were encouraged to follow up with their physician. Subjects were contacted one month after the recruitment period and their adherence to the follow up recommendation was recorded. Results: Data from 287 participants were analyzed and 146 were referred due to at least one abnormal laboratory test. The results showed 26 patients with cardiovascular disease risk greater than 20%, 32 high systolic blood pressure, 22 high diastolic blood pressures, 50 high total cholesterol levels, 108 low HDL-C levels, and 22 abnormal blood glucose levels. Approximately half of the individuals who received a follow up recommendation had made an appointment with their physician. Overall, 15.9% of the individuals received medications and 15.9% received appropriate advice for risk factor modification. Moreover, 7.5% were under evaluation by a physician. Conclusion: A screening program in a community pharmacy has the potential to identify patients with elevated cardiovascular risk factor. A plan for increased patient adherence to follow up recommendations is required. PMID:28690693

Mutation Analysis of SLC26A4 for Pendred Syndrome and Nonsyndromic Hearing Loss by High-Resolution Melting

PubMed Central

Chen, Neng; Tranebjærg, Lisbeth; Rendtorff, Nanna Dahl; Schrijver, Iris

2011-01-01

Pendred syndrome and DFNB4 (autosomal recessive nonsyndromic congenital deafness, locus 4) are associated with autosomal recessive congenital sensorineural hearing loss and mutations in the SLC26A4 gene. Extensive allelic heterogeneity, however, necessitates analysis of all exons and splice sites to identify mutations for individual patients. Although Sanger sequencing is the gold standard for mutation detection, screening methods supplemented with targeted sequencing can provide a cost-effective alternative. One such method, denaturing high-performance liquid chromatography, was developed for clinical mutation detection in SLC26A4. However, this method inherently cannot distinguish homozygous changes from wild-type sequences. High-resolution melting (HRM), on the other hand, can detect heterozygous and homozygous changes cost-effectively, without any post-PCR modifications. We developed a closed-tube HRM mutation detection method specific for SLC26A4 that can be used in the clinical diagnostic setting. Twenty-eight primer pairs were designed to cover all 21 SLC26A4 exons and splice junction sequences. Using the resulting amplicons, initial HRM analysis detected all 45 variants previously identified by sequencing. Subsequently, a 384-well plate format was designed for up to three patient samples per run. Blinded HRM testing on these plates of patient samples collected over 1 year in a clinical diagnostic laboratory accurately detected all variants identified by sequencing. In conclusion, HRM with targeted sequencing is a reliable, simple, and cost-effective method for SLC26A4 mutation screening and detection. PMID:21704276

Rhodotorula taiwanensis MD1149 produces hypoacetylated PEFA compounds with increased surface activity compared to Rhodotorula babjevae MD1169

PubMed Central

Rubinfeld, Bonnee; Leif, Roald; Mulcahy, Heather; Dugan, Lawrence; Souza, Brian

2018-01-01

Biosurfactants have several desirable characteristics in the industrial sector: detergency, antimicrobial effects, skin hydration, and emulsibility. Several yeast glycolipids are currently being utilized in these capacities: sophorolipids, ustilagic acid, and mannosylerythritol lipids (MELs). An emerging class of glycolipids, termed polyol esters of fatty acids (PEFA), have recently been reported for Rhodotorula babjevae, a basidiomycetous yeast species that secretes hyperacetylated congeners of PEFA (typically with 3–6 acetylation modifications). While screening Rhodotorula species for surfactant production, we identified a new environmental isolate identified as Rhodotorula taiwanensis MD1149 that dropped the surface tension of the liquid medium, indicating that it produced a potent biosurfactant. Acid depolymerization of the purified biosurfactants, followed by gas chromatography-mass spectrometry (GC-MS) analysis revealed that the biosurfactants were composed of PEFA compounds composed mainly of mannitol and arabitol esters of 3-hydroxy fatty acid, 3-methoxy fatty acid, and fatty acids with a single double bond; chain lengths were mainly C16 and C18. Liquid chromatography-mass spectrometry (LC-MS) confirmed the predicted accurate mass of these compounds. Interestingly, PEFA compounds produced by Rhodotorula taiwanensis MD1149 were more surface active due to their hypoacetylation profile (0–4 acetylation modifications) compared to Rhodotorula babjevae MD1169. These disparate surface active properties, based on acetylation, change the hydrophilic-lipophilic balance (HLB) of these compounds, and their potential utility within industrial applications. PMID:29293588

Synthesis and Antibacterial Screening of Novel Derivatives of Embelin

NASA Astrophysics Data System (ADS)

Subramanian, L.; Leema, M.; Pradeep, N. S.; Joy, B.; Pillai, Z. S.

2018-02-01

Embelin, a naturally occurring compound extracted from Embelia ribes is used in Ayurvedic system of medicine owing to its wide spectrum of biological activities. In the present work, we have aimed at improving the efficacy of Embelin by appropriate structural modifications. A few novel derivatives of Embelin have been prepared. The antibacterial screening of these derivatives were carried out and compared with a well known antibiotic, Streptomycin. The derivatives exhibited better activity than Streptomycin and the lead molecule, Embelin.

Self-Organizing Maps for In Silico Screening and Data Visualization.

PubMed

Digles, Daniela; Ecker, Gerhard F

2011-10-01

Self-organizing maps, which are unsupervised artificial neural networks, have become a very useful tool in a wide area of disciplines, including medicinal chemistry. Here, we will focus on two applications of self-organizing maps: the use of self-organizing maps for in silico screening and for clustering and visualisation of large datasets. Additionally, the importance of parameter selection is discussed and some modifications to the original algorithm are summarised. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Profiling Changes in Histone Post-translational Modifications by Top-Down Mass Spectrometry.

PubMed

Zhou, Mowei; Wu, Si; Stenoien, David L; Zhang, Zhaorui; Connolly, Lanelle; Freitag, Michael; Paša-Tolić, Ljiljana

2017-01-01

Top-down mass spectrometry is a valuable tool for understanding gene expression through characterization of combinatorial histone post-translational modifications (i.e., histone code). In this protocol, we describe a top-down workflow that employs liquid chromatography (LC) coupled to mass spectrometry (MS), for fast global profiling of changes in histone proteoforms, and apply LCMS top-down approach for comparative analysis of a wild-type and a mutant fungal species. The proteoforms exhibiting differential abundances can be subjected to further targeted studies by other MS or orthogonal (e.g., biochemical) assays. This method can be generally adapted for screening of changes in histone modifications between samples such as wild type vs. mutant or healthy vs. diseased.

Small Molecule DFPM Derivative-Activated Plant Resistance Protein Signaling in Roots Is Unaffected by EDS1 Subcellular Targeting Signal and Chemical Genetic Isolation of victr R-Protein Mutants

PubMed Central

Mevers, Emily; García, Ana V.; Highhouse, Samantha; Gerwick, William H.; Parker, Jane E.; Schroeder, Julian I.

2016-01-01

The small molecule DFPM ([5-(3,4-dichlorophenyl)furan-2-yl]-piperidine-1-ylmethanethione) was recently shown to trigger signal transduction via early effector-triggered immunity signaling genes including EDS1 and PAD4 in Arabidopsis thaliana accession Col-0. Chemical genetic analyses of A. thaliana natural variants identified the plant Resistance protein-like Toll/Interleukin1 Receptor (TIR)-Nucleotide Binding (NB)-Leucine-Rich Repeat (LRR) protein VICTR as required for DFPM-mediated root growth arrest. Here a chemical genetic screen for mutants which disrupt DFPM-mediated root growth arrest in the Col-0 accession identified new mutant alleles of the TIR-NB-LRR gene VICTR. One allele, victr-6, carries a Gly216-to-Asp mutation in the Walker A domain supporting an important function of the VICTR nucleotide binding domain in DFPM responses consistent with VICTR acting as a canonical Resistance protein. The essential nucleo-cytoplasmic regulator of TIR-NB-LRR-mediated effector-triggered immunity, EDS1, was reported to have both nuclear and cytoplasmic actions in pathogen resistance. DFPM was used to investigate the requirements for subcellular EDS1 localization in DFPM-mediated root growth arrest. EDS1-YFP fusions engineered to localize mainly in the cytoplasm or the nucleus by tagging with a nuclear export signal (NES) or a nuclear localization signal (NLS), respectively, were tested. We found that wild-type EDS1-YFP and both the NES and NLS-tagged EDS1 variants were induced by DFPM treatments and fully complemented eds1 mutant plants in root responses to DFPM, suggesting that enrichment of EDS1 in either compartment could confer DFPM-mediated root growth arrest. We further found that a light and O2-dependent modification of DFPM is necessary to mediate DFPM signaling in roots. Chemical analyses including Liquid Chromatography-Mass Spectrometry and High-Resolution Atmospheric Pressure Chemical Ionization Mass Spectrometry identified a DFPM modification product that is likely responsible for bioactivity mediating root growth arrest. We propose a chemical structure of this product and a possible reaction mechanism for DFPM modification. PMID:27219122

Forward genetics defines Xylt1 as a key, conserved regulator of early chondrocyte maturation and skeletal length.

PubMed

Mis, Emily K; Liem, Karel F; Kong, Yong; Schwartz, Nancy B; Domowicz, Miriam; Weatherbee, Scott D

2014-01-01

The long bones of the vertebrate body are built by the initial formation of a cartilage template that is later replaced by mineralized bone. The proliferation and maturation of the skeletal precursor cells (chondrocytes) within the cartilage template and their replacement by bone is a highly coordinated process which, if misregulated, can lead to a number of defects including dwarfism and other skeletal deformities. This is exemplified by the fact that abnormal bone development is one of the most common types of human birth defects. Yet, many of the factors that initiate and regulate chondrocyte maturation are not known. We identified a recessive dwarf mouse mutant (pug) from an N-ethyl-N-nitrosourea (ENU) mutagenesis screen. pug mutant skeletal elements are patterned normally during development, but display a ~20% length reduction compared to wild-type embryos. We show that the pug mutation does not lead to changes in chondrocyte proliferation but instead promotes premature maturation and early ossification, which ultimately leads to disproportionate dwarfism. Using sequence capture and high-throughput sequencing, we identified a missense mutation in the Xylosyltransferase 1 (Xylt1) gene in pug mutants. Xylosyltransferases catalyze the initial step in glycosaminoglycan (GAG) chain addition to proteoglycan core proteins, and these modifications are essential for normal proteoglycan function. We show that the pug mutation disrupts Xylt1 activity and subcellular localization, leading to a reduction in GAG chains in pug mutants. The pug mutant serves as a novel model for mammalian dwarfism and identifies a key role for proteoglycan modification in the initiation of chondrocyte maturation. © 2013 Published by Elsevier Inc.

Design and Validation of CRISPR/Cas9 Systems for Targeted Gene Modification in Induced Pluripotent Stem Cells.

PubMed

Lee, Ciaran M; Zhu, Haibao; Davis, Timothy H; Deshmukh, Harshahardhan; Bao, Gang

2017-01-01

The CRISPR/Cas9 system is a powerful tool for precision genome editing. The ability to accurately modify genomic DNA in situ with single nucleotide precision opens up new possibilities for not only basic research but also biotechnology applications and clinical translation. In this chapter, we outline the procedures for design, screening, and validation of CRISPR/Cas9 systems for targeted modification of coding sequences in the human genome and how to perform genome editing in induced pluripotent stem cells with high efficiency and specificity.

Abscisic acid dynamics in roots detected with genetically encoded FRET sensors

PubMed Central

Jones, Alexander M; Danielson, Jonas ÅH; ManojKumar, Shruti N; Lanquar, Viviane; Grossmann, Guido; Frommer, Wolf B

2014-01-01

Cytosolic hormone levels must be tightly controlled at the level of influx, efflux, synthesis, degradation and compartmentation. To determine ABA dynamics at the single cell level, FRET sensors (ABACUS) covering a range ∼0.2–800 µM were engineered using structure-guided design and a high-throughput screening platform. When expressed in yeast, ABACUS1 detected concentrative ABA uptake mediated by the AIT1/NRT1.2 transporter. Arabidopsis roots expressing ABACUS1-2µ (Kd∼2 µM) and ABACUS1-80µ (Kd∼80 µM) respond to perfusion with ABA in a concentration-dependent manner. The properties of the observed ABA accumulation in roots appear incompatible with the activity of known ABA transporters (AIT1, ABCG40). ABACUS reveals effects of external ABA on homeostasis, that is, ABA-triggered induction of ABA degradation, modification, or compartmentation. ABACUS can be used to study ABA responses in mutants and quantitatively monitor ABA translocation and regulation, and identify missing components. The sensor screening platform promises to enable rapid fine-tuning of the ABA sensors and engineering of plant and animal hormone sensors to advance our understanding of hormone signaling. DOI: http://dx.doi.org/10.7554/eLife.01741.001 PMID:24737862

A human XPC protein interactome--a resource.

PubMed

Lubin, Abigail; Zhang, Ling; Chen, Hua; White, Victoria M; Gong, Feng

2013-12-23

Global genome nucleotide excision repair (GG-NER) is responsible for identifying and removing bulky adducts from non-transcribed DNA that result from damaging agents such as UV radiation and cisplatin. Xeroderma pigmentosum complementation group C (XPC) is one of the essential damage recognition proteins of the GG-NER pathway and its dysfunction results in xeroderma pigmentosum (XP), a disorder involving photosensitivity and a predisposition to cancer. To better understand the identification of DNA damage by XPC in the context of chromatin and the role of XPC in the pathogenesis of XP, we characterized the interactome of XPC using a high throughput yeast two-hybrid screening. Our screening showed 49 novel interactors of XPC involved in DNA repair and replication, proteolysis and post-translational modifications, transcription regulation, signal transduction, and metabolism. Importantly, we validated the XPC-OTUD4 interaction by co-IP and provided evidence that OTUD4 knockdown in human cells indeed affects the levels of ubiquitinated XPC, supporting a hypothesis that the OTUD4 deubiquitinase is involved in XPC recycling by cleaving the ubiquitin moiety. This high-throughput characterization of the XPC interactome provides a resource for future exploration and suggests that XPC may have many uncharacterized cellular functions.

A review of patients with glutaric aciduria type 1 at Inkosi Albert Luthuli Central Hospital, Durban, South Africa.

PubMed

Govender, R; Mitha, A; Mubaiwa, L

2017-02-27

Glutaric aciduria type 1 (GA1) is an organic acidaemia. The objective of this study was to describe the profile of patients diagnosed with GA1 at Inkosi Albert Luthuli Central Hospital, Durban, South Africa from 2007 to 2015. We identified 6 children (4 girls, 2 boys) in a retrospective review. The mean age at diagnosis was 12 months. Clinical findings on presentation were encephalopathic crises (n=4), hypotonia (n=4) and macrocephaly (n=5). Other complications included seizures (n=4), dystonia (n=3) and bulbar dysfunction (n=4). Urine organic acid screens showed elevated glutaric acid levels (n=6). Five patients tested positive for the A293T mutation on the glutarylco-enzyme A (CoA) dehydrogenase gene. Abnormalities on magnetic resonance imaging screening included hyperintense basal ganglia (n=6), widened perisylvian fissures (n=6), and an abnormal signal in the cerebral peduncles (n=5) and central tegmental tract (n=4). All patients were treated with L-carnitine and dietary modification. Two patients had a static clinical course, 1 patient gained milestones, and 3 have shown further neuroregression.

A computational search for box C/D snoRNA genes in the Drosophila melanogaster genome.

PubMed

Accardo, M C; Giordano, E; Riccardo, S; Digilio, F A; Iazzetti, G; Calogero, R A; Furia, M

2004-12-12

In eukaryotes, the family of non-coding RNA genes includes a number of genes encoding small nucleolar RNAs (mainly C/D and H/ACA snoRNAs), which act as guides in the maturation or post-transcriptional modifications of target RNA molecules. Since in Drosophila melanogaster (Dm) only few examples of snoRNAs have been identified so far by cDNA libraries screening, integration of the molecular data with in silico identification of these types of genes could throw light on their organization in the Dm genome. We have performed a computational screening of the Dm genome for C/D snoRNA genes, followed by experimental validation of the putative candidates. Few of the 26 confirmed snoRNAs had been recognized by cDNA library analysis. Organization of the Dm genome was also found to be more variegated than previously suspected, with snoRNA genes nested in both the introns and exons of protein-coding genes. This finding suggests that the presence of additional mechanisms of snoRNA biogenesis based on the alternative production of overlapping mRNA/snoRNA molecules. Additional information is available at http://www.bioinformatica.unito.it/bioinformatics/snoRNAs.

Laboratory evaluations of erectile dysfunction: an evidence based approach.

PubMed

Bodie, Joshua; Lewis, Jean; Schow, Doug; Monga, Manoj

2003-06-01

We evaluate the prevalence of laboratory abnormalities in men presenting for initial evaluation and therapy of erectile dysfunction. The computerized charts of men receiving treatment for erectile dysfunction from 1987 to 2002 were retrospectively reviewed. We pooled laboratory data for 3,547 men with erectile dysfunction to assess the prevalence of laboratory abnormalities. Values of the common laboratory screening tests for erectile dysfunction were recorded for testosterone, prolactin, luteinizing hormone, thyroid-stimulating hormone, hemoglobin A(Ic), prostate specific antigen, hemoglobin, cholesterol and creatinine. Of those patients evaluated 18.7% had low testosterone, 4.6% had increased prolactin, 14.6% had abnormal luteinizing hormone, 4.0% had increased thyroid-stimulating hormone, 8.3% had increased prostate specific antigen, 26.5% had anemia and 11.9% tested had renal insufficiency. A high percentage of patients presenting with a primary complaint of erectile dysfunction had increased hemoglobin A(Ic) and total serum cholesterol levels (52.9% and 48.4%, respectively). An evidence based approach to standardization of laboratory evaluations for men presenting with erectile dysfunction is recommended. Laboratory screening should be directed to identify those risk factors that may benefit from lifestyle modification and pharmacological intervention.

75 FR 22675 - Notice of Passenger Facility Charge (PFC) Approvals and Disapprovals

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-29

... expansion. Security screening expansion. Terminal restroom design. Terminal restroom remodel. Terminal... remodeling. Pavement management system. Master plan, phase 1. Decision Date: September 23, 2009. FOR FURTHER... modifications, passenger terminal. Rehabilitation of taxilane K-1. Design and implement noise mitigation...

Lifestyle modification: A primary prevention approach to colorectal cancer

USDA-ARS?s Scientific Manuscript database

Early detection of cancer through screening is an important step in decreasing both morbidity and mortality. Likewise, specific modifiable lifestyle behaviors are associated with reduced risk of colorectal cancer. Lifestyle practices have also been shown to maximize health after the primary treatmen...

Validating a dance-specific screening test for balance: preliminary results from multisite testing.

PubMed

Batson, Glenna

2010-09-01

Few dance-specific screening tools adequately capture balance. The aim of this study was to administer and modify the Star Excursion Balance Test (oSEBT) to examine its utility as a balance screen for dancers. The oSEBT involves standing on one leg while lightly targeting with the opposite foot to the farthest distance along eight spokes of a star-shaped grid. This task simulates dance in the spatial pattern and movement quality of the gesturing limb. The oSEBT was validated for distance on athletes with history of ankle sprain. Thirty-three dancers (age 20.1 +/- 1.4 yrs) participated from two contemporary dance conservatories (UK and US), with or without a history of lower extremity injury. Dancers were verbally instructed (without physical demonstration) to execute the oSEBT and four modifications (mSEBT): timed (speed), timed with cognitive interference (answering questions aloud), and sensory disadvantaging (foam mat). Stepping strategies were tracked and performance strategies video-recorded. Unlike the oSEBT results, distances reached were not significant statistically (p = 0.05) or descriptively (i.e., shorter) for either group. Performance styles varied widely, despite sample homogeneity and instructions to control for strategy. Descriptive analysis of mSEBT showed an increased number of near-falls and decreased timing on the injured limb. Dancers appeared to employ variable strategies to keep balance during this test. Quantitative analysis is warranted to define balance strategies for further validation of SEBT modifications to determine its utility as a balance screening tool.

Fast tandem mass spectra-based protein identification regardless of the number of spectra or potential modifications examined.

PubMed

Falkner, Jayson; Andrews, Philip

2005-05-15

Comparing tandem mass spectra (MSMS) against a known dataset of protein sequences is a common method for identifying unknown proteins; however, the processing of MSMS by current software often limits certain applications, including comprehensive coverage of post-translational modifications, non-specific searches and real-time searches to allow result-dependent instrument control. This problem deserves attention as new mass spectrometers provide the ability for higher throughput and as known protein datasets rapidly grow in size. New software algorithms need to be devised in order to address the performance issues of conventional MSMS protein dataset-based protein identification. This paper describes a novel algorithm based on converting a collection of monoisotopic, centroided spectra to a new data structure, named 'peptide finite state machine' (PFSM), which may be used to rapidly search a known dataset of protein sequences, regardless of the number of spectra searched or the number of potential modifications examined. The algorithm is verified using a set of commercially available tryptic digest protein standards analyzed using an ABI 4700 MALDI TOFTOF mass spectrometer, and a free, open source PFSM implementation. It is illustrated that a PFSM can accurately search large collections of spectra against large datasets of protein sequences (e.g. NCBI nr) using a regular desktop PC; however, this paper only details the method for identifying peptide and subsequently protein candidates from a dataset of known protein sequences. The concept of using a PFSM as a peptide pre-screening technique for MSMS-based search engines is validated by using PFSM with Mascot and XTandem. Complete source code, documentation and examples for the reference PFSM implementation are freely available at the Proteome Commons, http://www.proteomecommons.org and source code may be used both commercially and non-commercially as long as the original authors are credited for their work.

Understanding RNA modifications: the promises and technological bottlenecks of the ‘epitranscriptome’

PubMed Central

Kapoor, Utkarsh

2017-01-01

The discovery of mechanisms that alter genetic information via RNA editing or introducing covalent RNA modifications points towards a complexity in gene expression that challenges long-standing concepts. Understanding the biology of RNA modifications represents one of the next frontiers in molecular biology. To this date, over 130 different RNA modifications have been identified, and improved mass spectrometry approaches are still adding to this list. However, only recently has it been possible to map selected RNA modifications at single-nucleotide resolution, which has created a number of exciting hypotheses about the biological function of RNA modifications, culminating in the proposition of the ‘epitranscriptome’. Here, we review some of the technological advances in this rapidly developing field, identify the conceptual challenges and discuss approaches that are needed to rigorously test the biological function of specific RNA modifications. PMID:28566301

Root Surface Bio-modification with Erbium Lasers- A Myth or a Reality??

PubMed Central

Lavu, Vamsi; Sundaram, Subramoniam; Sabarish, Ram; Rao, Suresh Ranga

2015-01-01

The objective of this literature review was to critically review the evidence available in the literature regarding the expediency of erbium family of lasers for root bio modification as a part of periodontal therapy. The literature search was performed on the Pubmed using MeSH words such as "lasers/therapeutic use, scaling, dental calculus, tooth root/anatomy and histology, ultrasonic therapy". The studies were screened and were grouped as follows: those evaluating a) efficacy for calculus removal with the Erbium family of laser b) root surface changes following Er YAG and Er Cr YSGG application c) comparative studies of the Er YAG, Er Cr YSGG lasers versus conventional methods of root surface modification d) Bio compatibility of root surface following Erbium laser treatment e) Studies on the combined efficacy of laser root modification with conventional methods towards root surface bio-modification f) Studies on effectiveness of root surface bio-modification prior to root coverage procedures. In conclusion, the erbium family has a proven anti-bacterial action, predictable calculus removal, minimal root substance removal, and appears to favor cell attachment. The Erbium family of lasers appears to be a useful adjunct for the management of periodontal disease. PMID:25713635

Studies of the expression of human poly(ADP-ribose) polymerase-1 in Saccharomyces cerevisiae and identification of PARP-1 substrates by yeast proteome microarray screening.

PubMed

Tao, Zhihua; Gao, Peng; Liu, Hung-Wen

2009-12-15

Poly(ADP-ribosyl)ation of various nuclear proteins catalyzed by a family of NAD(+)-dependent enzymes, poly(ADP-ribose) polymerases (PARPs), is an important posttranslational modification reaction. PARP activity has been demonstrated in all types of eukaryotic cells with the exception of yeast, in which the expression of human PARP-1 was shown to lead to retarded cell growth. We investigated the yeast growth inhibition caused by human PARP-1 expression in Saccharomyces cerevisiae. Flow cytometry analysis reveals that PARP-1-expressing yeast cells accumulate in the G(2)/M stage of the cell cycle. Confocal microscopy analysis shows that human PARP-1 is distributed throughout the nucleus of yeast cells but is enriched in the nucleolus. Utilizing yeast proteome microarray screening, we identified 33 putative PARP-1 substrates, six of which are known to be involved in ribosome biogenesis. The poly(ADP-ribosyl)ation of three of these yeast proteins, together with two human homologues, was confirmed by an in vitro PARP-1 assay. Finally, a polysome profile analysis using sucrose gradient ultracentrifugation demonstrated that the ribosome levels in yeast cells expressing PARP-1 are lower than those in control yeast cells. Overall, our data suggest that human PARP-1 may affect ribosome biogenesis by modifying certain nucleolar proteins in yeast. The artificial PARP-1 pathway in yeast may be used as a simple platform to identify substrates and verify function of this important enzyme.

Aging and Visual Impairment.

ERIC Educational Resources Information Center

Morse, A. R.; And Others

1987-01-01

Eye diseases of the aged include diabetic retinopathy, senile cataracts, senile macular degeneration, and glaucoma. Environmental modifications such as better levels of illumination and reduction of glare can enhance an individual's ability to function. Programs to screen and treat visual problems in elderly persons are called for. (Author/JDD)

Encoded libraries of chemically modified peptides.

PubMed

Heinis, Christian; Winter, Greg

2015-06-01

The use of powerful technologies for generating and screening DNA-encoded protein libraries has helped drive the development of proteins as pharmaceutical ligands. However the development of peptides as pharmaceutical ligands has been more limited. Although encoded peptide libraries are typically several orders of magnitude larger than classical chemical libraries, can be more readily screened, and can give rise to higher affinity ligands, their use as pharmaceutical ligands is limited by their intrinsic properties. Two of the intrinsic limitations include the rotational flexibility of the peptide backbone and the limited number (20) of natural amino acids. However these limitations can be overcome by use of chemical modification. For example, the libraries can be modified to introduce topological constraints such as cyclization linkers, or to introduce new chemical entities such as small molecule ligands, fluorophores and photo-switchable compounds. This article reviews the chemistry involved, the properties of the peptide ligands, and the new opportunities offered by chemical modification of DNA-encoded peptide libraries. Copyright © 2015. Published by Elsevier Ltd.

Thermal modifications of charmonia and bottomonia from spatial correlation functions

NASA Astrophysics Data System (ADS)

Ding, Heng-Tong; Kaczmarek, Olaf; Kruse, Anna-lena; Mukherjee, Swagato; Ohno, Hiroshi; Sandmeyer, Hauke; Shu, Hai-Tao

2018-03-01

We present our study on the thermal modifications of charmonia and bottomonia from spatial correlation functions at zero and nonzero momenta in quenched QCD. To accommodate the heavy quarks on the lattice we performed simulations on very fine lattices at a fixed beta value corresponding to a lattice spacing a-1 = 22:8 GeV on 1923×32, 1923 × 48, 1923 × 56, 1923 × 64 and 1923 × 96 lattices using clover-improved Wilson fermions. These lattices correspond to temperatures of 2.25Tc, 1.50Tc, 1.25Tc, 1.10Tc and 0.75Tc. To increase the signal to noise ratio in the axial-vector and scalar channels we used multi-sources for the measurement of spatial correlation functions. By investigating on the differences between spatial and temporal correlators as well as the temperature dependence of screening masses we will discuss the thermal effects in different channels of quarkonium states. Besides this the dispersion relation of the screening mass at different momenta is also discussed.

Comparison of Three Cognitive Screening Tools in Older Urban and Regional Aboriginal Australians.

PubMed

Radford, Kylie; Mack, Holly A; Draper, Brian; Chalkley, Simon; Delbaere, Kim; Daylight, Gail; Cumming, Robert G; Bennett, Hayley; Broe, Gerald A

2015-01-01

Validated cognitive screening tools for use in urban and regional Aboriginal populations in Australia are lacking. In a cross-sectional community-based study, 235 participants were assessed on the Mini-Mental State Examination (MMSE), the Rowland Universal Dementia Assessment Scale (RUDAS) and an urban modification of the Kimberley Indigenous Cognitive Assessment (mKICA). Performance on these cognitive screening tools was compared to dementia diagnosis by clinical consensus. All tests were culturally acceptable with good psychometric properties. Receiver operating characteristic curve analyses revealed that the MMSE and mKICA were the most accurate. The MMSE is an effective cognitive screening tool in urban Aboriginal populations. The mKICA is a good alternative when illiteracy, language or cultural considerations deem it appropriate. The RUDAS also has adequate validity in this population. © 2015 S. Karger AG, Basel.

Terrestrial Eco-Toxicological Tests as Screening Tool to Assess Soil Contamination in Krompachy Area

NASA Astrophysics Data System (ADS)

Ol'ga, Šestinová; Findoráková, Lenka; Hančuľák, Jozef; Fedorová, Erika; Tomislav, Špaldon

2016-10-01

In this study, we present screening tool of heavy metal inputs to agricultural and permanent grass vegetation of the soils in Krompachy. This study is devoted to Ecotoxicity tests, Terrestrial Plant Test (modification of OECD 208, Phytotoxkit microbiotest on Sinapis Alba) and chronic tests of Earthworm (Dendrobaena veneta, modification of OECD Guidelines for the testing of chemicals 317, Bioaccumulation in Terrestrial Oligochaetes) as practical and sensitive screening method for assessing the effects of heavy metals in Krompachy soils. The total Cu, Zn, As, Pb and Hg concentrations and eco-toxicological tests of soils from the Krompachy area were determined of 4 sampling sites in 2015. An influence of the sampling sites distance from the copper smeltery on the absolutely concentrations of metals were recorded for copper, lead, zinc, arsenic and mercury. The highest concentrations of these metals were detected on the sampling sites up to 3 km from the copper smeltery. The samples of soil were used to assess of phytotoxic effect. Total mortality was established at earthworms using chronic toxicity test after 7 exposure days. The results of our study confirmed that no mortality was observed in any of the study soils. Based on the phytotoxicity testing, phytotoxic effects of the metals contaminated soils from the samples 3KR (7-9) S.alba seeds was observed.

Effect of additional brief counselling after periodic health examination on motivation for health behavior change [corrected].

PubMed

Son, Ki Young; Lee, Cheol Min; Cho, BeLong; Lym, Youl Lee; Oh, Seung Won; Chung, Wonjoo; Lee, Jin-Seok; Park, DuShin; Kim, Han Suk

2012-11-01

This study was to evaluate the effect of additional brief counseling by a primary care physician on lifestyle modification of examinees after a periodic health examination. 1,000 participants of the 2007 Korean national health screening program were asked to note any variation in their health behavior after participating in the screening program. The degree of comprehensive motivation for lifestyle modification was assessed in terms of stages of health behavior change. We calculated odds ratio of positive change (enhanced stage of change) with multiple logistic regression analysis and age-adjusted proportion of positive changers. Of 989 respondents, 486 and 503 received the basic and additional programs, respectively. Additional group were more likely to be positive changer than basic group (adjusted OR 1.78; 95% CI 1.19-2.65), and this was more prominent in older age group (adjusted OR 2.38, 95% CI 1.23-4.58). The age-adjusted proportions of positive changers were 22.7% (95% CI, 17.9-28.3) and 36.2% (95% CI, 30.4-42.4) in the basic and additional groups, respectively (P < 0.001). The additional consultation led to improvements in the stage of health behavior change after the health examination. Thus, such a consultation should be considered when designing a health-screening program.

Effect of Aditional Brief Counselling after Periodic Health Examination on Motivation for Health Behavior Change

PubMed Central

Son, Ki Young; Lee, Cheol Min; Lym, Youl Lee; Oh, Seung Won; Chung, Wonjoo; Lee, Jin-Seok; Park, DuShin; Kim, Han Suk

2012-01-01

This study was to evaluate the effect of additional brief counseling by a primary care physician on lifestyle modification of examinees after a periodic health examination. 1,000 participants of the 2007 Korean national health screening program were asked to note any variation in their health behavior after participating in the screening program. The degree of comprehensive motivation for lifestyle modification was assessed in terms of stages of health behavior change. We calculated odds ratio of positive change (enhanced stage of change) with multiple logistic regression analysis and age-adjusted proportion of positive changers. Of 989 respondents, 486 and 503 received the basic and additional programs, respectively. Additional group were more likely to be positive changer than basic group (adjusted OR 1.78; 95% CI 1.19-2.65), and this was more prominent in older age group (adjusted OR 2.38, 95% CI 1.23-4.58). The age-adjusted proportions of positive changers were 22.7% (95% CI, 17.9-28.3) and 36.2% (95% CI, 30.4-42.4) in the basic and additional groups, respectively (P < 0.001). The additional consultation led to improvements in the stage of health behavior change after the health examination. Thus, such a consultation should be considered when designing a health-screening program. PMID:23166407

Improved silicon nitride for advanced heat engines

NASA Technical Reports Server (NTRS)

Yeh, Harry C.; Fang, Ho T.

1991-01-01

The results of a four year program to improve the strength and reliability of injection-molded silicon nitride are summarized. Statistically designed processing experiments were performed to identify and optimize critical processing parameters and compositions. Process improvements were monitored by strength testing at room and elevated temperatures, and microstructural characterization by optical, scanning electron microscopes, and scanning transmission electron microscope. Processing modifications resulted in a 20 percent strength and 72 percent Weibull slope improvement of the baseline material. Additional sintering aids screening and optimization experiments succeeded in developing a new composition (GN-10) capable of 581.2 MPa at 1399 C. A SiC whisker toughened composite using this material as a matrix achieved a room temperature toughness of 6.9 MPa m(exp .5) by the Chevron notched bar technique. Exploratory experiments were conducted on injection molding of turbocharger rotors.

Can abstract screening workload be reduced using text mining? User experiences of the tool Rayyan.

PubMed

Olofsson, Hanna; Brolund, Agneta; Hellberg, Christel; Silverstein, Rebecca; Stenström, Karin; Österberg, Marie; Dagerhamn, Jessica

2017-09-01

One time-consuming aspect of conducting systematic reviews is the task of sifting through abstracts to identify relevant studies. One promising approach for reducing this burden uses text mining technology to identify those abstracts that are potentially most relevant for a project, allowing those abstracts to be screened first. To examine the effectiveness of the text mining functionality of the abstract screening tool Rayyan. User experiences were collected. Rayyan was used to screen abstracts for 6 reviews in 2015. After screening 25%, 50%, and 75% of the abstracts, the screeners logged the relevant references identified. A survey was sent to users. After screening half of the search result with Rayyan, 86% to 99% of the references deemed relevant to the study were identified. Of those studies included in the final reports, 96% to 100% were already identified in the first half of the screening process. Users rated Rayyan 4.5 out of 5. The text mining function in Rayyan successfully helped reviewers identify relevant studies early in the screening process. Copyright © 2017 John Wiley & Sons, Ltd.

tRNAmodpred: a computational method for predicting posttranscriptional modifications in tRNAs

PubMed Central

Machnicka, Magdalena A.; Dunin-Horkawicz, Stanislaw; de Crécy-Lagard, Valerie; Bujnicki, Janusz M.

2016-01-01

tRNA molecules contain numerous chemically altered nucleosides, which are formed by enzymatic modification of the primary transcripts during the complex tRNA maturation process. Some of the modifications are introduced by single reactions, while other require complex series of reactions carried out by several different enzymes. The location and distribution of various types of modifications vary greatly between different tRNA molecules, organisms and organelles. We have developed a computational method tRNAmodpred, for predicting modifications in tRNA sequences. Briefly, our method takes as an input one or more unmodified tRNA sequences and a set of protein sequences corresponding to a proteome of a cell. Subsequently it identifies homologs of known tRNA modification enzymes in the proteome, predicts tRNA modification activities and maps them onto known pathways of RNA modification from the MODOMICS database. Thereby, theoretically possible modification pathways are identified, and products of these modification reactions are proposed for query tRNAs. This method allows for predicting modification patterns for newly sequenced genomes as well as for checking tentative modification status of tRNAs from one species treated with enzymes from another source, e.g. to predict the possible modifications of eukaryotic tRNAs expressed in bacteria. tRNAmodpred is freely available as web server at http://genesilico.pl/trnamodpred/. PMID:27016142

ChIP-Seq Analysis for Identifying Genome-Wide Histone Modifications Associated with Stress-Responsive Genes in Plants.

PubMed

Li, Guosheng; Jagadeeswaran, Guru; Mort, Andrew; Sunkar, Ramanjulu

2017-01-01

Histone modifications represent the crux of epigenetic gene regulation essential for most biological processes including abiotic stress responses in plants. Thus, identification of histone modifications at the genome-scale can provide clues for how some genes are 'turned-on' while some others are "turned-off" in response to stress. This chapter details a step-by-step protocol for identifying genome-wide histone modifications associated with stress-responsive gene regulation using chromatin immunoprecipitation (ChIP) followed by sequencing of the DNA (ChIP-seq).

Fragment-based screening in tandem with phenotypic screening provides novel antiparasitic hits.

PubMed

Blaazer, Antoni R; Orrling, Kristina M; Shanmugham, Anitha; Jansen, Chimed; Maes, Louis; Edink, Ewald; Sterk, Geert Jan; Siderius, Marco; England, Paul; Bailey, David; de Esch, Iwan J P; Leurs, Rob

2015-01-01

Methods to discover biologically active small molecules include target-based and phenotypic screening approaches. One of the main difficulties in drug discovery is elucidating and exploiting the relationship between drug activity at the protein target and disease modification, a phenotypic endpoint. Fragment-based drug discovery is a target-based approach that typically involves the screening of a relatively small number of fragment-like (molecular weight <300) molecules that efficiently cover chemical space. Here, we report a fragment screening on TbrPDEB1, an essential cyclic nucleotide phosphodiesterase (PDE) from Trypanosoma brucei, and human PDE4D, an off-target, in a workflow in which fragment hits and a series of close analogs are subsequently screened for antiparasitic activity in a phenotypic panel. The phenotypic panel contained T. brucei, Trypanosoma cruzi, Leishmania infantum, and Plasmodium falciparum, the causative agents of human African trypanosomiasis (sleeping sickness), Chagas disease, leishmaniasis, and malaria, respectively, as well as MRC-5 human lung cells. This hybrid screening workflow has resulted in the discovery of various benzhydryl ethers with antiprotozoal activity and low toxicity, representing interesting starting points for further antiparasitic optimization. © 2014 Society for Laboratory Automation and Screening.

A Chemogenomic Screen Reveals Novel Snf1p/AMPK Independent Regulators of Acetyl-CoA Carboxylase.

PubMed

Bozaquel-Morais, Bruno L; Madeira, Juliana B; Venâncio, Thiago M; Pacheco-Rosa, Thiago; Masuda, Claudio A; Montero-Lomeli, Monica

2017-01-01

Acetyl-CoA carboxylase (Acc1p) is a key enzyme in fatty acid biosynthesis and is essential for cell viability. To discover new regulators of its activity, we screened a Saccharomyces cerevisiae deletion library for increased sensitivity to soraphen A, a potent Acc1p inhibitor. The hits identified in the screen (118 hits) were filtered using a chemical-phenotype map to exclude those associated with pleiotropic drug resistance. This enabled the identification of 82 ORFs that are genetic interactors of Acc1p. The main functional clusters represented by these hits were "transcriptional regulation", "protein post-translational modifications" and "lipid metabolism". Further investigation of the "transcriptional regulation" cluster revealed that soraphen A sensitivity is poorly correlated with ACC1 transcript levels. We also studied the three top unknown ORFs that affected soraphen A sensitivity: SOR1 (YDL129W), SOR2 (YIL092W) and SOR3 (YJR039W). Since the C18/C16 ratio of lipid acyl lengths reflects Acc1p activity levels, we evaluated this ratio in the three mutants. Deletion of SOR2 and SOR3 led to reduced acyl lengths, suggesting that Acc1p is indeed down-regulated in these strains. Also, these mutants showed no differences in Snf1p/AMPK activation status and deletion of SNF1 in these backgrounds did not revert soraphen A sensitivity completely. Furthermore, plasmid maintenance was reduced in sor2Δ strain and this trait was shared with 18 other soraphen A sensitive hits. In summary, our screen uncovered novel Acc1p Snf1p/AMPK-independent regulators.

Electric-field-induced modification of the magnon energy, exchange interaction, and curie temperature of transition-metal thin films.

PubMed

Oba, M; Nakamura, K; Akiyama, T; Ito, T; Weinert, M; Freeman, A J

2015-03-13

The electric-field-induced modification in the Curie temperature of prototypical transition-metal thin films with the perpendicular magnetic easy axis, a freestanding Fe(001) monolayer and a Co monolayer on Pt(111), is investigated by first-principles calculations of spin-spiral structures in an external electric field (E field). An applied E field is found to modify the magnon (spin-spiral formation) energy; the change arises from the E-field-induced screening charge density in the spin-spiral states due to p-d hybridizations. The Heisenberg exchange parameters obtained from the magnon energy suggest an E-field-induced modification of the Curie temperature, which is demonstrated via Monte Carlo simulations that take the magnetocrystalline anisotropy into account.

Biotinylation of lysine method identifies acetylated histone H3 lysine 79 in Saccharomyces cerevisiae as a substrate for Sir2.

PubMed

Bheda, Poonam; Swatkoski, Stephen; Fiedler, Katherine L; Boeke, Jef D; Cotter, Robert J; Wolberger, Cynthia

2012-04-17

Although the biological roles of many members of the sirtuin family of lysine deacetylases have been well characterized, a broader understanding of their role in biology is limited by the challenges in identifying new substrates. We present here an in vitro method that combines biotinylation and mass spectrometry (MS) to identify substrates deacetylated by sirtuins. The method permits labeling of deacetylated residues with amine-reactive biotin on the ε-nitrogen of lysine. The biotin can be utilized to purify the substrate and identify the deacetylated lysine by MS. The biotinyl-lysine method was used to compare deacetylation of chemically acetylated histones by the yeast sirtuins, Sir2 and Hst2. Intriguingly, Sir2 preferentially deacetylates histone H3 lysine 79 as compared to Hst2. Although acetylation of K79 was not previously reported in Saccharomyces cerevisiae, we demonstrate that a minor population of this residue is indeed acetylated in vivo and show that Sir2, and not Hst2, regulates the acetylation state of H3 lysine 79. The in vitro biotinyl-lysine method combined with chemical acetylation made it possible to identify this previously unknown, low-abundance histone acetyl modification in vivo. This method has further potential to identify novel sirtuin deacetylation substrates in whole cell extracts, enabling large-scale screens for new deacetylase substrates.

Mapping Base Modifications in DNA by Transverse-Current Sequencing

NASA Astrophysics Data System (ADS)

Alvarez, Jose R.; Skachkov, Dmitry; Massey, Steven E.; Kalitsov, Alan; Velev, Julian P.

2018-02-01

Sequencing DNA modifications and lesions, such as methylation of cytosine and oxidation of guanine, is even more important and challenging than sequencing the genome itself. The traditional methods for detecting DNA modifications are either insensitive to these modifications or require additional processing steps to identify a particular type of modification. Transverse-current sequencing in nanopores can potentially identify the canonical bases and base modifications in the same run. In this work, we demonstrate that the most common DNA epigenetic modifications and lesions can be detected with any predefined accuracy based on their tunneling current signature. Our results are based on simulations of the nanopore tunneling current through DNA molecules, calculated using nonequilibrium electron-transport methodology within an effective multiorbital model derived from first-principles calculations, followed by a base-calling algorithm accounting for neighbor current-current correlations. This methodology can be integrated with existing experimental techniques to improve base-calling fidelity.

Examination of segmental average mass spectra from liquid chromatography-tandem mass spectrometric (LC-MS/MS) data enables screening of multiple types of protein modifications.

PubMed

Liu, Nai-Yu; Lee, Hsiao-Hui; Chang, Zee-Fen; Tsay, Yeou-Guang

2015-09-10

It has been observed that a modified peptide and its non-modified counterpart, when analyzed with reverse phase liquid chromatography, usually share a very similar elution property [1-3]. Inasmuch as this property is common to many different types of protein modifications, we propose an informatics-based approach, featuring the generation of segmental average mass spectra ((sa)MS), that is capable of locating different types of modified peptides in two-dimensional liquid chromatography-mass spectrometric (LC-MS) data collected for regular protease digests from proteins in gels or solutions. To enable the localization of these peptides in the LC-MS map, we have implemented a set of computer programs, or the (sa)MS package, that perform the needed functions, including generating a complete set of segmental average mass spectra, compiling the peptide inventory from the Sequest/TurboSequest results, searching modified peptide candidates and annotating a tandem mass spectrum for final verification. Using ROCK2 as an example, our programs were applied to identify multiple types of modified peptides, such as phosphorylated and hexosylated ones, which particularly include those peptides that could have been ignored due to their peculiar fragmentation patterns and consequent low search scores. Hence, we demonstrate that, when complemented with peptide search algorithms, our approach and the entailed computer programs can add the sequence information needed for bolstering the confidence of data interpretation by the present analytical platforms and facilitate the mining of protein modification information out of complicated LC-MS/MS data. Copyright © 2015 Elsevier B.V. All rights reserved.

Radiogenomics: a systems biology approach to understanding genetic risk factors for radiotherapy toxicity ?

PubMed Central

Herskind, Carsten; Talbot, Christopher J.; Kerns, Sarah L.; Veldwijk, Marlon R.; Rosenstein, Barry S.; West, Catharine M. L.

2016-01-01

Adverse reactions in normal tissue after radiotherapy (RT) limit the dose that can be given to tumour cells. Since 80% of individual variation in clinical response is estimated to be caused by patient-related factors, identifying these factors might allow prediction of patients with increased risk of developing severe reactions. While inactivation of cell renewal is considered a major cause of toxicity in early-reacting normal tissues, complex interactions involving multiple cell types, cytokines, and hypoxia seem important for late reactions. Here, we review ‘omics’ approaches such as screening of genetic polymorphisms or gene expression analysis, and assess the potential of epigenetic factors, posttranslational modification, signal transduction, and metabolism. Furthermore, functional assays have suggested possible associations with clinical risk of adverse reaction. Pathway analysis incorporating different ‘omics’ approaches may be more efficient in identifying critical pathways than pathway analysis based on single ‘omics’ data sets. Integrating these pathways with functional assays may be powerful in identifying multiple subgroups of RT patients characterized by different mechanisms. Thus ‘omics’ and functional approaches may synergize if they are integrated into radiogenomics ‘systems biology’ to facilitate the goal of individualised radiotherapy. PMID:26944314

DNA methylation biomarkers for head and neck squamous cell carcinoma.

PubMed

Zhou, Chongchang; Ye, Meng; Ni, Shumin; Li, Qun; Ye, Dong; Li, Jinyun; Shen, Zhishen; Deng, Hongxia

2018-06-21

DNA methylation plays an important role in the etiology and pathogenesis of head and neck squamous cell carcinoma (HNSCC). The current study aimed to identify aberrantly methylated-differentially expressed genes (DEGs) by a comprehensive bioinformatics analysis. In addition, we screened for DEGs affected by DNA methylation modification and further investigated their prognostic values for HNSCC. We included microarray data of DNA methylation (GSE25093 and GSE33202) and gene expression (GSE23036 and GSE58911) from Gene Expression Omnibus. Aberrantly methylated-DEGs were analyzed with R software. The Cancer Genome Atlas (TCGA) RNA sequencing and DNA methylation (Illumina HumanMethylation450) databases were utilized for validation. In total, 27 aberrantly methylated genes accompanied by altered expression were identified. After confirmation by The Cancer Genome Atlas (TCGA) database, 2 hypermethylated-low-expression genes (FAM135B and ZNF610) and 2 hypomethylated-high-expression genes (HOXA9 and DCC) were identified. A receiver operating characteristic (ROC) curve confirmed the diagnostic value of these four methylated genes for HNSCC. Multivariate Cox proportional hazards analysis showed that FAM135B methylation was a favorable independent prognostic biomarker for overall survival of HNSCC patients.

Developing Novel Therapeutics Targeting Undifferentiated and Castration-Resistant Prostate Cancer Stem Cells

DTIC Science & Technology

2016-10-01

identify PCSC- specific homing peptides ; and 2) To perform unbiased drug library screening to identify novel PCSC-targeting chemicals. In the past...display library (PDL) screening in PSA-/lo PCa cells to identify PCSC- specific homing peptides ; and 2) To perform unbiased drug library screening to...Goals of the Project (SOW): Aim 1: To perform phage display library (PDL) screening in PSA-/lo PCa cells to identify PCSC- specific homing peptides

AUDIT-C scores as a scaled marker of mean daily drinking, alcohol use disorder severity, and probability of alcohol dependence in a U.S. general population sample of drinkers.

PubMed

Rubinsky, Anna D; Dawson, Deborah A; Williams, Emily C; Kivlahan, Daniel R; Bradley, Katharine A

2013-08-01

Brief alcohol screening questionnaires are increasingly used to identify alcohol misuse in routine care, but clinicians also need to assess the level of consumption and the severity of misuse so that appropriate intervention can be offered. Information provided by a patient's alcohol screening score might provide a practical tool for assessing the level of consumption and severity of misuse. This post hoc analysis of data from the 2001 to 2002 National Epidemiologic Survey on Alcohol and Related Conditions (NESARC) included 26,546 U.S. adults who reported drinking in the past year and answered additional questions about their consumption, including Alcohol Use Disorders Identification Test-Consumption questionnaire (AUDIT-C) alcohol screening. Linear or logistic regression models and postestimation methods were used to estimate mean daily drinking, the number of endorsed alcohol use disorder (AUD) criteria ("AUD severity"), and the probability of alcohol dependence associated with each individual AUDIT-C score (1 to 12), after testing for effect modification by gender and age. Among eligible past-year drinkers, mean daily drinking, AUD severity, and the probability of alcohol dependence increased exponentially across increasing AUDIT-C scores. Mean daily drinking ranged from < 0.1 to 18.0 drinks/d, AUD severity ranged from < 0.1 to 5.1 endorsed AUD criteria, and probability of alcohol dependence ranged from < 1 to 65% across scores 1 to 12. AUD severity increased more steeply across AUDIT-C scores among women than men. Both AUD severity and mean daily drinking increased more steeply across AUDIT-C scores among younger versus older age groups. Results of this study could be used to estimate patient-specific consumption and severity based on age, gender, and alcohol screening score. This information could be integrated into electronic decision support systems to help providers estimate and provide feedback about patient-specific risks and identify those patients most likely to benefit from further diagnostic assessment. Copyright © 2013 by the Research Society on Alcoholism.

A recessive mutation in the RUB1-conjugating enzyme, RCE1, reveals a requirement for RUB modification for control of ethylene biosynthesis and proper induction of basic chitinase and PDF1.2 in Arabidopsis.

PubMed

Larsen, Paul B; Cancel, Jesse D

2004-05-01

By screening etiolated Arabidopsis seedlings for mutants with aberrant ethylene-related phenotypes, we identified a mutant that displays features of the ethylene-mediated triple response even in the absence of ethylene. Further characterization showed that the phenotype observed for the dark-grown seedlings of this mutant is reversible by prevention of ethylene perception and is dependent on a modest increase in ethylene production correlated with an increase in 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase (ACO) activity in the hypocotyl. Molecular characterization of leaves of the mutant revealed severely impaired induction of basic chitinase (chiB) and plant defensin (PDF)1.2 following treatment with jasmonic acid and/or ethylene. Positional cloning of the mutation resulted in identification of a 49-bp deletion in RCE1 (related to ubiquitin 1 (RUB1)-conjugating enzyme), which has been demonstrated to be responsible for covalent attachment of RUB1 to the SCF (Skpl Cdc 53 F-box) ubiquitin ligase complex to modify its activity. Our analyses with rce1-2 demonstrate a previously unknown requirement for RUB1 modification for regulation of ethylene biosynthesis and proper induction of defense-related genes in Arabidopsis.

In vitro study of the effects of ELF electric fields on gene expression in human epidermal cells.

PubMed

Collard, Jean-Francois; Mertens, Benjamin; Hinsenkamp, Maurice

2011-01-01

An acceleration of differentiation, at the expense of proliferation, is observed after exposure of various biological models to low frequency and low amplitude electric and electromagnetic fields. Following these results showing significant modifications, we try to identify the biological mechanism involved at the cell level through microarray screening. For this study, we use epidermis cultures harvested from human abdominoplasty. Two platinum electrodes are used to apply the electric signal. The gene expressions of 38,500 well-characterized human genes are analyzed using Affymetrix(®) microarray U133 Plus 2.0 chips. The protocol is repeated on three different patients. After three periods of exposure, a total of 24 chips have been processed. After the application of ELF electric fields, the microarray analysis confirms a modification of the gene expression of epidermis cells. Particularly, four up-regulated genes (DKK1, TXNRD1, ATF3, and MME) and one down-regulated gene (MACF1) are involved in the regulation of proliferation and differentiation. Expression of these five genes was also confirmed by real-time rtPCR in all samples used for microarray analysis. These results corroborate an acceleration of cell differentiation at the expense of cell proliferation. © 2010 Wiley-Liss, Inc.

PlasmoGEM, a database supporting a community resource for large-scale experimental genetics in malaria parasites.

PubMed

Schwach, Frank; Bushell, Ellen; Gomes, Ana Rita; Anar, Burcu; Girling, Gareth; Herd, Colin; Rayner, Julian C; Billker, Oliver

2015-01-01

The Plasmodium Genetic Modification (PlasmoGEM) database (http://plasmogem.sanger.ac.uk) provides access to a resource of modular, versatile and adaptable vectors for genome modification of Plasmodium spp. parasites. PlasmoGEM currently consists of >2000 plasmids designed to modify the genome of Plasmodium berghei, a malaria parasite of rodents, which can be requested by non-profit research organisations free of charge. PlasmoGEM vectors are designed with long homology arms for efficient genome integration and carry gene specific barcodes to identify individual mutants. They can be used for a wide array of applications, including protein localisation, gene interaction studies and high-throughput genetic screens. The vector production pipeline is supported by a custom software suite that automates both the vector design process and quality control by full-length sequencing of the finished vectors. The PlasmoGEM web interface allows users to search a database of finished knock-out and gene tagging vectors, view details of their designs, download vector sequence in different formats and view available quality control data as well as suggested genotyping strategies. We also make gDNA library clones and intermediate vectors available for researchers to produce vectors for themselves. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Transcriptome-wide analysis of alternative RNA splicing events in Epstein-Barr virus-associated gastric carcinomas

PubMed Central

Armero, Victoria E. S.; Tremblay, Marie-Pier; Allaire, Andréa; Boudreault, Simon; Martenon-Brodeur, Camille; Duval, Cyntia; Durand, Mathieu; Lapointe, Elvy; Thibault, Philippe; Tremblay-Létourneau, Maude; Perreault, Jean-Pierre; Scott, Michelle S.

2017-01-01

Multiple human diseases including cancer have been associated with a dysregulation in RNA splicing patterns. In the current study, modifications to the global RNA splicing landscape of cellular genes were investigated in the context of Epstein-Barr virus-associated gastric cancer. Global alterations to the RNA splicing landscape of cellular genes was examined in a large-scale screen from 295 primary gastric adenocarcinomas using high-throughput RNA sequencing data. RT-PCR analysis, mass spectrometry, and co-immunoprecipitation studies were also used to experimentally validate and investigate the differential alternative splicing (AS) events that were observed through RNA-seq studies. Our study identifies alterations in the AS patterns of approximately 900 genes such as tumor suppressor genes, transcription factors, splicing factors, and kinases. These findings allowed the identification of unique gene signatures for which AS is misregulated in both Epstein-Barr virus-associated gastric cancer and EBV-negative gastric cancer. Moreover, we show that the expression of Epstein–Barr nuclear antigen 1 (EBNA1) leads to modifications in the AS profile of cellular genes and that the EBNA1 protein interacts with cellular splicing factors. These findings provide insights into the molecular differences between various types of gastric cancer and suggest a role for the EBNA1 protein in the dysregulation of cellular AS. PMID:28493890

Transcriptome-wide analysis of alternative RNA splicing events in Epstein-Barr virus-associated gastric carcinomas.

PubMed

Armero, Victoria E S; Tremblay, Marie-Pier; Allaire, Andréa; Boudreault, Simon; Martenon-Brodeur, Camille; Duval, Cyntia; Durand, Mathieu; Lapointe, Elvy; Thibault, Philippe; Tremblay-Létourneau, Maude; Perreault, Jean-Pierre; Scott, Michelle S; Bisaillon, Martin

2017-01-01

Multiple human diseases including cancer have been associated with a dysregulation in RNA splicing patterns. In the current study, modifications to the global RNA splicing landscape of cellular genes were investigated in the context of Epstein-Barr virus-associated gastric cancer. Global alterations to the RNA splicing landscape of cellular genes was examined in a large-scale screen from 295 primary gastric adenocarcinomas using high-throughput RNA sequencing data. RT-PCR analysis, mass spectrometry, and co-immunoprecipitation studies were also used to experimentally validate and investigate the differential alternative splicing (AS) events that were observed through RNA-seq studies. Our study identifies alterations in the AS patterns of approximately 900 genes such as tumor suppressor genes, transcription factors, splicing factors, and kinases. These findings allowed the identification of unique gene signatures for which AS is misregulated in both Epstein-Barr virus-associated gastric cancer and EBV-negative gastric cancer. Moreover, we show that the expression of Epstein-Barr nuclear antigen 1 (EBNA1) leads to modifications in the AS profile of cellular genes and that the EBNA1 protein interacts with cellular splicing factors. These findings provide insights into the molecular differences between various types of gastric cancer and suggest a role for the EBNA1 protein in the dysregulation of cellular AS.

Evaluation of the smoke density chamber as an apparatus for fire toxicity screening tests

NASA Technical Reports Server (NTRS)

Hilado, C. J.; Labossiere, L. A.

1976-01-01

The smoke density chamber is perhaps the most widely used apparatus for smoke measurements. Because of its availability, it has been proposed as an apparatus for evaluating fire toxicity. The standard apparatus and procedure were not found suitable for toxicity screening tests using laboratory animals, because not enough materials of interest produced animal mortality or even incapacitation under standard test conditions. With modifications, the chamber offers greater promise as a screening tool, but other tests specifically designed to measure relative toxicity may be more cost-effective. Where one-dimensional heat flux is a requirement, the chamber is the most suitable apparatus available. It should be improved in regard to visibility of animals and ease of cleaning.

Integrating Routine HIV Screening in the New York City Community Health Center Collaborative.

PubMed

Rodriguez, Vanessa; Lester, Deborah; Connelly-Flores, Alison; Barsanti, Franco A; Hernandez, Paloma

2016-01-01

One in seven of the 1.1 million people living in the United States infected with HIV are not aware of their HIV status. At the same time, many clinical settings have not adopted routine HIV screening, which promotes linkage to specialist medical care. We sought to improve HIV screening in a large community health center network by using a data-driven, collaborative learning approach and system-wide modifications, where counselor-based HIV screening and testing were replaced by health-care providers and medical assistants. Urban Health Plan, Inc., a network of federally qualified health centers in the boroughs of the Bronx and Queens in New York City, provided HIV screening training for its health-care providers. In January 2011, it modified its electronic medical record system to incorporate HIV test offering. This study compared the 2010 baseline year with the three-year implementation follow-up period (January 2011 through December 2013) to determine the number of eligible individuals for HIV testing, HIV tests offered and performed, HIV-positive individuals, and HIV cases linked to specialty care. A total of 26,853 individuals at baseline and 100,369 individuals in the implementation period were eligible for HIV testing. HIV testing was performed on 2,079 (8%) of 26,853 eligible individuals in 2010 and 49,646 (50%) of 100,369 eligible individuals from 2011 through 2013. HIV-positive status was determined in 19 (0.9%) of 2,079 tested individuals in 2010 and 166 (0.3%) of 49,646 tested individuals from 2011 through 2013. Linkage to care was observed in all 19 eligible individuals and 127 (77%) of 166 eligible individuals who tested HIV positive in 2010 and 2011-2013, respectively. This study enabled routine HIV implementation testing at a community health center network, which resulted in enhanced HIV testing, an increased number of HIV-positive cases identified, and a rise in the number of patients linked to HIV specialist care.

Evaluation of Cloud and Aerosol Screening of Early Orbiting Carbon Observatory-2 (OCO-2) Observations with Collocated MODIS Cloud Mask

NASA Astrophysics Data System (ADS)

Nelson, R. R.; Taylor, T.; O'Dell, C.; Cronk, H. Q.; Partain, P.; Frankenberg, C.; Eldering, A.; Crisp, D.; Gunson, M. R.; Chang, A.; Fisher, B.; Osterman, G. B.; Pollock, H. R.; Savtchenko, A.; Rosenthal, E. J.

2015-12-01

Effective cloud and aerosol screening is critically important to the Orbiting Carbon Observatory-2 (OCO-2), which can accurately determine column averaged dry air mole fraction of carbon dioxide (XCO2) only when scenes are sufficiently clear of scattering material. It is crucial to avoid sampling biases, in order to maintain a globally unbiased XCO2 record for inversion modeling to determine sources and sinks of carbon dioxide. This work presents analysis from the current operational B7 data set, which is identifying as clear approximately 20% of the order one million daily soundings. Of those soundings that are passed to the L2 retrieval algorithm, we find that almost 80% are yielding XCO2 estimates that converge. Two primary preprocessor algorithms are used to cloud screen the OCO-2 soundings. The A-Band Preprocessor (ABP) uses measurements in the Oxygen-A band near 0.76 microns (mm) to determine scenes with large photon path length modifications due to scattering by aerosol and clouds. The Iterative Maximum A-Posteriori (IMAP) Differential Optical Absorption Spectroscopy (DOAS) algorithm (IDP) computes ratios of retrieved CO2 (and H2O) in the 1.6mm (weak CO2) and 2.0mm (strong CO2) spectral bands to determine scenes with spectral differences, indicating contamination by scattering materials. We demonstrate that applying these two algorithms in tandem provides robust cloud screening of the OCO-2 data set. We compare the OCO-2 cloud screening results to collocated Moderate Resolution Imaging Spectroradiometer (MODIS) cloud mask data and show that agreement between the two sensors is approximately 85-90%. A detailed statistical analysis is performed on a winter and spring 16-day repeat cycle for the nadir-land, glint-land and glint-water viewing geometries. No strong seasonal, spatial or footprint dependencies are found, although the agreement tends to be worse at high solar zenith angles and for snow and ice covered surfaces.

Characterizing the O-glycosylation landscape of human plasma, platelets, and endothelial cells

PubMed Central

King, Sarah L.; Joshi, Hiren J.; Schjoldager, Katrine T.; Halim, Adnan; Madsen, Thomas D.; Dziegiel, Morten H.; Woetmann, Anders; Vakhrushev, Sergey Y.

2017-01-01

The hemostatic system comprises platelet aggregation, coagulation, and fibrinolysis, and is critical to the maintenance of vascular integrity. Multiple studies indicate that glycans play important roles in the hemostatic system; however, most investigations have focused on N-glycans because of the complexity of O-glycan analysis. Here we performed the first systematic analysis of native-O-glycosylation using lectin affinity chromatography coupled to liquid chromatography mass spectrometry (LC-MS)/MS to determine the precise location of O-glycans in human plasma, platelets, and endothelial cells, which coordinately regulate hemostasis. We identified the hitherto largest O-glycoproteome from native tissue with a total of 649 glycoproteins and 1123 nonambiguous O-glycosites, demonstrating that O-glycosylation is a ubiquitous modification of extracellular proteins. Investigation of the general properties of O-glycosylation established that it is a heterogeneous modification, frequently occurring at low density within disordered regions in a cell-dependent manner. Using an unbiased screen to identify associations between O-glycosites and protein annotations we found that O-glycans were over-represented close (± 15 amino acids) to tandem repeat regions, protease cleavage sites, within propeptides, and located on a select group of protein domains. The importance of O-glycosites in proximity to proteolytic cleavage sites was further supported by in vitro peptide assays demonstrating that proteolysis of key hemostatic proteins can be inhibited by the presence of O-glycans. Collectively, these data illustrate the global properties of native O-glycosylation and provide the requisite roadmap for future biomarker and structure-function studies. PMID:29296958

How can the uptake of cervical cytology screening be improved?

PubMed

Perry, M A

Cervical cancer remains a killer, despite a screening programme designed to detect cases in the early stages of development. A number of factors appear to influence a woman's decision to attend for a smear test. This literature review considers these factors, and whether nurses can play a part in reducing the death rate by dispelling the misapprehensions and misinformation that deter vulnerable women from attending. There is a great need for modification and improvement of the present screening programme if all women who are at risk from cervical cancer are to be encouraged to attend for screening. The attitude of those who conduct smear tests is often crucial in gaining women's confidence--an unpleasant experience might deter a patient from attending again. Other barriers to attendance include administrative errors and lack of knowledge. Given the impact of mass advertising and health promotion campaigns in other areas, such as smoking cessation, there is clearly a need for a similar strategy to be applied to cervical screening.

School-Based Screening for Suicide Risk: Balancing Costs and Benefits

PubMed Central

Wilcox, Holly; Huo, Yanling; Turner, J. Blake; Fisher, Prudence; Shaffer, David

2010-01-01

Objectives. We examined the effects of a scoring algorithm change on the burden and sensitivity of a screen for adolescent suicide risk. Methods. The Columbia Suicide Screen was used to screen 641 high school students for high suicide risk (recent ideation or lifetime attempt and depression, or anxiety, or substance use), determined by subsequent blind assessment with the Diagnostic Interview Schedule for Children. We compared the accuracy of different screen algorithms in identifying high-risk cases. Results. A screen algorithm comprising recent ideation or lifetime attempt or depression, anxiety, or substance-use problems set at moderate-severity level classed 35% of students as positive and identified 96% of high-risk students. Increasing the algorithm's threshold reduced the proportion identified to 24% and identified 92% of high-risk cases. Asking only about recent suicidal ideation or lifetime suicide attempt identified 17% of the students and 89% of high-risk cases. The proportion of nonsuicidal diagnosis–bearing students found with the 3 algorithms was 62%, 34%, and 12%, respectively. Conclusions. The Columbia Suicide Screen threshold can be altered to reduce the screen-positive population, saving costs and time while identifying almost all students at high risk for suicide. PMID:20634467

Risk analysis of analytical validations by probabilistic modification of FMEA.

PubMed

Barends, D M; Oldenhof, M T; Vredenbregt, M J; Nauta, M J

2012-05-01

Risk analysis is a valuable addition to validation of an analytical chemistry process, enabling not only detecting technical risks, but also risks related to human failures. Failure Mode and Effect Analysis (FMEA) can be applied, using a categorical risk scoring of the occurrence, detection and severity of failure modes, and calculating the Risk Priority Number (RPN) to select failure modes for correction. We propose a probabilistic modification of FMEA, replacing the categorical scoring of occurrence and detection by their estimated relative frequency and maintaining the categorical scoring of severity. In an example, the results of traditional FMEA of a Near Infrared (NIR) analytical procedure used for the screening of suspected counterfeited tablets are re-interpretated by this probabilistic modification of FMEA. Using this probabilistic modification of FMEA, the frequency of occurrence of undetected failure mode(s) can be estimated quantitatively, for each individual failure mode, for a set of failure modes, and the full analytical procedure. Copyright © 2012 Elsevier B.V. All rights reserved.

Ultrasensitive Direct Quantification of Nucleobase Modifications in DNA by Surface-Enhanced Raman Scattering: The Case of Cytosine.

PubMed

Morla-Folch, Judit; Xie, Hai-nan; Gisbert-Quilis, Patricia; Gómez-de Pedro, Sara; Pazos-Perez, Nicolas; Alvarez-Puebla, Ramon A; Guerrini, Luca

2015-11-09

Recognition of chemical modifications in canonical nucleobases of nucleic acids is of key importance since such modified variants act as different genetic encoders, introducing variability in the biological information contained in DNA. Herein, we demonstrate the feasibility of direct SERS in combination with chemometrics and microfluidics for the identification and relative quantification of 4 different cytosine modifications in both single- and double-stranded DNA. The minute amount of DNA required per measurement, in the sub-nanogram regime, removes the necessity of pre-amplification or enrichment steps (which are also potential sources of artificial DNA damages). These findings show great potentials for the development of fast, low-cost and high-throughput screening analytical devices capable of detecting known and unknown modifications in nucleic acids (DNA and RNA) opening new windows of activity in several fields such as biology, medicine and forensic sciences. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Modification of the mycotoxin deoxynivalenol using microorganisms isolated from environmental samples

USDA-ARS?s Scientific Manuscript database

The trichothecene mycotoxin deoxynivalenol (DON) is a common contaminant of wheat, barley, and maize. New strategies are needed to reduce or eliminate DON in feed and food products. Microorganisms from plant and soil samples collected in Blacksburg, VA, USA, were screened by incubation in a mineral ...

Advanced Gas Turbine (AGT) powertrain system development for automotive applications

NASA Technical Reports Server (NTRS)

1982-01-01

Topics covered include the AGT 101 engine test; compressor design modification; cold air turbine testing; Mod 1 alloy turbine rotor fabrication; combustion aspects; regenerator development; and thermal screening tests for ceramic materials. The foil gas bearings, rotor dynamics, and AGT controls and accessories are also considered.

How-to-Do-It: Further Improvements to the Steucek & Hill Assay of Photosynthesis.

ERIC Educational Resources Information Center

Juliao, Fernando; Butcher, Henry C., IV

1989-01-01

Several modifications that improve upon the assay of photosynthesis are suggested. Described are the apparatus, materials, light intensity and photosynthesis measurements, and results. A table of the average light intensity values versus the screen number and a sketch of the experimental set-up is included. (RT)

Cultural Context and Modification of Behavior Change Theory

ERIC Educational Resources Information Center

Sanders Thompson, Vetta L.

2009-01-01

Although social and cultural contexts act on each level of the multilevel ecologic model to affect cancer risk, health behavior, and cancer screening and promotion in health behavior research, people have yet to develop theories that sufficiently integrate the social and environmental context with group and individual behavior. The "Behavioral…

Process relevant screening of cellulolytic organisms for consolidated bioprocessing.

PubMed

Antonov, Elena; Schlembach, Ivan; Regestein, Lars; Rosenbaum, Miriam A; Büchs, Jochen

2017-01-01

Although the biocatalytic conversion of cellulosic biomass could replace fossil oil for the production of various compounds, it is often not economically viable due to the high costs of cellulolytic enzymes. One possibility to reduce costs is consolidated bioprocessing (CBP), integrating cellulase production, hydrolysis of cellulose, and the fermentation of the released sugars to the desired product into one process step. To establish such a process, the most suitable cellulase-producing organism has to be identified. Thereby, it is crucial to evaluate the candidates under target process conditions. In this work, the chosen model process was the conversion of cellulose to the platform chemical itaconic acid by a mixed culture of a cellulolytic fungus with Aspergillus terreus as itaconic acid producer. Various cellulase producers were analyzed by the introduced freeze assay that measures the initial carbon release rate, quantifying initial cellulase activity under target process conditions. Promising candidates were then characterized online by monitoring their respiration activity metabolizing cellulose to assess the growth and enzyme production dynamics. The screening of five different cellulase producers with the freeze assay identified Trichoderma   reesei and Penicillium   verruculosum as most promising. The measurement of the respiration activity revealed a retarded induction of cellulase production for P.   verruculosum but a similar cellulase production rate afterwards, compared to T.   reesei . The freeze assay measurement depicted that P.   verruculosum reaches the highest initial carbon release rate among all investigated cellulase producers. After a modification of the cultivation procedure, these results were confirmed by the respiration activity measurement. To compare both methods, a correlation between the measured respiration activity and the initial carbon release rate of the freeze assay was introduced. The analysis revealed that the different initial enzyme/cellulose ratios as well as a discrepancy in cellulose digestibility are the main differences between the two approaches. With two complementary methods to quantify cellulase activity and the dynamics of cellulase production for CBP applications, T.   reesei and P.   verruculosum were identified as compatible candidates for the chosen model process. The presented methods can easily be adapted to screen for suitable cellulose degrading organisms for various other applications.

A simple ergonomic measure reduces fluoroscopy time during ERCP: A multivariate analysis.

PubMed

Jowhari, Fahd; Hopman, Wilma M; Hookey, Lawrence

2017-03-01

Background and study aims  Endoscopic retrograde cholangiopancreatgraphy (ERCP) carries a radiation risk to patients undergoing the procedure and the team performing it. Fluoroscopy time (FT) has been shown to have a linear relationship with radiation exposure during ERCP. Recent modifications to our ERCP suite design were felt to impact fluoroscopy time and ergonomics. This multivariate analysis was therefore undertaken to investigate these effects, and to identify and validate various clinical, procedural and ergonomic factors influencing the total fluoroscopy time during ERCP. This would better assist clinicians with predicting prolonged fluoroscopic durations and to undertake relevant precautions accordingly. Patients and methods  A retrospective analysis of 299 ERCPs performed by 4 endoscopists over an 18-month period, at a single tertiary care center was conducted. All inpatients/outpatients (121 males, 178 females) undergoing ERCP for any clinical indication from January 2012 to June 2013 in the chosen ERCP suite were included in the study. Various predetermined clinical, procedural and ergonomic factors were obtained via chart review. Univariate analyses identified factors to be included in the multivariate regression model with FT as the dependent variable. Results  Bringing the endoscopy and fluoroscopy screens next to each other was associated with a significantly lesser FT than when the screens were separated further (-1.4 min, P  = 0.026). Other significant factors associated with a prolonged FT included having a prior ERCP (+ 1.4 min, P  = 0.031), and more difficult procedures (+ 4.2 min for each level of difficulty, P  < 0.001). ERCPs performed by high-volume endoscopists used lesser FT vs. low-volume endoscopists (-1.82, P = 0.015). Conclusions  Our study has identified and validated various factors that affect the total fluoroscopy time during ERCP. This is the first study to show that decreasing the distance between the endoscopy and fluoroscopy screens in the ERCP suite significantly reduces the total fluoroscopy time, and therefore radiation exposure to patients and staff involved in the procedure.

LIFECHECK: a successful, low touch, low tech, in-plant, cardiovascular disease risk identification and modification program.

PubMed

Henritze, J; Brammell, H L; McGloin, J

1992-01-01

LIFECHECK, a voluntary, in-plant cardiovascular risk identification and modification program, was developed to complement Coors Wellness Center-based programs. LIFECHECK was offered to the 1,320 employees located at the Coors Engineering Center and Can Manufacturing Complex at the Coors Brewing Company. The initial 30-minute screening included height, weight, blood pressure, cholesterol, smoking history, weekly Kcal expenditure, self-rating of health, and health effects of stress. Participants concluded the screening session with a wellness counselor who reviewed results and referred them to the appropriate intervention activities. The eight-week intervention was provided at the worksite and was available to all shifts. The intervention included an activity competition and activity classes; nutrition, hypertension, smoking, and lipid classes; a smoke-out day; one-on-one counseling; exercise equipment at four worksites; posters; traymats; table tents; and electronic messages. A total of 692 employees, 52% of those eligible, participated in the initial screening. Of these, 91% had one or more risk factors, and 33% had three to five cardiovascular disease risk factors. A total of 499 employees, 72% of those eligible, completed the follow-up screening. Thirty-two percent of the employees who participated in LIFECHECK had not used the Wellness Center in the eight years it had been open. There were significant changes in employees who completed the eight-week program for systolic blood pressure, total cholesterol, weight, physical activity, and risk of ischemic heart disease within eight years as measured by the Framingham score (p less than 0.05).(ABSTRACT TRUNCATED AT 250 WORDS)

Identification of drug interactions in hospitals--computerized screening vs. bedside recording.

PubMed

Blix, H S; Viktil, K K; Moger, T A; Reikvam, A

2008-04-01

Managing drug interactions in hospitalized patients is important and challenging. The objective of the study was to compare two methods for identification of drug interactions (DDIs)--computerized screening and prospective bedside recording--with regard to capability of identifying DDIs. Patient characteristics were recorded for patients admitted to five hospitals. By bedside evaluation drug-related problems, including DDIs, were prospectively recorded by pharmacists and discussed in multidisciplinary teams. A computer screening programme was used to identify DDIs retrospectively--dividing DDIs into four classes: A, avoid; B, avoid/take precautions; C, take precautions; D, no action needed. Among 827 patients, computer screening identified DDIs in 544 patients (66%); 351 had DDIs introduced in hospital. The 1513 computer-identified DDIs had the following distribution: type A 78; type B 915; type C 38; type D 482. By bedside evaluation, 99 DDIs were identified in 73 patients (9%). The proportions of computer recorded DDIs which were also identified at the bedside were: 5%, 8%, 8%, 2% DDIs of types A, B, C and D respectively. In 10 patients, DDIs not registered by computer screening were identified by bedside evaluation. The drugs most frequently involved in DDIs, identified by computerized screening were acetylsalicylic acid, warfarin, furosemide and digitoxin compared with warfarin, simvastatin, theophylline and carbamazepine, by bedside evaluation. Despite an active prospective bedside search for DDIs, this approach identified less than one in 10 of the DDIs recorded by computer screening, including those regarded as hazardous. However, computer screening overestimates considerably when the objective is to identify clinically relevant DDIs.

RNA-ID, a Powerful Tool for Identifying and Characterizing Regulatory Sequences.

PubMed

Brule, C E; Dean, K M; Grayhack, E J

2016-01-01

The identification and analysis of sequences that regulate gene expression is critical because regulated gene expression underlies biology. RNA-ID is an efficient and sensitive method to discover and investigate regulatory sequences in the yeast Saccharomyces cerevisiae, using fluorescence-based assays to detect green fluorescent protein (GFP) relative to a red fluorescent protein (RFP) control in individual cells. Putative regulatory sequences can be inserted either in-frame or upstream of a superfolder GFP fusion protein whose expression, like that of RFP, is driven by the bidirectional GAL1,10 promoter. In this chapter, we describe the methodology to identify and study cis-regulatory sequences in the RNA-ID system, explaining features and variations of the RNA-ID reporter, as well as some applications of this system. We describe in detail the methods to analyze a single regulatory sequence, from construction of a single GFP variant to assay of variants by flow cytometry, as well as modifications required to screen libraries of different strains simultaneously. We also describe subsequent analyses of regulatory sequences. © 2016 Elsevier Inc. All rights reserved.

Meat consumption as a risk factor for type 2 diabetes.

PubMed

Barnard, Neal; Levin, Susan; Trapp, Caroline

2014-02-21

Disease risk factors identified in epidemiological studies serve as important public health tools, helping clinicians identify individuals who may benefit from more aggressive screening or risk-modification procedures, allowing policymakers to prioritize intervention programs, and encouraging at-risk individuals to modify behavior and improve their health. These factors have been based primarily on evidence from cross-sectional and prospective studies, as most do not lend themselves to randomized trials. While some risk factors are not modifiable, eating habits are subject to change through both individual action and broader policy initiatives. Meat consumption has been frequently investigated as a variable associated with diabetes risk, but it has not yet been described as a diabetes risk factor. In this article, we evaluate the evidence supporting the use of meat consumption as a clinically useful risk factor for type 2 diabetes, based on studies evaluating the risks associated with meat consumption as a categorical dietary characteristic (i.e., meat consumption versus no meat consumption), as a scalar variable (i.e., gradations of meat consumption), or as part of a broader dietary pattern.

Structural basis of O-GlcNAc recognition by mammalian 14-3-3 proteins.

PubMed

Toleman, Clifford A; Schumacher, Maria A; Yu, Seok-Ho; Zeng, Wenjie; Cox, Nathan J; Smith, Timothy J; Soderblom, Erik J; Wands, Amberlyn M; Kohler, Jennifer J; Boyce, Michael

2018-06-05

O-GlcNAc is an intracellular posttranslational modification that governs myriad cell biological processes and is dysregulated in human diseases. Despite this broad pathophysiological significance, the biochemical effects of most O-GlcNAcylation events remain uncharacterized. One prevalent hypothesis is that O-GlcNAc moieties may be recognized by "reader" proteins to effect downstream signaling. However, no general O-GlcNAc readers have been identified, leaving a considerable gap in the field. To elucidate O-GlcNAc signaling mechanisms, we devised a biochemical screen for candidate O-GlcNAc reader proteins. We identified several human proteins, including 14-3-3 isoforms, that bind O-GlcNAc directly and selectively. We demonstrate that 14-3-3 proteins bind O-GlcNAc moieties in human cells, and we present the structures of 14-3-3β/α and γ bound to glycopeptides, providing biophysical insights into O-GlcNAc-mediated protein-protein interactions. Because 14-3-3 proteins also bind to phospho-serine and phospho-threonine, they may integrate information from O-GlcNAc and O-phosphate signaling pathways to regulate numerous physiological functions.

Meat Consumption as a Risk Factor for Type 2 Diabetes

PubMed Central

Barnard, Neal; Levin, Susan; Trapp, Caroline

2014-01-01

Disease risk factors identified in epidemiological studies serve as important public health tools, helping clinicians identify individuals who may benefit from more aggressive screening or risk-modification procedures, allowing policymakers to prioritize intervention programs, and encouraging at-risk individuals to modify behavior and improve their health. These factors have been based primarily on evidence from cross-sectional and prospective studies, as most do not lend themselves to randomized trials. While some risk factors are not modifiable, eating habits are subject to change through both individual action and broader policy initiatives. Meat consumption has been frequently investigated as a variable associated with diabetes risk, but it has not yet been described as a diabetes risk factor. In this article, we evaluate the evidence supporting the use of meat consumption as a clinically useful risk factor for type 2 diabetes, based on studies evaluating the risks associated with meat consumption as a categorical dietary characteristic (i.e., meat consumption versus no meat consumption), as a scalar variable (i.e., gradations of meat consumption), or as part of a broader dietary pattern. PMID:24566443

Enzyme-substrate relationships in the ubiquitin system: approaches for identifying substrates of ubiquitin ligases.

PubMed

O'Connor, Hazel F; Huibregtse, Jon M

2017-09-01

Protein ubiquitylation is an important post-translational modification, regulating aspects of virtually every biochemical pathway in eukaryotic cells. Hundreds of enzymes participate in the conjugation and deconjugation of ubiquitin, as well as the recognition, signaling functions, and degradation of ubiquitylated proteins. Regulation of ubiquitylation is most commonly at the level of recognition of substrates by E3 ubiquitin ligases. Characterization of the network of E3-substrate relationships is a major goal and challenge in the field, as this expected to yield fundamental biological insights and opportunities for drug development. There has been remarkable success in identifying substrates for some E3 ligases, in many instances using the standard protein-protein interaction techniques (e.g., two-hybrid screens and co-immunoprecipitations paired with mass spectrometry). However, some E3s have remained refractory to characterization, while others have simply not yet been studied due to the sheer number and diversity of E3s. This review will discuss the range of tools and techniques that can be used for substrate profiling of E3 ligases.

Ergot Alkaloids (Re)generate New Leads as Antiparasitics

PubMed Central

Chan, John D.; Agbedanu, Prince N.; Grab, Thomas; Zamanian, Mostafa; Dosa, Peter I.; Day, Timothy A.; Marchant, Jonathan S.

2015-01-01

Abstract Praziquantel (PZQ) is a key therapy for treatment of parasitic flatworm infections of humans and livestock, but the mechanism of action of this drug is unresolved. Resolving PZQ-engaged targets and effectors is important for identifying new druggable pathways that may yield novel antiparasitic agents. Here we use functional, genetic and pharmacological approaches to reveal that serotonergic signals antagonize PZQ action in vivo. Exogenous 5-hydroxytryptamine (5-HT) rescued PZQ-evoked polarity and mobility defects in free-living planarian flatworms. In contrast, knockdown of a prevalently expressed planarian 5-HT receptor potentiated or phenocopied PZQ action in different functional assays. Subsequent screening of serotonergic ligands revealed that several ergot alkaloids possessed broad efficacy at modulating regenerative outcomes and the mobility of both free living and parasitic flatworms. Ergot alkaloids that phenocopied PZQ in regenerative assays to cause bipolar regeneration exhibited structural modifications consistent with serotonergic blockade. These data suggest that serotonergic activation blocks PZQ action in vivo, while serotonergic antagonists phenocopy PZQ action. Importantly these studies identify the ergot alkaloid scaffold as a promising structural framework for designing potent agents targeting parasitic bioaminergic G protein coupled receptors. PMID:26367744

Technical standards and guidelines: prenatal screening for Down syndrome that includes first-trimester biochemistry and/or ultrasound measurements.

PubMed

Palomaki, Glenn E; Lee, Jo Ellen S; Canick, Jacob A; McDowell, Geraldine A; Donnenfeld, Alan E

2009-09-01

This statement is intended to augment the current general ACMG Standards and Guidelines for Clinical Genetics Laboratories and to address guidelines specific to first-trimester screening for Down syndrome. The aim is to provide the laboratory the necessary information to ensure accurate and reliable Down syndrome screening results given a screening protocol (e.g., combined first trimester and integrated testing). Information about various test combinations and their expected performance are provided, but other issues such as availability of reagents, patient interest in early test results, access to open neural tube defect screening, and availability of chorionic villus sampling are all contextual factors in deciding which screening protocol(s) will be selected by individual health care providers. Individual laboratories are responsible for meeting the quality assurance standards described by the Clinical Laboratory Improvement Act, the College of American Pathologists, and other regulatory agencies, with respect to appropriate sample documentation, assay validation, general proficiency, and quality control measures. These guidelines address first-trimester screening that includes ultrasound measurement and interpretation of nuchal translucency thickness and protocols that combine markers from both the first and second trimesters. Laboratories can use their professional judgment to make modification or additions.

Energy dependence of J/ψ production in Au + Au collisions at √{sNN} = 39 , 62.4 and 200GeV

NASA Astrophysics Data System (ADS)

Adamczyk, L.; Adkins, J. K.; Agakishiev, G.; Aggarwal, M. M.; Ahammed, Z.; Ajitanand, N. N.; Alekseev, I.; Anderson, D. M.; Aoyama, R.; Aparin, A.; Arkhipkin, D.; Aschenauer, E. C.; Ashraf, M. U.; Attri, A.; Averichev, G. S.; Bai, X.; Bairathi, V.; Behera, A.; Bellwied, R.; Bhasin, A.; Bhati, A. K.; Bhattarai, P.; Bielcik, J.; Bielcikova, J.; Bland, L. C.; Bordyuzhin, I. G.; Bouchet, J.; Brandenburg, J. D.; Brandin, A. V.; Brown, D.; Bunzarov, I.; Butterworth, J.; Caines, H.; Calderón de la Barca Sánchez, M.; Campbell, J. M.; Cebra, D.; Chakaberia, I.; Chaloupka, P.; Chang, Z.; Chankova-Bunzarova, N.; Chatterjee, A.; Chattopadhyay, S.; Chen, X.; Chen, J. H.; Chen, X.; Cheng, J.; Cherney, M.; Christie, W.; Contin, G.; Crawford, H. J.; Das, S.; De Silva, L. C.; Debbe, R. R.; Dedovich, T. G.; Deng, J.; Derevschikov, A. A.; Didenko, L.; Dilks, C.; Dong, X.; Drachenberg, J. L.; Draper, J. E.; Dunkelberger, L. E.; Dunlop, J. C.; Efimov, L. G.; Elsey, N.; Engelage, J.; Eppley, G.; Esha, R.; Esumi, S.; Evdokimov, O.; Ewigleben, J.; Eyser, O.; Fatemi, R.; Fazio, S.; Federic, P.; Federicova, P.; Fedorisin, J.; Feng, Z.; Filip, P.; Finch, E.; Fisyak, Y.; Flores, C. E.; Fujita, J.; Fulek, L.; Gagliardi, C. A.; Garand, D.; Geurts, F.; Gibson, A.; Girard, M.; Grosnick, D.; Gunarathne, D. S.; Guo, Y.; Gupta, A.; Gupta, S.; Guryn, W.; Hamad, A. I.; Hamed, A.; Harlenderova, A.; Harris, J. W.; He, L.; Heppelmann, S.; Heppelmann, S.; Hirsch, A.; Hoffmann, G. W.; Horvat, S.; Huang, B.; Huang, H. Z.; Huang, T.; Huang, X.; Humanic, T. J.; Huo, P.; Igo, G.; Jacobs, W. W.; Jentsch, A.; Jia, J.; Jiang, K.; Jowzaee, S.; Judd, E. G.; Kabana, S.; Kalinkin, D.; Kang, K.; Kauder, K.; Ke, H. W.; Keane, D.; Kechechyan, A.; Khan, Z.; Kikoła, D. P.; Kisel, I.; Kisiel, A.; Kochenda, L.; Kocmanek, M.; Kollegger, T.; Kosarzewski, L. K.; Kraishan, A. F.; Kravtsov, P.; Krueger, K.; Kulathunga, N.; Kumar, L.; Kvapil, J.; Kwasizur, J. H.; Lacey, R.; Landgraf, J. M.; Landry, K. D.; Lauret, J.; Lebedev, A.; Lednicky, R.; Lee, J. H.; Li, Y.; Li, X.; Li, W.; Li, C.; Lidrych, J.; Lin, T.; Lisa, M. A.; Liu, Y.; Liu, H.; Liu, F.; Liu, P.; Ljubicic, T.; Llope, W. J.; Lomnitz, M.; Longacre, R. S.; Luo, S.; Luo, X.; Ma, G. L.; Ma, L.; Ma, Y. G.; Ma, R.; Magdy, N.; Majka, R.; Mallick, D.; Margetis, S.; Markert, C.; Matis, H. S.; Meehan, K.; Mei, J. C.; Miller, Z. W.; Minaev, N. G.; Mioduszewski, S.; Mishra, D.; Mizuno, S.; Mohanty, B.; Mondal, M. M.; Morozov, D. A.; Mustafa, M. K.; Nasim, Md.; Nayak, T. K.; Nelson, J. M.; Nie, M.; Nigmatkulov, G.; Niida, T.; Nogach, L. V.; Nonaka, T.; Nurushev, S. B.; Odyniec, G.; Ogawa, A.; Oh, K.; Okorokov, V. A.; Olvitt, D.; Page, B. S.; Pak, R.; Pandit, Y.; Panebratsev, Y.; Pawlik, B.; Pei, H.; Perkins, C.; Pile, P.; Pluta, J.; Poniatowska, K.; Porter, J.; Posik, M.; Pruthi, N. K.; Przybycien, M.; Putschke, J.; Qiu, H.; Quintero, A.; Ramachandran, S.; Ray, R. L.; Reed, R.; Rehbein, M. J.; Ritter, H. G.; Roberts, J. B.; Rogachevskiy, O. V.; Romero, J. L.; Roth, J. D.; Ruan, L.; Rusnak, J.; Rusnakova, O.; Sahoo, N. R.; Sahu, P. K.; Salur, S.; Sandweiss, J.; Saur, M.; Schambach, J.; Schmah, A. M.; Schmidke, W. B.; Schmitz, N.; Schweid, B. R.; Seger, J.; Sergeeva, M.; Seyboth, P.; Shah, N.; Shahaliev, E.; Shanmuganathan, P. V.; Shao, M.; Sharma, A.; Sharma, M. K.; Shen, W. Q.; Shi, S. S.; Shi, Z.; Shou, Q. Y.; Sichtermann, E. P.; Sikora, R.; Simko, M.; Singha, S.; Skoby, M. J.; Smirnov, N.; Smirnov, D.; Solyst, W.; Song, L.; Sorensen, P.; Spinka, H. M.; Srivastava, B.; Stanislaus, T. D. S.; Strikhanov, M.; Stringfellow, B.; Sugiura, T.; Sumbera, M.; Summa, B.; Sun, X.; Sun, Y.; Sun, X. M.; Surrow, B.; Svirida, D. N.; Tang, A. H.; Tang, Z.; Taranenko, A.; Tarnowsky, T.; Tawfik, A.; Thäder, J.; Thomas, J. H.; Timmins, A. R.; Tlusty, D.; Todoroki, T.; Tokarev, M.; Trentalange, S.; Tribble, R. E.; Tribedy, P.; Tripathy, S. K.; Trzeciak, B. A.; Tsai, O. D.; Ullrich, T.; Underwood, D. G.; Upsal, I.; Van Buren, G.; van Nieuwenhuizen, G.; Vasiliev, A. N.; Videbæk, F.; Vokal, S.; Voloshin, S. A.; Vossen, A.; Wang, G.; Wang, Y.; Wang, F.; Wang, Y.; Webb, J. C.; Webb, G.; Wen, L.; Westfall, G. D.; Wieman, H.; Wissink, S. W.; Witt, R.; Wu, Y.; Xiao, Z. G.; Xie, W.; Xie, G.; Xu, J.; Xu, N.; Xu, Q. H.; Xu, Y. F.; Xu, Z.; Yang, Y.; Yang, Q.; Yang, C.; Yang, S.; Ye, Z.; Ye, Z.; Yi, L.; Yip, K.; Yoo, I.-K.; Yu, N.; Zbroszczyk, H.; Zha, W.; Zhang, Z.; Zhang, X. P.; Zhang, J. B.; Zhang, S.; Zhang, J.; Zhang, Y.; Zhang, J.; Zhang, S.; Zhao, J.; Zhong, C.; Zhou, L.; Zhou, C.; Zhu, X.; Zhu, Z.; Zyzak, M.; STAR Collaboration

2017-08-01

The inclusive J / ψ transverse momentum spectra and nuclear modification factors are reported at mid-rapidity (| y | < 1.0) in Au + Au collisions at √{sNN} = 39, 62.4 and 200 GeV taken by the STAR experiment. A suppression of J / ψ production, with respect to the production in p + p scaled by the number of binary nucleon-nucleon collisions, is observed in central Au + Au collisions at these three energies. No significant energy dependence of nuclear modification factors is found within uncertainties. The measured nuclear modification factors can be described by model calculations that take into account both suppression of direct J / ψ production due to the color screening effect and J / ψ regeneration from recombination of uncorrelated charm-anticharm quark pairs.

Simple modification of basic dyes with bulky &symmetric WCAs for improving their solubilities in organic solvents without color change.

PubMed

Kim, Jeong Yun; Hwang, Tae Gyu; Woo, Sung Wun; Lee, Jae Moon; Namgoong, Jin Woong; Yuk, Sim Bum; Chung, Sei-Won; Kim, Jae Pil

2017-04-06

A simple and easy solubility enhancement of basic dyes was performed with bulky and symmetric weakly coordinating anions (WCAs). The WCAs decreased the ionic character of the dyes by broadening the partial charge distribution and causing a screening effect on the ionic bonding. This new modification with WCAs has advantages in that it has no influence on the optical properties of the dyes. The solubilities of unmodified and modified dyes were tested in several organic solvents. X-ray powder diffraction patterns of the dyes were measured. Color films were prepared with the dyes and their color loci were analyzed to evaluate the optical properties. By the modification with WCAs, commercial basic dyes showed sufficient solubilities for be applied to various applications while preserving their superior optical properties.

A Systematic Evaluation of Field-Based Screening Methods for the Assessment of Anterior Cruciate Ligament (ACL) Injury Risk.

PubMed

Fox, Aaron S; Bonacci, Jason; McLean, Scott G; Spittle, Michael; Saunders, Natalie

2016-05-01

Laboratory-based measures provide an accurate method to identify risk factors for anterior cruciate ligament (ACL) injury; however, these methods are generally prohibitive to the wider community. Screening methods that can be completed in a field or clinical setting may be more applicable for wider community use. Examination of field-based screening methods for ACL injury risk can aid in identifying the most applicable method(s) for use in these settings. The objective of this systematic review was to evaluate and compare field-based screening methods for ACL injury risk to determine their efficacy of use in wider community settings. An electronic database search was conducted on the SPORTDiscus™, MEDLINE, AMED and CINAHL databases (January 1990-July 2015) using a combination of relevant keywords. A secondary search of the same databases, using relevant keywords from identified screening methods, was also undertaken. Studies identified as potentially relevant were independently examined by two reviewers for inclusion. Where consensus could not be reached, a third reviewer was consulted. Original research articles that examined screening methods for ACL injury risk that could be undertaken outside of a laboratory setting were included for review. Two reviewers independently assessed the quality of included studies. Included studies were categorized according to the screening method they examined. A description of each screening method, and data pertaining to the ability to prospectively identify ACL injuries, validity and reliability, recommendations for identifying 'at-risk' athletes, equipment and training required to complete screening, time taken to screen athletes, and applicability of the screening method across sports and athletes were extracted from relevant studies. Of 1077 citations from the initial search, a total of 25 articles were identified as potentially relevant, with 12 meeting all inclusion/exclusion criteria. From the secondary search, eight further studies met all criteria, resulting in 20 studies being included for review. Five ACL-screening methods-the Landing Error Scoring System (LESS), Clinic-Based Algorithm, Observational Screening of Dynamic Knee Valgus (OSDKV), 2D-Cam Method, and Tuck Jump Assessment-were identified. There was limited evidence supporting the use of field-based screening methods in predicting ACL injuries across a range of populations. Differences relating to the equipment and time required to complete screening methods were identified. Only screening methods for ACL injury risk were included for review. Field-based screening methods developed for lower-limb injury risk in general may also incorporate, and be useful in, screening for ACL injury risk. Limited studies were available relating to the OSDKV and 2D-Cam Method. The LESS showed predictive validity in identifying ACL injuries, however only in a youth athlete population. The LESS also appears practical for community-wide use due to the minimal equipment and set-up/analysis time required. The Clinic-Based Algorithm may have predictive value for ACL injury risk as it identifies athletes who exhibit high frontal plane knee loads during a landing task, but requires extensive additional equipment and time, which may limit its application to wider community settings.

A comprehensive algorithm for determining whether a run-in strategy will be a cost-effective design modification in a randomized clinical trial.

PubMed

Schechtman, K B; Gordon, M E

1993-01-30

In randomized clinical trials, poor compliance and treatment intolerance lead to reduced between-group differences, increased sample size requirements, and increased cost. A run-in strategy is intended to reduce these problems. In this paper, we develop a comprehensive set of measures specifically sensitive to the effect of a run-in on cost and sample size requirements, both before and after randomization. Using these measures, we describe a step-by-step algorithm through which one can estimate the cost-effectiveness of a potential run-in. Because the cost-effectiveness of a run-in is partly mediated by its effect on sample size, we begin by discussing the likely impact of a planned run-in on the required number of randomized, eligible, and screened subjects. Run-in strategies are most likely to be cost-effective when: (1) per patient costs during the post-randomization as compared to the screening period are high; (2) poor compliance is associated with a substantial reduction in response to treatment; (3) the number of screened patients needed to identify a single eligible patient is small; (4) the run-in is inexpensive; (5) for most patients, the run-in compliance status is maintained following randomization and, most importantly, (6) many subjects excluded by the run-in are treatment intolerant or non-compliant to the extent that we expect little or no treatment response. Our analysis suggests that conditions for the cost-effectiveness of run-in strategies are stringent. In particular, if the only purpose of a run-in is to exclude ordinary partial compliers, the run-in will frequently add to the cost of the trial. Often, the cost-effectiveness of a run-in requires that one can identify and exclude a substantial number of treatment intolerant or otherwise unresponsive subjects.

Applying operations research to optimize a novel population management system for cancer screening.

PubMed

Zai, Adrian H; Kim, Seokjin; Kamis, Arnold; Hung, Ken; Ronquillo, Jeremiah G; Chueh, Henry C; Atlas, Steven J

2014-02-01

To optimize a new visit-independent, population-based cancer screening system (TopCare) by using operations research techniques to simulate changes in patient outreach staffing levels (delegates, navigators), modifications to user workflow within the information technology (IT) system, and changes in cancer screening recommendations. TopCare was modeled as a multiserver, multiphase queueing system. Simulation experiments implemented the queueing network model following a next-event time-advance mechanism, in which systematic adjustments were made to staffing levels, IT workflow settings, and cancer screening frequency in order to assess their impact on overdue screenings per patient. TopCare reduced the average number of overdue screenings per patient from 1.17 at inception to 0.86 during simulation to 0.23 at steady state. Increases in the workforce improved the effectiveness of TopCare. In particular, increasing the delegate or navigator staff level by one person improved screening completion rates by 1.3% or 12.2%, respectively. In contrast, changes in the amount of time a patient entry stays on delegate and navigator lists had little impact on overdue screenings. Finally, lengthening the screening interval increased efficiency within TopCare by decreasing overdue screenings at the patient level, resulting in a smaller number of overdue patients needing delegates for screening and a higher fraction of screenings completed by delegates. Simulating the impact of changes in staffing, system parameters, and clinical inputs on the effectiveness and efficiency of care can inform the allocation of limited resources in population management.

Approaches to virtual screening and screening library selection.

PubMed

Wildman, Scott A

2013-01-01

The ease of access to virtual screening (VS) software in recent years has resulted in a large increase in literature reports. Over 300 publications in the last year report the use of virtual screening techniques to identify new chemical matter or present the development of new virtual screening techniques. The increased use is accompanied by a corresponding increase in misuse and misinterpretation of virtual screening results. This review aims to identify many of the common difficulties associated with virtual screening and allow researchers to better assess the reliability of their virtual screening effort.

Walla Walla River Basin Fish Screens Evaluations, 2006 Annual Report.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chamness, Mickie; Abernethy, Scott; Tunnicliffe, Cherylyn

2007-01-01

Pacific Northwest National Laboratory evaluated Gardena Farms, Little Walla Walla, and Garden City/Lowden II Phase II fish screen facilities and provided underwater videography beneath a leaking rubber dam in the Walla Walla River basin in 2006. Evaluations of the fish screen facilities took place in early May 2006, when juvenile salmonids are generally outmigrating. At the Gardena Farms site, extended high river levels caused accumulations of debris and sediment in the forebay. This debris covered parts of the bottom drum seals, which could lead to early deterioration of the seals and drum screen. Approach velocities were excessive at the upstreammore » corners of most of the drums, leading to 14% of the total approach velocities exceeding 0.4 feet per second (ft/s). Consequently, the approach velocities did not meet National Marine Fisheries Service (NMFS) design criteria guidelines for juvenile fish screens. The Little Walla Walla site was found to be in good condition, with all approach, sweep, and bypass velocities within NMFS criteria. Sediment buildup was minor and did not affect the effectiveness of the screens. At Garden City/Lowden II, 94% of approach velocities met NMFS criteria of 0.4 ft/s at any time. Sweep velocities increased toward the fish ladder. The air-burst mechanism appears to keep large debris off the screens, although it does not prevent algae and periphyton from growing on the screen face, especially near the bottom of the screens. In August 2006, the Gardena Farm Irrigation District personnel requested that we look for a leak beneath the inflatable rubber dam at the Garden City/Lowden II site that was preventing water movement through the fish ladder. Using our underwater video equipment, we were able to find a gap in the sheet piling beneath the dam. Erosion of the riverbed was occurring around this gap, allowing water and cobbles to move beneath the dam. The construction engineers and irrigation district staff were able to use the video footage to resolve the problem within a couple weeks. We had hoped to also evaluate the effectiveness of modifications to louvers behind the Nursery Bridge screens when flows were higher than 350 cubic feet per second, (cfs) but were unable to do so. Based on the one measurement made in early 2006 after the modified louvers were set, it appears the modified louvers may help reduce approach velocities. The auxiliary supply water system gates also control water through the screens. Evaluating the effect of different combinations of gate and louver positions on approach velocities through the screens may help identify optimum settings for both at different river discharges.« less

Molecular docking studies on tetrahydroimidazo-[4,5,1-jk][1,4]-benzodiazepinone (TIBO) derivatives as HIV-1 NNRT inhibitors

NASA Astrophysics Data System (ADS)

Sapre, Nitin S.; Gupta, Swagata; Pancholi, Nilanjana; Sapre, Neelima

2008-02-01

At present, chemotherapy seems to be the main weapon in the arsenal of remedies for the ongoing crusade against AIDS. The mode of binding of the TIBO family of inhibitors has been of interest because these compounds do not fit the two-hinged-ring model as generally observed in the NNRTIs. Flexible docking simulations were performed with a series of 53 TIBO derivatives as NNRTIs. Binding preferences as well as the structural and energetic factors associated with them were studied. A good correlation ( r 2 = 0.849, q 2 = 0.843) was observed between the biological activity and binding affinity of the compounds which suggest that the identified binding conformations of these inhibitors are reliable. Further screening of PubChem database yielded novel scaffolds. Our studies suggest that modifications to the TIBO group of inhibitors might enhance their binding efficacy and hence, potentially, their therapeutic utility.

Design modification and optimisation of the perfusion system of a tri-axial bioreactor for tissue engineering.

PubMed

Hussein, Husnah; Williams, David J; Liu, Yang

2015-07-01

A systematic design of experiments (DOE) approach was used to optimize the perfusion process of a tri-axial bioreactor designed for translational tissue engineering exploiting mechanical stimuli and mechanotransduction. Four controllable design parameters affecting the perfusion process were identified in a cause-effect diagram as potential improvement opportunities. A screening process was used to separate out the factors that have the largest impact from the insignificant ones. DOE was employed to find the settings of the platen design, return tubing configuration and the elevation difference that minimise the load on the pump and variation in the perfusion process and improve the controllability of the perfusion pressures within the prescribed limits. DOE was very effective for gaining increased knowledge of the perfusion process and optimizing the process for improved functionality. It is hypothesized that the optimized perfusion system will result in improved biological performance and consistency.

Somatic mutation detection in human biomonitoring.

PubMed

Olsen, L S; Nielsen, L R; Nexø, B A; Wassermann, K

1996-06-01

Somatic cell gene mutation arising in vivo may be considered to be a biomarker for genotoxicity. Assays detecting mutations of the haemoglobin and glycophorin A genes in red blood cells and of the hypoxanthine-guanine phosphoribosyltransferase and human leucocyte antigenes in T-lymphocytes are available in humans. This MiniReview describes these assays and their application to studies of individuals exposed to genotoxic agents. Moreover, with the implementation of techniques of molecular biology mutation spectra can now be defined in addition to the quantitation of in vivo mutant frequencies. We describe current screening methods for unknown mutations, including the denaturing gradient gel electrophoresis, single strand conformation polymorphism analysis, heteroduplex analysis, chemical modification techniques and enzymatic cleavage methods. The advantage of mutation detection as a biomarker is that it integrates exposure and sensitivity in one measurement. With the analysis of mutation spectra it may thus be possible to identify the causative genotoxic agent.

QT Interval Screening in Methadone Maintenance Treatment: Report of a SAMHSA Expert Panel

PubMed Central

Martin, Judith A.; Campbell, Anthony; Killip, Thomas; Kotz, Margaret; Krantz, Mori J.; Kreek, Mary Jeanne; McCarroll, Brian A.; Mehta, Davendra; Payte, J. Thomas; Stimmel, Barry; Taylor, Trusandra; Wilford, Bonnie B.

2014-01-01

In an effort to enhance patient safety in Opioid Treatment Programs (OTPs), the Substance Abuse and Mental Health Services Administration (SAMHSA) convened a multi-disciplinary Expert Panel on the Cardiac Effects of Methadone. Panel members reviewed the literature, regulatory actions, professional guidances, and OTPs’ experiences regarding adverse cardiac events associated with methadone. The Panel concluded that, to the extent possible, every OTP should have a universal Cardiac Risk Management Plan (incorporating clinical assessment, ECG assessment, risk stratification, and prevention of drug interactions) for all patients, and should strongly consider patient-specific risk minimization strategies (such as careful patient monitoring, obtaining ECGs as indicated by a particular patient’s risk profile, and adjusting the methadone dose as needed) for patients with identified risk factors for adverse cardiac events. The Panel also suggested specific modifications to informed consent documents, patient education, staff education, and methadone protocols. PMID:22026519

Aiding planning in air traffic control: an experimental investigation of the effects of perceptual information integration.

PubMed

Moertl, Peter M; Canning, John M; Gronlund, Scott D; Dougherty, Michael R P; Johansson, Joakim; Mills, Scott H

2002-01-01

Prior research examined how controllers plan in their traditional environment and identified various information uncertainties as detriments to planning. A planning aid was designed to reduce this uncertainty by perceptually representing important constraints. This included integrating spatial information on the radar screen with discrete information (planned sequences of air traffic). Previous research reported improved planning performance and decreased workload in the planning aid condition. The purpose of this paper was to determine the source of these performance improvements. Analysis of computer interactions using log-linear modeling showed that the planning interface led to less repetitive--but more integrated--information retrieval compared with the traditional planning environment. Ecological interface design principles helped explain how the integrated information retrieval gave rise to the performance improvements. Actual or potential applications of this research include the design and evaluation of interface automation that keeps users in active control by modification of perceptual task characteristics.

Cardiovascular Disease and Primary Ovarian Insufficiency

PubMed Central

Wellons, Melissa

2012-01-01

Cardiovascular disease (CVD) is the number-one killer of women. Women with primary ovarian insufficiency (POI) may be more burdened by cardiovascular disease, such as myocardial infarction and stroke, as compared with women with normal menopause. The increased burden may be mediated by a worsening of cardiovascular risk factors, such as lipids, corresponding with the loss of ovarian function. In contrast, the increased burden may be caused by factors that precede and potentially contribute to both CVD events and ovarian decline, such as X-chromosome abnormalities and smoking. Regardless of the cause, women with POI may serve as an important population to target for CVD screening and prevention strategies. These strategies should include the use of CVD risk stratification tools to identify women that may benefit from lifestyle modification and pharmacological therapy to prevent CVD. Sex steroid therapy for the sole purpose of CVD prevention in women with POI cannot be recommended, based on a lack of evidence. PMID:21969267

Risk factors for the development of paclitaxel-induced neuropathy in breast cancer patients.

PubMed

Robertson, Jetter; Raizer, Jeffrey; Hodges, James S; Gradishar, William; Allen, Jeffrey A

2018-06-01

Peripheral neuropathy is a common side effect of many chemotherapeutic agents including paclitaxel. We prospectively evaluated demographic and laboratory data in a cohort of 61 woman with breast cancer prior to paclitaxel exposure to explore factors that predispose to neuropathy development. Neuropathy was graded based on the total neuropathy score reduced version (rTNS) at baseline and at 4 months after initiation of chemotherapy. A multivariate analysis identified predictors with the strongest association with a change in rTNS. Serum albumin (P = .002), paclitaxel dose (P = .001), and body surface area (P = .006) were statistically significantly associated with a positive rTNS change (worsening neuropathy). These results suggest that poor nutritional status and obesity increase the risk of paclitaxel induced neuropathy, and that screening for these factors prior to chemotherapy exposure may improve early neuropathy detection or decrease risk with dietary modifications. © 2018 Peripheral Nerve Society.

A high-throughput and rapid computational method for screening of RNA post-transcriptional modifications that can be recognized by target proteins.

PubMed

Orr, Asuka A; Gonzalez-Rivera, Juan C; Wilson, Mark; Bhikha, P Reena; Wang, Daiqi; Contreras, Lydia M; Tamamis, Phanourios

2018-02-01

There are over 150 currently known, highly diverse chemically modified RNAs, which are dynamic, reversible, and can modulate RNA-protein interactions. Yet, little is known about the wealth of such interactions. This can be attributed to the lack of tools that allow the rapid study of all the potential RNA modifications that might mediate RNA-protein interactions. As a promising step toward this direction, here we present a computational protocol for the characterization of interactions between proteins and RNA containing post-transcriptional modifications. Given an RNA-protein complex structure, potential RNA modified ribonucleoside positions, and molecular mechanics parameters for capturing energetics of RNA modifications, our protocol operates in two stages. In the first stage, a decision-making tool, comprising short simulations and interaction energy calculations, performs a fast and efficient search in a high-throughput fashion, through a list of different types of RNA modifications categorized into trees according to their structural and physicochemical properties, and selects a subset of RNA modifications prone to interact with the target protein. In the second stage, RNA modifications that are selected as recognized by the protein are examined in-detail using all-atom simulations and free energy calculations. We implement and experimentally validate this protocol in a test case involving the study of RNA modifications in complex with Escherichia coli (E. coli) protein Polynucleotide Phosphorylase (PNPase), depicting the favorable interaction between 8-oxo-7,8-dihydroguanosine (8-oxoG) RNA modification and PNPase. Further advancement of the protocol can broaden our understanding of protein interactions with all known RNA modifications in several systems. Copyright © 2018 Elsevier Inc. All rights reserved.

Designer drugs: the evolving science of drug discovery.

PubMed

Wanke, L A; DuBose, R F

1998-07-01

Drug discovery and design are fundamental to drug development. Until recently, most drugs were discovered through random screening or developed through molecular modification. New technologies are revolutionizing this phase of drug development. Rational drug design, using powerful computers and computational chemistry and employing X-ray crystallography, nuclear magnetic resonance spectroscopy, and three-dimensional quantitative structure activity relationship analysis, is creating highly specific, biologically active molecules by virtual reality modeling. Sophisticated screening technologies are eliminating all but the most active lead compounds. These new technologies promise more efficacious, safe, and cost-effective medications, while minimizing drug development time and maximizing profits.

A paper-based microbial fuel cell array for rapid and high-throughput screening of electricity-producing bacteria.

PubMed

Choi, Gihoon; Hassett, Daniel J; Choi, Seokheun

2015-06-21

There is a large global effort to improve microbial fuel cell (MFC) techniques and advance their translational potential toward practical, real-world applications. Significant boosts in MFC performance can be achieved with the development of new techniques in synthetic biology that can regulate microbial metabolic pathways or control their gene expression. For these new directions, a high-throughput and rapid screening tool for microbial biopower production is needed. In this work, a 48-well, paper-based sensing platform was developed for the high-throughput and rapid characterization of the electricity-producing capability of microbes. 48 spatially distinct wells of a sensor array were prepared by patterning 48 hydrophilic reservoirs on paper with hydrophobic wax boundaries. This paper-based platform exploited the ability of paper to quickly wick fluid and promoted bacterial attachment to the anode pads, resulting in instant current generation upon loading of the bacterial inoculum. We validated the utility of our MFC array by studying how strategic genetic modifications impacted the electrochemical activity of various Pseudomonas aeruginosa mutant strains. Within just 20 minutes, we successfully determined the electricity generation capacity of eight isogenic mutants of P. aeruginosa. These efforts demonstrate that our MFC array displays highly comparable performance characteristics and identifies genes in P. aeruginosa that can trigger a higher power density.

The knowledge, attitudes and beliefs of patients and their healthcare professionals around oral dosage form modification: A systematic review of the qualitative literature.

PubMed

Mc Gillicuddy, Aoife; Kelly, Maria; Crean, Abina M; Sahm, Laura J

The objective of this systematic review was to synthesize the available qualitative evidence on the knowledge, attitudes and beliefs of adult patients, healthcare professionals and carers about oral dosage form modification. A systematic review and synthesis of qualitative studies was undertaken, utilising the thematic synthesis approach. The following databases were searched from inception to September 2015: PubMed, Medline (EBSCO), EMBASE, CINAHL, PsycINFO, Web of Science, ProQuest Databases, Scopus, Turning Research Into Practice (TRIP), Cochrane Central Register of Controlled Trials (CENTRAL) and the Cochrane Database of Systematic Reviews (CDSR). Citation tracking and searching the references lists of included studies was also undertaken. Grey literature was searched using the OpenGrey database, internet searching and personal knowledge. An updated search was undertaken in June 2016. Studies meeting the following criteria were eligible for inclusion; (i) used qualitative data collection and analysis methods; (ii) full-text was available in English; (iii) included adult patients who require oral dosage forms to be modified to meet their needs or; (iv) carers or healthcare professionals of patients who require oral dosage forms to be modified. Two reviewers independently appraised the quality of the included studies using the Critical Appraisal Skills Programme Checklist. A thematic synthesis was conducted and analytical themes were generated. Of 5455 records screened, seven studies were eligible for inclusion; three involved healthcare professionals and the remaining four studies involved patients. Four analytical themes emerged from the thematic synthesis: (i) patient-centred individuality and variability; (ii) communication; (iii) knowledge and uncertainty and; (iv) complexity. The variability of individual patient's requirements, poor communication practices and lack of knowledge about oral dosage form modification, when combined with the complex and multi-faceted healthcare environment complicate decision making regarding oral dosage form modification and administration. This systematic review has highlighted the key factors influencing the knowledge, attitudes and beliefs of patients and healthcare professionals about oral dosage form modifications. The findings suggest that in order to optimise oral medicine modification practices the needs of individual patients should be routinely and systematically assessed and decision-making should be supported by evidence based recommendations with multidisciplinary input. Further research is needed to optimise oral dosage form modification practices and the factors identified in this review should be considered in the development of future interventions. Copyright © 2016 Elsevier Inc. All rights reserved.

Functional crosstalk between histone H2B ubiquitylation and H2A modifications and variants.

PubMed

Wojcik, Felix; Dann, Geoffrey P; Beh, Leslie Y; Debelouchina, Galia T; Hofmann, Raphael; Muir, Tom W

2018-04-11

Ubiquitylation of histone H2B at lysine residue 120 (H2BK120ub) is a prominent histone posttranslational modification (PTM) associated with the actively transcribed genome. Although H2BK120ub triggers several critical downstream histone modification pathways and changes in chromatin structure, less is known about the regulation of the ubiquitylation reaction itself, in particular with respect to the modification status of the chromatin substrate. Here we employ an unbiased library screening approach to profile the impact of pre-existing chromatin modifications on de novo ubiquitylation of H2BK120 by the cognate human E2:E3 ligase pair, UBE2A:RNF20/40. Deposition of H2BK120ub is found to be highly sensitive to PTMs on the N-terminal tail of histone H2A, a crosstalk that extends to the common histone variant H2A.Z. Based on a series of biochemical and cell-based studies, we propose that this crosstalk contributes to the spatial organization of H2BK120ub on gene bodies, and is thus important for transcriptional regulation.

The Identification and Modification of Defense Mechanisms in Counseling.

ERIC Educational Resources Information Center

Clark, Arthur J.

1991-01-01

Suggests considerations and strategies for identifying and modifying a client's defense mechanisms in counseling. Provides definitions of individual defenses and indicators for identifying the mechanisms. Literature review focuses on counseling implications of defenses. Process of defense mechanism modification is illustrated through case example.…

Characterization of Proteoforms with Unknown Post-translational Modifications Using the MIScore

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kou, Qiang; Zhu, Binhai; Wu, Si

Various proteoforms may be generated from a single gene due to primary structure alterations (PSAs) such as genetic variations, alternative splicing, and post-translational modifications (PTMs). Top-down mass spectrometry is capable of analyzing intact proteins and identifying patterns of multiple PSAs, making it the method of choice for studying complex proteoforms. In top-down proteomics, proteoform identification is often performed by searching tandem mass spectra against a protein sequence database that contains only one reference protein sequence for each gene or transcript variant in a proteome. Because of the incompleteness of the protein database, an identified proteoform may contain unknown PSAs comparedmore » with the reference sequence. Proteoform characterization is to identify and localize PSAs in a proteoform. Although many software tools have been proposed for proteoform identification by top-down mass spectrometry, the characterization of proteoforms in identified proteoform-spectrum matches still relies mainly on manual annotation. We propose to use the Modification Identification Score (MIScore), which is based on Bayesian models, to automatically identify and localize PTMs in proteoforms. Experiments showed that the MIScore is accurate in identifying and localizing one or two modifications.« less

Current challenges and future perspectives of plant and agricultural biotechnology.

PubMed

Moshelion, Menachem; Altman, Arie

2015-06-01

Advances in understanding plant biology, novel genetic resources, genome modification, and omics technologies generate new solutions for food security and novel biomaterials production under changing environmental conditions. New gene and germplasm candidates that are anticipated to lead to improved crop yields and other plant traits under stress have to pass long development phases based on trial and error using large-scale field evaluation. Therefore, quantitative, objective, and automated screening methods combined with decision-making algorithms are likely to have many advantages, enabling rapid screening of the most promising crop lines at an early stage followed by final mandatory field experiments. The combination of novel molecular tools, screening technologies, and economic evaluation should become the main goal of the plant biotechnological revolution in agriculture. Copyright © 2015 Elsevier Ltd. All rights reserved.

Fabrication of a wettability-gradient surface on copper by screen-printing techniques

NASA Astrophysics Data System (ADS)

Huang, Ding-Jun; Leu, Tzong-Shyng

2015-08-01

In this study, a screen-printing technique is utilized to fabricate a wettability-gradient surface on a copper substrate. The pattern definitions on the copper surface were freely fabricated to define the regions with different wettabilities, for which the printing definition technique was developed as an alternative to the existing costly photolithography techniques. This fabrication process using screen printing in tandem with chemical modification methods can easily realize an excellent wettability-gradient surface with superhydrophobicity and superhydrophilicity. Surface analyses were performed to characterize conditions in some fabrication steps. A water droplet movement sequence is provided to clearly demonstrate the droplet-driving effectiveness of the fabricated gradient surface. The droplet-driving efficiency offers a promising solution for condensation heat transfer applications in the foreseeable future.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharma, R K; Freeman, III, R F

Region III of the US Fish and Wildlife Service contracted with the Division of Environmental Impact Studies, Argonne National Laboratory, to make the 316(b) determination for the Donald C. Cook Nuclear Power Plant of the Indiana and Michigan Power Company and to make recommendations for improvement in intake design to facilitate compliance. To conduct this assessment, appropriate literature on screening systems and reports furnished by the applicant on intake design and operation and on ecological studies at the site were reviewed. Modifications of the location and design of the existing intake and possibilities of retrofitting with fine-mesh screening to screenmore » larval forms of fishes were examined. It was determined that currently there is no dictated need for fine-mesh screening of intake flow at the D.C. Cook Nuclear Power Plant.« less

ADAPTATION OF THE ADVANCED STATISTICAL TRAJECTORY REGIONAL AIR POLLUTION (ASTRAP) MODEL TO THE EPA VAX COMPUTER - MODIFICATIONS AND TESTING

EPA Science Inventory

The Advanced Statistical Trajectory Regional Air Pollution (ASTRAP) model simulates long-term transport and deposition of oxides of and nitrogen. t is a potential screening tool for assessing long-term effects on regional visibility from sulfur emission sources. owever, a rigorou...

Post processing of protein-compound docking for fragment-based drug discovery (FBDD): in-silico structure-based drug screening and ligand-binding pose prediction.

PubMed

Fukunishi, Yoshifumi

2010-01-01

For fragment-based drug development, both hit (active) compound prediction and docking-pose (protein-ligand complex structure) prediction of the hit compound are important, since chemical modification (fragment linking, fragment evolution) subsequent to the hit discovery must be performed based on the protein-ligand complex structure. However, the naïve protein-compound docking calculation shows poor accuracy in terms of docking-pose prediction. Thus, post-processing of the protein-compound docking is necessary. Recently, several methods for the post-processing of protein-compound docking have been proposed. In FBDD, the compounds are smaller than those for conventional drug screening. This makes it difficult to perform the protein-compound docking calculation. A method to avoid this problem has been reported. Protein-ligand binding free energy estimation is useful to reduce the procedures involved in the chemical modification of the hit fragment. Several prediction methods have been proposed for high-accuracy estimation of protein-ligand binding free energy. This paper summarizes the various computational methods proposed for docking-pose prediction and their usefulness in FBDD.

Screening for autism identifies behavioral disorders in children functional defecation disorders.

PubMed

Kuizenga-Wessel, Sophie; Di Lorenzo, Carlo; Nicholson, Lisa M; Butter, Eric M; Ratliff-Schaub, Karen L; Benninga, Marc A; Williams, Kent C

2016-10-01

This study prospectively assessed whether positive screening surveys for autism spectrum disorders (ASDs) in children with functional defecation disorders (FDDs) accurately identify ASD. Parents of children (4-12 years) who met Rome III criteria for functional constipation (FC), FC with fecal incontinence (FI) and functional nonretentive FI (FNRFI) completed two ASD screening surveys. Children with positive screens were referred for psychological evaluation, and a year later, follow-up surveys were conducted. Of the 97 study participants, 30.9 % were diagnosed with FC, 62.9 % with FC with FI, and 6.2 % with FNRFI. ASD surveys were positive for 27 children (27.8 %). New DSM diagnoses were made in 10 out of the 15 children that completed further evaluation. Two (2.1 %) met criteria for ASD, and 12 (12.4 %) met criteria for other behavioral disorders. Average SRS and SCQ-L scores were higher in subjects with FC with FI as compared to FC alone and in those who reported no improvement versus those who reported improvement 1 year later. While positive ASD screening surveys did not correctly identify ASD in the majority, it did help to identify other unrecognized behavioral disorders in children with FDD. High screening scores were more common in children with FC with FI and in children with poorer responses to current medical treatments. •A prior study found that 29 % of children with FDD scored positive on ASD screening questionnaires. •Whether positive screens correctly identify ASD in children with FDD is unknown. What is New: •This study shows that positive ASD screens do not correctly identify ASD in children with FDD. However, the use of ASD screening questionnaires can identify previously unrecognized and untreated behavioral/developmental disorders in children with FDD. •High screening scores are more common in children with FC with FI and in children with poorer responses to current medical treatments.

Understanding of diabetes mellitus and health-preventive behaviour among Singaporeans.

PubMed

Wong, Lai Yin; Toh, Matthias P H S

2009-06-01

To study the understanding and perceived vulnerability of diabetes mellitus among Singapore residents, and determine the predictors associated with screening for diabetes mellitus among the people without the condition. A population-based survey was conducted from December 2004 to October 2005 involving Singapore residents aged 15 to 69 years. Using a standard questionnaire, Health Survey Officers interviewed household members on their understanding and perceived vulnerability of diabetes mellitus and associated cardiovascular risk factors. Data were analysed using SPSS v13. The response rate was 84.5%. Of 2,632 respondents, 291 (11.1%) have diabetes mellitus. Compared to respondents without diabetes, respondents with the disease had better understanding of diabetes and they had favourable health practice of screening for cardiovascular risk factors. Having diabetes mellitus was not associated with a healthier lifestyle. Among non-diabetics, those who had a family history of diabetes had better knowledge and health practices than those who had not. They were significantly more likely to recognise the symptoms and signs (61.5% vs 54.5%) and the causes of diabetes (70% vs 58.2%); and were more likely to have ever tested for diabetes (76.1% vs 60.4%), with P <0.001. Socio-demographic characteristics, family history, understanding and perception on the vulnerability of diabetes were identified as predictors associated with health screening for the disease. Among all respondents, better understanding was found to be associated with favourable health-preventive behaviours. However, it did not translate into healthier lifestyle. Cultural and socio-demographic profiles must be factored in for any effort on lifestyle modifications.

Patient Navigation in Medically Underserved Areas study design: A trial with implications for efficacy, effect modification, and full continuum assessment.

PubMed

Molina, Yamile; Glassgow, Anne E; Kim, Sage J; Berrios, Nerida M; Pauls, Heather; Watson, Karriem S; Darnell, Julie S; Calhoun, Elizabeth A

2017-02-01

The Patient Navigation in Medically Underserved Areas study objectives are to assess if navigation improves: 1) care uptake and time to diagnosis; and 2) outcomes depending on patients' residential medically underserved area (MUA) status. Secondary objectives include the efficacy of navigation across 1) different points of the care continuum among patients diagnosed with breast cancer; and 2) multiple regular screening episodes among patients who did not obtain breast cancer diagnoses. Our randomized controlled trial was implemented in three community hospitals in South Chicago. Eligible participants were: 1) female, 2) 18+years old, 3) not pregnant, 4) referred from a primary care provider for a screening or diagnostic mammogram based on an abnormal clinical breast exam. Participants were randomized to 1) control care or 2) receive longitudinal navigation, through treatment if diagnosed with cancer or across multiple years if asymptomatic, by a lay health worker. Participants' residential areas were identified as: 1) established MUA (before 1998), 2) new MUA (after 1998), 3) eligible/but not designated as MUA, and 4) affluent/ineligible for MUA. Primary outcomes include days to initially recommended care after randomization and days to diagnosis for women with abnormal results. Secondary outcomes concern days to treatment initiation following a diagnosis and receipt of subsequent screening following normal/benign results. This intervention aims to assess the efficacy of patient navigation on breast cancer care uptake across the continuum. If effective, the program may improve rates of early cancer detection and breast cancer morbidity. Copyright © 2016 Elsevier Inc. All rights reserved.

Identifying Nursing Interventions in a Cancer Screening Program Using Nursing Interventions Classification Taxonomy.

PubMed

Benito, Llucia; Lluch, María Teresa; Falcó, Anna Marta; García, Montse; Puig, Montse

2017-04-01

This study aimed to investigate which Nursing Interventions Classification (NIC) labels correspond to specific nursing interventions provided during cancer screening to establish a nursing documentation system. This descriptive study was conducted to identify and classify the interventions that cancer screening nurses perform based on an initial list. The initial list was grouped into 15 interventions that corresponded to four domains and eight classes. The study found expert consensus regarding the duties of cancer screening nurses and identified 15 interventions that should be implemented in clinical practice for cancer screening care, according to the NIC taxonomy. This study is the first step in developing indicators to assess nursing performance in cancer screening, and it helps to establish the core competency requirements for cancer screening nurses. © 2015 NANDA International, Inc.

A simplified immunoprecipitation method for quantitatively measuring antibody responses in clinical sera samples by using mammalian-produced Renilla luciferase-antigen fusion proteins.

PubMed

Burbelo, Peter D; Goldman, Radoslav; Mattson, Thomas L

2005-08-18

Assays detecting human antigen-specific antibodies are medically useful. However, the usefulness of existing simple immunoassay formats is limited by technical considerations such as sera antibodies to contaminants in insufficiently pure antigen, a problem likely exacerbated when antigen panels are screened to obtain clinically useful data. We developed a novel and simple immunoprecipitation technology for identifying clinical sera containing antigen-specific antibodies and for generating quantitative antibody response profiles. This method is based on fusing protein antigens to an enzyme reporter, Renilla luciferase (Ruc), and expressing these fusions in mammalian cells, where mammalian-specific post-translational modifications can be added. After mixing crude extracts, sera and protein A/G beads together and incubating, during which the Ruc-antigen fusion become immobilized on the A/G beads, antigen-specific antibody is quantitated by washing the beads and adding coelenterazine substrate and measuring light production. We have characterized this technology with sera from patients having three different types of cancers. We show that 20-85% of these sera contain significant titers of antibodies against at least one of five frequently mutated and/or overexpressed tumor-associated proteins. Five of six colon cancer sera tested gave responses that were statistically significantly greater than the average plus three standard deviations of 10 control sera. The results of competition experiments, preincubating positive sera with unmodified E. coli-produced antigens, varied dramatically. This technology has several advantages over current quantitative immunoassays including its relative simplicity, its avoidance of problems associated with E. coli-produced antigens and its use of antigens that can carry mammalian or disease-specific post-translational modifications. This assay should be generally useful for analyzing sera for antibodies recognizing any protein or its post-translational modifications.

A simplified immunoprecipitation method for quantitatively measuring antibody responses in clinical sera samples by using mammalian-produced Renilla luciferase-antigen fusion proteins

PubMed Central

Burbelo, Peter D; Goldman, Radoslav; Mattson, Thomas L

2005-01-01

Background Assays detecting human antigen-specific antibodies are medically useful. However, the usefulness of existing simple immunoassay formats is limited by technical considerations such as sera antibodies to contaminants in insufficiently pure antigen, a problem likely exacerbated when antigen panels are screened to obtain clinically useful data. Results We developed a novel and simple immunoprecipitation technology for identifying clinical sera containing antigen-specific antibodies and for generating quantitative antibody response profiles. This method is based on fusing protein antigens to an enzyme reporter, Renilla luciferase (Ruc), and expressing these fusions in mammalian cells, where mammalian-specific post-translational modifications can be added. After mixing crude extracts, sera and protein A/G beads together and incubating, during which the Ruc-antigen fusion become immobilized on the A/G beads, antigen-specific antibody is quantitated by washing the beads and adding coelenterazine substrate and measuring light production. We have characterized this technology with sera from patients having three different types of cancers. We show that 20–85% of these sera contain significant titers of antibodies against at least one of five frequently mutated and/or overexpressed tumor-associated proteins. Five of six colon cancer sera tested gave responses that were statistically significantly greater than the average plus three standard deviations of 10 control sera. The results of competition experiments, preincubating positive sera with unmodified E. coli-produced antigens, varied dramatically. Conclusion This technology has several advantages over current quantitative immunoassays including its relative simplicity, its avoidance of problems associated with E. coli-produced antigens and its use of antigens that can carry mammalian or disease-specific post-translational modifications. This assay should be generally useful for analyzing sera for antibodies recognizing any protein or its post-translational modifications. PMID:16109166

Screening for Intimate Partner Violence in Orthopedic Patients: A Comparison of Three Screening Tools

ERIC Educational Resources Information Center

Sprague, Sheila; Madden, Kim; Dosanjh, Sonia; Petrisor, Brad; Schemitsch, Emil H.; Bhandari, Mohit

2012-01-01

Accurately identifying victims of intimate partner violence (IPV) can be a challenge for clinicians and clinical researchers. Multiple instruments have been developed and validated to identify IPV in patients presenting to health care practitioners, including the Woman Abuse Screening Tool (WAST) and the Partner Violence Screen (PVS). The purpose…

City and County Solar PV Training Program, Module 2: Screening and Identifying PV Projects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elgqvist, Emma M

When screening and identifying PV projects, cities and counties should understand the different factors that impact the technical and economic potential of a PV project, the steps of the PV screening process, and how to use REopt Lite to screen a site for PV and storage project potential.

A Putative O-Linked β-N-Acetylglucosamine Transferase Is Essential for Hormogonium Development and Motility in the Filamentous Cyanobacterium Nostoc punctiforme.

PubMed

Khayatan, Behzad; Bains, Divleen K; Cheng, Monica H; Cho, Ye Won; Huynh, Jessica; Kim, Rachelle; Omoruyi, Osagie H; Pantoja, Adriana P; Park, Jun Sang; Peng, Julia K; Splitt, Samantha D; Tian, Mason Y; Risser, Douglas D

2017-05-01

Most species of filamentous cyanobacteria are capable of gliding motility, likely via a conserved type IV pilus-like system that may also secrete a motility-associated polysaccharide. In a subset of these organisms, motility is achieved only after the transient differentiation of hormogonia, which are specialized filaments that enter a nongrowth state dedicated to motility. Despite the fundamental importance of hormogonia to the life cycles of many filamentous cyanobacteria, the molecular regulation of hormogonium development is largely undefined. To systematically identify genes essential for hormogonium development and motility in the model heterocyst-forming filamentous cyanobacterium Nostoc punctiforme , a forward genetic screen was employed. The first gene identified using this screen, designated ogtA , encodes a putative O-linked β- N -acetylglucosamine transferase (OGT). The deletion of ogtA abolished motility, while ectopic expression of ogtA induced hormogonium development even under hormogonium-repressing conditions. Transcription of ogtA is rapidly upregulated (1 h) following hormogonium induction, and an OgtA-GFPuv fusion protein localized to the cytoplasm. In developing hormogonia, accumulation of PilA but not HmpD is dependent on ogtA Reverse transcription-quantitative PCR (RT-qPCR) analysis indicated equivalent levels of pilA transcript in the wild-type and Δ ogtA mutant strains, while a reporter construct consisting of the intergenic region in the 5' direction of pilA fused to gfp produced lower levels of fluorescence in the Δ ogtA mutant strain than in the wild type. The production of hormogonium polysaccharide in the Δ ogtA mutant strain is reduced compared to that in the wild type but comparable to that in a pilA deletion strain. Collectively, these results imply that O -GlcNAc protein modification regulates the accumulation of PilA via a posttranscriptional mechanism in developing hormogonia. IMPORTANCE Filamentous cyanobacteria are among the most developmentally complex prokaryotes. Species such as Nostoc punctiforme develop an array of cell types, including nitrogen-fixing heterocysts, spore-like akinetes, and motile hormogonia, that function in dispersal as well as the establishment of nitrogen-fixing symbioses with plants and fungi. These symbioses are major contributors to global nitrogen fixation. Despite the fundamental importance of hormogonia to the life cycle of filamentous cyanobacteria and the establishment of symbioses, the molecular regulation of hormogonium development is largely undefined. We employed a genetic screen to identify genes essential for hormogonium development and motility in Nostoc punctiforme The first gene identified using this screen encodes a eukaryotic-like O-linked β- N -acetylglucosamine transferase that is required for accumulation of PilA in hormogonia. Copyright © 2017 American Society for Microbiology.

Energy dependence of J/ψ production in Au + Au collisions at s N N = 39 , 62.4  and  200 GeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adamczyk, L.; Adkins, J. K.; Agakishiev, G.

The inclusive J/ψ transverse momentum spectra and nuclear modification factors are reported at mid-rapidity (|y|<1.0) in Au + Au collisions at √sNN = 39, 62.4 and 200 GeV taken by the STAR experiment. A suppression of J/ψ production, with respect to the production in p+p scaled by the number of binary nucleon–nucleon collisions, is observed in central Au + Au collisions at these three energies. No significant energy dependence of nuclear modification factors is found within uncertainties. The measured nuclear modification factors can be described by model calculations that take into account both suppression of direct J/ψ production due tomore » the color screening effect and J/ψ regeneration from recombination of uncorrelated charm–anticharm quark pairs.« less

Energy dependence of J/ψ production in Au + Au collisions at s N N = 39 , 62.4  and  200 GeV

DOE PAGES

Adamczyk, L.; Adkins, J. K.; Agakishiev, G.; ...

2017-05-10

The inclusive J/ψ transverse momentum spectra and nuclear modification factors are reported at mid-rapidity (|y|<1.0) in Au + Au collisions at √sNN = 39, 62.4 and 200 GeV taken by the STAR experiment. A suppression of J/ψ production, with respect to the production in p+p scaled by the number of binary nucleon–nucleon collisions, is observed in central Au + Au collisions at these three energies. No significant energy dependence of nuclear modification factors is found within uncertainties. The measured nuclear modification factors can be described by model calculations that take into account both suppression of direct J/ψ production due tomore » the color screening effect and J/ψ regeneration from recombination of uncorrelated charm–anticharm quark pairs.« less

Screening for Victims of Sex Trafficking in the Emergency Department: A Pilot Program

PubMed Central

Mumma, Bryn E.; Scofield, Marisa E.; Mendoza, Lydia P.; Toofan, Yalda; Youngyunpipatkul, Justin; Hernandez, Bryan

2017-01-01

Introduction Estimates suggest that hundreds of thousands of sex trafficking victims live in the United States. Several screening tools for healthcare professionals to identify sex trafficking victims have been proposed, but the effectiveness of these tools in the emergency department (ED) remains unclear. Our primary objective in this study was to evaluate the feasibility of a screening survey to identify adult victims of sex trafficking in the ED. We also compared the sensitivity of emergency physician concern and a screening survey for identifying sex trafficking victims in the ED and determined the most effective question(s) for identifying adult victims of sex trafficking. Methods We enrolled a convenience sample of medically stable female ED patients, age 18–40 years. Patients completed a 14-question survey. Physician concern for sex trafficking was documented prior to informing the physician of the survey results. A “yes” answer to any question or physician concern was considered a positive screen, and the patient was offered social work consultation. We defined a “true positive” as a patient admission for or social work documentation of sex trafficking. Demographic and clinical information were collected from the electronic medical record. Results We enrolled 143 patients, and of those 39 (27%, 95% confidence interval [CI] [20%–35%]) screened positive, including 10 (25%, 95% CI [13%–41%]) ultimately identified as victims of sex trafficking. Sensitivity of the screening survey (100%, 95% CI [74%–100%]) was better than physician concern (40%, 95% CI [12%–74%]) for identifying victims of sex trafficking, difference 60%, 95% CI [30%–90%]. Physician specificity (91%, 95% CI [85%–95%]), however, was slightly better than the screening survey (78%, 95% CI [70%–85%]), difference 13%, 95% CI [4%–21%]. All 10 (100%, 95%CI [74%–100%]) “true positive” cases answered “yes” to the screening question regarding abuse. Conclusion Identifying adult victims of sex trafficking in the ED is feasible. A screening survey appears to have greater sensitivity than physician concern, and a single screening question may be sufficient to identify all adult victims of sex trafficking in the ED. PMID:28611881

Screening for Victims of Sex Trafficking in the Emergency Department: A Pilot Program.

PubMed

Mumma, Bryn E; Scofield, Marisa E; Mendoza, Lydia P; Toofan, Yalda; Youngyunpipatkul, Justin; Hernandez, Bryan

2017-06-01

Estimates suggest that hundreds of thousands of sex trafficking victims live in the United States. Several screening tools for healthcare professionals to identify sex trafficking victims have been proposed, but the effectiveness of these tools in the emergency department (ED) remains unclear. Our primary objective in this study was to evaluate the feasibility of a screening survey to identify adult victims of sex trafficking in the ED. We also compared the sensitivity of emergency physician concern and a screening survey for identifying sex trafficking victims in the ED and determined the most effective question(s) for identifying adult victims of sex trafficking. We enrolled a convenience sample of medically stable female ED patients, age 18-40 years. Patients completed a 14-question survey. Physician concern for sex trafficking was documented prior to informing the physician of the survey results. A "yes" answer to any question or physician concern was considered a positive screen, and the patient was offered social work consultation. We defined a "true positive" as a patient admission for or social work documentation of sex trafficking. Demographic and clinical information were collected from the electronic medical record. We enrolled 143 patients, and of those 39 (27%, 95% confidence interval [CI] [20%-35%]) screened positive, including 10 (25%, 95% CI [13%-41%]) ultimately identified as victims of sex trafficking. Sensitivity of the screening survey (100%, 95% CI [74%-100%]) was better than physician concern (40%, 95% CI [12%-74%]) for identifying victims of sex trafficking, difference 60%, 95% CI [30%-90%]. Physician specificity (91%, 95% CI [85%-95%]), however, was slightly better than the screening survey (78%, 95% CI [70%-85%]), difference 13%, 95% CI [4%-21%]. All 10 (100%, 95%CI [74%-100%]) "true positive" cases answered "yes" to the screening question regarding abuse. Identifying adult victims of sex trafficking in the ED is feasible. A screening survey appears to have greater sensitivity than physician concern, and a single screening question may be sufficient to identify all adult victims of sex trafficking in the ED.

Web Extensible Display Manager

DOE Office of Scientific and Technical Information (OSTI.GOV)

Slominski, Ryan; Larrieu, Theodore L.

Jefferson Lab's Web Extensible Display Manager (WEDM) allows staff to access EDM control system screens from a web browser in remote offices and from mobile devices. Native browser technologies are leveraged to avoid installing and managing software on remote clients such as browser plugins, tunnel applications, or an EDM environment. Since standard network ports are used firewall exceptions are minimized. To avoid security concerns from remote users modifying a control system, WEDM exposes read-only access and basic web authentication can be used to further restrict access. Updates of monitored EPICS channels are delivered via a Web Socket using a webmore » gateway. The software translates EDM description files (denoted with the edl suffix) to HTML with Scalable Vector Graphics (SVG) following the EDM's edl file vector drawing rules to create faithful screen renderings. The WEDM server parses edl files and creates the HTML equivalent in real-time allowing existing screens to work without modification. Alternatively, the familiar drag and drop EDM screen creation tool can be used to create optimized screens sized specifically for smart phones and then rendered by WEDM.« less

Application of ToxCast High-Throughput Screening and ...

EPA Pesticide Factsheets

Slide presentation at the SETAC annual meeting on High-Throughput Screening and Modeling Approaches to Identify Steroidogenesis Distruptors Slide presentation at the SETAC annual meeting on High-Throughput Screening and Modeling Approaches to Identify Steroidogenssis Distruptors

Applying operations research to optimize a novel population management system for cancer screening

PubMed Central

Zai, Adrian H; Kim, Seokjin; Kamis, Arnold; Hung, Ken; Ronquillo, Jeremiah G; Chueh, Henry C; Atlas, Steven J

2014-01-01

Objective To optimize a new visit-independent, population-based cancer screening system (TopCare) by using operations research techniques to simulate changes in patient outreach staffing levels (delegates, navigators), modifications to user workflow within the information technology (IT) system, and changes in cancer screening recommendations. Materials and methods TopCare was modeled as a multiserver, multiphase queueing system. Simulation experiments implemented the queueing network model following a next-event time-advance mechanism, in which systematic adjustments were made to staffing levels, IT workflow settings, and cancer screening frequency in order to assess their impact on overdue screenings per patient. Results TopCare reduced the average number of overdue screenings per patient from 1.17 at inception to 0.86 during simulation to 0.23 at steady state. Increases in the workforce improved the effectiveness of TopCare. In particular, increasing the delegate or navigator staff level by one person improved screening completion rates by 1.3% or 12.2%, respectively. In contrast, changes in the amount of time a patient entry stays on delegate and navigator lists had little impact on overdue screenings. Finally, lengthening the screening interval increased efficiency within TopCare by decreasing overdue screenings at the patient level, resulting in a smaller number of overdue patients needing delegates for screening and a higher fraction of screenings completed by delegates. Conclusions Simulating the impact of changes in staffing, system parameters, and clinical inputs on the effectiveness and efficiency of care can inform the allocation of limited resources in population management. PMID:24043318

Barriers to Breast and Cervical Cancer Screening in Singapore: a Mixed Methods Analysis.

PubMed

Malhotra, Chetna; Bilger, Marcel; Liu, Joy; Finkelstein, Eric

2016-01-01

In order to increase breast and cervical cancer screening uptake in Singapore, women's perceived barriers to screening need to be identified and overcome. Using data from both focus groups and surveys, we aimed to assess perceived barriers and motivations for breast and cervical cancer screening. We conducted 8 focus groups with 64 women, using thematic analysis to identify overarching themes related to women's attitudes towards screening. Based on recurring themes from focus groups, several hypotheses regarding potential barriers and motivations to screen were generated and tested through a national survey of 801 women aged 25-64. Focus group participants had misconceptions related to screening, believing that the procedures were painful. Cost was an issue, as well as efficacy and fatalism. By identifying barriers to and motivators for screening through a mixed-method design that has both nuance and external validity, this study offers valuable suggestions to policymakers to improve breast and cervical cancer screening uptake in Singapore.

Tailoring an Alcohol Intervention for American Indian Alaska Native Women of Childbearing Age: Listening to the Community.

PubMed

Montag, Annika C; Dusek, Marlené L; Ortega, Marina L; Camp-Mazzetti, Alexandrea; Calac, Dan J; Chambers, Christina D

2017-11-01

Reduction of risky drinking in women of childbearing age is 1 strategy that may be employed to prevent fetal alcohol spectrum disorder, a sequela of prenatal alcohol exposure. Communities differ in risk and protective factors, necessitating culturally informed interventions for maximal efficacy. This article describes the modification of an existing web-based screening, brief intervention, and referral to treatment intervention to reduce risky drinking among American Indian Alaska Native (AIAN) women of childbearing age in Southern California into a peer-to-peer-based intervention using motivational interviewing (MI). The modification process was iterative and included various community focus groups, interviews, and a final review. Intervention modification was required for cultural congruence. Components of the peer-to-peer intervention designed by this project included a flip chart used to guide the motivational interviewing, charts of the financial and physical costs of alcohol consumption, revised baseline and follow-up questionnaires, and guidance regarding the application of MI techniques. This study may inform the modification of future interventions among AIAN communities. Copyright © 2017 by the Research Society on Alcoholism.

DNA Replication Origin Function Is Promoted by H3K4 Di-methylation in Saccharomyces cerevisiae

PubMed Central

Rizzardi, Lindsay F.; Dorn, Elizabeth S.; Strahl, Brian D.; Cook, Jeanette Gowen

2012-01-01

DNA replication is a highly regulated process that is initiated from replication origins, but the elements of chromatin structure that contribute to origin activity have not been fully elucidated. To identify histone post-translational modifications important for DNA replication, we initiated a genetic screen to identify interactions between genes encoding chromatin-modifying enzymes and those encoding proteins required for origin function in the budding yeast Saccharomyces cerevisiae. We found that enzymes required for histone H3K4 methylation, both the histone methyltransferase Set1 and the E3 ubiquitin ligase Bre1, are required for robust growth of several hypomorphic replication mutants, including cdc6-1. Consistent with a role for these enzymes in DNA replication, we found that both Set1 and Bre1 are required for efficient minichromosome maintenance. These phenotypes are recapitulated in yeast strains bearing mutations in the histone substrates (H3K4 and H2BK123). Set1 functions as part of the COMPASS complex to mono-, di-, and tri-methylate H3K4. By analyzing strains lacking specific COMPASS complex members or containing H2B mutations that differentially affect H3K4 methylation states, we determined that these replication defects were due to loss of H3K4 di-methylation. Furthermore, histone H3K4 di-methylation is enriched at chromosomal origins. These data suggest that H3K4 di-methylation is necessary and sufficient for normal origin function. We propose that histone H3K4 di-methylation functions in concert with other histone post-translational modifications to support robust genome duplication. PMID:22851644

DNA replication origin function is promoted by H3K4 di-methylation in Saccharomyces cerevisiae.

PubMed

Rizzardi, Lindsay F; Dorn, Elizabeth S; Strahl, Brian D; Cook, Jeanette Gowen

2012-10-01

DNA replication is a highly regulated process that is initiated from replication origins, but the elements of chromatin structure that contribute to origin activity have not been fully elucidated. To identify histone post-translational modifications important for DNA replication, we initiated a genetic screen to identify interactions between genes encoding chromatin-modifying enzymes and those encoding proteins required for origin function in the budding yeast Saccharomyces cerevisiae. We found that enzymes required for histone H3K4 methylation, both the histone methyltransferase Set1 and the E3 ubiquitin ligase Bre1, are required for robust growth of several hypomorphic replication mutants, including cdc6-1. Consistent with a role for these enzymes in DNA replication, we found that both Set1 and Bre1 are required for efficient minichromosome maintenance. These phenotypes are recapitulated in yeast strains bearing mutations in the histone substrates (H3K4 and H2BK123). Set1 functions as part of the COMPASS complex to mono-, di-, and tri-methylate H3K4. By analyzing strains lacking specific COMPASS complex members or containing H2B mutations that differentially affect H3K4 methylation states, we determined that these replication defects were due to loss of H3K4 di-methylation. Furthermore, histone H3K4 di-methylation is enriched at chromosomal origins. These data suggest that H3K4 di-methylation is necessary and sufficient for normal origin function. We propose that histone H3K4 di-methylation functions in concert with other histone post-translational modifications to support robust genome duplication.

Identifying Relationships between High-Risk Sexual Behaviors and Screening Positive for Chlamydia and Gonorrhea in School-Wide Screening Events

ERIC Educational Resources Information Center

Salerno, Jennifer; Darling-Fisher, Cindy; Hawkins, Nicole M.; Fraker, Elizabeth

2013-01-01

Background: This article describes a school-wide sexually transmitted infection (STI) screening to identify adolescent high-risk sexual behaviors, STI history/incidence, and presence of chlamydia and gonorrhea, and examines relationships between high-risk behaviors and screening positive for chlamydia and gonorrhea in an alternative high school…

Regional Differences as Barriers to Body Mass Index Screening Described by Ohio School Nurses

ERIC Educational Resources Information Center

Stalter, Ann M.; Chaudry, Rosemary V.; Polivka, Barbara J.

2011-01-01

Background: Body mass index (BMI) screening is advocated by the National Association of School Nurses (NASN). Research identifying barriers to BMI screening in public elementary school settings has been sparse. The purpose of the study was to identify barriers and facilitating factors of BMI screening practices among Ohio school nurses working in…

Barley callus: a model system for bioengineering of starch in cereals.

PubMed

Carciofi, Massimiliano; Blennow, Andreas; Nielsen, Morten M; Holm, Preben B; Hebelstrup, Kim H

2012-09-07

Starch is the most important source of calories for human nutrition and the majority of it is produced by cereal farming. Starch is also used as a renewable raw material in a range of industrial sectors. It can be chemically modified to introduce new physicochemical properties. In this way starch is adapted to a variety of specific end-uses. Recombinant DNA technologies offers an alternative to starch industrial processing. The plant biosynthetic pathway can be manipulated to design starches with novel structure and improved technological properties. In the future this may reduce or eliminate the economical and environmental costs of industrial modification. Recently, many advances have been achieved to clarify the genetic mechanism that controls starch biosynthesis. Several genes involved in the synthesis and modification of complex carbohydrates in many organisms have been identified and cloned. This knowledge suggests a number of strategies and a series of candidate genes for genetic transformation of crops to generate new types of starch-based polymers. However transformation of cereals is a slow process and there is no easy model system available to test the efficiency of candidate genes in planta. We explored the possibility to use transgenic barley callus generated from immature embryo for a fast test of transgenic modification strategies of starch biosynthesis. We found that this callus contains 4% (w/w dw) starch granules, which we could modify by generating fully transgenic calli by Agrobacterium-transformation. A Green Fluorescent Protein reporter protein tag was used to identify and propagate only fully transgenic callus explants. Around 1 - 1.5 g dry weight of fully transgenic callus could be produced in 9 weeks. Callus starch granules were smaller than endosperm starch granules and contained less amylose. Similarly the expression profile of starch biosynthesis genes were slightly different in callus compared with developing endosperm. In this study we have developed an easy and rapid in planta model system for starch bioengineering in cereals. We suggest that this method can be used as a time-efficient model system for fast screening of candidate genes for the generation of modified starch or new types of carbohydrate polymers.

Barley callus: a model system for bioengineering of starch in cereals

PubMed Central

2012-01-01

Background Starch is the most important source of calories for human nutrition and the majority of it is produced by cereal farming. Starch is also used as a renewable raw material in a range of industrial sectors. It can be chemically modified to introduce new physicochemical properties. In this way starch is adapted to a variety of specific end-uses. Recombinant DNA technologies offers an alternative to starch industrial processing. The plant biosynthetic pathway can be manipulated to design starches with novel structure and improved technological properties. In the future this may reduce or eliminate the economical and environmental costs of industrial modification. Recently, many advances have been achieved to clarify the genetic mechanism that controls starch biosynthesis. Several genes involved in the synthesis and modification of complex carbohydrates in many organisms have been identified and cloned. This knowledge suggests a number of strategies and a series of candidate genes for genetic transformation of crops to generate new types of starch-based polymers. However transformation of cereals is a slow process and there is no easy model system available to test the efficiency of candidate genes in planta. Results We explored the possibility to use transgenic barley callus generated from immature embryo for a fast test of transgenic modification strategies of starch biosynthesis. We found that this callus contains 4% (w/w dw) starch granules, which we could modify by generating fully transgenic calli by Agrobacterium-transformation. A Green Fluorescent Protein reporter protein tag was used to identify and propagate only fully transgenic callus explants. Around 1 – 1.5 g dry weight of fully transgenic callus could be produced in 9 weeks. Callus starch granules were smaller than endosperm starch granules and contained less amylose. Similarly the expression profile of starch biosynthesis genes were slightly different in callus compared with developing endosperm. Conclusions In this study we have developed an easy and rapid in planta model system for starch bioengineering in cereals. We suggest that this method can be used as a time-efficient model system for fast screening of candidate genes for the generation of modified starch or new types of carbohydrate polymers. PMID:22958600

[Absorption of Uranium with Tea Oil Tree Sawdust Modified by Succinic Acid].

PubMed

Zhang, Xiao-feng; Chen, Di-yun; Peng, Yan; Liu, Yong-sheng; Xiong, Xue-ying

2015-05-01

In order to explore how the modification of succinic acid improves the adsorption of tea oil tree sawdust for uranium, the tea oil tree sawdust was modified by succinic acid, after the pretreatments of crushing, screening, alkalization and acidification. Infrared analysis indicated carboxylic acid groups and ester groups were added to the sawdust after modification, and scanning electron microscope demonstrated after modification the appearance of tea oil tree sawdust was transferred from the structure like compact and straight stripped into the structure like loose and wrinkled leaves, which meant modification increased its inner pores. By the static experiments, effects of reaction time between adsorbent and solvent, dosage of adsorbent, temperature, pH value and initial concentration of uranium were investigated. The results showed that after the modification by succinic acid, the absorption rate of tea oil tree sawdust for uranium increased significantly by about 20% in 12.5 mg · L(-1) initial concentration uranium solution. Adsorption equilibrium was achieved within 180 min, and the kinetic data can be well described by the pseudo-second-order kinetic model. The experimental adsorption isotherm followed the Langmuir and Freundlich models. In addition, the maximum adsorption amounts of tea oil tree sawdust after modification calculated from Langmuir equation raised from 21.413 3 to 31.545 7 mg · g(-1) at 35°C and pH 4.0.

Probing superfast quarks in nuclei through dijet production at the LHC

DOE PAGES

Freese, Adam J.; Sargsian, Misak M.; Strikman, Mark I.

2015-11-12

We investigate dijet production from proton-nucleus collisions at the Large Hadron Collider (LHC) as a means for observing superfast quarks in nuclei with Bjorken x>1 . Kinematically, superfast quarks can be identified through directly measurable jet kinematics. Dynamically, their description requires understanding several elusive properties of nuclear QCD, such as nuclear forces at very short distances, as well as medium modification of parton distributions in nuclei. In the present work, we develop a model for nuclear parton distributions at large x in which the nuclear dynamics at short distance scales are described by two- and three-nucleon short range correlations (SRCs).more » Nuclear modifications are accounted for using the color screening model, and an improved description of the EMC effect is reached by using a structure function parametrization that includes higher-twist contributions. We apply QCD evolution at the leading order to obtain nuclear parton distributions in the kinematic regime of the LHC, and based on the obtained distributions calculate the cross section for dijet production. We find that the rates of the dijet production in pA collisions at kinematics accessible by ATLAS and CMS are sufficient not only to observe superfast quarks but also to get information about the practically unexplored three-nucleon SRCs in nuclei. Additionally, the LHC can extend our knowledge of the EMC effect to large Q 2 where higher-twist effects are negligible.« less

Elongator-dependent modification of cytoplasmic tRNALysUUU is required for mitochondrial function under stress conditions

PubMed Central

Tigano, Marco; Ruotolo, Roberta; Dallabona, Cristina; Fontanesi, Flavia; Barrientos, Antoni; Donnini, Claudia; Ottonello, Simone

2015-01-01

To gain a wider view of the pathways that regulate mitochondrial function, we combined the effect of heat stress on respiratory capacity with the discovery potential of a genome-wide screen in Saccharomyces cerevisiae. We identified 105 new genes whose deletion impairs respiratory growth at 37°C by interfering with processes such as transcriptional regulation, ubiquitination and cytosolic tRNA wobble uridine modification via 5-methoxycarbonylmethyl-2-thiouridine formation. The latter process, specifically required for efficient decoding of AA-ending codons under stress conditions, was covered by multiple genes belonging to the Elongator (e.g. ELP3) and urmylation (e.g., NCS6) pathways. ELP3 or NCS6 deletants had impaired mitochondrial protein synthesis. Their respiratory deficiency was selectively rescued by overexpression of tRNALysUUU as well by overexpression of genes (BCK1 and HFM1) with a strong bias for the AAA codon read by this tRNA. These data extend the mitochondrial regulome, demonstrate that heat stress can impair respiration by disturbing cytoplasmic translation of proteins critically involved in mitochondrial function and document, for the first time, the involvement in such process of the Elongator and urmylation pathways. Given the conservation of these pathways, the present findings may pave the way to a better understanding of the human mitochondrial regulome in health and disease. PMID:26240381

Probing superfast quarks in nuclei through dijet production at the LHC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freese, Adam J.; Sargsian, Misak M.; Strikman, Mark I.

2015-11-01

We investigate dijet production from proton-nucleus collisions at the Large Hadron Collider (LHC) as a means for observing superfast quarks in nuclei with Bjorken x>1 . Kinematically, superfast quarks can be identified through directly measurable jet kinematics. Dynamically, their description requires understanding several elusive properties of nuclear QCD, such as nuclear forces at very short distances, as well as medium modification of parton distributions in nuclei. In the present work, we develop a model for nuclear parton distributions at large x in which the nuclear dynamics at short distance scales are described by two- and three-nucleon short range correlations (SRCs).more » Nuclear modifications are accounted for using the color screening model, and an improved description of the EMC effect is reached by using a structure function parametrization that includes higher-twist contributions. We apply QCD evolution at the leading order to obtain nuclear parton distributions in the kinematic regime of the LHC, and based on the obtained distributions calculate the cross section for dijet production. We find that the rates of the dijet production in pA collisions at kinematics accessible by ATLAS and CMS are sufficient not only to observe superfast quarks but also to get information about the practically unexplored three-nucleon SRCs in nuclei. Additionally, the LHC can extend our knowledge of the EMC effect to large Q2 where higher-twist effects are negligible.« less

A Kinetic Analysis of the Auxin Transcriptome Reveals Cell Wall Remodeling Proteins That Modulate Lateral Root Development in Arabidopsis[W][OPEN

PubMed Central

Lewis, Daniel R.; Olex, Amy L.; Lundy, Stacey R.; Turkett, William H.; Fetrow, Jacquelyn S.; Muday, Gloria K.

2013-01-01

To identify gene products that participate in auxin-dependent lateral root formation, a high temporal resolution, genome-wide transcript abundance analysis was performed with auxin-treated Arabidopsis thaliana roots. Data analysis identified 1246 transcripts that were consistently regulated by indole-3-acetic acid (IAA), partitioning into 60 clusters with distinct response kinetics. We identified rapidly induced clusters containing auxin-response functional annotations and clusters exhibiting delayed induction linked to cell division temporally correlated with lateral root induction. Several clusters were enriched with genes encoding proteins involved in cell wall modification, opening the possibility for understanding mechanistic details of cell structural changes that result in root formation following auxin treatment. Mutants with insertions in 72 genes annotated with a cell wall remodeling function were examined for alterations in IAA-regulated root growth and development. This reverse-genetic screen yielded eight mutants with root phenotypes. Detailed characterization of seedlings with mutations in CELLULASE3/GLYCOSYLHYDROLASE9B3 and LEUCINE RICH EXTENSIN2, genes not normally linked to auxin response, revealed defects in the early and late stages of lateral root development, respectively. The genes identified here using kinetic insight into expression changes lay the foundation for mechanistic understanding of auxin-mediated cell wall remodeling as an essential feature of lateral root development. PMID:24045021

75 FR 61148 - Food and Drug Administration Modernization Act of 1997: Modifications to the List of Recognized...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-04

... Evaluation and testing within a risk management process 2-100 ASTM E1372-95 (2003) Standard Test Method...) Standard Title, Type of Test Method for Agar Diffusion Cell standard , Relevant Culture Screening for... Biological evaluation of medical devices - Office(s) and Part 3: Tests for genotoxicity, Division(s...

Videotape Replay: Positive Reinforcement in Behavioral Modification with the Adult Retardate. Final Report.

ERIC Educational Resources Information Center

Burnell, Diana P.

The use of videotape replay was evaluated as a new therapeutic and educational technique in the treatment of mental retardation. It was hypothesized that the retardate would improve his behavior after seeing himself interacting with others on the television screen. The behavior of the control and experimental groups was rated by four therapists…

Risk stratification in cervical cancer screening by complete screening history: Applying bioinformatics to a general screening population.

PubMed

Baltzer, Nicholas; Sundström, Karin; Nygård, Jan F; Dillner, Joakim; Komorowski, Jan

2017-07-01

Women screened for cervical cancer in Sweden are currently treated under a one-size-fits-all programme, which has been successful in reducing the incidence of cervical cancer but does not use all of the participants' available medical information. This study aimed to use women's complete cervical screening histories to identify diagnostic patterns that may indicate an increased risk of developing cervical cancer. A nationwide case-control study was performed where cervical cancer screening data from 125,476 women with a maximum follow-up of 10 years were evaluated for patterns of SNOMED diagnoses. The cancer development risk was estimated for a number of different screening history patterns and expressed as Odds Ratios (OR), with a history of 4 benign cervical tests as reference, using logistic regression. The overall performance of the model was moderate (64% accuracy, 71% area under curve) with 61-62% of the study population showing no specific patterns associated with risk. However, predictions for high-risk groups as defined by screening history patterns were highly discriminatory with ORs ranging from 8 to 36. The model for computing risk performed consistently across different screening history lengths, and several patterns predicted cancer outcomes. The results show the presence of risk-increasing and risk-decreasing factors in the screening history. Thus it is feasible to identify subgroups based on their complete screening histories. Several high-risk subgroups identified might benefit from an increased screening density. Some low-risk subgroups identified could likely have a moderately reduced screening density without additional risk. © 2017 UICC.

Screening for Behavioral Health Issues in Children Enrolled in Massachusetts Medicaid

PubMed Central

Penfold, Robert; Arsenault, Lisa; Zhang, Fang; Murphy, Michael; Wissow, Larry

2014-01-01

OBJECTIVES: To understand mandated behavioral health (BH) screening in Massachusetts Medicaid including characteristics of screened children, predictors of positive screens, and whether screening identifies children without a previous BH history. METHODS: Massachusetts mandated BH screening in particularly among underidentified groups. 2008. Providers used a billing code and modifier to indicate a completed screen and whether a BH need was identified. Using MassHealth claims data, children with ≥300 days of eligibility in fiscal year (FY) 2009 were identified and categorized into groups based on first use of the modifier, screening code, or claim. Bivariate analyses were conducted to determine differences among groups. BH history was examined by limiting the sample to those continuously enrolled in FY 2008 and 2009. Multivariate logistic regression was used to determine predictors of positive screens. RESULTS: Of 355 490 eligible children, 46% had evidence of screening. Of those with modifiers, 12% were positive. Among continuously enrolled children (FY 2008 and FY 2009) with evidence of screening, 43% with positive modifiers had no BH history. This “newly identified” group were more likely to be female, younger, minority, and from rural residences (P < .0001). Among children with modifiers; gender (male), age (5–7), being in foster care, recent BH history, and Hispanic ethnicity predicted having a positive modifier. CONCLUSIONS: The high rate of newly identified Medicaid children with a BH need suggests that screening is performing well, particularly among underidentified groups. To better assess screening value, future work on cost-effectiveness and the impact on subsequent mental health treatment is needed. PMID:24298005

Feasibility of interdisciplinary community-based fall risk screening.

PubMed

Elliott, Sharon J; Ivanescu, Andrada; Leland, Natalie E; Fogo, Jennifer; Painter, Jane A; Trujillo, Leonard G

2012-01-01

This pilot study examined the feasibility of (1) conducting interdisciplinary fall risk screens at a communitywide adult fall prevention event and (2) collecting preliminary follow-up data from people screened at the event about balance confidence and home and activity modifications made after receiving educational information at the event. We conducted a pilot study with pre- and posttesting (4-mo follow-up) with 35 community-dwelling adults ≥55 yr old. Approximately half the participants were at risk for falls. Most participants who anticipated making environmental or activity changes to reduce fall risk initiated changes (n = 8/11; 72.7%) during the 4-mo follow-up period. We found no significant difference in participants' balance confidence between baseline (median = 62.81) and follow-up (median = 64.06) as measured by the Activities-specific Balance Confidence scale. Conducting interdisciplinary fall risk screens at an adult fall prevention event is feasible and can facilitate environmental and behavior changes to reduce fall risk. Copyright © 2012 by the American Occupational Therapy Association, Inc.

Consistency and sources of divergence in recommendations on screening with questionnaires for presently experienced health problems or symptoms: a comparison of recommendations from the Canadian Task Force on Preventive Health Care, UK National Screening Committee, and US Preventive Services Task Force.

PubMed

Thombs, Brett D; Saadat, Nazanin; Riehm, Kira E; Karter, Justin Michael; Vaswani, Akansha; Andrews, Bonnie K; Simons, Peter; Cosgrove, Lisa

2017-08-09

Recently, health screening recommendations have gone beyond screening for early-stage, asymptomatic disease to include "screening" for presently experienced health problems and symptoms using self-report questionnaires. We examined recommendations from three major national guideline organizations to determine the consistency of recommendations, identify sources of divergent recommendations, and determine if guideline organizations have identified any direct randomized controlled trial (RCT) evidence for the effectiveness of questionnaire-based screening. We reviewed recommendation statements listed by the Canadian Task Force on Preventive Health Care (CTFPHC), the United Kingdom National Screening Committee (UKNSC), and the United States Preventive Services Task Force (USPSTF) as of 5 September 2016. Eligible recommendations focused on using self-report questionnaires to identify patients with presently experienced health problems or symptoms. Within each recommendation and accompanying evidence review we identified screening RCTs. We identified 22 separate recommendations on questionnaire-based screening, including three CTFPHC recommendations against screening, eight UKNSC recommendations against screening, four USPSTF recommendations in favor of screening (alcohol misuse, adolescent depression, adult depression, intimate partner violence), and seven USPSTF recommendations that did not recommend for or against screening. In the four cases where the USPSTF recommended screening, either the CTFPHC, the UKNSC, or both recommended against. When recommendations diverged, the USPSTF expressed confidence in benefits based on indirect evidence, evaluated potential harms as minimal, and did not consider cost or resource use. CTFPHC and UKNSC recommendations against screening, on the other hand, focused on the lack of direct evidence of benefit and raised concerns about harms to patients and resource use. Of six RCTs that directly evaluated screening interventions, five did not report any statistically significant primary or secondary health outcomes in favor of screening, and one trial reported equivocal results. Only the USPSTF has made any recommendations for screening with questionnaires for presently experienced problems or symptoms. The CTFPHC and UKNSC recommended against screening in all of their recommendations. Differences in recommendations appear to reflect differences in willingness to assume benefit from indirect evidence and different approaches to assessing possible harms and resource consumption. There were no examples in any recommendations of RCTs with direct evidence of improved health outcomes.

Development and Validation of 2D Difference Intensity Analysis for Chemical Library Screening by Protein-Detected NMR Spectroscopy.

PubMed

Egner, John M; Jensen, Davin R; Olp, Michael D; Kennedy, Nolan W; Volkman, Brian F; Peterson, Francis C; Smith, Brian C; Hill, R Blake

2018-03-02

An academic chemical screening approach was developed by using 2D protein-detected NMR, and a 352-chemical fragment library was screened against three different protein targets. The approach was optimized against two protein targets with known ligands: CXCL12 and BRD4. Principal component analysis reliably identified compounds that induced nonspecific NMR crosspeak broadening but did not unambiguously identify ligands with specific affinity (hits). For improved hit detection, a novel scoring metric-difference intensity analysis (DIA)-was devised that sums all positive and negative intensities from 2D difference spectra. Applying DIA quickly discriminated potential ligands from compounds inducing nonspecific NMR crosspeak broadening and other nonspecific effects. Subsequent NMR titrations validated chemotypes important for binding to CXCL12 and BRD4. A novel target, mitochondrial fission protein Fis1, was screened, and six hits were identified by using DIA. Screening these diverse protein targets identified quinones and catechols that induced nonspecific NMR crosspeak broadening, hampering NMR analyses, but are currently not computationally identified as pan-assay interference compounds. The results established a streamlined screening workflow that can easily be scaled and adapted as part of a larger screening pipeline to identify fragment hits and assess relative binding affinities in the range of 0.3-1.6 mm. DIA could prove useful in library screening and other applications in which NMR chemical shift perturbations are measured. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Graph-based similarity concepts in virtual screening.

PubMed

Hutter, Michael C

2011-03-01

Applying similarity for finding new promising compounds is a key issue in drug design. Conversely, quantifying similarity between molecules has remained a difficult task despite the numerous approaches. Here, some general aspects along with recent developments regarding similarity criteria are collected. For the purpose of virtual screening, the compounds have to be encoded into a computer-readable format that permits a comparison, according to given similarity criteria, comprising the use of the 3D structure, fingerprints, graph-based and alignment-based approaches. Whereas finding the most common substructures is the most obvious method, more recent approaches take into account chemical modifications that appear throughout existing drugs, from various therapeutic categories and targets.

Retrospective review of lung cancers diagnosed in annual rounds of CT screening.

PubMed

Xu, Dong Ming; Yip, Rowena; Smith, James P; Yankelevitz, David F; Henschke, Claudia I

2014-11-01

The purpose of this study was to review the records of patients with diagnoses of lung cancer in annual repeat rounds of CT screening in the International Early Lung Cancer Action Program to determine whether the cancer could have been identified in the previous round of screening. Three radiologists reviewed the scans of 104 lung cancer patients and assigned the findings to one of three categories: 1, cancer was not visible at previous CT screening; 2, cancer was visible at previous CT screening but not identified; 3, abnormality was identified at previous CT screening but not classified as malignant. Nodule size, nodule consistency, cell type, and stage at the previous screening and when identified for further workup for each of the three categories were tabulated. Twenty-four (23%) patients had category 1 findings; 56 (54%) category 2; and 24 (23%) category 3. When diagnosed, seven (29%) category 1, 10 (18%) category 2, and four (17%) category three cancers had progressed beyond stage I. All cancers seen in retrospect were in clinical stage I at the previous screening. Category 1 cancers, compared with categories 2 and 3, had faster growth rates, were less frequently adenocarcinomas (29% vs 54% and 67%, p = 0.01), and were more often small cell carcinomas (29% vs 14% and 12%, p = 0.12). Lung cancers found on annual repeat screenings were frequently identified in the previous round of screening, suggesting that review of the varied appearance and incorporation of advanced image display may be useful for earlier detection.

Epigenetic Modifications of Major Depressive Disorder

PubMed Central

Saavedra, Kathleen; Molina-Márquez, Ana María; Saavedra, Nicolás; Zambrano, Tomás; Salazar, Luis A.

2016-01-01

Major depressive disorder (MDD) is a chronic disease whose neurological basis and pathophysiology remain poorly understood. Initially, it was proposed that genetic variations were responsible for the development of this disease. Nevertheless, several studies within the last decade have provided evidence suggesting that environmental factors play an important role in MDD pathophysiology. Alterations in epigenetics mechanism, such as DNA methylation, histone modification and microRNA expression could favor MDD advance in response to stressful experiences and environmental factors. The aim of this review is to describe genetic alterations, and particularly altered epigenetic mechanisms, that could be determinants for MDD progress, and how these alterations may arise as useful screening, diagnosis and treatment monitoring biomarkers of depressive disorders. PMID:27527165

Nitrilases in nitrile biocatalysis: recent progress and forthcoming research

PubMed Central

2012-01-01

Over the past decades, nitrilases have drawn considerable attention because of their application in nitrile degradation as prominent biocatalysts. Nitrilases are derived from bacteria, filamentous fungi, yeasts, and plants. In-depth investigations on their natural sources function mechanisms, enzyme structure, screening pathways, and biocatalytic properties have been conducted. Moreover, the immobilization, purification, gene cloning and modifications of nitrilase have been dwelt upon. Some nitrilases are used commercially as biofactories for carboxylic acids production, waste treatment, and surface modification. This critical review summarizes the current status of nitrilase research, and discusses a number of challenges and significant attempts in its further development. Nitrilase is a significant and promising biocatalyst for catalytic applications. PMID:23106943

High-Content, High-Throughput Screening for the Identification of Cytotoxic Compounds Based on Cell Morphology and Cell Proliferation Markers

PubMed Central

Martin, Heather L.; Adams, Matthew; Higgins, Julie; Bond, Jacquelyn; Morrison, Ewan E.; Bell, Sandra M.; Warriner, Stuart; Nelson, Adam; Tomlinson, Darren C.

2014-01-01

Toxicity is a major cause of failure in drug discovery and development, and whilst robust toxicological testing occurs, efficiency could be improved if compounds with cytotoxic characteristics were identified during primary compound screening. The use of high-content imaging in primary screening is becoming more widespread, and by utilising phenotypic approaches it should be possible to incorporate cytotoxicity counter-screens into primary screens. Here we present a novel phenotypic assay that can be used as a counter-screen to identify compounds with adverse cellular effects. This assay has been developed using U2OS cells, the PerkinElmer Operetta high-content/high-throughput imaging system and Columbus image analysis software. In Columbus, algorithms were devised to identify changes in nuclear morphology, cell shape and proliferation using DAPI, TOTO-3 and phosphohistone H3 staining, respectively. The algorithms were developed and tested on cells treated with doxorubicin, taxol and nocodazole. The assay was then used to screen a novel, chemical library, rich in natural product-like molecules of over 300 compounds, 13.6% of which were identified as having adverse cellular effects. This assay provides a relatively cheap and rapid approach for identifying compounds with adverse cellular effects during screening assays, potentially reducing compound rejection due to toxicity in subsequent in vitro and in vivo assays. PMID:24505478

Empirical evaluation demonstrated importance of validating biomarkers for early detection of cancer in screening settings to limit the number of false-positive findings.

PubMed

Chen, Hongda; Knebel, Phillip; Brenner, Hermann

2016-07-01

Search for biomarkers for early detection of cancer is a very active area of research, but most studies are done in clinical rather than screening settings. We aimed to empirically evaluate the role of study setting for early detection marker identification and validation. A panel of 92 candidate cancer protein markers was measured in 35 clinically identified colorectal cancer patients and 35 colorectal cancer patients identified at screening colonoscopy. For each case group, we selected 38 controls without colorectal neoplasms at screening colonoscopy. Single-, two- and three-marker combinations discriminating cases and controls were identified in each setting and subsequently validated in the alternative setting. In all scenarios, a higher number of predictive biomarkers were initially detected in the clinical setting, but a substantially lower proportion of identified biomarkers could subsequently be confirmed in the screening setting. Confirmation rates were 50.0%, 84.5%, and 74.2% for one-, two-, and three-marker algorithms identified in the screening setting and were 42.9%, 18.6%, and 25.7% for algorithms identified in the clinical setting. Validation of early detection markers of cancer in a true screening setting is important to limit the number of false-positive findings. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Identifying DNA methylation in a nanochannel

NASA Astrophysics Data System (ADS)

Sun, Xiaoyin; Yasui, Takao; Yanagida, Takeshi; Kaji, Noritada; Rahong, Sakon; Kanai, Masaki; Nagashima, Kazuki; Kawai, Tomoji; Baba, Yoshinobu

2016-01-01

DNA methylation is a stable epigenetic modification, which is well known to be involved in gene expression regulation. In general, however, analyzing DNA methylation requires rather time consuming processes (24-96 h) via DNA replication and protein modification. Here we demonstrate a methodology to analyze DNA methylation at a single DNA molecule level without any protein modifications by measuring the contracted length and relaxation time of DNA within a nanochannel. Our methodology is based on the fact that methylation makes DNA molecules stiffer, resulting in a longer contracted length and a longer relaxation time (a slower contraction rate). The present methodology offers a promising way to identify DNA methylation without any protein modification at a single DNA molecule level within 2 h.

Using lessons from breast, cervical, and colorectal cancer screening to inform the development of lung cancer screening programs.

PubMed

Armstrong, Katrina; Kim, Jane J; Halm, Ethan A; Ballard, Rachel M; Schnall, Mitchell D

2016-05-01

Multiple advisory groups now recommend that high-risk smokers be screened for lung cancer by low-dose computed tomography. Given that the development of lung cancer screening programs will face many of the same issues that have challenged other cancer screening programs, the National Cancer Institute-funded Population-based Research Optimizing Screening through Personalized Regimens (PROSPR) consortium was used to identify lessons learned from the implementation of breast, cervical, and colorectal cancer screening that should inform the introduction of lung cancer screening. These lessons include the importance of developing systems for identifying and recruiting eligible individuals in primary care, ensuring that screening centers are qualified and performance is monitored, creating clear communication standards for reporting screening results to referring physicians and patients, ensuring follow-up is available for individuals with abnormal test results, avoiding overscreening, remembering primary prevention, and leveraging advances in cancer genetics and immunology. Overall, this experience emphasizes that effective cancer screening is a multistep activity that requires robust strategies to initiate, report, follow up, and track each step as well as a dynamic and ongoing oversight process to revise current screening practices as new evidence regarding screening is created, new screening technologies are developed, new biological markers are identified, and new approaches to health care delivery are disseminated. Cancer 2016;122:1338-1342. © 2016 American Cancer Society. © 2016 American Cancer Society.

Identification of high-efficiency 3'GG gRNA motifs in indexed FASTA files with ngg2.

PubMed

Roberson, Elisha D O

CRISPR/Cas9 is emerging as one of the most-used methods of genome modification in organisms ranging from bacteria to human cells. However, the efficiency of editing varies tremendously site-to-site. A recent report identified a novel motif, called the 3'GG motif, which substantially increases the efficiency of editing at all sites tested in C. elegans . Furthermore, they highlighted that previously published gRNAs with high editing efficiency also had this motif. I designed a python command-line tool, ngg2, to identify 3'GG gRNA sites from indexed FASTA files. As a proof-of-concept, I screened for these motifs in six model genomes: Saccharomyces cerevisiae , Caenorhabditis elegans , Drosophila melanogaster , Danio rerio , Mus musculus , and Homo sapiens. I also scanned the genomes of pig ( Sus scrofa ) and African elephant ( Loxodonta africana ) to demonstrate the utility in non-model organisms. I identified more than 60 million single match 3'GG motifs in these genomes. Greater than 61% of all protein coding genes in the reference genomes had at least one unique 3'GG gRNA site overlapping an exon. In particular, more than 96% of mouse and 93% of human protein coding genes have at least one unique, overlapping 3'GG gRNA. These identified sites can be used as a starting point in gRNA selection, and the ngg2 tool provides an important ability to identify 3'GG editing sites in any species with an available genome sequence.

Fisher: a program for the detection of H/ACA snoRNAs using MFE secondary structure prediction and comparative genomics - assessment and update.

PubMed

Freyhult, Eva; Edvardsson, Sverker; Tamas, Ivica; Moulton, Vincent; Poole, Anthony M

2008-07-21

The H/ACA family of small nucleolar RNAs (snoRNAs) plays a central role in guiding the pseudouridylation of ribosomal RNA (rRNA). In an effort to systematically identify the complete set of rRNA-modifying H/ACA snoRNAs from the genome sequence of the budding yeast, Saccharomyces cerevisiae, we developed a program - Fisher - and previously presented several candidate snoRNAs based on our analysis 1. In this report, we provide a brief update of this work, which was aborted after the publication of experimentally-identified snoRNAs 2 identical to candidates we had identified bioinformatically using Fisher. Our motivation for revisiting this work is to report on the status of the candidate snoRNAs described in 1, and secondly, to report that a modified version of Fisher together with the available multiple yeast genome sequences was able to correctly identify several H/ACA snoRNAs for modification sites not identified by the snoGPS program 3. While we are no longer developing Fisher, we briefly consider the merits of the Fisher algorithm relative to snoGPS, which may be of use for workers considering pursuing a similar search strategy for the identification of small RNAs. The modified source code for Fisher is made available as supplementary material. Our results confirm the validity of using minimum free energy (MFE) secondary structure prediction to guide comparative genomic screening for RNA families with few sequence constraints.

Newborn Screening for Glutaric Aciduria-II: The New England Experience.

PubMed

Sahai, I; Garganta, C L; Bailey, J; James, P; Levy, H L; Martin, M; Neilan, E; Phornphutkul, C; Sweetser, D A; Zytkovicz, T H; Eaton, R B

2014-01-01

Newborn screening (NBS) using tandem mass spectrometry (MS/MS) permits detection of neonates with Glutaric Aciduria-Type II (GA-II). We report follow-up of positive GA-II screens by the New England Newborn Screening Program. 1.5 million infants were screened for GA-II (Feb 1999-Dec 2012). Specialist consult was suggested for infants with two or more acylcarnitine elevations suggestive of GA-II. 82 neonates screened positive for GA-II, 21 weighing > 1.5 kg and 61 weighing ≤ 1.5 kg. Seven (one weighing < 1.5 kg), were confirmed with GA-II. Four of these had the severe form (died < 1 week). The other three have a milder form and were identified because of newborn screening. Two (ages > 5 years) have a G-Tube in place, had multiple hospitalizations and are slightly hypotonic. The third infant remains asymptomatic (9 months old). Two GA-II carriers were also identified. The remaining positive screens were classified as false positives (FP). Six infants (> 1.5 kg) classified as FP had limited diagnostic work-up. Characteristics and outcomes of all specimens and neonates with a positive screen were reviewed, and marker profiles of the cases and FP were compared to identify characteristic profiles. In addition to the severe form of GA-II, milder forms of GA-II and some GA-II carriers are identified by newborn screening. Some positive screens classified as FP may be affected with a milder form of the disorder. Characteristic GA-II profiles, quantified as GA-II indexes, may be utilized to predict probability of disorder and direct urgency of intervention for positive screens.

Proteomic Approaches to Quantify Cysteine Reversible Modifications in Aging and Neurodegenerative Diseases

PubMed Central

Gu, Liqing; Robinson, Renã A. S.

2016-01-01

Cysteine is a highly reactive amino acid and is subject to a variety of reversible post-translational modifications (PTMs), including nitrosylation, glutathionylation, palmitoylation, as well as formation of sulfenic acid and disulfides. These modifications are not only involved in normal biological activities, such as enzymatic catalysis, redox signaling and cellular homeostasis, but can also be the result of oxidative damage. Especially in aging and neurodegenerative diseases, oxidative stress leads to aberrant cysteine oxidations that affect protein structure and function leading to neurodegeneration as well as other detrimental effects. Methods that can identify cysteine modifications by type, including the site of modification, as well as the relative stoichiometry of the modification can be very helpful for understanding the role of the thiol proteome and redox homeostasis in the context of disease. Cysteine reversible modifications however, are challenging to investigate as they are low abundant, diverse, and labile especially under endogenous conditions. Thanks to the development of redox proteomic approaches, large-scale quantification of cysteine reversible modifications is possible. These approaches cover a range of strategies to enrich, identify, and quantify cysteine reversible modifications from biological samples. This review will focus on nongel-based redox proteomics workflows that give quantitative information about cysteine PTMs and highlight how these strategies have been useful for investigating the redox thiol proteome in aging and neurodegenerative diseases. PMID:27666938

Pnp gene modification for improved xylose utilization in Zymomonas

DOEpatents

Caimi, Perry G G; Qi, Min; Tao, Luan; Viitanen, Paul V; Yang, Jianjun

2014-12-16

The endogenous pnp gene encoding polynucleotide phosphorylase in the Zymomonas genome was identified as a target for modification to provide improved xylose utilizing cells for ethanol production. The cells are in addition genetically modified to have increased expression of ribose-5-phosphate isomerase (RPI) activity, as compared to cells without this genetic modification, and are not limited in xylose isomerase activity in the absence of the pnp modification.

The design and development of a complex multifactorial falls assessment intervention for falls prevention: The Prevention of Falls Injury Trial (PreFIT).

PubMed

Bruce, Julie; Ralhan, Shvaita; Sheridan, Ray; Westacott, Katharine; Withers, Emma; Finnegan, Susanne; Davison, John; Martin, Finbarr C; Lamb, Sarah E

2017-06-01

This paper describes the design and development of a complex multifactorial falls prevention (MFFP) intervention for implementation and testing within the framework of a large UK-based falls prevention randomised controlled trial (RCT). A complex intervention was developed for inclusion within the Prevention of Falls Injury Trial (PreFIT), a multicentre pragmatic RCT. PreFIT aims to compare the clinical and cost-effectiveness of three alternative primary care falls prevention interventions (advice, exercise and MFFP), on outcomes of fractures and falls. Community-dwelling adults, aged 70 years and older, were recruited from primary care in the National Health Service (NHS), England. Development of the PreFIT MFFP intervention was informed by the existing evidence base and clinical guidelines for the assessment and management of falls in older adults. After piloting and modification, the final MFFP intervention includes seven falls risk factors: a detailed falls history interview with consideration of 'red flags'; assessment of balance and gait; vision; medication screen; cardiac screen; feet and footwear screen and home environment assessment. This complex intervention has been fully manualised with clear, documented assessment and treatment pathways for each risk factor. Each risk factor is assessed in every trial participant referred for MFFP. Referral for assessment is based upon a screening survey to identify those with a history of falling or balance problems. Intervention delivery can be adapted to the local setting. This complex falls prevention intervention is currently being tested within the framework of a large clinical trial. This paper adheres to TIDieR and CONSORT recommendations for the comprehensive and explicit reporting of trial interventions. Results from the PreFIT study will be published in due course. The effectiveness and cost-effectiveness of the PreFIT MFFP intervention, compared to advice and exercise, on the prevention of falls and fractures, will be reported at the conclusion of the trial.

Tiered High-Throughput Screening Approach to Identify ...

EPA Pesticide Factsheets

High-throughput screening (HTS) for potential thyroid–disrupting chemicals requires a system of assays to capture multiple molecular-initiating events (MIEs) that converge on perturbed thyroid hormone (TH) homeostasis. Screening for MIEs specific to TH-disrupting pathways is limited in the US EPA ToxCast screening assay portfolio. To fill one critical screening gap, the Amplex UltraRed-thyroperoxidase (AUR-TPO) assay was developed to identify chemicals that inhibit TPO, as decreased TPO activity reduces TH synthesis. The ToxCast Phase I and II chemical libraries, comprised of 1,074 unique chemicals, were initially screened using a single, high concentration to identify potential TPO inhibitors. Chemicals positive in the single concentration screen were retested in concentration-response. Due to high false positive rates typically observed with loss-of-signal assays such as AUR-TPO, we also employed two additional assays in parallel to identify possible sources of nonspecific assay signal loss, enabling stratification of roughly 300 putative TPO inhibitors based upon selective AUR-TPO activity. A cell-free luciferase inhibition assay was used to identify nonspecific enzyme inhibition among the putative TPO inhibitors, and a cytotoxicity assay using a human cell line was used to estimate the cellular tolerance limit. Additionally, the TPO inhibition activities of 150 chemicals were compared between the AUR-TPO and an orthogonal peroxidase oxidation assay using

[Validation of a nutritional screening tool for hospitalized pediatric patients].

PubMed

Lama More, R A; Moráis López, A; Herrero Álvarez, M; Caraballo Chicano, S; Galera Martínez, R; López Ruzafa, E; Rodríguez Martínez, G; de la Mano Hernández, A; Rivero de la Rosa, M C

2012-01-01

Malnutrition among hospitalized patients has clinical implications, and interest has arisen to find screening tools able to identify subjects under risk. At present, there is no consensus about the most suitable nutrition screening tool for pediatric patients. To validate STAMP (Screening Tool for the Assessment of Malnutrition in Pediatrics) pediatric screening tool in Spain. Descriptive cross-sectional study of patients admitted to a 3rd level children's hospital with both medical and surgical specialities. During the first 24 hours of admission, STAMP screening tool was applied. For its validation, results were compared with those obtained from a nutritional assessment performed by specialist staff, which included clinical, anthropometric and body composition data. A sample of 250 children was studied. Nutritional assessment identified 64 patients (25.6%) under risk, 40 of whom were malnourished (16%). STAMP classified 48.4% of the patients as being under nutritional risk. This tool showed 75% sensitivity and 60.8% specificity when identifying patients under risk according to nutritional assessment. It showed 90% sensitivity and 59.5% specificity when identifying malnourished patients. Malnutrition was less frequent than that reported in other European countries, although diagnosis technique was different. STAMP is a simple and useful tool for nutritional screening, avoiding the need to assess all patients on admission in order to identify those under nutritional risk.

Automated Solid-Phase Protein Modification with Integrated Enzymatic Digest for Reaction Validation: Application of a Compartmented Microfluidic Reactor for Rapid Optimization and Analysis of Protein Biotinylation

PubMed Central

Fraas, Regina; Diehm, Juliane; Franzreb, Matthias

2017-01-01

Protein modification by covalent coupling of small ligands or markers is an important prerequisite for the use of proteins in many applications. Well-known examples are the use of proteins with fluorescent markers in many in vivo experiments or the binding of biotinylated antibodies via biotin–streptavidin coupling in the frame of numerous bioassays. Multiple protocols were established for the coupling of the respective molecules, e.g., via the C and N-terminus, or via cysteines and lysines exposed at the protein surface. Still, in most cases the conditions of these standard protocols are only an initial guess. Optimization of the coupling parameters like reagent concentrations, pH, or temperature may strongly increase coupling yield and the biological activity of the modified protein. In order to facilitate the process of optimizing coupling conditions, a method was developed which uses a compartmented microfluidic reactor for the rapid screening of different coupling conditions. In addition, the system allows for the integration of an enzymatic digest of the modified protein directly after modification. In combination with a subsequent MALDI-TOF analysis of the resulting fragments, this gives a fast and detailed picture not only of the number and extent of the generated modifications but also of their position within the protein sequence. The described process was demonstrated for biotinylation of green fluorescent protein. Different biotin-excesses and different pH-values were tested in order to elucidate the influence on the modification extent and pattern. In addition, the results of solid-phase based modifications within the microfluidic reactor were compared to modification patterns resulting from coupling trials with unbound protein. As expected, modification patterns of immobilized proteins showed clear differences to the ones of dissolved proteins. PMID:29181376

Optimal healthcare decision making under multiple mathematical models: application in prostate cancer screening.

PubMed

Bertsimas, Dimitris; Silberholz, John; Trikalinos, Thomas

2018-03-01

Important decisions related to human health, such as screening strategies for cancer, need to be made without a satisfactory understanding of the underlying biological and other processes. Rather, they are often informed by mathematical models that approximate reality. Often multiple models have been made to study the same phenomenon, which may lead to conflicting decisions. It is natural to seek a decision making process that identifies decisions that all models find to be effective, and we propose such a framework in this work. We apply the framework in prostate cancer screening to identify prostate-specific antigen (PSA)-based strategies that perform well under all considered models. We use heuristic search to identify strategies that trade off between optimizing the average across all models' assessments and being "conservative" by optimizing the most pessimistic model assessment. We identified three recently published mathematical models that can estimate quality-adjusted life expectancy (QALE) of PSA-based screening strategies and identified 64 strategies that trade off between maximizing the average and the most pessimistic model assessments. All prescribe PSA thresholds that increase with age, and 57 involve biennial screening. Strategies with higher assessments with the pessimistic model start screening later, stop screening earlier, and use higher PSA thresholds at earlier ages. The 64 strategies outperform 22 previously published expert-generated strategies. The 41 most "conservative" ones remained better than no screening with all models in extensive sensitivity analyses. We augment current comparative modeling approaches by identifying strategies that perform well under all models, for various degrees of decision makers' conservativeness.

Influence of qualitative research on women's health screening guidelines.

PubMed

Abadir, Anna Maria; Lang, Ariella; Klein, Talia; Abenhaim, Haim Arie

2014-01-01

Considerable time and resources are allocated to carry out qualitative research. The purpose of our study was to evaluate the availability of qualitative research on women's health screening and assess its influence on screening practice guidelines in the United States, Canada, and the United Kingdom. Medline, CINHAL, and WEB of Science databases were used to identify the availability of qualitative research conducted in the past 15 years on 3 different women's health screening topics: cervical cancer screening, breast cancer screening, and prenatal first-trimester screening. Key national practice guidelines on women's health screening were selected using the National Guideline Clearinghouse web site. Bibliometric analysis was used to determine the frequency of qualitative references cited in the guidelines. A total of 272 qualitative research papers on women's health screening was identified: 109 on cervical cancer screening, 104 on breast cancer screening, and 59 on prenatal first-trimester screening. The qualitative studies focused on health care provider perspectives as well as ethical, ethnographic, psychological, and social issues surrounding screening. Fifteen national clinical practice guidelines on women's health screening were identified. A total of 943 references was cited, only 2 of which comprised of qualitative research cited by only 1 clinical practice guideline. Although there is considerable qualitative research that has been carried out on women's health screening, its incorporation into clinical practice guidelines is minimal. Further exploration of the disconnect between the two is important for enhancing knowledge translation of qualitative research within clinical practice. Copyright © 2014 Mosby, Inc. All rights reserved.

SPATA2 promotes CYLD activity and regulates TNF-induced NF-κB signaling and cell death.

PubMed

Schlicher, Lisa; Wissler, Manuela; Preiss, Florian; Brauns-Schubert, Prisca; Jakob, Celia; Dumit, Veronica; Borner, Christoph; Dengjel, Joern; Maurer, Ulrich

2016-10-01

K63- and Met1-linked ubiquitylation are crucial posttranslational modifications for TNF receptor signaling. These non-degradative ubiquitylations are counteracted by deubiquitinases (DUBs), such as the enzyme CYLD, resulting in an appropriate signal strength, but the regulation of this process remains incompletely understood. Here, we describe an interaction partner of CYLD, SPATA2, which we identified by a mass spectrometry screen. We find that SPATA2 interacts via its PUB domain with CYLD, while a PUB interaction motif (PIM) of SPATA2 interacts with the PUB domain of the LUBAC component HOIP SPATA2 is required for the recruitment of CYLD to the TNF receptor signaling complex upon TNFR stimulation. Moreover, SPATA2 acts as an allosteric activator for the K63- and M1-deubiquitinase activity of CYLD In consequence, SPATA2 substantially attenuates TNF-induced NF-κB and MAPK signaling. Conversely, SPATA2 is required for TNF-induced complex II formation, caspase activation, and apoptosis. Thus, this study identifies SPATA2 as an important factor in the TNF signaling pathway with a substantial role for the effects mediated by the cytokine. © 2016 The Authors.

A biochemical landscape of A-to-I RNA editing in the human brain transcriptome

PubMed Central

Sakurai, Masayuki; Ueda, Hiroki; Yano, Takanori; Okada, Shunpei; Terajima, Hideki; Mitsuyama, Toutai; Toyoda, Atsushi; Fujiyama, Asao; Kawabata, Hitomi; Suzuki, Tsutomu

2014-01-01

Inosine is an abundant RNA modification in the human transcriptome and is essential for many biological processes in modulating gene expression at the post-transcriptional level. Adenosine deaminases acting on RNA (ADARs) catalyze the hydrolytic deamination of adenosines to inosines (A-to-I editing) in double-stranded regions. We previously established a biochemical method called “inosine chemical erasing” (ICE) to directly identify inosines on RNA strands with high reliability. Here, we have applied the ICE method combined with deep sequencing (ICE-seq) to conduct an unbiased genome-wide screening of A-to-I editing sites in the transcriptome of human adult brain. Taken together with the sites identified by the conventional ICE method, we mapped 19,791 novel sites and newly found 1258 edited mRNAs, including 66 novel sites in coding regions, 41 of which cause altered amino acid assignment. ICE-seq detected novel editing sites in various repeat elements as well as in short hairpins. Gene ontology analysis revealed that these edited mRNAs are associated with transcription, energy metabolism, and neurological disorders, providing new insights into various aspects of human brain functions. PMID:24407955

Rapid Detection of Dendritic Cell and Monocyte Disorders Using CD4 as a Lineage Marker of the Human Peripheral Blood Antigen-Presenting Cell Compartment

PubMed Central

Jardine, Laura; Barge, Dawn; Ames-Draycott, Ashley; Pagan, Sarah; Cookson, Sharon; Spickett, Gavin; Haniffa, Muzlifah; Collin, Matthew; Bigley, Venetia

2013-01-01

Dendritic cells (DCs) and monocytes are critical regulators and effectors of innate and adaptive immune responses. Monocyte expansion has been described in many pathological states while monocyte and DC deficiency syndromes are relatively recent additions to the catalog of human primary immunodeficiency disorders. Clinically applicable screening tests to diagnose and monitor these conditions are lacking. Conventional strategies for identifying human DCs and monocytes have been based on the use of a lineage gate to exclude lymphocytes, thus preventing simultaneous detection of DCs, monocytes, and lymphocyte subsets. Here we demonstrate that CD4 is a reliable lineage marker for the human peripheral blood antigen-presenting cell compartment that can be used to identify DCs and monocytes in parallel with lymphocytes. Based on this principle, simple modification of a standard lymphocyte phenotyping assay permits simultaneous enumeration of four lymphocyte and five DC/monocyte populations from a single sample. This approach is applicable to clinical samples and facilitates the diagnosis of DC and monocyte disorders in a wide range of clinical settings, including genetic deficiency, neoplasia, and inflammation. PMID:24416034

Assessment of deoxyhypusine hydroxylase as a putative, novel drug target.

PubMed

Kerscher, B; Nzukou, E; Kaiser, A

2010-02-01

Antimalarial drug resistance has nowadays reached each drug class on the market for longer than 10 years. The focus on validated, classical targets has severe drawbacks. If resistance is arising or already present in the field, a target-based High-Throughput-Screening (HTS) with the respective target involves the risk of identifying compounds to which field populations are also resistant. Thus, it appears that a rewarding albeit demanding challenge for target-based drug discovery is to identify novel drug targets. In the search for new targets for antimalarials, we have investigated the biosynthesis of hypusine, present in eukaryotic initiation factor 5A (eIF5A). Deoxyhypusine hydroxylase (DOHH), which has recently been cloned and expressed from P. falciparum, completes the modification of eIF5A through hydroxylation. Here, we assess the present druggable data on Plasmodium DOHH and its human counterpart. Plasmodium DOHH arose from a cyanobacterial phycobilin lyase by loss of function. It has a low FASTA score of 27 to its human counterpart. The HEAT-like repeats present in the parasite DOHH differ in number and amino acid identity from its human ortholog and might be of considerable interest for inhibitor design.

Inhibitors for the Vitamin D Receptor–Coregulator Interaction

PubMed Central

Teske, Kelly A.; Yu, Olivia; Arnold, Leggy A.

2016-01-01

The vitamin D receptor (VDR) belongs to the superfamily of nuclear receptors and is activated by the endogenous ligand 1,25-dihydroxyvitamin D3. The genomic effects mediated by VDR consist of the activation and repression of gene transcription, which includes the formation of multi-protein complexes with coregulator proteins. Coregulators bind many nuclear receptors and can be categorized according their role as coactivators (gene activation) or corepressors (gene repression). Herein, different approaches to develop compounds that modulate the interaction between VDR and coregulators are summarized. This include coregulator peptides that were identified by creating phage display libraries. Subsequent modification of these peptides including the introduction of a tether or non-hydrolysable bonds resulted in the first direct VDR–coregulator inhibitors. Later, small molecules that inhibit VDR–coregulator inhibitors were identified using rational drug design and high throughput screening. Early on, allosteric inhibition of VDR–coregulator interactions was achieved with VDR antagonists that change the conformation of VDR and modulate the interactions with coregulators. A detailed discussion of their dual agonist/antagonist effects is given as well as a summary of their biological effects in cell-based assays and in vivo studies. PMID:26827948

Accessible Home Environments for People with Functional Limitations: A Systematic Review.

PubMed

Cho, Hea Young; MacLachlan, Malcolm; Clarke, Michael; Mannan, Hasheem

2016-08-17

The aim of this review is to evaluate the health and social effects of accessible home environments for people with functional limitations, in order to provide evidence to promote well-informed decision making for policy guideline development and choices about public health interventions. MEDLINE and nine other electronic databases were searched between December 2014 and January 2015, for articles published since 2004. All study types were included in this review. Two reviewers independently screened 12,544 record titles or titles and abstracts based on our pre-defined eligibility criteria. We identified 94 articles as potentially eligible; and assessed their full text. Included studies were critically appraised using the Mixed Method Appraisal Tool, version 2011. Fourteen studies were included in the review. We did not identify any meta-analysis or systematic review directly relevant to the question for this systematic review. A narrative approach was used to synthesise the findings of the included studies due to methodological and statistical heterogeneity. Results suggest that certain interventions to enhance the accessibility of homes can have positive health and social effects. Home environments that lack accessibility modifications appropriate to the needs of their users are likely to result in people with physical impairments becoming disabled at home.

Review of Operational Challenges and Changing Conditions associated with Offshore Submerged Vertical Pumping Station

NASA Astrophysics Data System (ADS)

Samsudin, M. L.; Munisamy, K. M.; Thangaraju, S. K.

2015-09-01

Cooling water system is one of the essential auxiliary systems for a power generating plant. The decision to have an offshore pumping station, instead of onshore station, may have been driven by the scarcity in land area or for direct water supply access. However, the design has several disadvantages such as tendency for sediment intakes, limited condition monitoring activities and inaccessible sump for maintenance and modification. The paper reviews and lists several potential operational challenges and difficulties experienced with the offshore station. The influences of changing conditions such as varying seawater tide level, clogged intake screen, intake sedimentation issues and marine fouling on the sump walls and structures, are discussed and mitigating solutions are identified. While it is impractical to conduct physical model test for studying flow pattern, the CFD method can be an attractive assessment tools. In addition to this, a review of plant operating parameters can assist in identifying flow anomalies to anticipate potential deterioration. Finally the difficulty in incorporating the solutions to vortex and sediment problems within the sump is highlighted with preference for those which can be managed by limited access or those which are moveable with the vertical pump.

False-positive cancer screens and health-related quality of life.

PubMed

McGovern, Patricia M; Gross, Cynthia R; Krueger, Richard A; Engelhard, Deborah A; Cordes, Jill E; Church, Timothy R

2004-01-01

By design, screening tests are imperfect-unresponsive to some cancers (false negatives) while occasionally raising suspicion of cancer where none exists (false positives). This pilot study describes patients' responses to having a false-positive screening test for cancer, and identifies screening effects on health-related quality of life (HRQoL). The pilot findings suggest issues important for incorporation in future evaluations of the impact of screening for prostate, lung, colon, or ovarian (PLCO) cancers. Seven focus groups were conducted to identify the nature and meaning of all phases of PLCO screening. Minnesota participants in the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial who had completed screening, with at least 1 false-positive screen, participated (N = 47). Participants' reactions to abnormal screens and diagnostic work-ups were primarily emotional (eg, anxiety and distress), not physical, and ultimately positive for the majority. Health distress and fear of cancer and death were the major negative aspects of HRQoL identified. These concepts are not typically included in generic HRQoL questionnaires like the SF-36, but are highly relevant to PLCO screening. Clinicians were regarded as underestimating the discomfort of follow-up diagnostic testing. However, relief and assurance appeared to eventually outweigh the negative emotions for most participants. Implications for oncology nurses include the need to consider the emotional consequences of screening in association with screen reliability and validity.

A parallel genome-wide RNAi screening strategy to identify host proteins important for entry of Marburg virus and H5N1 influenza virus.

PubMed

Cheng, Han; Koning, Katie; O'Hearn, Aileen; Wang, Minxiu; Rumschlag-Booms, Emily; Varhegyi, Elizabeth; Rong, Lijun

2015-11-24

Genome-wide RNAi screening has been widely used to identify host proteins involved in replication and infection of different viruses, and numerous host factors are implicated in the replication cycles of these viruses, demonstrating the power of this approach. However, discrepancies on target identification of the same viruses by different groups suggest that high throughput RNAi screening strategies need to be carefully designed, developed and optimized prior to the large scale screening. Two genome-wide RNAi screens were performed in parallel against the entry of pseudotyped Marburg viruses and avian influenza virus H5N1 utilizing an HIV-1 based surrogate system, to identify host factors which are important for virus entry. A comparative analysis approach was employed in data analysis, which alleviated systematic positional effects and reduced the false positive number of virus-specific hits. The parallel nature of the strategy allows us to easily identify the host factors for a specific virus with a greatly reduced number of false positives in the initial screen, which is one of the major problems with high throughput screening. The power of this strategy is illustrated by a genome-wide RNAi screen for identifying the host factors important for Marburg virus and/or avian influenza virus H5N1 as described in this study. This strategy is particularly useful for highly pathogenic viruses since pseudotyping allows us to perform high throughput screens in the biosafety level 2 (BSL-2) containment instead of the BSL-3 or BSL-4 for the infectious viruses, with alleviated safety concerns. The screening strategy together with the unique comparative analysis approach makes the data more suitable for hit selection and enables us to identify virus-specific hits with a much lower false positive rate.

CRISPR screen identifies the NCOR/HDAC3 complex as a major suppressor of differentiation in rhabdomyosarcoma

PubMed Central

Phelps, Michael P.; Bailey, Jenna N.; Vleeshouwer-Neumann, Terra

2016-01-01

Dysregulated gene expression resulting from abnormal epigenetic alterations including histone acetylation and deacetylation has been demonstrated to play an important role in driving tumor growth and progression. However, the mechanisms by which specific histone deacetylases (HDACs) regulate differentiation in solid tumors remains unclear. Using pediatric rhabdomyosarcoma (RMS) as a paradigm to elucidate the mechanism blocking differentiation in solid tumors, we identified HDAC3 as a major suppressor of myogenic differentiation from a high-efficiency Clustered regularly interspaced short palindromic repeats (CRISPR)-based phenotypic screen of class I and II HDAC genes. Detailed characterization of the HDAC3-knockout phenotype in vitro and in vivo using a tamoxifen-inducible CRISPR targeting strategy demonstrated that HDAC3 deacetylase activity and the formation of a functional complex with nuclear receptor corepressors (NCORs) were critical in restricting differentiation in RMS. The NCOR/HDAC3 complex specifically functions by blocking myoblast determination protein 1 (MYOD1)-mediated activation of myogenic differentiation. Interestingly, there was also a transient up-regulation of growth-promoting genes upon initial HDAC3 targeting, revealing a unique cancer-specific response to the forced transition from a neoplastic state to terminal differentiation. Our study applied modifications of CRISPR/CRISPR-associated endonuclease 9 (Cas9) technology to interrogate the function of essential cancer genes and pathways and has provided insights into cancer cell adaptation in response to altered differentiation status. Because current pan-HDAC inhibitors have shown disappointing results in clinical trials of solid tumors, therapeutic targets specific to HDAC3 function represent a promising option for differentiation therapy in malignant tumors with dysregulated HDAC3 activity. PMID:27956629

Genome-wide Escherichia coli stress response and improved tolerance towards industrially relevant chemicals.

PubMed

Rau, Martin Holm; Calero, Patricia; Lennen, Rebecca M; Long, Katherine S; Nielsen, Alex T

2016-10-13

Economically viable biobased production of bulk chemicals and biofuels typically requires high product titers. During microbial bioconversion this often leads to product toxicity, and tolerance is therefore a critical element in the engineering of production strains. Here, a systems biology approach was employed to understand the chemical stress response of Escherichia coli, including a genome-wide screen for mutants with increased fitness during chemical stress. Twelve chemicals with significant production potential were selected, consisting of organic solvent-like chemicals (butanol, hydroxy-γ-butyrolactone, 1,4-butanediol, furfural), organic acids (acetate, itaconic acid, levulinic acid, succinic acid), amino acids (serine, threonine) and membrane-intercalating chemicals (decanoic acid, geraniol). The transcriptional response towards these chemicals revealed large overlaps of transcription changes within and between chemical groups, with functions such as energy metabolism, stress response, membrane modification, transporters and iron metabolism being affected. Regulon enrichment analysis identified key regulators likely mediating the transcriptional response, including CRP, RpoS, OmpR, ArcA, Fur and GadX. These regulators, the genes within their regulons and the above mentioned cellular functions therefore constitute potential targets for increasing E. coli chemical tolerance. Fitness determination of genome-wide transposon mutants (Tn-seq) subjected to the same chemical stress identified 294 enriched and 336 depleted mutants and experimental validation revealed up to 60 % increase in mutant growth rates. Mutants enriched in several conditions contained, among others, insertions in genes of the Mar-Sox-Rob regulon as well as transcription and translation related gene functions. The combination of the transcriptional response and mutant screening provides general targets that can increase tolerance towards not only single, but multiple chemicals.

CRISPR screen identifies the NCOR/HDAC3 complex as a major suppressor of differentiation in rhabdomyosarcoma.

PubMed

Phelps, Michael P; Bailey, Jenna N; Vleeshouwer-Neumann, Terra; Chen, Eleanor Y

2016-12-27

Dysregulated gene expression resulting from abnormal epigenetic alterations including histone acetylation and deacetylation has been demonstrated to play an important role in driving tumor growth and progression. However, the mechanisms by which specific histone deacetylases (HDACs) regulate differentiation in solid tumors remains unclear. Using pediatric rhabdomyosarcoma (RMS) as a paradigm to elucidate the mechanism blocking differentiation in solid tumors, we identified HDAC3 as a major suppressor of myogenic differentiation from a high-efficiency Clustered regularly interspaced short palindromic repeats (CRISPR)-based phenotypic screen of class I and II HDAC genes. Detailed characterization of the HDAC3-knockout phenotype in vitro and in vivo using a tamoxifen-inducible CRISPR targeting strategy demonstrated that HDAC3 deacetylase activity and the formation of a functional complex with nuclear receptor corepressors (NCORs) were critical in restricting differentiation in RMS. The NCOR/HDAC3 complex specifically functions by blocking myoblast determination protein 1 (MYOD1)-mediated activation of myogenic differentiation. Interestingly, there was also a transient up-regulation of growth-promoting genes upon initial HDAC3 targeting, revealing a unique cancer-specific response to the forced transition from a neoplastic state to terminal differentiation. Our study applied modifications of CRISPR/CRISPR-associated endonuclease 9 (Cas9) technology to interrogate the function of essential cancer genes and pathways and has provided insights into cancer cell adaptation in response to altered differentiation status. Because current pan-HDAC inhibitors have shown disappointing results in clinical trials of solid tumors, therapeutic targets specific to HDAC3 function represent a promising option for differentiation therapy in malignant tumors with dysregulated HDAC3 activity.

Pilot study on use of home telephoning to identify and recruit high-risk individuals for lung cancer screening.

PubMed

Veronesi, Giulia; Colombo, Paolo; Novellis, Pierluigi; Crepaldi, Alessandro; Lutman, Romano Fabio; Dieci, Elisa; Profili, Manuel; Siracusano, Licia; Alloisio, Marco

2017-03-01

Widespread lung cancer screening with low-dose computed tomography is urgently needed in Europe to identify lung cancers early and reduce lung cancer deaths. The most effective method of identifying high-risk individuals and recruiting them for screening has not been determined. In the present pilot study we investigated direct telephoning to families as a way of identifying high risk individuals and recruiting them to a screening/smoking cessation program, that avoided the selection bias of voluntary screening. Families in the province of Milan, Italy, were contacted by telephone at their homes and asked about family members over 50 years who were heavy smokers (30 or more pack-years). Persons meeting these criteria were contacted and asked to participate in the program. Those who agreed were given an appointment to undergo screening and receive smoking cessation counseling. Among the 1000 contacted families, involving 2300 persons, 44 (1.9%) were eligible for LDCT screening, and 12 (27%) of these participated in the program. The cost of this recruitment strategy pilot study was around 150 euro per screened subject. We obtained useful information on the proportion of the general population eligible for lung cancer screening and the proportion of those who responded. However the cost of home telephone calling is probably too high to be practicable as a method of recruiting high risk persons for screening. Alternative recruitment methods, possibly involving family physicians practitioners, need to be investigated. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

Screening for colorectal cancer.

PubMed

Ross, C C

1988-12-01

Efforts to decrease the number of deaths from colorectal cancer have focused on screening techniques, since no etiologic agent has been identified. Current screening regimens are designed to detect colorectal cancer in a large population in a cost-efficient manner and to minimize the risks associated with work-ups for false-positive tests. A two-part screening questionnaire for colorectal cancer helps identify patients who are at moderate risk for this cancer.

Compounds with species and cell type specific toxicity identified in a 2000 compound drug screen of neural stem cells and rat mixed cortical neurons.

PubMed

Malik, Nasir; Efthymiou, Anastasia G; Mather, Karly; Chester, Nathaniel; Wang, Xiantao; Nath, Avindra; Rao, Mahendra S; Steiner, Joseph P

2014-12-01

Human primary neural tissue is a vital component for the quick and simple determination of chemical compound neurotoxicity in vitro. In particular, such tissue would be ideal for high-throughput screens that can be used to identify novel neurotoxic or neurotherapeutic compounds. We have previously established a high-throughput screening platform using human induced pluripotent stem cell (iPSC)-derived neural stem cells (NSCs) and neurons. In this study, we conducted a 2000 compound screen with human NSCs and rat cortical cells to identify compounds that are selectively toxic to each group. Approximately 100 of the tested compounds showed specific toxicity to human NSCs. A secondary screen of a small subset of compounds from the primary screen on human iPSCs, NSC-derived neurons, and fetal astrocytes validated the results from >80% of these compounds with some showing cell specific toxicity. Amongst those compounds were several cardiac glycosides, all of which were selectively toxic to the human cells. As the screen was able to reliably identify neurotoxicants, many with species and cell-type specificity, this study demonstrates the feasibility of this NSC-driven platform for higher-throughput neurotoxicity screens. Published by Elsevier B.V.

Cross-species extrapolation of toxicity information using the ...

EPA Pesticide Factsheets

In the United States, the Endocrine Disruptor Screening Program (EDSP) was established to identify chemicals that may lead to adverse effects via perturbation of the endocrine system (i.e., estrogen, androgen, and thyroid hormone systems). In the mid-1990s the EDSP adopted a two tiered approach for screening chemicals that applied standardized in vitro and in vivo toxicity tests. The Tier 1 screening assays were designed to identify substances that have the potential of interacting with the endocrine system and Tier 2 testing was developed to identify adverse effects caused by the chemical, with documentation of dose-response relationships. While this tiered approach was effective in identifying possible endocrine disrupting chemicals, the cost and time to screen a single chemical was significant. Therefore, in 2012 the EDSP proposed a transition to make greater use of computational approaches (in silico) and high-throughput screening (HTS; in vitro) assays to more rapidly and cost-efficiently screen chemicals for endocrine activity. This transition from resource intensive, primarily in vivo, screening methods to more pathway-based approaches aligns with the simultaneously occurring transformation in toxicity testing termed “Toxicity Testing in the 21st Century” which shifts the focus to the disturbance of the biological pathway predictive of the observable toxic effects. An example of such screening tools include the US Environmental Protection Agency’s

Elevation and igneous crater modification on Venus: Implications for magmatic volatile content

NASA Technical Reports Server (NTRS)

Wichman, R. W.

1993-01-01

Although most impact craters on Venus preserve nearly pristine crater rim and ejecta features, a small number of craters have been identified showing clear evidence of either igneous intrusion emplacement (floor-fracturing) beneath the crater floor or of volcanically embayed exterior ejecta deposits. Since the volcanically embayed craters consistently occur at higher elevations than the identified floor-fractured craters, this report proposes that igneous crater modification on Venus is elevation dependent. This report describes how regional variations in magmatic neutral buoyancy could produce such elevation dependent crater modification and considers the implications for typical magmatic volatile contents on Venus.

A novel mutation (ASn244Lys) in the peripherin/RDS gene causing autosomal dominant retinitis pigmentosa associated with bull's eye maculopathy detected by nonradioisotopic SSCP

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kikawa, Emi; Nakazawa, Mitsuru; Chida, Yasushi

1994-03-01

Retinitis pigmentosa (RP) is characterized by night blindness, an eventual loss of visual field, a diminished response on the electroretinogram, and pigmentary retinal degeneration. These features are primarily explained by the degeneration of photoreceptors. The recent development of the molecular genetic approach has enabled the identification of genes responsible for parts of autosomal dominant RP (ADRP). Rhodopsin and peripherin/RDS genes, in particular, have been successfully shown to cosegregate with ADRP. The authors, therefore, screened 42 unrelated Japanese patients with ADRP to search for mutations in the peripherin/RDS gene. The method we employed for screening was a nonradioisotopic modification of single-strandmore » conformation polymorphism. Among 42 unrelated patients with ADRP, the DNA from one patient (SY) showed an abnormal pattern in exon 2 on SSCP. The DNA fragments were then amplified from affected and nonaffected members of the same family as SY. The alteration in the DNA sequence that was commonly found in the affected members of the family was identified as a heterozygous transversional change of C to A at the third nucleotide in codon 244, resulting in the amino acid replacement of asparagine residue with lysine residue. None of unaffected family members or 30 normal control individuals had this alteration.« less

Detecting Cancer Quickly and Accurately

NASA Astrophysics Data System (ADS)

Gourley, Paul; McDonald, Anthony; Hendricks, Judy; Copeland, Guild; Hunter, John; Akhil, Ohmar; Capps, Heather; Curry, Marc; Skirboll, Steve

2000-03-01

We present a new technique for high throughput screening of tumor cells in a sensitive nanodevice that has the potential to quickly identify a cell population that has begun the rapid protein synthesis and mitosis characteristic of cancer cell proliferation. Currently, pathologists rely on microscopic examination of cell morphology using century-old staining methods that are labor-intensive, time-consuming and frequently in error. New micro-analytical methods for automated, real time screening without chemical modification are critically needed to advance pathology and improve diagnoses. We have teamed scientists with physicians to create a microlaser biochip (based upon our R&D award winning bio-laser concept)1 which evaluates tumor cells by quantifying their growth kinetics. The key new discovery was demonstrating that the lasing spectra are sensitive to the biomolecular mass in the cell, which changes the speed of light in the laser microcavity. Initial results with normal and cancerous human brain cells show that only a few hundred cells -- the equivalent of a billionth of a liter -- are required to detect abnormal growth. The ability to detect cancer in such a minute tissue sample is crucial for resecting a tumor margin or grading highly localized tumor malignancy. 1. P. L. Gourley, NanoLasers, Scientific American, March 1998, pp. 56-61. This work supported under DOE contract DE-AC04-94AL85000 and the Office of Basic Energy Sciences.

Screening Procedures Used to Identify Children with Hearing Loss.

ERIC Educational Resources Information Center

Barringer, Donald G.; And Others

1993-01-01

Analysis of data on 1,404 young children with hearing losses indicated that 80% of the children were identified via informal hearing-screening procedures, such as parental suspicion and referral. Auditory brainstem response technology provided the lowest mean identification age. The study concludes that formal screening programs are not locating…

Assessment of the structural validity of the domestic violence healthcare providers’ survey questionnaire using a Nigerian sample

PubMed Central

John, Ime A; Lawoko, Stephen

2010-01-01

Abstract: Background: There has been increased advocacy to involve healthcare providers in the prevention of intimate partner violence (IPV) through screening for it in healthcare. Yet, only one in ten providers screen for IPV, suggesting barriers. Understanding the readiness of healthcare providers to screen for IPV is therefore paramount. The Domestic Violence Healthcare Provider Survey Scales (DVHPSS) is a previously validated, comprehensive scale to study readiness of healthcare providers to screen for IPV. However, an understanding of its usefulness in the Sub-Saharan African context remains elusive. The current study undertook to examine the structural validity of the DVHPSS in Nigeria. Methods: Exploratory factor analysis and Cronbach's Alpha were run to reveal the factorial structure and reliability of the instrument/subscales respectively. Established thresholds were used to determine significant factor loadings and alphas coefficient. Results: A six factor model emerged, with 2 factors similar to the original scale, another two differing slightly and a further two factors resulting from a splitting up of the original combination of victim/provider safety to having distinct victim and provider safety subscales. Conclusions: With slight modifications, the DVHPSS can be use to study IPV screening among Nigerian healthcare professionals. Introducing screening protocols could promote better understanding of crucial questions that were lost in the analysis. PMID:21483202

Pilot study on the use of data mining to identify cochlear implant candidates.

PubMed

Grisel, Jedidiah J; Schafer, Erin; Lam, Anne; Griffin, Terry

2018-05-01

The goal of this pilot study was to determine the clinical utility of data-mining software that screens for cochlear implant (CI) candidacy. The Auditory Implant Initiative developed a software module that screens for CI candidates via integration with a software system (Noah 4) that serves as a depository for hearing test data. To identify candidates, patient audiograms from one practice were exported into the screening module. Candidates were tracked to determine if any eventually underwent implantation. After loading 4836 audiograms from the Noah 4 system, the screening module identified 558 potential CI candidates. After reviewing the data for the potential candidates, 117 were targeted and invited to an educational event. Following the event, a total of six candidates were evaluated, and two were implanted. This objective approach to identifying candidates has the potential to address the gross underutilization of CIs by removing any bias or lack of knowledge regarding the management of severe to profound sensorineural hearing loss with CIs. The screening module was an effective tool for identifying potential CI candidates at one ENT practice. On a larger scale, the screening module has the potential to impact thousands of CI candidates worldwide.

2-Guanidino-quinazolines as a novel class of translation inhibitors.

PubMed

Komarova Andreyanova, E S; Osterman, I A; Pletnev, P I; Ivanenkov, Y A; Majouga, A G; Bogdanov, A A; Sergiev, P V

2017-02-01

A variety of structurally unrelated organic compounds has been reported to have antibacterial activity. Among these, certain small-molecule translation inhibitors have attracted a great deal of attention, due to their relatively high selectivity against prokaryotes, and an appropriate therapeutic index with minor "off target" effects. However, ribosomes are being considered as poorly druggable biological targets, thereby making some routine computational-based approaches to rational drug design and its development rather ineffective. Taking this into account, diversity-oriented biological screening can reasonably be considered as the most advantageous strategy. Thus, using a high-throughput screening (HTS) platform, we applied a unique biological assay for in vitro evaluation of thousands of organic molecules, especially targeted against bacterial ribosomes and translation. As a result, we have identified a series of structurally diverse small-molecule compounds that induce a reporter strain sensitive to translation and DNA biosynthesis inhibitors. In a cell free system, several molecules were found to strongly inhibit protein biosynthesis. Among them, compounds bearing a 2-guanidino-quinazoline core demonstrated the most promising antibacterial activity. With regard to the preliminary structure-activity relationship (SAR) study, we revealed that relatively small substituents at positions 4, 6 and 8 of the quinazoline ring significantly enhance the target activity whereas modification of the guanidine group leads to decrease or loss of antibacterial potency. This novel class of translation inhibitors can properly be regarded as a promising starting point for the development of novel antibacterial therapeutic or screening tools. Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

The C. elegans Excretory Canal as a Model for Intracellular Lumen Morphogenesis and In Vivo Polarized Membrane Biogenesis in a Single Cell: labeling by GFP-fusions, RNAi Interaction Screen and Imaging.

PubMed

Zhang, Nan; Membreno, Edward; Raj, Susan; Zhang, Hongjie; Khan, Liakot A; Gobel, Verena

2017-10-03

The four C. elegans excretory canals are narrow tubes extended through the length of the animal from a single cell, with almost equally far extended intracellular endotubes that build and stabilize the lumen with a membrane and submembraneous cytoskeleton of apical character. The excretory cell expands its length approximately 2,000 times to generate these canals, making this model unique for the in vivo assessment of de novo polarized membrane biogenesis, intracellular lumen morphogenesis and unicellular tubulogenesis. The protocol presented here shows how to combine standard labeling, gain- and loss-of-function genetic or RNA interference (RNAi)-, and microscopic approaches to use this model to visually dissect and functionally analyze these processes on a molecular level. As an example of a labeling approach, the protocol outlines the generation of transgenic animals with fluorescent fusion proteins for live analysis of tubulogenesis. As an example of a genetic approach, it highlights key points of a visual RNAi-based interaction screen designed to modify a gain-of-function cystic canal phenotype. The specific methods described are how to: label and visualize the canals by expressing fluorescent proteins; construct a targeted RNAi library and strategize RNAi screening for the molecular analysis of canal morphogenesis; visually assess modifications of canal phenotypes; score them by dissecting fluorescence microscopy; characterize subcellular canal components at higher resolution by confocal microscopy; and quantify visual parameters. The approach is useful for the investigator who is interested in taking advantage of the C. elegans excretory canal for identifying and characterizing genes involved in the phylogenetically conserved processes of intracellular lumen and unicellular tube morphogenesis.

Practices to improve identification of Adult Antiretroviral Therapy failure at the Lighthouse Trust clinic in Lilongwe, Malawi

PubMed Central

Vorkas, Charles Kyriakos; Tweya, Hannock; Mzinganjira, Dalitso; Dickie, George; Weigel, Ralf; Phiri, Sam; Hosseinipour, Mina C.

2011-01-01

Summary Background Evaluating treatment failure is critical when deciding to modify antiretroviral therapy (ART). Virologic Assessment Forms (VAFs) were implemented in July 2008 as a prerequisite for ordering viral load. The form requires assessment of clinical and immunologic status. Methods Using the Electronic Medical Record (EMR), we retrospectively evaluated patients who met 2006 WHO guidelines for immunologic failure (≥15 years old; on ART ≥6 months; CD4 count 50% drop from peak OR CD4 persistently <100 cells) at the Lighthouse Trust clinic from 12/2007–12/2009. We compared virologic screening, VAF implementation and ART modification during the same period using Fisher’s exact tests and unpaired t-tests as appropriate. Results Of 7,000 enrolled ART patients ≥ 15 years old with at least two CD4 counts, 10% had immunologic failure with a median follow-up time on ART of 1.4 years (IQR: 0.8–2.3). Forty (6%) viral loads were ordered: 14 (35%) were detectable (>400 HIV RNA copies/mL) and 1 (7%) patient was switched to second-line therapy. Overall, 259 VAFs were completed: 67% for immunologic failure and 33% for WHO Stage 4 condition. Before VAF implementation, 1% of patients had viral loads drawn during routine care, whereas afterwards, 8% did (p<0.0001; 95% CI 0.03–0.08). Conclusions Clinicians did not identify a large proportion of immunologic failure patients for screening. Implementation of VAFs produced little improvement in virologic screening during routine care. Better training and monitoring systems are needed. PMID:22039960

An in vitro approach for lipolysis measurement using high-resolution mass spectrometry and partial least squares based analysis.

PubMed

Chang, Wen-Qi; Zhou, Jian-Liang; Li, Yi; Shi, Zi-Qi; Wang, Li; Yang, Jie; Li, Ping; Liu, Li-Fang; Xin, Gui-Zhong

2017-01-15

The elevation of free fatty acids (FFAs) has been regarded as a universal metabolic signature of excessive adipocyte lipolysis. Nowadays, in vitro lipolysis assay is generally essential for drug screening prior to the animal study. Here, we present a novel in vitro approach for lipolysis measurement combining UHPLC-Orbitrap and partial least squares (PLS) based analysis. Firstly, the calibration matrix was constructed by serial proportions of mixed samples (blended with control and model samples). Then, lipidome profiling was performed by UHPLC-Orbitrap, and 403 variables were extracted and aligned as dataset. Owing to the high resolution of Orbitrap analyzer and open source lipid identification software, 28 FFAs were further screened and identified. Based on the relative intensity of the screened FFAs, PLS regression model was constructed for lipolysis measurement. After leave-one-out cross-validation, ten principal components have been designated to build the final PLS model with excellent performances (RMSECV, 0.0268; RMSEC, 0.0173; R 2 , 0.9977). In addition, the high predictive accuracy (R 2  = 0.9907 and RMSEP = 0.0345) of the trained PLS model was also demonstrated using test samples. Finally, taking curcumin as a model compound, its antilipolytic effect on palmitic acid-induced lipolysis was successfully predicted as 31.78% by the proposed approach. Besides, supplementary evidences of curcumin induced modification in FFAs compositions as well as lipidome were given by PLS extended methods. Different from general biological assays, high resolution MS-based method provide more sophisticated information included in biological events. Thus, the novel biological evaluation model proposed here showed promising perspectives for drug evaluation or disease diagnosis. Copyright © 2016 Elsevier B.V. All rights reserved.

Evaluation of a Noncontact, Alternative Mosquito Repellent Assay System.

PubMed

Tisgratog, Rungarun; Kongmee, Monthathip; Sanguanpong, Unchalee; Prabaripai, Atchariya; Bangs, Michael J; Chareonviriyaphap, Theeraphap

2016-09-01

A novel noncontact repellency assay system (NCRAS) was designed and evaluated as a possible alternative method for testing compounds that repel or inhibit mosquitoes from blood feeding. Deet and Aedes aegypti were used in a controlled laboratory setting. Using 2 study designs, a highly significant difference were seen between deet-treated and untreated skin placed behind the protective screens, indicating that deet was detected and was acting as a deterrence to mosquito landing and probing behavior. However, a 2nd study showed significant differences between protected (behind a metal screen barrier) and unprotected (exposed) deet-treated forearms, indicating the screen mesh might restrict the detection of deet and thus influences landing/biting response. These findings indicate the prototype NCRAS shows good promise but requires further evaluation and possible modification in design and testing protocol to achieve more desirable operational attributes in comparison with direct skin-contact repellency mosquito assays.

Biometric health screening for employers: consensus statement of the health enhancement research organization, American College of Occupational and Environmental Medicine, and care continuum alliance.

PubMed

2013-10-01

Employer wellness programs have grown rapidly in recent years with the interest in making an impact on employees' health. Successful programs are delivered through comprehensive solutions that are linked to an organization's business strategy and championed by senior leadership. Successful employee health management programs vary in the services, yet typically include the core components of health risk identification tools, behavior modification programs, educational programs, as well as changes to the workplace environment and culture. This article focuses on biometric screenings and was intended to provide employers and other stakeholders with information and guidance to help implement a successful screening program as part of an overall employee health management approach. The article is organized into four sections: goals and key success factors; methods and oversight; operations and delivery; and engagement and evaluation.

Hydrophobic and porous cellulose nanofibrous screen for efficient particulate matter (PM2.5) blocking

NASA Astrophysics Data System (ADS)

Chen, Liping; Guo, Yi; Peng, Xinsheng

2017-10-01

Particulate matter (PM2.5) pollution in air seriously affects public health. However, both bulk thickness and the accumulation of PM particles typically lead to a quick decline in the air permeability and large pressure drops of the conventional air clean membranes. In this work, we choose cellulose nanofibers (CNFs, a low cost, biodegradable and sustainable material) to form a hydrophobic and porous CNF thin layer on a stainless steel screen (300 mesh with pore size of 48 µm) through a simple filtration-assisted gelation process and subsequent polydimethylsiloxane modification. The prepared hydrophobic CNFs/stainless steel screen demonstrates highly efficient PM2.5 blocking based on size-sieving effect, fast air permeability and long-term durability under natural ventilation conditions in the relative humidity range from 45% to 93%. This technique holds great potential for indoor PM2.5 blocking under natural ventilation conditions.

The anticancer natural product ophiobolin A induces cytotoxicity by covalent modification of phosphatidylethanolamine.

PubMed

Chidley, Christopher; Trauger, Sunia A; Birsoy, Kıvanç; O'Shea, Erin K

2016-07-12

Phenotypic screens allow the identification of small molecules with promising anticancer activity, but the difficulty in characterizing the mechanism of action of these compounds in human cells often undermines their value as drug leads. Here, we used a loss-of-function genetic screen in human haploid KBM7 cells to discover the mechanism of action of the anticancer natural product ophiobolin A (OPA). We found that genetic inactivation of de novo synthesis of phosphatidylethanolamine (PE) mitigates OPA cytotoxicity by reducing cellular PE levels. OPA reacts with the ethanolamine head group of PE in human cells to form pyrrole-containing covalent cytotoxic adducts and these adducts lead to lipid bilayer destabilization. Our characterization of this unusual cytotoxicity mechanism, made possible by unbiased genetic screening in human cells, suggests that the selective antitumor activity displayed by OPA may be due to altered membrane PE levels in cancer cells.

Newborn screening for spinal muscular atrophy: Anticipating an imminent need.

PubMed

Phan, Han C; Taylor, Jennifer L; Hannon, Harry; Howell, Rodney

2015-04-01

Spinal muscular atrophy (SMA) is the most common genetic cause of infant mortality. Children with type I SMA typically die by the age of 2 years. Recent progress in gene modification and other innovative therapies suggest that improved outcomes may soon be forthcoming. In animal models, therapeutic intervention initiated before the loss of motor neurons alters SMA phenotype and increases lifespan. Presently, supportive care including respiratory, nutritional, physiatry, and orthopedic management can ameliorate clinical symptoms and improve survival rates if SMA is diagnosed early in life. Newborn screening could help optimize these potential benefits. A recent report demonstrated that SMA detection can be multiplexed at minimal additional cost with the assay for severe combined immunodeficiency, already implemented by many newborn screening programs. The public health community should remain alert to the rapidly changing developments in early detection and treatment of SMA. Copyright © 2015 Elsevier Inc. All rights reserved.

The influence of surface modification on sound absorption coefficient of albizzia wood absorber

NASA Astrophysics Data System (ADS)

Diharjo, Kuncoro; Prabowo, Anditya E.; Jamasri, Suharty, Neng Sri

2017-01-01

The purpose of this research is to investigate the influence of surface modification to sound absorption on absorber based albizia wood and kenaf fiber. The absorber was produced using the albizia wood as main materials, and the kenaf fiber was used as acoustic fill. The albizia wood used for producing the absorber was cut in the transverse direction so that its surface had good porosity. The size of specimens had 100 mm in diameter and 40 mm in thickness. The configuration of resonator cavities was 30 mm in diameter and 20 mm in depth, and each resonator was completed with a neck hole of the resonator. The types of surface modification were the addition of screen printing ink, fabric (with and without neck hole), and vinyl-wallpaper (with and without neck hole). According to ISO 10534-2, the absorber specimens were tested using two microphones impedance tube with random noise source to get the curve of noise absorption coefficient (NAC) for each specimen. The result shows that both unmodified absorber and absorber modified with screen printing ink have the similar characteristic of NAC and they are feasible to be used as an absorber in conversation rooms. The addition of fabric and vinyl-wallpaper as cover on the absorber surface give the positive effect of the air gap, and it increases the NAC in low frequency (100-400 Hz). However, the covers decrease the NAC in high frequency (400-1,400 Hz). The holes on the fabric and wallpaper covers give the improvement of NAC.

Reverse Induced Fit-Driven MAS-Downstream Transduction: Looking for Metabotropic Agonists.

PubMed

Pernomian, Larissa; Gomes, Mayara S; de Paula da Silva, Carlos H Tomich; Rosa, Joaquin M C

2017-01-01

Protective effects of MAS activation have spurred clinical interests in developing MAS agonists. However, current bases that drive this process preclude that physiological concentrations of peptide MAS agonists induce an atypical signaling that does not reach the metabotropic efficacy of constitutive activation. Canonical activation of MAS-coupled G proteins is only achieved by supraphysiological concentrations of peptide MAS agonists or physiological concentrations of chemically modified analogues. These pleiotropic differences are because of two overlapped binding domains: one non-metabotropic site that recognizes peptide agonists and one metabotropic domain that recognizes modified analogues. It is feasible that supraphysiological concentrations of peptide MAS agonists undergo to chemical modifications required for binding to metabotropic domain. Receptor oligomerization enhances pharmacological parameters coupled to metabotropic signaling. The formation of receptor-signalosome complex makes the transduction of agonists more adaptive. Considering the recent identification of MAS-signalosome, we aimed to postulate the reverse induced fit hypothesis in which MAS-signalosome would trigger chemical modifications required for agonists bind to MAS metabotropic domain. Here we cover rational perspectives for developing novel metabotropic MAS agonists in the view of the reverse induced-fit hypothesis. Predicting a 3D model of MAS metabotropic domain may guide the screening of chemical modifications required for metabotropic efficacy. Pharmacophore-based virtual screening would select potential metabotropic MAS agonists from virtual libraries from human proteome. Rational perspectives that consider reverse induced fit hypothesis during MAS activation for developing metabotropic MAS agonists represents the best approach in providing MAS ligands with constitutive efficacy at physiological concentrations. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Attention and Cognitive Bias Modification Apps: Review of the Literature and of Commercially Available Apps

PubMed Central

Ying, JiangBo; Song, Guo; Fung, Daniel SS; Smith, Helen

2018-01-01

Background Automatic processes, such as attentional biases or interpretative biases, have been purported to be responsible for several psychiatric disorders. Recent reviews have highlighted that cognitive biases may be modifiable. Advances in eHealth and mHealth have been harnessed for the delivery of cognitive bias modification. While several studies have evaluated mHealth-based bias modification intervention, no review, to our knowledge, has synthesized the evidence for it. In addition, no review has looked at commercial apps and their functionalities and methods of bias modification. A review is essential in determining whether scientifically validated apps are available commercially and the proportion of commercial apps that have been evaluated scientifically. Objective The objective of this review was primarily to determine the proportion of attention or cognitive bias modification apps that have been evaluated scientifically and secondarily to determine whether the scientifically evaluated apps were commercially available. We also sought to identify commercially available bias modification apps and determine the functionalities of these apps, the methods used for attention or cognitive bias modification, and whether these apps had been evaluated scientifically. Methods To identify apps in the published literature, we searched PubMed, MEDLINE, PsycINFO, and Scopus for studies published from 2000 to April 17, 2018. The search terms used were “attention bias” OR “cognitive bias” AND “smartphone” OR “smartphone application” OR “smartphone app” OR “mobile phones” OR “mobile application” OR mobile app” OR “personal digital assistant.” To identify commercial apps, we conducted a manual cross-sectional search between September 15 and 25, 2017 in the Apple iTunes and Google Play app stores. The search terms used to identify the apps were “attention bias” and “cognitive bias.” We also conducted a manual search on the apps with published evaluations. Results The effectiveness of bias modification was reported in 7 of 8 trials that we identified in the published literature. Only 1 of the 8 previously evaluated apps was commercially available. The 17 commercial apps we identified tended to use either an attention visual search or gamified task. Only 1 commercial app had been evaluated in the published literature. Conclusions This is perhaps the first review to synthesize the evidence for published mHealth attention bias apps. Our review demonstrated that evidence for mHealth attention bias apps is inconclusive, and quite a few commercial apps have not been validated scientifically. PMID:29793899

Attention and Cognitive Bias Modification Apps: Review of the Literature and of Commercially Available Apps.

PubMed

Zhang, Melvyn; Ying, JiangBo; Song, Guo; Fung, Daniel Ss; Smith, Helen

2018-05-24

Automatic processes, such as attentional biases or interpretative biases, have been purported to be responsible for several psychiatric disorders. Recent reviews have highlighted that cognitive biases may be modifiable. Advances in eHealth and mHealth have been harnessed for the delivery of cognitive bias modification. While several studies have evaluated mHealth-based bias modification intervention, no review, to our knowledge, has synthesized the evidence for it. In addition, no review has looked at commercial apps and their functionalities and methods of bias modification. A review is essential in determining whether scientifically validated apps are available commercially and the proportion of commercial apps that have been evaluated scientifically. The objective of this review was primarily to determine the proportion of attention or cognitive bias modification apps that have been evaluated scientifically and secondarily to determine whether the scientifically evaluated apps were commercially available. We also sought to identify commercially available bias modification apps and determine the functionalities of these apps, the methods used for attention or cognitive bias modification, and whether these apps had been evaluated scientifically. To identify apps in the published literature, we searched PubMed, MEDLINE, PsycINFO, and Scopus for studies published from 2000 to April 17, 2018. The search terms used were "attention bias" OR "cognitive bias" AND "smartphone" OR "smartphone application" OR "smartphone app" OR "mobile phones" OR "mobile application" OR mobile app" OR "personal digital assistant." To identify commercial apps, we conducted a manual cross-sectional search between September 15 and 25, 2017 in the Apple iTunes and Google Play app stores. The search terms used to identify the apps were "attention bias" and "cognitive bias." We also conducted a manual search on the apps with published evaluations. The effectiveness of bias modification was reported in 7 of 8 trials that we identified in the published literature. Only 1 of the 8 previously evaluated apps was commercially available. The 17 commercial apps we identified tended to use either an attention visual search or gamified task. Only 1 commercial app had been evaluated in the published literature. This is perhaps the first review to synthesize the evidence for published mHealth attention bias apps. Our review demonstrated that evidence for mHealth attention bias apps is inconclusive, and quite a few commercial apps have not been validated scientifically. ©Melvyn Zhang, JiangBo Ying, Guo Song, Daniel SS Fung, Helen Smith. Originally published in JMIR Mhealth and Uhealth (http://mhealth.jmir.org), 24.05.2018.

A Novel Plasmid-Based Microarray Screen Identifies Suppressors of rrp6Δ in Saccharomyces cerevisiae▿†

PubMed Central

Abruzzi, Katharine; Denome, Sylvia; Olsen, Jens Raabjerg; Assenholt, Jannie; Haaning, Line Lindegaard; Jensen, Torben Heick; Rosbash, Michael

2007-01-01

Genetic screens in Saccharomyces cerevisiae provide novel information about interacting genes and pathways. We screened for high-copy-number suppressors of a strain with the gene encoding the nuclear exosome component Rrp6p deleted, with either a traditional plate screen for suppressors of rrp6Δ temperature sensitivity or a novel microarray enhancer/suppressor screening (MES) strategy. MES combines DNA microarray technology with high-copy-number plasmid expression in liquid media. The plate screen and MES identified overlapping, but also different, suppressor genes. Only MES identified the novel mRNP protein Nab6p and the tRNA transporter Los1p, which could not have been identified in a traditional plate screen; both genes are toxic when overexpressed in rrp6Δ strains at 37°C. Nab6p binds poly(A)+ RNA, and the functions of Nab6p and Los1p suggest that mRNA metabolism and/or protein synthesis are growth rate limiting in rrp6Δ strains. Microarray analyses of gene expression in rrp6Δ strains and a number of suppressor strains support this hypothesis. PMID:17101774

Modifications of Glycans: Biological Significance and Therapeutic Opportunities

PubMed Central

Muthana, Saddam M.; Campbell, Christopher; Gildersleeve, Jeffrey C.

2012-01-01

Carbohydrates play a central role in a wide range of biological processes. As with nucleic acids and proteins, modifications of specific sites within the glycan chain can modulate a carbohydrate’s overall biological function. For example, acylation, methylation, sulfation, epimerization, and phosphorylation can occur at various positions within a carbohydrate to modulate bioactivity. Therefore, there is significant interest in identifying discrete carbohydrate modifications and understanding their biological effects. Additionally, enzymes that catalyze those modifications and proteins that bind modified glycans provide numerous targets for therapeutic intervention. This review will focus on modifications of glycans that occur after the oligomer/polymer has been assembled, generally referred to as postglycosylational modifications. PMID:22195988

Vainshtein screening in scalar-tensor theories before and after GW170817: Constraints on theories beyond Horndeski

NASA Astrophysics Data System (ADS)

Dima, Alexandru; Vernizzi, Filippo

2018-05-01

Screening mechanisms are essential features of dark energy models mediating a fifth force on large scales. We study the regime of strong scalar field nonlinearities, known as Vainshtein screening, in the most general scalar-tensor theories propagating a single scalar degree of freedom. We first develop an effective approach to parametrize cosmological perturbations beyond linear order for these theories. In the quasistatic limit, the fully nonlinear effective Lagrangian contains six independent terms, one of which starts at cubic order in perturbations. We compute the two gravitational potentials around a spherical body. Outside and near the body, screening reproduces standard gravity, with a modified gravitational coupling. Inside the body, the two potentials are different and depend on the density profile, signalling the breaking of the Vainshtein screening. We provide the most general expressions for these modifications, revising and extending previous results. We apply our findings to show that the combination of the GW170817 event, the Hulse-Taylor pulsar and stellar structure physics, constrain the parameters of these general theories at the level of 10-1, and of Gleyzes-Langlois-Piazza-Vernizzi theories at the level of 10-2.

Spontaneous Swallow Frequency Compared with Clinical Screening in the Identification of Dysphagia in Acute Stroke

PubMed Central

Crary, Michael A.; Carnaby, Giselle D.; Sia, Isaac

2017-01-01

Background The aim of this study was to compare spontaneous swallow frequency analysis (SFA) with clinical screening protocols for identification of dysphagia in acute stroke. Methods In all, 62 patients with acute stroke were evaluated for spontaneous swallow frequency rates using a validated acoustic analysis technique. Independent of SFA, these same patients received a routine nurse-administered clinical dysphagia screening as part of standard stroke care. Both screening tools were compared against a validated clinical assessment of dysphagia for acute stroke. In addition, psychometric properties of SFA were compared against published, validated clinical screening protocols. Results Spontaneous SFA differentiates patients with versus without dysphagia after acute stroke. Using a previously identified cut point based on swallows per minute, spontaneous SFA demonstrated superior ability to identify dysphagia cases compared with a nurse-administered clinical screening tool. In addition, spontaneous SFA demonstrated equal or superior psychometric properties to 4 validated, published clinical dysphagia screening tools. Conclusions Spontaneous SFA has high potential to identify dysphagia in acute stroke with psychometric properties equal or superior to clinical screening protocols. PMID:25088166

Spontaneous swallow frequency compared with clinical screening in the identification of dysphagia in acute stroke.

PubMed

Crary, Michael A; Carnaby, Giselle D; Sia, Isaac

2014-09-01

The aim of this study was to compare spontaneous swallow frequency analysis (SFA) with clinical screening protocols for identification of dysphagia in acute stroke. In all, 62 patients with acute stroke were evaluated for spontaneous swallow frequency rates using a validated acoustic analysis technique. Independent of SFA, these same patients received a routine nurse-administered clinical dysphagia screening as part of standard stroke care. Both screening tools were compared against a validated clinical assessment of dysphagia for acute stroke. In addition, psychometric properties of SFA were compared against published, validated clinical screening protocols. Spontaneous SFA differentiates patients with versus without dysphagia after acute stroke. Using a previously identified cut point based on swallows per minute, spontaneous SFA demonstrated superior ability to identify dysphagia cases compared with a nurse-administered clinical screening tool. In addition, spontaneous SFA demonstrated equal or superior psychometric properties to 4 validated, published clinical dysphagia screening tools. Spontaneous SFA has high potential to identify dysphagia in acute stroke with psychometric properties equal or superior to clinical screening protocols. Copyright © 2014 National Stroke Association. Published by Elsevier Inc. All rights reserved.

Environmental screening of dark matter haloes in f(R) gravity

NASA Astrophysics Data System (ADS)

Shi, Difu; Li, Baojiu; Han, Jiaxin

2017-07-01

In certain theories of modified gravity, Solar system constraints on deviations from general relativity (GR) are satisfied by virtue of a so-called screening mechanism, which enables the theory to revert to GR in regions where the matter density is high or the gravitational potential is deep. In the case of chameleon theories, the screening has two contributions - self-screening, which is due to the mass of an object itself, and environmental screening, which is caused by the surrounding matter - which are often entangled, with the second contribution being more crucial for less massive objects. A quantitative understanding of the effect of the environment on the screening can prove critical in observational tests of such theories using systems such as the Local Group and dwarf galaxies, for which the environment may be inferred in various ways. We use the high-resolution liminality simulation of Shi et al. to test the fidelity of different definitions of environment. We find that, although the different ways to define environment in practice do not agree with one another perfectly, they can provide useful guidance, and cross checks about how well a dark matter halo is screened. In addition, the screening of subhaloes in dark matter haloes is primarily determined by the environment, with the subhalo mass playing a minor role, which means that lower resolution simulations where subhaloes are not well resolved can still be useful for understanding the modification of gravity inside subhaloes.

Diagnosis, treatment and outcome of glutaric aciduria type I in Zhejiang Province, China

PubMed Central

Yang, Lili; Yin, Huaiming; Yang, Rongwang; Huang, Xinwen

2011-01-01

Summary Background Glutaric aciduria type I (GA I; MIM 231670) is a rare autosomal recessive disorder resulting from glutaryl-CoA dehydrogenase deficiency. This article reports our experience in the diagnosis, treatment and outcome of GA I patients in Zhejiang Province, China. Material/Methods A total of 129,415 newborns (accounting for approximately one-tenth of the annual births in Zhejiang Province) and 9640 high-risk infants were screened for inborn errors of metabolism in the Neonatal Screening Center of Zhejiang Province during a 3-year period. Tandem mass spectrometry and gas chromatography-mass spectrometry were used for diagnosis of the patients. Dietary modification, carnitine supplementation and aggressive treatment of intercurrent illnesses were adapted for GA I patients. Results Three infants were diagnosed with GA I by high-risk screening (detection rate: 1/3,213) and 2 were diagnosed by newborn screening (incidence: 1/64,708). Four patients (3 by high-risk screening and 1 by neonatal screening) undergoing MRI examination showed remarkable changes on T2-weighted image. Four patients accepted timely treatment, and in the patient diagnosed by neonatal screening, treatment was delayed until hypotonia appeared 3 months later. Neuropsychological assessment showed mental and motor retardation in 3 patients after treatment, including the patient diagnosed by neonatal screening. Conclusions Individualized timely treatment and close monitoring of GA I patients needs to be optimized in China. Appropriate communication with parents may help to achieve successful management of GA I patients. PMID:21709643

A Robotic Platform for Quantitative High-Throughput Screening

PubMed Central

Michael, Sam; Auld, Douglas; Klumpp, Carleen; Jadhav, Ajit; Zheng, Wei; Thorne, Natasha; Austin, Christopher P.; Inglese, James

2008-01-01

Abstract High-throughput screening (HTS) is increasingly being adopted in academic institutions, where the decoupling of screening and drug development has led to unique challenges, as well as novel uses of instrumentation, assay formulations, and software tools. Advances in technology have made automated unattended screening in the 1,536-well plate format broadly accessible and have further facilitated the exploration of new technologies and approaches to screening. A case in point is our recently developed quantitative HTS (qHTS) paradigm, which tests each library compound at multiple concentrations to construct concentration-response curves (CRCs) generating a comprehensive data set for each assay. The practical implementation of qHTS for cell-based and biochemical assays across libraries of > 100,000 compounds (e.g., between 700,000 and 2,000,000 sample wells tested) requires maximal efficiency and miniaturization and the ability to easily accommodate many different assay formats and screening protocols. Here, we describe the design and utilization of a fully integrated and automated screening system for qHTS at the National Institutes of Health's Chemical Genomics Center. We report system productivity, reliability, and flexibility, as well as modifications made to increase throughput, add additional capabilities, and address limitations. The combination of this system and qHTS has led to the generation of over 6 million CRCs from > 120 assays in the last 3 years and is a technology that can be widely implemented to increase efficiency of screening and lead generation. PMID:19035846

The national one week prevalence audit of universal meticillin-resistant Staphylococcus aureus (MRSA) admission screening 2012.

PubMed

Fuller, Christopher; Robotham, Julie; Savage, Joanne; Hopkins, Susan; Deeny, Sarah R; Stone, Sheldon; Cookson, Barry

2013-01-01

The English Department of Health introduced universal MRSA screening of admissions to English hospitals in 2010. It commissioned a national audit to review implementation, impact on patient management, admission prevalence and extra yield of MRSA identified compared to "high-risk" specialty or "checklist-activated" screening (CLAS) of patients with MRSA risk factors. National audit May 2011. Questionnaires to infection control teams in all English NHS acute trusts, requesting number patients admitted and screened, new or previously known MRSA; MRSA point prevalence; screening and isolation policies; individual risk factors and patient management for all new MRSA patients and random sample of negatives. 144/167 (86.2%) trusts responded. Individual patient data for 760 new MRSA patients and 951 negatives. 61% of emergency admissions (median 67.3%), 81% (median 59.4%) electives and 47% (median 41.4%) day-cases were screened. MRSA admission prevalence: 1% (median 0.9%) emergencies, 0.6% (median 0.4%) electives, 0.4% (median 0%) day-cases. Approximately 50% all MRSA identified was new. Inpatient MRSA point prevalence: 3.3% (median 2.9%). 104 (77%) trusts pre-emptively isolated patients with previous MRSA, 63 (35%) pre-emptively isolated admissions to "high-risk" specialties; 7 (5%) used PCR routinely. Mean time to MRSA positive result: 2.87 days (±1.33); 37% (219/596) newly identified MRSA patients discharged before result available; 55% remainder (205/376) isolated post-result. In an average trust, CLAS would reduce screening by 50%, identifying 81% of all MRSA. "High risk" specialty screening would reduce screening by 89%, identifying 9% of MRSA. Implementation of universal screening was poor. Admission prevalence (new cases) was low. CLAS reduced screening effort for minor decreases in identification, but implementation may prove difficult. Cost effectiveness of this and other policies, awaits evaluation by transmission dynamic economic modelling, using data from this audit. Until then trusts should seek to improve implementation of current policy and use of isolation facilities.

Questions About Cervical and Breast Cancer Screening Knowledge, Practice, and Outcomes: A Review of Demographic and Health Surveys.

PubMed

Viens, Laura; Perin, Doug; Senkomago, Virginia; Neri, Antonio; Saraiya, Mona

2017-05-01

United Nation's Sustainable Development Goals and the World Health Organization's Global Monitoring Framework support a strong global commitment to reducing the high burden of cervical and breast cancers among low- and middle-income countries. Strategies include vaccination, screening, and early diagnosis. Population-based surveys, such as those conducted by the Demographic and Health Surveys (DHS) Program, can collect the information needed to guide cancer control efforts in a standardized comparable manner. We identified and evaluated the breadth of breast and cervical cancer screening information that was collected by the DHS from 1984 through 2015. Then, we determined if these surveys currently provide the specific and measurable data about both the quantity and quality of cancer screening needed to guide national efforts to reduce the overall effects of cervical and breast cancers. We searched the DHS website to identify surveys conducted between the start of the DHS Program in 1984 and November 2015 that included questions about breast and cervical cancer screening. The relevant questions were extracted from the questionnaire, translated into English, and grouped by themes. Of the 90 countries where DHS surveys have been implemented, cervical cancer screening questions were included in 22 countries (24.4%) and breast cancer screening questions in 18 countries (20.0%). The common themes identified were disease knowledge, screening knowledge, screening practice, and screening outcomes. Most countries with survey questionnaires available for review addressed at least one aspect of screening practice (88.9% of cervical and 87.5% of breast), although few countries queried knowledge and outcomes. Questions that assess varied aspects of breast and cervical cancer screening have been incorporated into relatively few DHS surveys. The themes identified could guide the design of a standard set of questions for use in future population-based surveys and enable evaluation beyond the existence of screening, which would include assessment of the quality and impact of cervical and breast cancer screening.

Newborn screening education on the internet: a content analysis of North American newborn screening program websites.

PubMed

Araia, Makda H; Potter, Beth K

2011-09-01

The Internet is a potentially important medium for communication about public health programs including newborn screening. This study explores whether the information available on official newborn screening program websites is consistent with existing guidelines regarding educational content for parents. We conducted a systematic search of the public websites of newborn screening programs in the US and Canada, identifying web pages and downloadable brochures that contained educational information. Two researchers independently reviewed all documents to determine the extent to which they included 14 key recommended educational messages. We identified 85 documents containing educational information on 46 US and 6 Canadian newborn screening program websites. The documents contained from 1 to 14 of the recommended messages. The majority of identified materials emphasized the importance and benefits of screening. The differences between US and Canadian materials were related to the importance of parental involvement in follow-up and issues of consent and storage of blood spots. Our findings are consistent with studies of non-web-based newborn screening education materials. The results emphasize the need for further evaluation of newborn screening education, including internet-based resources, particularly in terms of the impact of particular messages on parental attitudes and behaviors.

Screening of ground water samples for volatile organic compounds using a portable gas chromatograph

USGS Publications Warehouse

Buchmiller, R.C.

1989-01-01

A portable gas chromatograph was used to screen 32 ground water samples for volatile organic compounds. Seven screened samples were positive; four of the seven samples had volatile organic substances identified by second-column confirmation. Four of the seven positive, screened samples also tested positive in laboratory analyses of duplicate samples. No volatile organic compounds were detected in laboratory analyses of samples that headspace screening indicated to be negative. Samples that contained volatile organic compounds, as identified by laboratory analysis, and that contained a volatile organic compound present in a standard of selected compounds were correctly identified by using the portable gas chromatography. Comparisons of screened-sample data with laboratory data indicate the ability to detect selected volatile organic compounds at concentrations of about 1 microgram per liter in the headspace of water samples by use of a portable gas chromatography. -Author

Neutron stars in screened modified gravity: Chameleon versus dilaton

NASA Astrophysics Data System (ADS)

Brax, Philippe; Davis, Anne-Christine; Jha, Rahul

2017-04-01

We consider the scalar field profile around relativistic compact objects such as neutron stars for a range of modified gravity models with screening mechanisms of the chameleon and Damour-Polyakov types. We focus primarily on inverse power law chameleons and the environmentally dependent dilaton as examples of both mechanisms. We discuss the modified Tolman-Oppenheimer-Volkoff equation and then implement a relaxation algorithm to solve for the scalar profiles numerically. We find that chameleons and dilatons behave in a similar manner and that there is a large degeneracy between the modified gravity parameters and the neutron star equation of state. This is exemplified by the modifications to the mass-radius relationship for a variety of model parameters.

Lattice energy calculation - A quick tool for screening of cocrystals and estimation of relative solubility. Case of flavonoids

NASA Astrophysics Data System (ADS)

Kuleshova, L. N.; Hofmann, D. W. M.; Boese, R.

2013-03-01

Cocrystals (or multicomponent crystals) have physico-chemical properties that are different from crystals of pure components. This is significant in drug development, since the desired properties, e.g. solubility, stability and bioavailability, can be tailored by binding two substances into a single crystal without chemical modification of an active component. Here, the FLEXCRYST program suite, implemented with a data mining force field, was used to estimate the relative stability and, consequently, the relative solubility of cocrystals of flavonoids vs their pure crystals, stored in the Cambridge Structural Database. The considerable potency of this approach for in silico screening of cocrystals, as well as their relative solubility, was demonstrated.

Suppression of background noise in a transonic wind-tunnel test section

NASA Technical Reports Server (NTRS)

Schutzenhofer, L. A.; Howard, P. W.

1975-01-01

Some exploratory tests were recently performed in the transonic test section of the NASA Marshall Space Flight Center 14-in. wind tunnel to suppress the background noise. In these tests, the perforated walls of the test section were covered with fine wire screens. The screens eliminated the edge tones generated by the holes in the perforated walls and significantly reduced the tunnel background noise. The tunnel noise levels were reduced to such a degree by this simple modification at Mach numbers 0.75, 0.9, 1.1, 1.2, and 1.46 that the fluctuating pressure levels of a turbulent boundary layer could be measured on a 5-deg half-angle cone.

Site specific modification of the human plasma proteome by methylglyoxal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kimzey, Michael J.; Kinsky, Owen R.; Yassine, Hussein N.

Increasing evidence identifies dicarbonyl stress from reactive glucose metabolites, such as methylglyoxal (MG), as a major pathogenic link between hyperglycemia and complications of diabetes. MG covalently modifies arginine residues, yet the site specificity of this modification has not been thoroughly investigated. Sites of MG adduction in the plasma proteome were identified using LC–MS/MS analysis in vitro following incubation of plasma proteins with MG. Treatment of plasma proteins with MG yielded 14 putative MG hotspots from five plasma proteins (albumin [nine hotspots], serotransferrin, haptoglobin [2 hotspots], hemopexin, and Ig lambda-2 chain C regions). The search results revealed two versions of MG-argininemore » modification, dihydroxyimidazolidine (R + 72) and hydroimidazolone (R + 54) adducts. One of the sites identified was R257 in human serum albumin, which is a critical residue located in drug binding site I. This site was validated as a target for MG modification by a fluorescent probe displacement assay, which revealed significant drug dissociation at 300 μM MG from a prodan–HSA complex (75 μM). Moreover, twelve human plasma samples (six male, six female, with two type 2 diabetic subjects from both genders) were analyzed using multiple reaction monitoring (MRM) tandem mass spectrometry and revealed the presence of the MG-modified albumin R257 peptide. These data provide insights into the nature of the site-specificity of MG modification of arginine, which may be useful for therapeutic treatments that aim to prevent MG-mediated adverse responses in patients. - Highlights: • Methylglyoxal (MG) selectively modifies arginine sites in human plasma proteome. • Dihydroxyimidazolidine and hydroimidazolone adducts on serum albumin identified • MG modification on albumin R257 associated with loss of drug site I binding capacity • MRM-tandem mass spectrometry enables sensitive detection of albumin MG-R257. • Site-specific MG modification may represent a useful monitor of effective therapy of T2DM.« less

Cystic fibrosis heterozygote screening in 5,161 pregnant women

DOE Office of Scientific and Technical Information (OSTI.GOV)

Witt, D.R.; Hallam, P.; Blumberg, B.

A screening program for cystic fibrosis (CF) heterozygotes was conducted in a large HMO prenatal population, to evaluate the level of interest among eligible patients, the effectiveness of prescreening education, attitudes toward the screening process, psychological effects, and utilization of prenatal diagnosis and its outcomes. The heterozygote identification rate and frequency of specific CFTR mutations were also assessed. Identified carriers were offered genetic counseling and testing of male partners. Prenatal diagnosis was offered if both partners were identified as carriers. A total of 5,161 women underwent carrier testing; 947 others completed survey instruments only. The acceptance rate of screening wasmore » high (78%), and pretest education by videotape was generally effective. Adverse psychological effects were not reported. Participants generally found screening to be desirable and useful. Screening identified 142 female heterozygotes, 109 couples in which the male partner was not a carrier, and 7 high-risk couples. The incidence of R117H mutations was much higher than expected. The number of identified carriers was much lower in Hispanics than in Caucasians. We conclude that large-scale prenatal screening for CF heterozygotes in the absence of a family history of CF is an acceptable method for identifying couples at risk for affected fetuses. Sufficient pretest education can be accomplished efficiently, test insensitivity is well accepted, adverse psychological events are not observed, and general patient satisfaction is high. 66 refs., 1 fig., 8 tabs.« less

Data from Tiered High-Throughput Screening Approach to Identify Thyroperoxidase Inhibitors within the ToxCast Phase I and II Chemical Libraries

EPA Pesticide Factsheets

High-throughput screening for potential thyroid-disrupting chemicals requires a system of assays to capture multiple molecular-initiating events (MIEs) that converge on perturbed thyroid hormone (TH) homeostasis. Screening for MIEs specific to TH-disrupting pathways is limited in the U.S. Environmental Protection Agency ToxCast screening assay portfolio. To fill 1 critical screening gap, the Amplex UltraRed-thyroperoxidase (AUR-TPO) assay was developed to identify chemicals that inhibit TPO, as decreased TPO activity reduces TH synthesis. The ToxCast phase I and II chemical libraries, comprised of 1074 unique chemicals, were initially screened using a single, high concentration to identify potential TPO inhibitors. Chemicals positive in the single-concentration screen were retested in concentration-response. Due to high false-positive rates typically observed with loss-of-signal assays such as AUR-TPO, we also employed 2 additional assays in parallel to identify possible sources of nonspecific assay signal loss, enabling stratification of roughly 300 putative TPO inhibitors based upon selective AUR-TPO activity. A cell-free luciferase inhibition assay was used to identify nonspecific enzyme inhibition among the putative TPO inhibitors, and a cytotoxicity assay using a human cell line was used to estimate the cellular tolerance limit. Additionally, the TPO inhibition activities of 150 chemicals were compared between the AUR-TPO and an orthogonal peroxidase oxidat

Identification of histone modifications in biomedical text for supporting epigenomic research

PubMed Central

Kolářik, Corinna; Klinger, Roman; Hofmann-Apitius, Martin

2009-01-01

Background Posttranslational modifications of histones influence the structure of chromatine and in such a way take part in the regulation of gene expression. Certain histone modification patterns, distributed over the genome, are connected to cell as well as tissue differentiation and to the adaption of organisms to their environment. Abnormal changes instead influence the development of disease states like cancer. The regulation mechanisms for modifying histones and its functionalities are the subject of epigenomics investigation and are still not completely understood. Text provides a rich resource of knowledge on epigenomics and modifications of histones in particular. It contains information about experimental studies, the conditions used, and results. To our knowledge, no approach has been published so far for identifying histone modifications in text. Results We have developed an approach for identifying histone modifications in biomedical literature with Conditional Random Fields (CRF) and for resolving the recognized histone modification term variants by term standardization. For the term identification F1 measures of 0.84 by 10-fold cross-validation on the training corpus and 0.81 on an independent test corpus have been obtained. The standardization enabled the correct transformation of 96% of the terms from training and 98% from test the corpus. Due to the lack of terminologies exhaustively covering specific histone modification types, we developed a histone modification term hierarchy for use in a semantic text retrieval system. Conclusion The developed approach highly improves the retrieval of articles describing histone modifications. Since text contains context information about performed studies and experiments, the identification of histone modifications is the basis for supporting literature-based knowledge discovery and hypothesis generation to accelerate epigenomic research. PMID:19208128

Identification of histone modifications in biomedical text for supporting epigenomic research.

PubMed

Kolárik, Corinna; Klinger, Roman; Hofmann-Apitius, Martin

2009-01-30

Posttranslational modifications of histones influence the structure of chromatine and in such a way take part in the regulation of gene expression. Certain histone modification patterns, distributed over the genome, are connected to cell as well as tissue differentiation and to the adaption of organisms to their environment. Abnormal changes instead influence the development of disease states like cancer. The regulation mechanisms for modifying histones and its functionalities are the subject of epigenomics investigation and are still not completely understood. Text provides a rich resource of knowledge on epigenomics and modifications of histones in particular. It contains information about experimental studies, the conditions used, and results. To our knowledge, no approach has been published so far for identifying histone modifications in text. We have developed an approach for identifying histone modifications in biomedical literature with Conditional Random Fields (CRF) and for resolving the recognized histone modification term variants by term standardization. For the term identification F1 measures of 0.84 by 10-fold cross-validation on the training corpus and 0.81 on an independent test corpus have been obtained. The standardization enabled the correct transformation of 96% of the terms from training and 98% from test the corpus. Due to the lack of terminologies exhaustively covering specific histone modification types, we developed a histone modification term hierarchy for use in a semantic text retrieval system. The developed approach highly improves the retrieval of articles describing histone modifications. Since text contains context information about performed studies and experiments, the identification of histone modifications is the basis for supporting literature-based knowledge discovery and hypothesis generation to accelerate epigenomic research.

Barriers to colorectal cancer screening among women in rural central Pennsylvania: Primary care physicians’ perspective

PubMed Central

Rosenwasser, Lara A.; McCall-Hosenfeld, Jennifer S.; Weisman, Carol S.; Hillemeier, Marianne M.; Perry, Amanda N.; Chuang, Cynthia H.

2014-01-01

Introduction Colorectal cancer (CRC) is the third leading cause of death among U.S. women. Rural populations have lower rates of CRC screening than their urban counterparts, and rural women have lower screening rates compared with rural men. The purpose of this qualitative study was to identify (1) primary care physicians’ (PCP) beliefs regarding CRC screening in rural communities, (2) factors that may cause gender disparities in CRC screening in rural areas, and (3) solutions to overcome those barriers. Methods Semi-structured interviews were conducted with 17 PCPs practicing in rural central Pennsylvania. PCPs were asked about their CRC screening practices for women, availability of CRC screening services, reminder systems for CRC screening, and barriers to screening specific to their rural communities and to gender. Thematic analysis was used to identify major themes. Results All 17 PCPs endorsed the importance of CRC screening, but believed that there are barriers to CRC screening specific to women and to rural location. All PCPs identified colonoscopy as their screening method of choice, and generally reported that access to colonoscopy services in their rural areas was not a significant barrier. Barriers to CRC screening for women in rural communities were related to: 1) PCPs’ CRC screening practices (e.g., not using alternative screening modalities when colonoscopy is not possible), 2) gender-specific barriers to CRC screening (e.g., patients’ belief that CRC mostly affects men, embarrassment of knowing people at the endoscopy center, prioritization of family issues over personal health), 3) patient-related barriers (e.g., low educational attainment, low health literacy, poverty, under- or uninsured), 4) community-related barriers (e.g., inadequate public education about CRC, “rural culture” that does not emphasize importance of preventive health services), and 5) physician practice-related barriers (e.g., lack of effective reminder systems, lack of time, busy practices). Physicians overwhelmingly identified patient education as necessary for improving CRC screening in their rural communities, but believed that education would have to come from a source outside the rural primary care office due to lack of resources, personnel, and time. Conclusions Overall, the PCPs in this study were motivated to identify ways to improve their ability to engage more eligible patients in CRC screening. These findings suggest several interventions to potentially improve CRC screening for women in rural areas, including encouraging use of other effective CRC screening modalities (i.e., FOBT) when colonoscopy is not possible; systems-based reminders that leverage electronic resources and are not visit dependent; and public health education campaigns aimed specifically at women in rural communities. PMID:24099635

Exposure-based screening for Nipah virus encephalitis, Bangladesh.

PubMed

Sazzad, Hossain M S; Luby, Stephen P; Ströher, Ute; Daszak, Peter; Sultana, Sharmin; Afroj, Sayma; Rahman, Mahmudur; Gurley, Emily S

2015-02-01

We measured the performance of exposure screening questions to identify Nipah virus encephalitis in hospitalized encephalitis patients during the 2012-13 Nipah virus season in Bangladesh. The sensitivity (93%), specificity (82%), positive predictive value (37%), and negative predictive value (99%) results suggested that screening questions could more quickly identify persons with Nipah virus encephalitis.

Case Definitions for Conditions Identified by Newborn Screening Public Health Surveillance.

PubMed

Sontag, Marci K; Sarkar, Deboshree; Comeau, Anne M; Hassell, Kathryn; Botto, Lorenzo D; Parad, Richard; Rose, Susan R; Wintergerst, Kupper A; Smith-Whitley, Kim; Singh, Sikha; Yusuf, Careema; Ojodu, Jelili; Copeland, Sara; Hinton, Cynthia F

2018-01-01

Newborn screening (NBS) identifies infants with rare conditions to prevent death or the onset of irreversible morbidities. Conditions on the Health and Human Services Secretary's Recommended Uniform Screening Panel have been adopted by most state NBS programs, providing a consistent approach for identification of affected newborns across the United States. Screen-positive newborns are identified and referred for confirmatory diagnosis and follow-up. The designation of a clinically significant phenotype precursor to a clinical diagnosis may vary between clinical specialists, resulting in diagnostic variation. Determination of disease burden and birth prevalence of the screened conditions by public health tracking is made challenging by these variations. This report describes the development of a core group of new case definitions, along with implications, plans for their use, and links to the definitions that were developed by panels of clinical experts. These definitions have been developed through an iterative process and are piloted in NBS programs. Consensus public health surveillance case definitions for newborn screened disorders will allow for consistent categorization and tracking of short- and long-term follow-up of identified newborns at the local, regional, and national levels.

Case Definitions for Conditions Identified by Newborn Screening Public Health Surveillance

PubMed Central

Sontag, Marci K.; Sarkar, Deboshree; Comeau, Anne M.; Hassell, Kathryn; Botto, Lorenzo D.; Parad, Richard; Rose, Susan R.; Wintergerst, Kupper A.; Smith-Whitley, Kim; Singh, Sikha; Yusuf, Careema; Ojodu, Jelili; Copeland, Sara; Hinton, Cynthia F.

2018-01-01

Newborn screening (NBS) identifies infants with rare conditions to prevent death or the onset of irreversible morbidities. Conditions on the Health and Human Services Secretary’s Recommended Uniform Screening Panel have been adopted by most state NBS programs, providing a consistent approach for identification of affected newborns across the United States. Screen-positive newborns are identified and referred for confirmatory diagnosis and follow-up. The designation of a clinically significant phenotype precursor to a clinical diagnosis may vary between clinical specialists, resulting in diagnostic variation. Determination of disease burden and birth prevalence of the screened conditions by public health tracking is made challenging by these variations. This report describes the development of a core group of new case definitions, along with implications, plans for their use, and links to the definitions that were developed by panels of clinical experts. These definitions have been developed through an iterative process and are piloted in NBS programs. Consensus public health surveillance case definitions for newborn screened disorders will allow for consistent categorization and tracking of short- and long-term follow-up of identified newborns at the local, regional, and national levels.

Identification and characterization of ana o 3 modifications on arginine-111 residue in heated cashew nuts

USDA-ARS?s Scientific Manuscript database

Heating foods can alter the physical, chemical, and biological characteristics of the proteins we consume. Raw and roasted cashew nut extracts were evaluated for allergen modifications by mass-spectrometry. We did not identify modifications on Ana o 1 or Ana o 2, but we observed two independent mo...

Tiered High-Throughput Screening Approach to Identify Thyroperoxidase Inhibitors Within the ToxCast Phase I and II Chemical Libraries

PubMed Central

Watt, Eric D.; Hornung, Michael W.; Hedge, Joan M.; Judson, Richard S.; Crofton, Kevin M.; Houck, Keith A.; Simmons, Steven O.

2016-01-01

High-throughput screening for potential thyroid-disrupting chemicals requires a system of assays to capture multiple molecular-initiating events (MIEs) that converge on perturbed thyroid hormone (TH) homeostasis. Screening for MIEs specific to TH-disrupting pathways is limited in the U.S. Environmental Protection Agency ToxCast screening assay portfolio. To fill 1 critical screening gap, the Amplex UltraRed-thyroperoxidase (AUR-TPO) assay was developed to identify chemicals that inhibit TPO, as decreased TPO activity reduces TH synthesis. The ToxCast phase I and II chemical libraries, comprised of 1074 unique chemicals, were initially screened using a single, high concentration to identify potential TPO inhibitors. Chemicals positive in the single-concentration screen were retested in concentration-response. Due to high false-positive rates typically observed with loss-of-signal assays such as AUR-TPO, we also employed 2 additional assays in parallel to identify possible sources of nonspecific assay signal loss, enabling stratification of roughly 300 putative TPO inhibitors based upon selective AUR-TPO activity. A cell-free luciferase inhibition assay was used to identify nonspecific enzyme inhibition among the putative TPO inhibitors, and a cytotoxicity assay using a human cell line was used to estimate the cellular tolerance limit. Additionally, the TPO inhibition activities of 150 chemicals were compared between the AUR-TPO and an orthogonal peroxidase oxidation assay using guaiacol as a substrate to confirm the activity profiles of putative TPO inhibitors. This effort represents the most extensive TPO inhibition screening campaign to date and illustrates a tiered screening approach that focuses resources, maximizes assay throughput, and reduces animal use. PMID:26884060

Irradiation influence on the detection of genetic-modified soybeans

NASA Astrophysics Data System (ADS)

Villavicencio, A. L. C. H.; Araújo, M. M.; Baldasso, J. G.; Aquino, S.; Konietzny, U.; Greiner, R.

2004-09-01

Three soybean varieties were analyzed to evaluate the irradiation influence on the detection of genetic modification. Samples were treated in a 60Co facility at dose levels of 0, 500, 800, and 1000Gy. The seeds were at first analyzed by Comet Assay as a rapid screening irradiation detection method. Secondly, germination test was performed to detect the viability of irradiated soybeans. Finally, because of its high sensitivity, its specificity and rapidity the polimerase chain reaction was the method applied for genetic modified organism detection. The analysis of DNA by the single technique of microgel electrophoresis of single cells (DNA Comet Assay) showed that DNA damage increased with increasing radiation doses. No negative influence of irradiation on the genetic modification detection was found.

Current reprogramming systems in regenerative medicine: from somatic cells to induced pluripotent stem cells.

PubMed

Hu, Chenxia; Li, Lanjuan

2016-01-01

Induced pluripotent stem cells (iPSCs) paved the way for research fields including cell therapy, drug screening, disease modeling and the mechanism of embryonic development. Although iPSC technology has been improved by various delivery systems, direct transduction and small molecule regulation, low reprogramming efficiency and genomic modification steps still inhibit its clinical use. Improvements in current vectors and the exploration of novel vectors are required to balance efficiency and genomic modification for reprogramming. Herein, we set out a comprehensive analysis of current reprogramming systems for the generation of iPSCs from somatic cells. By clarifying advantages and disadvantages of the current reprogramming systems, we are striding toward an effective route to generate clinical grade iPSCs.

Novel animal model defines genetic contributions for neuron-to-neuron transfer of α-synuclein.

PubMed

Tyson, Trevor; Senchuk, Megan; Cooper, Jason F; George, Sonia; Van Raamsdonk, Jeremy M; Brundin, Patrik

2017-08-08

Cell-to-cell spreading of misfolded α-synuclein (α-syn) is suggested to contribute to the progression of neuropathology in Parkinson's disease (PD). Compelling evidence supports the hypothesis that misfolded α-syn transmits from neuron-to-neuron and seeds aggregation of the protein in the recipient cells. Furthermore, α-syn frequently appears to propagate in the brains of PD patients following a stereotypic pattern consistent with progressive spreading along anatomical pathways. We have generated a C. elegans model that mirrors this progression and allows us to monitor α-syn neuron-to-neuron transmission in a live animal over its lifespan. We found that modulation of autophagy or exo/endocytosis, affects α-syn transfer. Furthermore, we demonstrate that silencing C. elegans orthologs of PD-related genes also increases the accumulation of α-syn. This novel worm model is ideal for screening molecules and genes to identify those that modulate prion-like spreading of α-syn in order to target novel strategies for disease modification in PD and other synucleinopathies.

A chemical proteomics approach for global analysis of lysine monomethylome profiling.

PubMed

Wu, Zhixiang; Cheng, Zhongyi; Sun, Mingwei; Wan, Xuelian; Liu, Ping; He, Tieming; Tan, Minjia; Zhao, Yingming

2015-02-01

Methylation of lysine residues on histone proteins is known to play an important role in chromatin structure and function. However, non-histone protein substrates of this modification remain largely unknown. An effective approach for system-wide analysis of protein lysine methylation, particularly lysine monomethylation, is lacking. Here we describe a chemical proteomics approach for global screening for monomethyllysine substrates, involving chemical propionylation of monomethylated lysine, affinity enrichment of the modified monomethylated peptides, and HPLC/MS/MS analysis. Using this approach, we identified with high confidence 446 lysine monomethylation sites in 398 proteins, including three previously unknown histone monomethylation marks, representing the largest data set of protein lysine monomethylation described to date. Our data not only confirms previously discovered lysine methylation substrates in the nucleus and spliceosome, but also reveals new substrates associated with diverse biological processes. This method hence offers a powerful approach for dynamic study of protein lysine monomethylation under diverse cellular conditions and in human diseases. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Small-Molecule Inhibitors of the SOX18 Transcription Factor.

PubMed

Fontaine, Frank; Overman, Jeroen; Moustaqil, Mehdi; Mamidyala, Sreeman; Salim, Angela; Narasimhan, Kamesh; Prokoph, Nina; Robertson, Avril A B; Lua, Linda; Alexandrov, Kirill; Koopman, Peter; Capon, Robert J; Sierecki, Emma; Gambin, Yann; Jauch, Ralf; Cooper, Matthew A; Zuegg, Johannes; Francois, Mathias

2017-03-16

Pharmacological modulation of transcription factors (TFs) has only met little success over the past four decades. This is mostly due to standard drug discovery approaches centered on blocking protein/DNA binding or interfering with post-translational modifications. Recent advances in the field of TF biology have revealed a central role of protein-protein interaction in their mode of action. In an attempt to modulate the activity of SOX18 TF, a known regulator of vascular growth in development and disease, we screened a marine extract library for potential small-molecule inhibitors. We identified two compounds, which inspired a series of synthetic SOX18 inhibitors, able to interfere with the SOX18 HMG DNA-binding domain, and to disrupt HMG-dependent protein-protein interaction with RBPJ. These compounds also perturbed SOX18 transcriptional activity in a cell-based reporter gene system. This approach may prove useful in developing a new class of anti-angiogenic compounds based on the inhibition of TF activity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Design and challenges of a randomized controlled trial for reducing risk factors of metabolic syndrome in Mexican women through water intake

PubMed Central

Hernández-Cordero, Sonia; González-Castell, Dinorah; Rodríguez-Ramírez, Sonia; Villanueva-Borbolla, María Ángeles; Unar, Mishel; Barquera, Simón; de Cossío, Teresita González; Rivera-Dommarco, Juan; Popkin, Barry M

2014-01-01

Objective To describe the design, methods, and challenges encountered during a randomized clinical trial aimed to promote water intake for reducing risks of metabolic syndrome in Mexican women. Materials and methods In a randomized clinical trial in Cuernavaca, Mexico, overweight and obese (body mass index [BMI] ≥ 25 < 39) women, 18 – < 45 years old with an intake of sugar-sweetened beverages ≥ 250 kilocalories per day (kcal/day) were randomly allocated to the water and education provision group (n = 120) or the education provision only group (n = 120). Results We screened 1 756 women. The main difficulties encountered were identifying participants with the recruitment criteria, delivering water to participants, and the time demanded from the study participants. Conclusions The trial’s main challenges were difficulties surrounding recruitment, delivery of the intervention, and the time demanded from the study participants. Modifications were effectively implemented without jeopardizing the original protocol. PMID:24715012

Assessment, Diagnosis, and Treatment of HIV-Associated Neurocognitive Disorder: A Consensus Report of the Mind Exchange Program

PubMed Central

Antinori, Andrea; Arendt, Gabriele; Grant, Igor; Letendre, Scott; Chair; Muñoz-Moreno, Jose A.; Eggers, Christian; Brew, Bruce; Brouillette, Marie-Josée; Bernal-Cano, Francisco; Carvalhal, Adriana; Christo, Paulo Pereira; Cinque, Paola; Cysique, Lucette; Ellis, Ronald; Everall, Ian; Gasnault, Jacques; Husstedt, Ingo; Korten, Volkan; Machala, Ladislav; Obermann, Mark; Ouakinin, Silvia; Podzamczer, Daniel; Portegies, Peter; Rackstraw, Simon; Rourke, Sean; Sherr, Lorraine; Streinu-Cercel, Adrian; Winston, Alan; Wojna, Valerie; Yazdanpannah, Yazdan; Arbess, Gordon; Baril, Jean-Guy; Begovac, Josip; Bergin, Colm; Bonfanti, Paolo; Bonora, Stefano; Brinkman, Kees; Canestri, Ana; Cholewińska-Szymańska, Graźyna; Chowers, Michal; Cooney, John; Corti, Marcelo; Doherty, Colin; Elbirt, Daniel; Esser, Stefan; Florence, Eric; Force, Gilles; Gill, John; Goffard, Jean-Christophe; Harrer, Thomas; Li, Patrick; de Kerckhove, Linos Van; Knecht, Gaby; Matsushita, Shuzo; Matulionyte, Raimonda; McConkey, Sam; Mouglignier, Antoine; Oka, Shinichi; Penalva, Augusto; Riesenberg, Klaris; Sambatakou, Helen; Tozzi, Valerio; Vassallo, Matteo; Wetterberg, Peter; Drapato, Alicia Wiercińska

2013-01-01

Many practical clinical questions regarding the management of human immunodeficiency virus (HIV)–associated neurocognitive disorder (HAND) remain unanswered. We sought to identify and develop practical answers to key clinical questions in HAND management. Sixty-six specialists from 30 countries provided input into the program, which was overseen by a steering committee. Fourteen questions were rated as being of greatest clinical importance. Answers were drafted by an expert group based on a comprehensive literature review. Sixty-three experts convened to determine consensus and level of evidence for the answers. Consensus was reached on all answers. For instance, good practice suggests that all HIV patients should be screened for HAND early in disease using standardized tools. Follow-up frequency depends on whether HAND is already present or whether clinical data suggest risk for developing HAND. Worsening neurocognitive impairment may trigger consideration of antiretroviral modification when other causes have been excluded. The Mind Exchange program provides practical guidance in the diagnosis, monitoring, and treatment of HAND. PMID:23175555

PARP12 suppresses Zika virus infection through PARP-dependent degradation of NS1 and NS3 viral proteins.

PubMed

Li, Lili; Zhao, Hui; Liu, Ping; Li, Chunfeng; Quanquin, Natalie; Ji, Xue; Sun, Nina; Du, Peishuang; Qin, Cheng-Feng; Lu, Ning; Cheng, Genhong

2018-06-19

Zika virus infection stimulates a type I interferon (IFN) response in host cells, which suppresses viral replication. Type I IFNs exert antiviral effects by inducing the expression of hundreds of IFN-stimulated genes (ISGs). To screen for antiviral ISGs that restricted Zika virus replication, we individually knocked out 21 ISGs in A549 lung cancer cells and identified PARP12 as a strong inhibitor of Zika virus replication. Our findings suggest that PARP12 mediated the ADP-ribosylation of NS1 and NS3, nonstructural viral proteins that are involved in viral replication and modulating host defense responses. This modification of NS1 and NS3 triggered their proteasome-mediated degradation. These data increase our understanding of the antiviral activity of PARP12 and suggest a molecular basis for the potential development of therapeutics against Zika virus. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Exploring the Yeast Acetylome Using Functional Genomics

PubMed Central

Duffy, Supipi Kaluarachchi; Friesen, Helena; Baryshnikova, Anastasia; Lambert, Jean-Philippe; Chong, Yolanda T.; Figeys, Daniel; Andrews, Brenda

2014-01-01

SUMMARY Lysine acetylation is a dynamic posttranslational modification with a well-defined role in regulating histones. The impact of acetylation on other cellular functions remains relatively uncharacterized. We explored the budding yeast acetylome with a functional genomics approach, assessing the effects of gene overexpression in the absence of lysine deacetylases (KDACs). We generated a network of 463 synthetic dosage lethal (SDL) interactions involving class I and II KDACs, revealing many cellular pathways regulated by different KDACs. A biochemical survey of genes interacting with the KDAC RPD3 identified 72 proteins acetylated in vivo. In-depth analysis of one of these proteins, Swi4, revealed a role for acetylation in G1-specific gene expression. Acetylation of Swi4 regulates interaction with its partner Swi6, both components of the SBF transcription factor. This study expands our view of the yeast acetylome, demonstrates the utility of functional genomic screens for exploring enzymatic pathways, and provides functional information that can be mined for future studies. PMID:22579291

Monitoring abacavir bioactivation in humans: screening for an aldehyde metabolite.

PubMed

Grilo, Nádia M; Antunes, Alexandra M M; Caixas, Umbelina; Marinho, Aline T; Charneira, Catarina; Conceição Oliveira, M; Monteiro, Emília C; Matilde Marques, M; Pereira, Sofia A

2013-05-10

The anti-HIV drug abacavir is associated with idiosyncratic hypersensitivity reactions and cardiotoxicity. Although the mechanism underlying abacavir-toxicity is not fully understood, drug bioactivation to reactive metabolites may be involved. This work was aimed at identifying abacavir-protein adducts in the hemoglobin of HIV patients as biomarkers of abacavir bioactivation and protein modification. The protocol received prior approval from the Hospital Ethics Committee, patients gave their written informed consent and adherence was controlled through a questionnaire. Abacavir-derived Edman adducts with the N-terminal valine of hemoglobin were analyzed by an established liquid chromatography-electrospray ionization-tandem mass spectrometry method. Abacavir-valine adducts were detected in three out of ten patients. This work represents the first evidence of abacavir-protein adduct formation in humans. The data confirm the ability of abacavir to modify self-proteins and suggest that the molecular mechanism(s) of some abacavir-induced adverse reactions may require bioactivation. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Chromogenic detection of aminoglycoside phosphotransferases.

PubMed

Amoroso, A M; Gutkind, G O

2001-01-01

Acquired resistance to aminoglycosides is most frequently due to the presence of the so-called aminoglycoside modifying enzymes (AGME) (1) able to catalyze one or more of three general reactions: N-acetylation, O-nucleotidylation and O-phosphorylation (2). Although resistance phenotype (to different (substrate or not for enzymatic modification) may serve as an approach for identifying actual enzymes present in a given isolate (3), results can be obscured or confusing, particularly when several different enzymes (4) (even, isoenzymes with different affinities) are superimposing their action in a single microorganism with potential "permeability" or target alterations. Thus, identification of the AGME content of a given strain also requires screening at the DNA level using probes specific to all the known AGME (5). However, the complete set of probes is available only to a few laboratories around the world, making surveillance for the appearance of novel enzymes, or the unlikely evolution of those already known, a relatively nonfeasible goal, as search for new enzymes may begin only after failing to hybridize to all known probes.

High-throughput Identification of Bacteria Repellent Polymers for Medical Devices

PubMed Central

Wu, Mei; Hardman, Ailsa; Lilienkampf, Annamaria; Pernagallo, Salvatore; Blakely, Garry; Swann, David G.; Bradley, Mark; Gallagher, Maurice P.

2016-01-01

Medical devices are often associated with hospital-acquired infections, which place enormous strain on patients and the healthcare system as well as contributing to antimicrobial resistance. One possible avenue for the reduction of device-associated infections is the identification of bacteria-repellent polymer coatings for these devices, which would prevent bacterial binding at the initial attachment step. A method for the identification of such repellent polymers, based on the parallel screening of hundreds of polymers using a microarray, is described here. This high-throughput method resulted in the identification of a range of promising polymers that resisted binding of various clinically relevant bacterial species individually and also as multi-species communities. One polymer, PA13 (poly(methylmethacrylate-co-dimethylacrylamide)), demonstrated significant reduction in attachment of a number of hospital isolates when coated onto two commercially available central venous catheters. The method described could be applied to identify polymers for a wide range of applications in which modification of bacterial attachment is important. PMID:27842360

Attitudes, norms and controls influencing lifestyle risk factor management in general practice.

PubMed

Ampt, Amanda J; Amoroso, Cheryl; Harris, Mark F; McKenzie, Suzanne H; Rose, Vanessa K; Taggart, Jane R

2009-08-26

With increasing rates of chronic disease associated with lifestyle behavioural risk factors, there is urgent need for intervention strategies in primary health care. Currently there is a gap in the knowledge of factors that influence the delivery of preventive strategies by General Practitioners (GPs) around interventions for smoking, nutrition, alcohol consumption and physical activity (SNAP). This qualitative study explores the delivery of lifestyle behavioural risk factor screening and management by GPs within a 45-49 year old health check consultation. The aims of this research are to identify the influences affecting GPs' choosing to screen and choosing to manage SNAP lifestyle risk factors, as well as identify influences on screening and management when multiple SNAP factors exist. A total of 29 audio-taped interviews were conducted with 15 GPs and one practice nurse over two stages. Transcripts from the interviews were thematically analysed, and a model of influencing factors on preventive care behaviour was developed using the Theory of Planned Behaviour as a structural framework. GPs felt that assessing smoking status was straightforward, however some found assessing alcohol intake only possible during a formal health check. Diet and physical activity were often inferred from appearance, only being assessed if the patient was overweight. The frequency and thoroughness of assessment were influenced by the GPs' personal interests and perceived congruence with their role, the level of risk to the patient, the capacity of the practice and availability of time. All GPs considered advising and educating patients part of their professional responsibility. However their attempts to motivate patients were influenced by perceptions of their own effectiveness, with smoking causing the most frustration. Active follow-up and referral of patients appeared to depend on the GPs' orientation to preventive care, the patient's motivation, and cost and accessibility of services to patients. General practitioner attitudes, normative influences from both patients and the profession, and perceived external control factors (time, cost, availability and practice capacity) all influence management of behavioural risk factors. Provider education, community awareness raising, support and capacity building may improve the uptake of lifestyle modification interventions.

Improved sugar yields from biomass sorghum feedstocks: comparing low-lignin mutants and pretreatment chemistries.

PubMed

Godin, Bruno; Nagle, Nick; Sattler, Scott; Agneessens, Richard; Delcarte, Jérôme; Wolfrum, Edward

2016-01-01

For biofuel production processes to be economically efficient, it is essential to maximize the production of monomeric carbohydrates from the structural carbohydrates of feedstocks. One strategy for maximizing carbohydrate production is to identify less recalcitrant feedstock cultivars by performing some type of experimental screening on a large and diverse set of candidate materials, or by identifying genetic modifications (random or directed mutations or transgenic plants) that provide decreased recalcitrance. Economic efficiency can also be increased using additional pretreatment processes such as deacetylation, which uses dilute NaOH to remove the acetyl groups of hemicellulose prior to dilute acid pretreatment. In this work, we used a laboratory-scale screening tool that mimics relevant thermochemical pretreatment conditions to compare the total sugar yield of three near-isogenic brown midrib ( bmr ) mutant lines and the wild-type (WT) sorghum cultivar. We then compared results obtained from the laboratory-scale screening pretreatment assay to a large-scale pretreatment system. After pretreatment and enzymatic hydrolysis, the bmr mutants had higher total sugar yields than the WT sorghum cultivar. Increased pretreatment temperatures increased reactivity for all sorghum samples reducing the differences observed at lower reaction temperatures. Deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples, and reduced the differences in total sugar yields among them, but solubilized a sizable fraction of the non-structural carbohydrates. The general trends of increased total sugar yield in the bmr mutant compared to the WT seen at the laboratory scale were observed at the large-scale system. However, in the larger reactor system, the measured total sugar yields were lower and the difference in total sugar yield between the WT and bmr sorghum was larger. Sorghum bmr mutants, which have a reduced lignin content showed higher total sugar yields than the WT cultivar after dilute acid pretreatment and enzymatic hydrolysis. Deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples. However, since deacetylation also solubilizes a large fraction of the non-structural carbohydrates, the ability to derive value from these solubilized sugars will depend greatly on the proposed conversion process.

Improved sugar yields from biomass sorghum feedstocks: comparing low-lignin mutants and pretreatment chemistries

DOE PAGES

Godin, Bruno; Nagle, Nick; Sattler, Scott; ...

2016-11-21

For biofuel production processes to be economically efficient, it is essential to maximize the production of monomeric carbohydrates from the structural carbohydrates of feedstocks. One strategy for maximizing carbohydrate production is to identify less recalcitrant feedstock cultivars by performing some type of experimental screening on a large and diverse set of candidate materials, or by identifying genetic modifications (random or directed mutations or transgenic plants) that provide decreased recalcitrance. Economic efficiency can also be increased using additional pretreatment processes such as deacetylation, which uses dilute NaOH to remove the acetyl groups of hemicellulose prior to dilute acid pretreatment. In thismore » work, we used a laboratory-scale screening tool that mimics relevant thermochemical pretreatment conditions to compare the total sugar yield of three near-isogenic brown midrib (bmr) mutant lines and the wild-type (WT) sorghum cultivar. We then compared results obtained from the laboratory-scale screening pretreatment assay to a large-scale pretreatment system. After pretreatment and enzymatic hydrolysis, the bmr mutants had higher total sugar yields than the WT sorghum cultivar. Increased pretreatment temperatures increased reactivity for all sorghum samples reducing the differences observed at lower reaction temperatures. Deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples, and reduced the differences in total sugar yields among them, but solubilized a sizable fraction of the non-structural carbohydrates. The general trends of increased total sugar yield in the bmr mutant compared to the WT seen at the laboratory scale were observed at the large-scale system. However, in the larger reactor system, the measured total sugar yields were lower and the difference in total sugar yield between the WT and bmr sorghum was larger. Sorghum bmr mutants, which have a reduced lignin content showed higher total sugar yields than the WT cultivar after dilute acid pretreatment and enzymatic hydrolysis. In conclusion, deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples. However, since deacetylation also solubilizes a large fraction of the non-structural carbohydrates, the ability to derive value from these solubilized sugars will depend greatly on the proposed conversion process.« less

The Plasmodium falciparum exported protein PF3D7_0402000 binds to erythrocyte ankyrin and band 4.1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shakya, Bikash; Penn, Wesley D.; Nakayasu, Ernesto S.

Plasmodium falciparum extensively modifies the infected red blood cell (RBC), resulting in changes in deformability, shape and surface properties. These alterations suggest that the RBC cytoskeleton is a major target for modification during infection. However, the molecular mechanisms leading to these changes are largely unknown. To begin to address this question, we screened for exported P. falciparum proteins that bound to the erythrocyte cytoskeleton proteins ankyrin 1 (ANK1) and band 4.1 (4.1R), which form critical interactions with other cytoskeletal proteins that contribute to the deformability and stability of RBCs. Yeast two-hybrid screens with ANK1 and 4.1R identified eight interactions withmore » P. falciparum exported proteins, including an interaction between 4.1R and PF3D7_0402000 (PFD0090c). This interaction was first identified in a large-scale screen (Vignali et al., Malaria J, 7:211, 2008), which also reported an interaction between PF3D7_0402000 and ANK1. We confirmed the interactions of PF3D7_0402000 with 4.1R and ANK1 in pair-wise yeast two-hybrid and co-precipitation assays. In both cases, an intact PHIST domain in PF3D7_0402000 was required for binding. Complex purification followed by mass spectrometry analysis provided additional support for the interaction of PF3D7_0402000 with ANK1 and 4.1R. RBC ghost cells loaded with maltose-binding protein (MBP)-PF3D7_0402000 passed through a metal microsphere column less efficiently than mock- or MBP-loaded controls, consistent with an effect of PF3D7_0402000 on RBC rigidity or membrane stability. This study confirmed the interaction of PF3D7_0402000 with 4.1R in multiple independent assays, provided the first evidence that PF3D7_0402000 also binds to ANK1, and suggested that PF3D7_0402000 affects deformability or membrane stability of uninfected RBC ghosts.« less

Improved sugar yields from biomass sorghum feedstocks: comparing low-lignin mutants and pretreatment chemistries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Godin, Bruno; Nagle, Nick; Sattler, Scott

For biofuel production processes to be economically efficient, it is essential to maximize the production of monomeric carbohydrates from the structural carbohydrates of feedstocks. One strategy for maximizing carbohydrate production is to identify less recalcitrant feedstock cultivars by performing some type of experimental screening on a large and diverse set of candidate materials, or by identifying genetic modifications (random or directed mutations or transgenic plants) that provide decreased recalcitrance. Economic efficiency can also be increased using additional pretreatment processes such as deacetylation, which uses dilute NaOH to remove the acetyl groups of hemicellulose prior to dilute acid pretreatment. In thismore » work, we used a laboratory-scale screening tool that mimics relevant thermochemical pretreatment conditions to compare the total sugar yield of three near-isogenic brown midrib (bmr) mutant lines and the wild-type (WT) sorghum cultivar. We then compared results obtained from the laboratory-scale screening pretreatment assay to a large-scale pretreatment system. After pretreatment and enzymatic hydrolysis, the bmr mutants had higher total sugar yields than the WT sorghum cultivar. Increased pretreatment temperatures increased reactivity for all sorghum samples reducing the differences observed at lower reaction temperatures. Deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples, and reduced the differences in total sugar yields among them, but solubilized a sizable fraction of the non-structural carbohydrates. The general trends of increased total sugar yield in the bmr mutant compared to the WT seen at the laboratory scale were observed at the large-scale system. However, in the larger reactor system, the measured total sugar yields were lower and the difference in total sugar yield between the WT and bmr sorghum was larger. Sorghum bmr mutants, which have a reduced lignin content showed higher total sugar yields than the WT cultivar after dilute acid pretreatment and enzymatic hydrolysis. In conclusion, deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples. However, since deacetylation also solubilizes a large fraction of the non-structural carbohydrates, the ability to derive value from these solubilized sugars will depend greatly on the proposed conversion process.« less

Pediatric provider processes for behavioral health screening, decision making, and referral in sites with colocated mental health services.

PubMed

Hacker, Karen; Goldstein, Joel; Link, David; Sengupta, Nandini; Bowers, Rachael; Tendulkar, Shalini; Wissow, Larry

2013-01-01

Validated behavioral health (BH) screens are recommended for use at well-child visits. This study aimed to explore how pediatricians experience and use these screens for subsequent care decisions in primary care. The study took place at 4 safety net health centers. Fourteen interviews were conducted with pediatricians who were mandated to use validated BH screens at well-child visits. Interview questions focused on key domains, including clinic BH context, screening processes, assessment of screening scores, and decision making about referral to mental health services. Qualitative analysis used the Framework Approach. A variety of themes emerged: BH screens were well accepted and valued for the way they facilitated discussion of mental health issues. However, screening results were not always used in the way that instrument designers intended. Providers' beliefs about the face validity of the instruments, and their observations about performance of instruments, led to discounting scored results. As a result, clinical decisions were made based on a variety of evidence, including individual item responses, parent or patient concerns, and perceived readiness for treatment. Additionally, providers, although interested in expanding their mental health discussions, perceived a lack of time and of their own skills to be major obstacles in this pursuit. Screens act as important prompts to stimulate discussion of BH problems, but their actual scored results play a variable role in problem identification and treatment decisions. Modifications to scheduling policies, additional provider training, and enhanced collaboration with mental health professionals could support better BH integration in pediatric primary care.

Crash Modification Factors Needs Assessment Workshop

DOT National Transportation Integrated Search

2015-03-01

The Federal Highway Administration (FHWA) hosted a Crash Modification Factor (CMF) Stakeholder Meeting to provide a forum for CMF stakeholders to communicate ongoing efforts and identify opportunities for future collaboration. CMF stakeholders repres...

A screen for over-secretion of proteins by yeast based on a dual component cellular phosphatase and immuno-chromogenic stain for exported bacterial alkaline phosphatase reporter

PubMed Central

2013-01-01

Background To isolate over-secretors, we subjected to saturation mutagenesis, a strain of P.pastoris exporting E. coli alkaline phosphatase (EAP) fused to the secretory domain of the yeast α factor pheromone through cellular PHO1/KEX2 secretory processing signals as the α-sec-EAP reporter protein. Direct chromogenic staining for α-sec-EAP activity is non-specific as its NBT/BCIP substrate cross-reacts with cellular phosphatases which can be inhibited with Levulinic acid. However, the parental E(P) strain only exports detectable levels of α-sec-EAP at 69 hours and not within the 36 hour period post-seeding required for effective screening with the consequent absence of a reference for secretion. We substituted the endogenous cellular phosphatase activity as a comparative reference for secretion rate and levels as well as for colony alignment while elevating specificity and sensitivity of detection of the exported protein with other innovative modifications of the immuno-chromogenic staining application for screening protein export mutants. Results Raising the specificity and utility of staining for α-sec-EAP activity required 5 modifications including some to published methods. These included, exploitation of endogenous phosphatase activity, reduction of the cell/protein burden, establishment of the direct relation between concentrations of transcriptional inducer and exported membrane immobilized protein and concentrations of protein exported into growth media, amplification of immuno-specificity and sensitivity of detection of α-sec-EAP reporter enzyme signal and restriction of staining to optimal concentrations of antisera and time periods. The resultant immuno-chromogenic screen allows for the detection of early secretion and as little as 1.3 fold over-secretion of α-sec-EAP reporter protein by E(M) mutants in the presence of 10 fold -216 fold higher concentrations of HSA. Conclusions The modified immuno-chromogenic screen is sensitive, specific and has led to the isolation of mutants E(M) over-secreting the α-sec-EAP reporter protein by a minimum of 50 fold higher levels than that exported by non-mutagenized E(P) parental strains. Unselected proteins were also over-secreted. PMID:23602005

Breast cancer screening in older women.

PubMed

Caplan, L S; Haynes, S G

1996-01-01

There is currently an epidemic of breast cancer in women 65 years of age and older. The purposes of this paper are to explore the breast cancer screening behaviors of older women and to identify some of the determinants of screening in these women. Data were analyzed from the 1987 National Health Interview Survey, a continuous nationwide household interview survey of the U.S. civilian, noninstitutionalized population. As in other studies, the utilization of breast cancer screening by older women was less in older women than in younger women. This was true for both mammography and clinical breast examination. A number of determinants of screening in older women were identified here. Women with a usual source of care and/or no activity limitation, as well as high school graduates, were the ones most likely to have received a screening mammogram and/or a screening clinical breast exam during the past year. The failure of older women to receive adequate breast cancer screening is an important concern which should be reevaluated, given the breast cancer epidemic in this population. This study identified a number of determinants of breast cancer screening in older women. For the most part, these determinants point to the primary care physician as the key to breast cancer screening in these women. Therefore, the primary care physician must be informed of, and encouraged to follow, the recommendations for periodic breast cancer screening in older women.

Identification of small molecule inhibitors of cytokinesis and single cell wound repair

PubMed Central

Clark, Andrew G.; Sider, Jenny R.; Verbrugghe, Koen; Fenteany, Gabriel; von Dassow, George; Bement, William M.

2013-01-01

Screening of small molecule libraries offers the potential to identify compounds that inhibit specific biological processes and, ultimately, to identify macromolecules that are important players in such processes. To date, however, most screens of small molecule libraries have focused on identification of compounds that inhibit known proteins or particular steps in a given process, and have emphasized automated primary screens. Here we have used “low tech” in vivo primary screens to identify small molecules that inhibit both cytokinesis and single cell wound repair, two complex cellular processes that possess many common features. The “diversity set”, an ordered array of 1990 compounds available from the National Cancer Institute, was screened in parallel to identify compounds that inhibit cytokinesis in D. excentricus (sand dollar) embryos and single cell wound repair in X. laevis (frog) oocytes. Two small molecules were thus identified: Sph1 and Sph2. Sph1 reduces Rho activation in wound repair and suppresses formation of the spindle midzone during cytokinesis. Sph2 also reduces Rho activation in wound repair and may inhibit cytokinesis by blocking membrane fusion. The results identify two small molecules of interest for analysis of wound repair and cytokinesis, reveal that these processes are more similar than often realized and reveal the potential power of low tech screens of small molecule libraries for analysis of complex cellular processes. PMID:23125193

Design Modification of Electrophoretic Equipment

NASA Technical Reports Server (NTRS)

Reddick, J. M.; Hirsch, I.

1973-01-01

The improved design of a zone electrophoretic sampler is reported that can be used in mass screening for hemoglobin S, the cause of sickle cell anemia. Considered is a high voltage multicell cellulose acetate device that requires 5 to 6 minutes electrophoresis periods; cells may be activitated individually or simultaneously. A multisample hemoglobin applicator standardizes the amount of sample applied and transfers the homolysate to the electrical wires.

STEVE -- a thinking person's screen editor

NASA Astrophysics Data System (ADS)

Fish, Adrian

STEve is an acronym for STarlink EVE and is an extended EDT-style EVE editor for use at Starlink nodes. The facility provides extra commands which are not part of standard EVE, and improves on one or two of the standard EVE commands. Help on all topics and keys is available from within the editor. The extensions and modifications present in STEve are particularly useful to Starlink users.

A Multiplexed High-Content Screening Approach Using the Chromobody Technology to Identify Cell Cycle Modulators in Living Cells.

PubMed

Schorpp, Kenji; Rothenaigner, Ina; Maier, Julia; Traenkle, Bjoern; Rothbauer, Ulrich; Hadian, Kamyar

2016-10-01

Many screening hits show relatively poor quality regarding later efficacy and safety. Therefore, small-molecule screening efforts shift toward high-content analysis providing more detailed information. Here, we describe a novel screening approach to identify cell cycle modulators with low toxicity by combining the Cell Cycle Chromobody (CCC) technology with the CytoTox-Glo (CTG) cytotoxicity assay. The CCC technology employs intracellularly functional single-domain antibodies coupled to a fluorescent protein (chromobodies) to visualize the cell cycle-dependent redistribution of the proliferating cell nuclear antigen (PCNA) in living cells. This image-based cell cycle analysis was combined with determination of dead-cell protease activity in cell culture supernatants by the CTG assay. We adopted this multiplex approach to high-throughput format and screened 960 Food and Drug Administration (FDA)-approved drugs. By this, we identified nontoxic compounds, which modulate different cell cycle stages, and validated selected hits in diverse cell lines stably expressing CCC. Additionally, we independently validated these hits by flow cytometry as the current state-of-the-art format for cell cycle analysis. This study demonstrates that CCC imaging is a versatile high-content screening approach to identify cell cycle modulators, which can be multiplexed with cytotoxicity assays for early elimination of toxic compounds during screening. © 2016 Society for Laboratory Automation and Screening.

ACT2 peer-driven intervention increases enrollment into HIV/AIDS medical studies among African-Americans/Blacks and Hispanics: A cluster randomized controlled trial

PubMed Central

Gwadz, Marya; Cleland, Charles M.; Belkin, Mindy; Ritchie, Amanda; Leonard, Noelle; Riedel, Marion; Banfield, Angela; Colon, Pablo; Elharrar, Vanessa; Kagan, Jonathan; Mildvan, Donna

2014-01-01

African American/Black and Hispanic persons living with HIV/AIDS (“AABH-PLHA”) are under-represented in HIV/AIDS medical studies (HAMS). This paper evaluates the efficacy of a social/behavioral intervention to increase rates of screening for and enrollment into HAMS in these populations. Participants (N=540) were enrolled into a cluster randomized controlled trial of an intervention designed to overcome multi-level barriers to HAMS. Primary endpoints were rates of screening for and enrollment into therapeutic/treatment-oriented and observational studies. Intervention arm participants were 30 times more likely to be screened than controls (49.3% vs. 3.7%; p < .001). Half (55.5%) of those screened were eligible for HAMS, primarily observational studies. Nine out of ten found eligible enrolled (91.7%), almost all into observational studies (95.2%), compared to no enrollments among controls. Achieving appropriate representation of AABH-PLHA in HAMS necessitates modification of study inclusion criteria to increase the proportion found eligible for therapeutic HAMS, in addition to social/behavioral interventions. PMID:24961193

[Evaluation of mass screening activity for cardiovascular disease risk factors in a rural environment].

PubMed

Boudreau, F

2001-01-01

The aim of this study was to evaluate the immediate and short-term impacts of a cardiovascular mass screening activity in a rural environment. A posttest-only control group design was used. Concerning the immediate impact, the results showed that the participants of the experimental group had, compared to the participants in the control group, a higher intention to participate regularly in physical activities and a higher intention to reduce their fat consumption. The participants' intention to stop smoking was not modified by the screening activity. After four months, the results revealed an increase in participation in physical activities and a decrease in fat consumption. The proportion of participants who smoked did not decrease. In conclusion, it is suggested that a cardiovascular mass screening activity such as the one performed in this study could be effective in motivating a population to adopt heart health-related behaviours. Others studies are necessary however to confirm the short-term impact of this type of activity on behaviour modification with regard to cardiovascular health.

Evidence that tRNA modifying enzymes are important in vivo targets for 5-fluorouracil in yeast

PubMed Central

Gustavsson, Marie; Ronne, Hans

2008-01-01

We have screened a collection of haploid yeast knockout strains for increased sensitivity to 5-fluorouracil (5-FU). A total of 138 5-FU sensitive strains were found. Mutants affecting rRNA and tRNA maturation were particularly sensitive to 5-FU, with the tRNA methylation mutant trm10 being the most sensitive mutant. This is intriguing since trm10, like many other tRNA modification mutants, lacks a phenotype under normal conditions. However, double mutants for nonessential tRNA modification enzymes are frequently temperature sensitive, due to destabilization of hypomodified tRNAs. We therefore tested if the sensitivity of our mutants to 5-FU is affected by the temperature. We found that the cytotoxic effect of 5-FU is strongly enhanced at 38°C for tRNA modification mutants. Furthermore, tRNA modification mutants show similar synthetic interactions for temperature sensitivity and sensitivity to 5-FU. A model is proposed for how 5-FU kills these mutants by reducing the number of tRNA modifications, thus destabilizing tRNA. Finally, we found that also wild-type cells are temperature sensitive at higher concentrations of 5-FU. This suggests that tRNA destabilization contributes to 5-FU cytotoxicity in wild-type cells and provides a possible explanation why hyperthermia can enhance the effect of 5-FU in cancer therapy. PMID:18314501

Effectiveness of motivational interviewing on lifestyle modification and health outcomes of clients at risk or diagnosed with cardiovascular diseases: A systematic review.

PubMed

Lee, Windy W M; Choi, K C; Yum, Royce W Y; Yu, Doris S F; Chair, S Y

2016-01-01

Clinically, there is an increasing trend in using motivational interviewing as a counseling method to help clients with cardiovascular diseases to modify their unhealthy lifestyle in order to decrease the risk of disease occurrence. As motivational interviewing has gained increased attention, research has been conducted to examine its effectiveness. This review attempts to identify the best available evidence related to the effectiveness of motivational interviewing on lifestyle modification, physiological and psychological outcomes for clients at risk of developing or with established cardiovascular diseases. Systematic review of studies incorporating motivational interviewing in modifying lifestyles, improving physiological and psychological outcomes for clients at risk of or diagnosed with cardiovascular diseases. Major English and Chinese electronic databases were searched to identify citations that reported the effectiveness of motivational interviewing. The searched databases included MEDLINE, British Nursing Index, CINAHL Plus, PsycINFO, SCOPUS, CJN, CBM, HyRead, WanFang Data, Digital Dissertation Consortium, and so on. Two reviewers independently assessed the relevance of citations based on the inclusion criteria. Full texts of potential citations were retrieved for more detailed review. Critical appraisal was conducted by using the standardized critical appraisal checklist for randomized and quasi-randomized controlled studies from the Joanna Briggs Institute - Meta Analysis of Statistics Assessment and Review Instrument (JBI-MAStaRI). After eligibility screening, 14 articles describing 9 studies satisfied the inclusion criteria and were included in the analysis. Only certain outcomes in certain studies were pooled for meta-analysis because of the large variability of the studies included, other findings were presented in narrative form. For lifestyle modification, the review showed that motivational interviewing could be more effective than usual care on altering smoking habits. For physiological outcomes, the review showed that motivational interviewing positively improved client's systolic and diastolic blood pressures but the result was not significant. For psychological outcomes, the review showed that motivational interviewing might have favorable effect on improving clients' depression. For other outcomes, the review showed that motivational interviewing did not differ from usual care or usual care was even more effective. The review showed that motivational interviewing might have favorable effects on changing clients' smoking habits, depression, and three SF-36 domains. For the other outcomes, most of the results were inconclusive. Further studies should be performed to identify the optimal format and frequency of motivational interviewing. Primary research on the effectiveness of motivational interviewing on increasing clients' motivation and their actual changes in healthy behavior is also recommended. Copyright © 2015 Elsevier Ltd. All rights reserved.

Fingerprints of Modified RNA Bases from Deep Sequencing Profiles.

PubMed

Kietrys, Anna M; Velema, Willem A; Kool, Eric T

2017-11-29

Posttranscriptional modifications of RNA bases are not only found in many noncoding RNAs but have also recently been identified in coding (messenger) RNAs as well. They require complex and laborious methods to locate, and many still lack methods for localized detection. Here we test the ability of next-generation sequencing (NGS) to detect and distinguish between ten modified bases in synthetic RNAs. We compare ultradeep sequencing patterns of modified bases, including miscoding, insertions and deletions (indels), and truncations, to unmodified bases in the same contexts. The data show widely varied responses to modification, ranging from no response, to high levels of mutations, insertions, deletions, and truncations. The patterns are distinct for several of the modifications, and suggest the future use of ultradeep sequencing as a fingerprinting strategy for locating and identifying modifications in cellular RNAs.

Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor.

PubMed

Williamson, Lynn L; Borlee, Bradley R; Schloss, Patrick D; Guan, Changhui; Allen, Heather K; Handelsman, Jo

2005-10-01

The goal of this study was to design and evaluate a rapid screen to identify metagenomic clones that produce biologically active small molecules. We built metagenomic libraries with DNA from soil on the floodplain of the Tanana River in Alaska. We extracted DNA directly from the soil and cloned it into fosmid and bacterial artificial chromosome vectors, constructing eight metagenomic libraries that contain 53,000 clones with inserts ranging from 1 to 190 kb. To identify clones of interest, we designed a high throughput "intracellular" screen, designated METREX, in which metagenomic DNA is in a host cell containing a biosensor for compounds that induce bacterial quorum sensing. If the metagenomic clone produces a quorum-sensing inducer, the cell produces green fluorescent protein (GFP) and can be identified by fluorescence microscopy or captured by fluorescence-activated cell sorting. Our initial screen identified 11 clones that induce and two that inhibit expression of GFP. The intracellular screen detected quorum-sensing inducers among metagenomic clones that a traditional overlay screen would not. One inducing clone carries a LuxI homologue that directs the synthesis of an N-acyl homoserine lactone quorum-sensing signal molecule. The LuxI homologue has 62% amino acid sequence identity to its closest match in GenBank, AmfI from Pseudomonas fluorescens, and is on a 78-kb insert that contains 67 open reading frames. Another inducing clone carries a gene with homology to homocitrate synthase. Our results demonstrate the power of an intracellular screen to identify functionally active clones and biologically active small molecules in metagenomic libraries.

High Throughput Screening Identifies Novel Lead Compounds with Activity against Larval, Juvenile and Adult Schistosoma mansoni

PubMed Central

Gardner, J. Mark F.; Bell, Andrew S.; Parkinson, Tanya; Bickle, Quentin

2016-01-01

An estimated 600 million people are affected by the helminth disease schistosomiasis caused by parasites of the genus Schistosoma. There is currently only one drug recommended for treating schistosomiasis, praziquantel (PZQ), which is effective against adult worms but not against the juvenile stage. In an attempt to identify improved drugs for treating the disease, we have carried out high throughput screening of a number of small molecule libraries with the aim of identifying lead compounds with balanced activity against all life stages of Schistosoma. A total of almost 300,000 compounds were screened using a high throughput assay based on motility of worm larvae and image analysis of assay plates. Hits were screened against juvenile and adult worms to identify broadly active compounds and against a mammalian cell line to assess cytotoxicity. A number of compounds were identified as promising leads for further chemical optimization. PMID:27128493

Screening for psychological distress in cancer: renewing the research agenda.

PubMed

Salmon, Peter; Clark, Louise; McGrath, Elly; Fisher, Peter

2015-03-01

Although health policy for cancer care promotes screening of patients for emotional distress, the utility and validity of screening have been questioned. Continued research to refine detection of distress or to evaluate outcomes of screening programmes is unlikely to end this controversy. Instead, we need to identify more fundamental research questions that address the validity or utility of screening in this context. We critically and selectively review research and policy literature on psychological screening in cancer care, drawing also from research literature about the nature of psychological needs in cancer care and from relevant literature on psychological screening in mental health. We identify three broad research questions: (i) Apart from intensity of distress, what further information should screening seek about the context of distress, psychological processes that promote distress and patients' own perspective on their needs? (ii) What are the implications of the contextual dependence of disclosure of emotional feelings, given that screening questions can be asked in contexts ranging from an impersonal questionnaire to dialogue with a trusted practitioner? (iii) How should a screen be responded to, given the inherent uncertainty associated with screening results and given that distress in a cancer context can indicate instrumental as well as psychological needs? Examining these questions will mean exchanging a diagnostic framework for screening, in which health need is indicated by the presence of a psychological disorder, for a public health framework, in which health need is identified from multiple perspectives. Copyright © 2014 John Wiley & Sons, Ltd.

New restriction enzymes discovered from Escherichia coli clinical strains using a plasmid transformation method

PubMed Central

Kasarjian, Julie K. A.; Iida, Masatake; Ryu, Junichi

2003-01-01

The presence of restriction enzymes in bacterial cells has been predicted by either classical phage restriction-modification (R-M) tests, direct in vitro enzyme assays or more recently from bacterial genome sequence analysis. We have applied phage R-M test principles to the transformation of plasmid DNA and established a plasmid R-M test. To validate this test, six plasmids that contain BamHI fragments of phage lambda DNA were constructed and transformed into Escherichia coli strains containing known R-M systems including: type I (EcoBI, EcoAI, Eco124I), type II (HindIII) and type III (EcoP1I). Plasmid DNA with a single recognition site showed a reduction of relative efficiency of transformation (EOT = 10–1–10–2). When multiple recognition sites were present, greater reductions in EOT values were observed. Once established in the cell, the plasmids were subjected to modification (EOT = 1.0). We applied this test to screen E.coli clinical strains and detected the presence of restriction enzymes in 93% (14/15) of cells. Using additional subclones and the computer program, RM Search, we identified four new restriction enzymes, Eco377I, Eco585I, Eco646I and Eco777I, along with their recognition sequences, GGA(8N)ATGC, GCC(6N)TGCG, CCA(7N)CTTC, and GGA(6N)TATC, respectively. Eco1158I, an isoschizomer of EcoBI, was also found in this study. PMID:12595571

Advances in genetic modification of pluripotent stem cells.

PubMed

Fontes, Andrew; Lakshmipathy, Uma

2013-11-15

Genetically engineered stem cells aid in dissecting basic cell function and are valuable tools for drug discovery, in vivo cell tracking, and gene therapy. Gene transfer into pluripotent stem cells has been a challenge due to their intrinsic feature of growing in clusters and hence not amenable to common gene delivery methods. Several advances have been made in the rapid assembly of DNA elements, optimization of culture conditions, and DNA delivery methods. This has lead to the development of viral and non-viral methods for transient or stable modification of cells, albeit with varying efficiencies. Most methods require selection and clonal expansion that demand prolonged culture and are not suited for cells with limited proliferative potential. Choosing the right platform based on preferred length, strength, and context of transgene expression is a critical step. Random integration of the transgene into the genome can be complicated due to silencing or altered regulation of expression due to genomic effects. An alternative to this are site-specific methods that target transgenes followed by screening to identify the genomic loci that support long-term expression with stem cell proliferation and differentiation. A highly precise and accurate editing of the genome driven by homology can be achieved using traditional methods as well as the newer technologies such as zinc finger nuclease, TAL effector nucleases and CRISPR. In this review, we summarize the different genetic engineering methods that have been successfully used to create modified embryonic and induced pluripotent stem cells. © 2013. Published by Elsevier Inc. All rights reserved.

Discovery of cellular substrates for protein kinase A using a peptide array screening protocol.

PubMed

Smith, F Donelson; Samelson, Bret K; Scott, John D

2011-08-15

Post-translational modification of proteins is a universal form of cellular regulation. Phosphorylation on serine, threonine, tyrosine or histidine residues by protein kinases is the most widespread and versatile form of covalent modification. Resultant changes in activity, localization or stability of phosphoproteins drives cellular events. MS and bioinformatic analyses estimate that ~30% of intracellular proteins are phosphorylated at any given time. Multiple approaches have been developed to systematically define targets of protein kinases; however, it is likely that we have yet to catalogue the full complement of the phosphoproteome. The amino acids that surround a phosphoacceptor site are substrate determinants for protein kinases. For example, basophilic enzymes such as PKA (protein kinase A), protein kinase C and calmodulin-dependent kinases recognize basic side chains preceding the target serine or threonine residues. In the present paper we describe a strategy using peptide arrays and motif-specific antibodies to identify and characterize previously unrecognized substrate sequences for protein kinase A. We found that the protein kinases PKD (protein kinase D) and MARK3 [MAP (microtubule-associated protein)-regulating kinase 3] can both be phosphorylated by PKA. Furthermore, we show that the adapter protein RIL [a product of PDLIM4 (PDZ and LIM domain protein 4)] is a PKA substrate that is phosphorylated on Ser(119) inside cells and that this mode of regulation may control its ability to affect cell growth. © The Authors Journal compilation © 2011 Biochemical Society

Elongator-dependent modification of cytoplasmic tRNALysUUU is required for mitochondrial function under stress conditions.

PubMed

Tigano, Marco; Ruotolo, Roberta; Dallabona, Cristina; Fontanesi, Flavia; Barrientos, Antoni; Donnini, Claudia; Ottonello, Simone

2015-09-30

To gain a wider view of the pathways that regulate mitochondrial function, we combined the effect of heat stress on respiratory capacity with the discovery potential of a genome-wide screen in Saccharomyces cerevisiae. We identified 105 new genes whose deletion impairs respiratory growth at 37°C by interfering with processes such as transcriptional regulation, ubiquitination and cytosolic tRNA wobble uridine modification via 5-methoxycarbonylmethyl-2-thiouridine formation. The latter process, specifically required for efficient decoding of AA-ending codons under stress conditions, was covered by multiple genes belonging to the Elongator (e.g. ELP3) and urmylation (e.g., NCS6) pathways. ELP3 or NCS6 deletants had impaired mitochondrial protein synthesis. Their respiratory deficiency was selectively rescued by overexpression of tRNA(Lys) UUU as well by overexpression of genes (BCK1 and HFM1) with a strong bias for the AAA codon read by this tRNA. These data extend the mitochondrial regulome, demonstrate that heat stress can impair respiration by disturbing cytoplasmic translation of proteins critically involved in mitochondrial function and document, for the first time, the involvement in such process of the Elongator and urmylation pathways. Given the conservation of these pathways, the present findings may pave the way to a better understanding of the human mitochondrial regulome in health and disease. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Development of a Brief Pre-Implementation Screening Tool to Identify Teachers Who Are at Risk for Not Implementing Intervention Curriculum and High-Implementing Teachers

ERIC Educational Resources Information Center

Wang, Bo; Stanton, Bonita; Lunn, Sonja; Patel, Pooja; Koci, Veronica; Deveaux, Lynette

2017-01-01

Few questionnaires have been developed to screen for potentially poor implementers of school-based interventions. This study combines teacher characteristics, perceptions, and teaching/training experiences to develop a short screening tool that can identify potential "low-performing" or "high-performing" teachers…

Validation of the Systematic Screening for Behavior Disorders in Middle and Junior High School

ERIC Educational Resources Information Center

Caldarella, Paul; Young, Ellie L.; Richardson, Michael J.; Young, Benjamin J.; Young, K. Richard

2008-01-01

The Systematic Screening for Behavior Disorders (SSBD), a multistage screening system designed to identify elementary school--age children at risk for emotional and behavioral disorders, was evaluated for use with middle and junior high school students. During SSBD Stage 1, teachers identified 123 students in grades 6 through 9 with…

In vitro and in vivo structure and activity relationship analysis of polymethoxylated flavonoids: identifying sinensetin as a novel antiangiogenesis agent.

PubMed

Lam, In Kei; Alex, Deepa; Wang, You-Hua; Liu, Ping; Liu, Ai-Lin; Du, Guan-Hua; Lee, Simon Ming Yuen

2012-06-01

Polymethoxylated flavonoids are present in citrus fruit in a range of chemical structures and abundance. These compounds have potential for anticarcinogenesis, antitumor, and cardiovascular protective activity, but the effect on angiogenesis has not been well studied. Human umbilical vein endothelial cells (HUVECs) in vitro and zebrafish (Danio rerio) in vivo models were used to screen and identify the antiangiogenesis activity of seven polymethoxylated flavonoids; namely, hesperetin, naringin, neohesperidin, nobiletin, scutellarein, scutellarein tetramethylether, and sinensetin. Five, excluding naringin and neohesperidin, showed different degrees of potency of antiangiogenesis activity. Sinensetin, which had the most potent antiangiogenesis activity and the lowest toxicity, inhibited angiogenesis by inducing cell cycle arrest in the G0/G1 phase in HUVEC culture and downregulating the mRNA expressions of angiogenesis genes flt1, kdrl, and hras in zebrafish. The in vivo structure-activity relationship (SAR) analysis indicated that a flavonoid with a methoxylated group at the C3' position offers a stronger antiangiogenesis activity, whereas the absence of a methoxylated group at the C8 position offers lower lethal toxicity in addition to enhancing the antiangiogenesis activity. This study provides new insight into how modification of the chemical structure of polymethoxylated flavonoids affects this newly identified antiangiogenesis activity. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chronic Kidney Disease Screening Methods and Its Implication for Malaysia: An in Depth Review

PubMed Central

Almualm, Yasmin; Huri, Hasniza Zaman

2015-01-01

Chronic Kidney Disease has become a public health problem, imposing heath, social and human cost on societies worldwide. Chronic Kidney Disease remains asymptomatic till late stage when intervention cannot stop the progression of the disease. Therefore, there is an urgent need to detect the disease early. Despite the high prevalence of Chronic Kidney Disease in Malaysia, screening is still lacking behind. This review discusses the strengths and limitations of current screening methods for Chronic Kidney Disease from a Malaysian point of view. Diabetic Kidney Disease was chosen as focal point as Diabetes is the leading cause of Chronic Kidney Disease in Malaysia. Screening for Chronic Kidney Disease in Malaysia includes a urine test for albuminuria and a blood test for serum creatinine. Recent literature indicates that albuminuria is not always present in Diabetic Kidney Disease patients and serum creatinine is only raised after substantial kidney damage has occurred. Recently, cystatin C was proposed as a potential marker for kidney disease but this has not been studied thoroughly in Malaysia. Glomerular Filtration Rate is the best method for measuring kidney function and is widely estimated using the Modification of Diet for Renal Disease equation. Another equation, the Chronic Kidney Disease Epidemiology Collaboration Creatinine equation was introduced in 2009. The new equation retained the precision and accuracy of the Modification of Diet for Renal Disease equation at GFR < 60ml/min/1.73m2, showed less bias and improved precision at GFR>60ml/min/1.73m2. In Asian countries, adding an ethnic coefficient to the equation enhanced its performance. In Malaysia, a multi-ethnic Asian population, the Chronic Kidney Disease Epidemiology Collaboration equation should be validated and the Glomerular Filtration Rate should be reported whenever serum creatinine is ordered. Reporting estimated Glomerular Filtration Rate will help diagnose patients who would have been otherwise missed if only albuminuria and serum creatinine are measured. PMID:25946939

Chronic kidney disease screening methods and its implication for Malaysia: an in depth review.

PubMed

Almualm, Yasmin; Zaman Huri, Hasniza

2015-01-01

Chronic Kidney Disease has become a public health problem, imposing heath, social and human cost on societies worldwide. Chronic Kidney Disease remains asymptomatic till late stage when intervention cannot stop the progression of the disease. Therefore, there is an urgent need to detect the disease early. Despite the high prevalence of Chronic Kidney Disease in Malaysia, screening is still lacking behind. This review discusses the strengths and limitations of current screening methods for Chronic Kidney Disease from a Malaysian point of view. Diabetic Kidney Disease was chosen as focal point as Diabetes is the leading cause of Chronic Kidney Disease in Malaysia. Screening for Chronic Kidney Disease in Malaysia includes a urine test for albuminuria and a blood test for serum creatinine. Recent literature indicates that albuminuria is not always present in Diabetic Kidney Disease patients and serum creatinine is only raised after substantial kidney damage has occurred.  Recently, cystatin C was proposed as a potential marker for kidney disease but this has not been studied thoroughly in Malaysia.  Glomerular Filtration Rate is the best method for measuring kidney function and is widely estimated using the Modification of Diet for Renal Disease equation. Another equation, the Chronic Kidney Disease Epidemiology Collaboration Creatinine equation was introduced in 2009. The new equation retained the precision and accuracy of the Modification of Diet for Renal Disease equation at GFR < 60ml/min/1.73m2, showed less bias and improved precision at GFR>60ml/min/1.73m2. In Asian countries, adding an ethnic coefficient to the equation enhanced its performance. In Malaysia, a multi-ethnic Asian population, the Chronic Kidney Disease Epidemiology Collaboration equation should be validated and the Glomerular Filtration Rate should be reported whenever serum creatinine is ordered. Reporting estimated Glomerular Filtration Rate will help diagnose patients who would have been otherwise missed if only albuminuria and serum creatinine are measured.

Knowledge of Parents of Children with Autism Spectrum Disorder of Behavior Modification Methods and Their Training Needs Accordingly

ERIC Educational Resources Information Center

Deeb, Raid Mousa Al-Shaik

2016-01-01

The study aimed at identifying knowledge of parents of children with autism spectrum disorder of behavior modification methods and their training needs accordingly. The sample of the study consisted of (98) parents in Jordan. A scale of behavior modification methods was constructed, and then validated. The results of the study showed that the…

A Genome-Wide Knockout Screen to Identify Genes Involved in Acquired Carboplatin Resistance

DTIC Science & Technology

2016-07-01

library screen to identify genes that when knocked out render human ovarian cells > 2.5-fold resistant to CBDCA; 2) Validate the ability of...a GeCKOv2 library screen to identify genes that when knocked out render human ovarian cells > 2.5-fold resistant to CBDCA; 2) validate the ability of...resistance in either cell lines or clinical samples. The CRIPSR-cas9 technology now provides us with a major new tool to introduce knock out mutations

Colorectal Cancer Screening: Preferences, Past Behavior, and Future Intentions.

PubMed

Mansfield, Carol; Ekwueme, Donatus U; Tangka, Florence K L; Brown, Derek S; Smith, Judith Lee; Guy, Gery P; Li, Chunyu; Hauber, Brett

2018-05-09

Screening rates for colorectal cancer are below the Healthy People 2020 goal. There are several colorectal cancer screening tests that differ in terms of accuracy, recommended frequency, and administration. In this article, we compare how a set of personal characteristics correlates with preferences for colorectal cancer screening test attributes, past colorectal cancer screening behavior, and future colorectal cancer screening intentions. We conducted a discrete-choice experiment survey to assess relative preferences for attributes of colorectal cancer screening tests among adults aged 50-75 years in USA. We used a latent class logit model to identify classes of preferences and calculated willingness to pay for changes in test attributes. A set of personal characteristics were included in the latent class analysis and analyses of self-reported past screening behavior and self-assessed likelihood of future colorectal cancer screening. Latent class analysis identified three types of respondents. Class 1 valued test accuracy, class 2 valued removing polyps and avoiding discomfort, and class 3 valued cost. Having had a prior colonoscopy and a higher income were predictors of the likelihood of future screening and membership in classes 1 and 2. Health insurance and a self-reported higher risk of developing colorectal cancer were associated with prior screening and higher future screening intentions, but not class membership. We identified distinct classes of preferences focusing on different test features and personal characteristics associated with reported behavior and intentions. Healthcare providers should engage in a careful assessment of patient preferences when recommending colorectal cancer test options to encourage colorectal cancer screening uptake.

Pregnant Women's Perceptions of Harms and Benefits of Mental Health Screening.

PubMed

Kingston, Dawn; Austin, Marie-Paule; McDonald, Sheila W; Vermeyden, Lydia; Heaman, Maureen; Hegadoren, Kathleen; Lasiuk, Gerri; Kingston, Joshua; Sword, Wendy; Jarema, Karly; Veldhuyzen van Zanten, Sander; McDonald, Sarah D; Biringer, Anne

2015-01-01

A widely held concern of screening is that its psychological harms may outweigh the benefits of early detection and treatment. This study describes pregnant women's perceptions of possible harms and benefits of mental health screening and factors associated with identifying screening as harmful or beneficial. This study analyzed a subgroup of women who had undergone formal or informal mental health screening from our larger multi-site, cross-sectional study. Pregnant women >16 years of age who spoke/read English were recruited (May-December 2013) from prenatal classes and maternity clinics in Alberta, Canada. Descriptive statistics were generated to summarize harms and benefits of screening and multivariable logistic regression identified factors associated with reporting at least one harm or affirming screening as a positive experience (January-December 2014). Overall study participation rate was 92% (N = 460/500). Among women screened for mental health concerns (n = 238), 63% viewed screening as positive, 69% were glad to be asked, and 87% took it as evidence their provider cared about them. Only one woman identified screening as a negative experience. Of the 6 harms, none was endorsed by >7% of women, with embarrassment being most cited. Women who were very comfortable (vs somewhat/not comfortable) with screening were more likely to report it as a positive experience. Women were largely Caucasian, well-educated, partnered women; thus, findings may not be generalizable to women with socioeconomic risk. Most women perceived prenatal mental health screening as having high benefit and low harm. These findings dispel popular concerns that mental health screening is psychologically harmful.

Enzymatic modification of schizophyllan

USDA-ARS?s Scientific Manuscript database

An enzymatic method was developed for the progressive modification of the polysaccharide schizophyllan. Fungal strains Hypocrea nigricans NRRL 62555, Penicillium crustosum NRRL 62558, and Penicillium simplicissimum NRRL 62550 were previously identified as novel sources of ß-endoglucanase with specif...

Successful outcomes of older adolescents and adults with profound biotinidase deficiency identified by newborn screening.

PubMed

Wolf, Barry

2017-04-01

We began screening newborns for biotinidase deficiency disorder in 1984, and now all states in the United States and many countries perform this screening. The purpose of this study was to determine the outcomes of older adolescent and adult individuals with the disorder identified by newborn screening. We located and surveyed, by questionnaire and telephone interviews, 44 individuals with profound biotinidase deficiency identified by newborn screening with a mean age of 23.1 years. All individuals had successfully completed high school, and many were attending or had completed college or graduate school. Compliance in using biotin has been excellent. Several individuals developed a variety of symptoms when they discontinued biotin for days or weeks. These features readily resolved when biotin was resumed. In addition, five treated women had nine uneventful pregnancies and deliveries. Newborn screening for profound biotinidase deficiency and early treatment with biotin result in excellent outcomes for older adolescents and adults with the disorder. In addition, mothers with profound biotinidase deficiency who were treated with biotin had pregnancies with good outcomes. These outcome results indicate that newborn screening for biotinidase deficiency is one of the most successful newborn screening programs.Genet Med 19 4, 396-402.

Patient-completed or symptom-based screening tools for endometriosis: a scoping review.

PubMed

Surrey, Eric; Carter, Cathryn M; Soliman, Ahmed M; Khan, Shahnaz; DiBenedetti, Dana B; Snabes, Michael C

2017-08-01

The objective of this review was to evaluate existing patient-completed screening questionnaires and/or symptom-based predictive models with respect to their potential for use as screening tools for endometriosis in adult women. Validated instruments were of particular interest. We conducted structured searches of PubMed and targeted searches of the gray literature to identify studies reporting on screening instruments used in endometriosis. Studies were screened according to inclusion and exclusion criteria that followed the PICOS (population, intervention, comparison, outcomes, study design) framework. A total of 16 studies were identified, of which 10 described measures for endometriosis in general, 2 described measures for endometriosis at specific sites, and 4 described measures for deep-infiltrating endometriosis. Only 1 study evaluated a questionnaire that was solely patient-completed. Most measures required physician, imaging, or laboratory assessments in addition to patient-completed questionnaires, and several measures relied on complex scoring. Validation for use as a screening tool in adult women with potential endometriosis was lacking in all studies, as most studies focused on diagnosis versus screening. This literature review did not identify any fully validated, symptom-based, patient-reported questionnaires for endometriosis screening in adult women.

Nutrition screening tools: an analysis of the evidence.

PubMed

Skipper, Annalynn; Ferguson, Maree; Thompson, Kyle; Castellanos, Victoria H; Porcari, Judy

2012-05-01

In response to questions about tools for nutrition screening, an evidence analysis project was developed to identify the most valid and reliable nutrition screening tools for use in acute care and hospital-based ambulatory care settings. An oversight group defined nutrition screening and literature search criteria. A trained analyst conducted structured searches of the literature for studies of nutrition screening tools according to predetermined criteria. Eleven nutrition screening tools designed to detect undernutrition in patients in acute care and hospital-based ambulatory care were identified. Trained analysts evaluated articles for quality using criteria specified by the American Dietetic Association's Evidence Analysis Library. Members of the oversight group assigned quality grades to the tools based on the quality of the supporting evidence, including reliability and validity data. One tool, the NRS-2002, received a grade I, and 4 tools-the Simple Two-Part Tool, the Mini-Nutritional Assessment-Short Form (MNA-SF), the Malnutrition Screening Tool (MST), and Malnutrition Universal Screening Tool (MUST)-received a grade II. The MST was the only tool shown to be both valid and reliable for identifying undernutrition in the settings studied. Thus, validated nutrition screening tools that are simple and easy to use are available for application in acute care and hospital-based ambulatory care settings.

Expression screening using a Medaka cDNA library identifies evolutionarily conserved regulators of the p53/Mdm2 pathway.

PubMed

Zhang, Ping; Kratz, Anne Sophie; Salama, Mohammed; Elabd, Seham; Heinrich, Thorsten; Wittbrodt, Joachim; Blattner, Christine; Davidson, Gary

2015-10-08

The p53 tumor suppressor protein is mainly regulated by alterations in the half-life of the protein, resulting in significant differences in p53 protein levels in cells. The major regulator of this process is Mdm2, which ubiquitinates p53 and targets it for proteasomal degradation. This process can be enhanced or reduced by proteins that associate with p53 or Mdm2 and several proteins have been identified with such an activity. Furthermore, additional ubiquitin ligases for p53 have been identified in recent years. Nevertheless, our understanding of how p53 abundance and Mdm2 activity are regulated remains incomplete. Here we describe a cell culture based overexpression screen to identify evolutionarily conserved regulators of the p53/Mdm2 circuit. The results from this large-scale screening method will contribute to a better understanding of the regulation of these important proteins. Expression screening was based on co-transfection of H1299 cells with pools of cDNA's from a Medaka library together with p53, Mdm2 and, as internal control, Ror2. After cell lysis, SDS-PAGE/WB analysis was used to detect alterations in these proteins. More than one hundred hits that altered the abundance of either p53, Mdm2, or both were identified in the primary screen. Subscreening of the library pools that were identified in the primary screen identified several potential novel regulators of p53 and/or Mdm2. We also tested whether the human orthologues of the Medaka genes regulate p53 and/or Mdm2 abundance. All human orthologues regulated p53 and/or Mdm2 abundance in the same manner as the proteins from Medaka, which underscores the suitability of this screening methodology for the identification of new modifiers of p53 and Mdm2. Despite enormous efforts in the last two decades, many unknown regulators for p53 and Mdm2 abundance are predicted to exist. This cross-species approach to identify evolutionarily conserved regulators demonstrates that our Medaka unigene cDNA library represents a powerful tool to screen for these novel regulators of the p53/Mdm2 pathway.

Atrial fibrillation screening in pharmacies using an iPhone ECG: a qualitative review of implementation.

PubMed

Lowres, Nicole; Krass, Ines; Neubeck, Lis; Redfern, Julie; McLachlan, Andrew J; Bennett, Alexandra A; Freedman, S Ben

2015-12-01

Atrial fibrillation guidelines advocate screening to identify undiagnosed atrial fibrillation. Community pharmacies may provide an opportunistic venue for such screening. To explore the experience of implementing an atrial fibrillation screening service from the pharmacist's perspective including: the process of study implementation; the perceived benefits; the barriers and enablers; and the challenges for future sustainability of atrial fibrillation screening within pharmacies. Setting Interviews were conducted face-to-face in the pharmacy or via telephone, according to pharmacist preference. The 'SEARCH-AF study' screened 1000 pharmacy customers aged ≥65 years using an iPhone electrocardiogram, identifying 1.5 % with undiagnosed atrial fibrillation. Nine pharmacists took part in semi-structured interviews. Interviews were transcribed in full and thematically analysed. Qualitative analysis of the experience of implementing an AF screening service from the pharmacist's perspective. Four broad themes relating to service provision were identified: (1) interest and engagement in atrial fibrillation screening by pharmacists, customers, and doctors with the novel, easy-to-use electrocardiogram technology serving as an incentive to undergo screening and an education tool for pharmacists to use with customers; (2) perceived benefits to the pharmacist including increased job satisfaction, improvement in customer relations and pharmacy profile by fostering enhanced customer care and the educational role of pharmacists; (3) implementation barriers including managing workflow, and enablers such as personal approaches for recruitment, and allocating time to discuss screening process and fears; and, (4) potential for sustainable future implementation including remuneration linked to government or pharmacy incentives, combined cardiovascular screening, and automating sections of risk-assessments using touch-screen technology. Atrial fibrillation screening in pharmacies is well accepted by pharmacists and customers. Many pharmacists combined atrial fibrillation screening with other health screens reporting improved time-efficiency and greater customer satisfaction. Widespread implementation of atrial fibrillation screening requires longterm funding, which could be provided for a combined cardiovascular screening service. Further research could focus on feasibility and cost-effectiveness of combined cardiovascular screening in pharmacies.

Validation of self-reported breast and cervical cancer screening tests among low-income minority women.

PubMed

Paskett, E D; Tatum, C M; Mack, D W; Hoen, H; Case, L D; Velez, R

1996-09-01

The objective of the Forsyth County Cancer Screening Project is to assess barriers to breast and cervical cancer screening among low-income women and to develop an educational program to address these barriers. To properly assess the barriers, it was first necessary to determine if self-reported rates of breast and cervical cancer screening were accurate. All women who participated in the baseline survey (n = 555) were asked to provide information regarding if, where, and when they had obtained mammograms and Pap smears. Identified health care facilities were then contacted to verify this information. Approximately 80% of responses were verified for at least one of the exams with the information provided. For mammography, 77% of self-reports were correct, whereas 67% of self-reports of Pap smear screening were correct (kappa = 0.54 and 0.15, respectively). For both tests, women thought they had received them more recently than they actually had, by an average of 3 months for mammography and 23 months for Pap smears. Using validated reports of screening did not substantially change identified predictors of screening for mammography. For Pap smear screening, however, most of the identified predictors of screening became nonsignificant when medical chart reports were used instead of self-reports, suggesting that caution should be used in relying on self-reports to design programs to improve cervical cancer screening practices.

Structural and mechanistic analysis of a β-glycoside phosphorylase identified by screening a metagenomic library.

PubMed

Macdonald, Spencer S; Patel, Ankoor; Larmour, Veronica L C; Morgan-Lang, Connor; Hallam, Steven J; Mark, Brian L; Withers, Stephen G

2018-03-02

Glycoside phosphorylases have considerable potential as catalysts for the assembly of useful glycans for products ranging from functional foods and prebiotics to novel materials. However, the substrate diversity of currently identified phosphorylases is relatively small, limiting their practical applications. To address this limitation, we developed a high-throughput screening approach using the activated substrate 2,4-dinitrophenyl β-d-glucoside (DNPGlc) and inorganic phosphate for identifying glycoside phosphorylase activity and used it to screen a large insert metagenomic library. The initial screen, based on release of 2,4-dinitrophenyl from DNPGlc in the presence of phosphate, identified the gene bglP, encoding a retaining β-glycoside phosphorylase from the CAZy GH3 family. Kinetic and mechanistic analysis of the gene product, BglP, confirmed a double displacement ping-pong mechanism involving a covalent glycosyl-enzyme intermediate. X-ray crystallographic analysis provided insights into the phosphate-binding mode and identified a key glutamine residue in the active site important for substrate recognition. Substituting this glutamine for a serine swapped the substrate specificity from glucoside to N -acetylglucosaminide. In summary, we present a high-throughput screening approach for identifying β-glycoside phosphorylases, which was robust, simple to implement, and useful in identifying active clones within a metagenomics library. Implementation of this screen enabled discovery of a new glycoside phosphorylase class and has paved the way to devising simple ways in which enzyme specificity can be encoded and swapped, which has implications for biotechnological applications. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Generation of an arrayed CRISPR-Cas9 library targeting epigenetic regulators: from high-content screens to in vivo assays

PubMed Central

2017-01-01

ABSTRACT The CRISPR-Cas9 system has revolutionized genome engineering, allowing precise modification of DNA in various organisms. The most popular method for conducting CRISPR-based functional screens involves the use of pooled lentiviral libraries in selection screens coupled with next-generation sequencing. Screens employing genome-scale pooled small guide RNA (sgRNA) libraries are demanding, particularly when complex assays are used. Furthermore, pooled libraries are not suitable for microscopy-based high-content screens or for systematic interrogation of protein function. To overcome these limitations and exploit CRISPR-based technologies to comprehensively investigate epigenetic mechanisms, we have generated a focused sgRNA library targeting 450 epigenetic regulators with multiple sgRNAs in human cells. The lentiviral library is available both in an arrayed and pooled format and allows temporally-controlled induction of gene knock-out. Characterization of the library showed high editing activity of most sgRNAs and efficient knock-out at the protein level in polyclonal populations. The sgRNA library can be used for both selection and high-content screens, as well as for targeted investigation of selected proteins without requiring isolation of knock-out clones. Using a variety of functional assays we show that the library is suitable for both in vitro and in vivo applications, representing a unique resource to study epigenetic mechanisms in physiological and pathological conditions. PMID:29327641

Cell-Based High-Throughput Screening for Aromatase Inhibitors in the Tox21 10K Library.

PubMed

Chen, Shiuan; Hsieh, Jui-Hua; Huang, Ruili; Sakamuru, Srilatha; Hsin, Li-Yu; Xia, Menghang; Shockley, Keith R; Auerbach, Scott; Kanaya, Noriko; Lu, Hannah; Svoboda, Daniel; Witt, Kristine L; Merrick, B Alex; Teng, Christina T; Tice, Raymond R

2015-10-01

Multiple mechanisms exist for endocrine disruption; one nonreceptor-mediated mechanism is via effects on aromatase, an enzyme critical for maintaining the normal in vivo balance of androgens and estrogens. We adapted the AroER tri-screen 96-well assay to 1536-well format to identify potential aromatase inhibitors (AIs) in the U.S. Tox21 10K compound library. In this assay, screening with compound alone identifies estrogen receptor alpha (ERα) agonists, screening in the presence of testosterone (T) identifies AIs and/or ERα antagonists, and screening in the presence of 17β-estradiol (E2) identifies ERα antagonists. Screening the Tox-21 library in the presence of T resulted in finding 302 potential AIs. These compounds, along with 31 known AI actives and inactives, were rescreened using all 3 assay formats. Of the 333 compounds tested, 113 (34%; 63 actives, 50 marginal actives) were considered to be potential AIs independent of cytotoxicity and ER antagonism activity. Structure-activity analysis suggested the presence of both conventional (eg, 1, 2, 4, - triazole class) and novel AI structures. Due to their novel structures, 14 of the 63 potential AI actives, including both drugs and fungicides, were selected for confirmation in the biochemical tritiated water-release aromatase assay. Ten compounds were active in the assay; the remaining 4 were only active in high-throughput screen assay, but with low efficacy. To further characterize these 10 novel AIs, we investigated their binding characteristics. The AroER tri-screen, in high-throughput format, accurately and efficiently identified chemicals in a large and diverse chemical library that selectively interact with aromatase. © The Author 2015. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Cell-Based High-Throughput Screening for Aromatase Inhibitors in the Tox21 10K Library

PubMed Central

Chen, Shiuan; Hsieh, Jui-Hua; Huang, Ruili; Sakamuru, Srilatha; Hsin, Li-Yu; Xia, Menghang; Shockley, Keith R.; Auerbach, Scott; Kanaya, Noriko; Lu, Hannah; Svoboda, Daniel; Witt, Kristine L.; Merrick, B. Alex; Teng, Christina T.; Tice, Raymond R.

2015-01-01

Multiple mechanisms exist for endocrine disruption; one nonreceptor-mediated mechanism is via effects on aromatase, an enzyme critical for maintaining the normal in vivo balance of androgens and estrogens. We adapted the AroER tri-screen 96-well assay to 1536-well format to identify potential aromatase inhibitors (AIs) in the U.S. Tox21 10K compound library. In this assay, screening with compound alone identifies estrogen receptor alpha (ERα) agonists, screening in the presence of testosterone (T) identifies AIs and/or ERα antagonists, and screening in the presence of 17β-estradiol (E2) identifies ERα antagonists. Screening the Tox-21 library in the presence of T resulted in finding 302 potential AIs. These compounds, along with 31 known AI actives and inactives, were rescreened using all 3 assay formats. Of the 333 compounds tested, 113 (34%; 63 actives, 50 marginal actives) were considered to be potential AIs independent of cytotoxicity and ER antagonism activity. Structure-activity analysis suggested the presence of both conventional (eg, 1, 2, 4, - triazole class) and novel AI structures. Due to their novel structures, 14 of the 63 potential AI actives, including both drugs and fungicides, were selected for confirmation in the biochemical tritiated water-release aromatase assay. Ten compounds were active in the assay; the remaining 4 were only active in high-throughput screen assay, but with low efficacy. To further characterize these 10 novel AIs, we investigated their binding characteristics. The AroER tri-screen, in high-throughput format, accurately and efficiently identified chemicals in a large and diverse chemical library that selectively interact with aromatase. PMID:26141389

Identification of a new peptide deformylase gene from enterococcus faecium and establishment of a new screening model targeted on PDF for novel antibiotics.

PubMed

Tang, Xian-Bing; Si, Shu-Yi; Zhang, Yue-Qin

2004-09-01

To identify a new peptide deformylase (PDF) gene (Genebank Accession AY238515) from Enterococcus faecium and to establish a new screening model targeted on PDF. A new PDF gene was identified by BLAST analysis and PCR and was subsequently over-expressed in the prokaryotic expression host E. coli B121(DE3). Over-expressed protein was purified for enzymatic assay by metal affinity chromatography and a new screening model was established for novel antibiotics. A new PDF gene of Enterococcus faecium was identified successfully. Ten positive samples were picked up from 8000 compound library and the microbial fermentation broth samples. A new PDF of gene Enterococcus faecium was first identified and the model had a high efficacy. Positive samples screened may be antibacterial agents of broad spectrum.

Screening tools to identify patients with complex health needs at risk of high use of health care services: A scoping review.

PubMed

Marcoux, Valérie; Chouinard, Maud-Christine; Diadiou, Fatoumata; Dufour, Isabelle; Hudon, Catherine

2017-01-01

Many people with chronic conditions have complex health needs often due to multiple chronic conditions, psychiatric comorbidities, psychosocial issues, or a combination of these factors. They are at high risk of frequent use of healthcare services. To offer these patients interventions adapted to their needs, it is crucial to be able to identify them early. The aim of this study was to find all existing screening tools that identify patients with complex health needs at risk of frequent use of healthcare services, and to highlight their principal characteristics. Our purpose was to find a short, valid screening tool to identify adult patients of all ages. A scoping review was performed on articles published between 1985 and July 2016, retrieved through a comprehensive search of the Scopus and CINAHL databases, following the methodological framework developed by Arksey and O'Malley (2005), and completed by Levac et al. (2010). Of the 3,818 articles identified, 30 were included, presenting 14 different screening tools. Seven tools were self-reported. Five targeted adult patients, and nine geriatric patients. Two tools were designed for specific populations. Four can be completed in 15 minutes or less. Most screening tools target elderly persons. The INTERMED self-assessment (IM-SA) targets adults of all ages and can be completed in less than 15 minutes. Future research could evaluate its usefulness as a screening tool for identifying patients with complex needs at risk of becoming high users of healthcare services.

Behavioral management of the obese patient

USDA-ARS?s Scientific Manuscript database

Despite countless diets, exercise regimens, drugs, and behavior modification strategies, the prevalence of obesity continues its relentless increase in both developed and developing nations. Although many necessary components to treat obesity have been identified, behavior modification remains the b...

Screening for Homelessness in the Veterans Health Administration: Monitoring Housing Stability through Repeat Screening.

PubMed

Byrne, Thomas; Fargo, Jamison D; Montgomery, Ann Elizabeth; Roberts, Christopher B; Culhane, Dennis P; Kane, Vincent

2015-01-01

This study examined veterans' responses to the Veterans Health Administration's (VHA's) universal screen for homelessness and risk of homelessness during the first 12 months of implementation. We calculated the baseline annual frequency of homelessness and risk of homelessness among all veterans who completed an initial screen during the study period. We measured changes in housing status among veterans who initially screened positive and then completed a follow-up screen, assessed factors associated with such changes, and identified distinct risk profiles of veterans who completed a follow-up screen. More than 4 million veterans completed an initial screen; 1.8% (n=77,621) screened positive for homelessness or risk of homelessness. Of those who initially screened positive for either homelessness or risk of homelessness and who completed a second screen during the study period, 85.0% (n=15,060) resolved their housing instability prior to their second screen. Age, sex, race, VHA eligibility, and screening location were all associated with changes in housing stability. We identified four distinct risk profiles for veterans with ongoing housing instability. To address homelessness among veterans, efforts should include increased and targeted engagement of veterans experiencing persistent housing instability.

Smartphone-based cyclic voltammetry system with graphene modified screen printed electrodes for glucose detection.

PubMed

Ji, Daizong; Liu, Lei; Li, Shuang; Chen, Chen; Lu, Yanli; Wu, Jiajia; Liu, Qingjun

2017-12-15

Smartphone-based electrochemical devices have such advantages as the low price, miniaturization, and obtaining the real-time data. As a popular electrochemical method, cyclic voltammetry (CV) has shown its great practicability for quantitative detection and electrodes modification. In this study, a smartphone-based CV system with a simple method of electrode modification was constructed to perform electrochemical detections. The system was composed of these main portions: modified electrodes, portable electrochemical detector and smartphone. Among them, the detector was comprised of an energy transformation module applying the stimuli signals, and a low-cost potentiostat module for CV measurements with a Bluetooth module for transmitting data and commands. With an Application (App), the smartphone was used as the controller and displayer of the system. Through controlling of different scan rates, the smartphone-based system could perform CV detections for redox couples with test errors less than 3.8% compared to that of commercial electrochemical workstation. Also, the reduced graphene oxide (rGO) and sensitive substance could be modified by the system on the screen printed electrodes for detections. As a demonstration, 3-amino phenylboronic acid (APBA) was used as the sensitive substance to fabricate a glucose sensor. Finally, the experimental data of the system were shown the linear, sensitive, and specific responses to glucose at different doses, even in blood serum as low as about 0.026mM with 3δ/slope calculation. Thus, the system could show great potentials of detection and modification of electrodes in various fields, such as public health, water monitoring, and food quality. Copyright © 2017 Elsevier B.V. All rights reserved.

A modified reverse one-hybrid screen identifies transcriptional activation in Phyochrome-Interacting Factor 3

USDA-ARS?s Scientific Manuscript database

Transcriptional activation domains (TAD) are difficult to predict and identify, since they are not conserved and have little consensus. Here, we describe a yeast-based screening method that is able to identify individual amino acid residues involved in transcriptional activation in a high throughput...

Space Shuttle orbiter modifications to support Space Station Freedom

NASA Technical Reports Server (NTRS)

Segert, Randall; Lichtenfels, Allyson

1992-01-01

The Space Shuttle will be the primary vehicle to support the launch, assembly, and maintenance of the Space Station Freedom (SSF). In order to accommodate this function, the Space Shuttle orbiter will require significant modifications. These modifications are currently in development in the Space Shuttle Program. The requirements for the planned modifications to the Space Shuttle orbiter are dependent on the design of the SSF. Therefore, extensive coordination is required with the Space Station Freedom Program (SSFP) in order to identify requirements and resolve integration issues. This paper describes the modifications to the Space Shuttle orbiter required to support SSF assembly and operations.

Outcomes analysis of new entrant screening for active tuberculosis in Heathrow and Gatwick airports, United Kingdom 2009/2010.

PubMed

Severi, Ettore; Maguire, Helen; Ihekweazu, Chikwe; Bickler, Graham; Abubakar, Ibrahim

2016-04-22

In 2012, the United Kingdom (UK) Government announced that the new entrant screening for active tuberculosis (TB) in Heathrow and Gatwick airports would end. Our study objective was to estimate screening yield and diagnostic accuracy, and identify those at risk of active TB after entry. We designed a retrospective cohort study and linked new entrants screened from June 2009 to September 2010 through probabilistic matching with UK Enhanced TB Surveillance (ETS) data (June 2009 to December 2010). Yield was the proportion of cases reported to ETS within three months of airport screening in the screened population. To estimate screening diagnostic accuracy we assessed sensitivity, specificity, positive and negative predictive values. Through Poisson regression we identified groups at increased risk of TB diagnosis after entry. We identified 200,199 screened entrants, of these 59 had suspected TB at screening and were reported within 3 months to ETS (yield = 0.03 %). Sensitivity was 26 %; specificity was 99.7 %; positive predictive value was 13.2 %; negative predictive value was 99.9 %. Overall, 350 entrants were reported in ETS. Persons from countries with annual TB incidence higher than 150 cases per 100,000 population and refugees and asylum seekers were at increased risk of TB diagnosis after entry (population attributable risk 77 and 3 % respectively). Airport screening has very low screening yields, sensitivity and positive predictive value. New entrants coming from countries with annual TB incidence higher than 150 per 100,000 population, refugees and asylum seekers should be prioritised at pre- or post-entry screening.

Making the Mark: The Role of Adenosine Modifications in the Lifecycle of RNA Viruses

PubMed Central

Gonzales-van Horn, Sarah R.; Sarnow, Peter

2017-01-01

Summary Viral epitranscriptomics is a newly emerging field that has identified unique roles for RNA modifications in modulating lifecycles of RNA viruses. Despite the observation of a handful of modified viral RNAs five decades ago, very little was known about how these modifications regulate viral lifecycles, until recently. Here we review the pro- and anti-viral effects of methyl-6-adenosine in distinct viral life cycles, the role of 2′ O-methyl modifications in RNA stability and innate immune sensing, and functions of adenosine to inosine modifications in retroviral life cycles. With roles for over 100 modifications in RNA still unknown, this is a rapidly emerging field that is destined to suggest novel antiviral therapies. PMID:28618265

Modern and prospective technologies for weather modification activities: A look at integrating unmanned aircraft systems

NASA Astrophysics Data System (ADS)

Axisa, Duncan; DeFelice, Tom P.

2016-09-01

Present-day weather modification technologies are scientifically based and have made controlled technological advances since the late 1990s, early 2000s. The technological advances directly related to weather modification have primarily been in the decision support and evaluation based software and modeling areas. However, there have been some technological advances in other fields that might now be advanced enough to start considering their usefulness for improving weather modification operational efficiency and evaluation accuracy. We consider the programmatic aspects underlying the development of new technologies for use in weather modification activities, identifying their potential benefits and limitations. We provide context and initial guidance for operators that might integrate unmanned aircraft systems technology in future weather modification operations.

Immobilized magnetic beads-based multi-target affinity selection coupled with HPLC-MS for screening active compounds from traditional Chinese medicine and natural products.

PubMed

Chen, Yaqi; Chen, Zhui; Wang, Yi

2015-01-01

Screening and identifying active compounds from traditional Chinese medicine (TCM) and other natural products plays an important role in drug discovery. Here, we describe a magnetic beads-based multi-target affinity selection-mass spectrometry approach for screening bioactive compounds from natural products. Key steps and parameters including activation of magnetic beads, enzyme/protein immobilization, characterization of functional magnetic beads, screening and identifying active compounds from a complex mixture by LC/MS, are illustrated. The proposed approach is rapid and efficient in screening and identification of bioactive compounds from complex natural products.

Development of Synthetic Spider Silk Fibers for High Performance Applications

DTIC Science & Technology

2013-08-08

complete with N- and C-termini. • Transformed all protein variants into a proprietary yeast strain and screened for expression. While all encoded...mammals1- 6,10-12. Among the most successfully expressing organisms has been the methylotropic yeast Pichia pastoris. Yeast are an attractive...modifications, recombinant proteins can be secreted into their culture media, and they are well adapted to high density fermentation . In addition, P

Simulation Learning: PC-Screen Based (PCSB) versus High Fidelity Simulation (HFS)

DTIC Science & Technology

2012-08-01

methods for the use of simulation for teaching clinical skills to military and civilian clinicians . High fidelity simulation is an expensive method of...without the knowledge and approval of the IRB. Changes include, but not limited to, modifications in study design, recruitment process and number of...Person C-Collar simulation algorithm Pathway A Scenario A - Spinal stabilization: Sub processes Legend: Pathway Points Complex task to be performed by

Considering Planetary Constraints and Dynamic Screening in Solar Evolution Modeling

NASA Astrophysics Data System (ADS)

Wood, Suzannah R.; Mussack, Katie; Guzik, Joyce A.

2018-01-01

The ‘faint early sun problem’ remains unsolved. This problem consists of the apparent contradiction between the standard solar model prediction of lower luminosity (70% of current luminosity) and the observations of liquid water on early Earth and Mars. The presence of liquid water on early Earth and Mars should not be neglected and should be used as a constraint for solar evolution modeling. In addition, modifications to standard solar models are needed to address the discrepancy with solar structure inferred from helioseismology given the latest solar abundance determinations. Here, we will utilize the three different solar abundances: GN93 (Grevesse & Noels, 1993), AGS05 (Asplund et al., 2005), AGSS09 (Asplund et al., 2009). Here, we propose an early mass loss model with an initial solar mass between 1.07 and 1.15 solar masses and an exponentially decreasing mass-loss rate to meet conditions in the early solar system (Wood et al, submitted). Additionally, we investigate the effects of dynamic screening and the new OPLIB opacities from Los Alamos (Colgan et al., 2016). We show the effects of these modifications to the standard solar evolution models on the interior structure, neutrino fluxes, sound speed, p-mode frequencies, convection zone depth, and envelope helium and element abundance of the model sun at the present day.

SPLICEFINDER – A Fast and Easy Screening Method for Active Protein Trans-Splicing Positions

PubMed Central

Eppmann, Simone; Busche, Alena; Dikovskaya, Dina; Dötsch, Volker; Mootz, Henning D.

2013-01-01

Split intein enabled protein trans-splicing (PTS) is a powerful method for the ligation of two protein fragments, thereby paving the way for various protein modification or protein function control applications. PTS activity is strongly influenced by the amino acids directly flanking the splice junctions. However, to date no reliable prediction can be made whether or not a split intein is active in a particular foreign extein context. Here we describe SPLICEFINDER, a PCR-based method, allowing fast and easy screening for active split intein insertions in any target protein. Furthermore we demonstrate the applicability of SPLICEFINDER for segmental isotopic labeling as well as for the generation of multi-domain and enzymatically active proteins. PMID:24023792

Digesting the data - Effects of predator ingestion on the oxygen isotopic signature of micro-mammal teeth

NASA Astrophysics Data System (ADS)

Barham, Milo; Blyth, Alison J.; Wallwork, Melinda D.; Joachimski, Michael M.; Martin, Laure; Evans, Noreen J.; Laming, Belinda; McDonald, Bradley J.

2017-11-01

Biogenic minerals such as dental apatite have become commonly analysed archives preserving geochemical indicators of past environmental conditions and palaeoecologies. However, post-mortem, biogenic minerals are modified due to the alteration/replacement of labile components, and recent moves to utilise micro-mammal tooth δ18O signatures for refined Cenozoic terrestrial palaeoclimate reconstructions has lacked consideration of the chemical effects of predator digestion. Here, the physical and chemical condition of laboratory-raised mouse (Mus musculus) teeth have been investigated in conjunction with their bulk phosphate and tissue-specific δ18O values prior, and subsequent, to ingestion and excretion by various predator species (owls, mammals and a reptile). Substantial variability (up to 2‰) in the δ18O values of both undigested teeth and those ingested by specific predators suggests significant natural heterogeneity of individual prey δ18O. Statistically distinct, lower δ18O values (∼0.7‰) are apparent in teeth ingested by barn owls compared to undigested controls as a result of the chemically and enzymatically active digestive and waste-pellet environments. Overall, dentine tissues preserve lower δ18O values than enamel, while the greatest modification of oxygen isotope signals is exhibited in the basal enamel of ingested teeth as a result of its incompletely mineralised state. However, recognition of 18O-depletion in chemically purified phosphate analyses demonstrates that modification of original δ18O values is not restricted to labile oxygen-bearing carbonate and organic phases. The style and magnitude of digestive-alteration varies with predator species and no correlation was identified between specific physical or minor/trace-element (patterns or concentrations) modification of ingested teeth and disruption of their primary oxygen isotope values. Therefore, there is a current lack of any screening tool for oxygen isotope disruption as a result of predation. These results point to the need for careful application of the micro-mammal oxygen isotope palaeoenvironmental proxy in future studies.

Estimating natural monthly streamflows in California and the likelihood of anthropogenic modification

USGS Publications Warehouse

Carlisle, Daren M.; Wolock, David M.; Howard, Jeannette K.; Grantham, Theodore E.; Fesenmyer, Kurt; Wieczorek, Michael

2016-12-12

Because natural patterns of streamflow are a fundamental property of the health of streams, there is a critical need to quantify the degree to which human activities have modified natural streamflows. A requirement for assessing streamflow modification in a given stream is a reliable estimate of flows expected in the absence of human influences. Although there are many techniques to predict streamflows in specific river basins, there is a lack of approaches for making predictions of natural conditions across large regions and over many decades. In this study conducted by the U.S. Geological Survey, in cooperation with The Nature Conservancy and Trout Unlimited, the primary objective was to develop empirical models that predict natural (that is, unaffected by land use or water management) monthly streamflows from 1950 to 2012 for all stream segments in California. Models were developed using measured streamflow data from the existing network of streams where daily flow monitoring occurs, but where the drainage basins have minimal human influences. Widely available data on monthly weather conditions and the physical attributes of river basins were used as predictor variables. Performance of regional-scale models was comparable to that of published mechanistic models for specific river basins, indicating the models can be reliably used to estimate natural monthly flows in most California streams. A second objective was to develop a model that predicts the likelihood that streams experience modified hydrology. New models were developed to predict modified streamflows at 558 streamflow monitoring sites in California where human activities affect the hydrology, using basin-scale geospatial indicators of land use and water management. Performance of these models was less reliable than that for the natural-flow models, but results indicate the models could be used to provide a simple screening tool for identifying, across the State of California, which streams may be experiencing anthropogenic flow modification.

Monotopic modifications derived from in vitro glycation of albumin with ribose.

PubMed

Pataridis, Statis; Stastná, Zdeňka; Sedláková, Pavla; Mikšík, Ivan

2013-06-01

Post-translational modifications are significant reactions that occur to proteins. One of these modifications is a non-enzymatic reaction between the oxo-group(s) of sugars and amino-group(s) of protein - glycation. This reaction plays an important role in the chronic complications of diabetes mellitus, or in the aging process of organisms, that is, it has an important role in the pathophysiology and "normal" physiology of animals. In the work presented here, we studied the glycation of albumins (HSA and BSA). Methodologically, we used nano-LC coupled to a QTOF mass spectrometer. In vitro-modified proteins were cleaved by trypsin and the arising peptides were separated on a C(18) nano column with a trap-column. Peptides and their modifications were analysed with a high-resolution QTOF mass spectrometer with a mass determination precision of better than 5 ppm. Non-enzymatic in vitro reaction products between albumin and ribose were identified. Besides well-known carboxymethyl lysine, new modifications were determined - creating mass shifts of 78 and 218. The origin of the first modification is discussed and its possible structure is presented. In addition, a mass shift of 132 belonging to a Schiff base was also identified. The location of all the modifications within the structure of the proteins was determined and their reactivity to various oxo-compounds was also examined. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Peer Health Educator Program for Breast Cancer Screening Promotion: Arabic, Chinese, South Asian, and Vietnamese Immigrant Women's Perspectives

PubMed Central

Parascandalo, Faye

2015-01-01

This study explored Arabic, Chinese, South Asian, and Vietnamese immigrant women's experiences with a peer health educator program, a public health program that facilitated access to breast health information and mammography screening. Framed within critical social theory, this participatory action research project took place from July 2009 to January 2011. Ten focus groups and 14 individual interviews were conducted with 82 immigrant women 40 years of age and older. Qualitative methods were utilized. Thematic content analysis derived from grounded theory and other qualitative literature was employed to analyze data. Four dominant themes emerged: Breast Cancer Prevention focused on learning within the program, Social Support provided by the peer health educator and other women, Screening Services Access for Women centered on service provision, and Program Enhancements related to specific modifications required to meet the needs of immigrant women accessing the program. The findings provide insights into strategies used to promote breast health, mammography screening, and the improvement of public health programming. Perceived barriers that continue to persist are structural barriers, such as the provision of information on breast cancer and screening by family physicians. A future goal is to improve collaborations between public health and primary care to minimize this barrier. PMID:25810922

Adolescents' Physical Activity and Sedentary Behavior: A Pathway in Reducing Overweight and Obesity. The PRALIMAP 2-Year Cluster Randomized Controlled Trial.

PubMed

Omorou, Abdou Y; Langlois, Johanne; Lecomte, Edith; Vuillemin, Anne; Briançon, Serge

2015-05-01

explaining why and how overweight prevention programs were effective was a real need; especially the potential role of physical activity (PA) and sedentary behavior (SB) should be highlighted. This study aimed to evaluate the 2-year effectiveness of a screening and care strategy in adolescents' weight reduction with regards to PA and SB change. 1745 adolescents aged 15.1 years from PRALIMAP trial was included (n = 840 for screening and care group and n = 905 for control group). PA and SB time (international physical activity questionnaire: IPAQ), body mass index (BMI), and BMI z-score were assessed at inclusion and after 2-year intervention. Hierarchical mixed models were applied. Compared with the control group, screening and care strategy was associated with an increase in global PA (58 min/week), a moderate PA (43 min/week), the adherence to the French PA guidelines (OR = 1.3), and a decrease in SB (-198 min/week). The 2-year weight change decreased when adjusted for PA and SB suggesting that the effect of screening and care strategy was partly mediated by PA and SB. Screening and care intervention seemed to be effective in increasing PA and decreasing SB. The induced PA and SB modifications contributed to the observed weight change.

Pediatric Eye Screening Instrumentation

NASA Astrophysics Data System (ADS)

Chen, Ying-Ling; Lewis, J. W. L.

2001-11-01

Computational evaluations are presented for binocular eye screening using the off-axis digital retinascope. The retinascope, such as the iScreen digital screening system, has been employed to perform pediatric binocular screening using a flash lamp and single-shot camera recording. The digital images are transferred electronically to a reading center for analysis. The method has been shown to detect refractive error, amblyopia, anisocoria, and ptosis. This computational work improves the performance of the system and forms the basis for automated data analysis. For this purpose, variouis published eye models are evaluated with simulated retinascope images. Two to ten million rays are traced in each image calculation. The poster will present the simulation results for a range of eye conditions of refractive error of -20 to +20 diopters with 0.5- to-1 diopter resolution, pupil size of 3 to 8 mm diameter (1-mm increment), and staring angle of 2 to 12 degree (2-degree increment). The variation of the results with the system conditions such as the off-axis distance of light source and the shutter size of camera are also evaluated. The quantitative analysis for each eye’s and system’s condition is then performed to obtain parameters for automatic reading. The summary of the system performance is given and performance-enhancement design modifications are presented.

A Peer Health Educator Program for Breast Cancer Screening Promotion: Arabic, Chinese, South Asian, and Vietnamese Immigrant Women's Perspectives.

PubMed

Crawford, Joanne; Frisina, Angela; Hack, Tricia; Parascandalo, Faye

2015-01-01

This study explored Arabic, Chinese, South Asian, and Vietnamese immigrant women's experiences with a peer health educator program, a public health program that facilitated access to breast health information and mammography screening. Framed within critical social theory, this participatory action research project took place from July 2009 to January 2011. Ten focus groups and 14 individual interviews were conducted with 82 immigrant women 40 years of age and older. Qualitative methods were utilized. Thematic content analysis derived from grounded theory and other qualitative literature was employed to analyze data. Four dominant themes emerged: Breast Cancer Prevention focused on learning within the program, Social Support provided by the peer health educator and other women, Screening Services Access for Women centered on service provision, and Program Enhancements related to specific modifications required to meet the needs of immigrant women accessing the program. The findings provide insights into strategies used to promote breast health, mammography screening, and the improvement of public health programming. Perceived barriers that continue to persist are structural barriers, such as the provision of information on breast cancer and screening by family physicians. A future goal is to improve collaborations between public health and primary care to minimize this barrier.

High-Throughput Screening Using a Whole-Cell Virus Replication Reporter Gene Assay to Identify Inhibitory Compounds against Rift Valley Fever Virus Infection.

PubMed

Islam, Md Koushikul; Baudin, Maria; Eriksson, Jonas; Öberg, Christopher; Habjan, Matthias; Weber, Friedemann; Överby, Anna K; Ahlm, Clas; Evander, Magnus

2016-04-01

Rift Valley fever virus (RVFV) is an emerging virus that causes serious illness in humans and livestock. There are no approved vaccines or treatments for humans. The purpose of the study was to identify inhibitory compounds of RVFV infection without any preconceived idea of the mechanism of action. A whole-cell-based high-throughput drug screening assay was developed to screen 28,437 small chemical compounds targeting RVFV infection. To accomplish both speed and robustness, a replication-competent NSs-deleted RVFV expressing a fluorescent reporter gene was developed. Inhibition of fluorescence intensity was quantified by spectrophotometry and related to virus infection in human lung epithelial cells (A549). Cell toxicity was assessed by the Resazurin cell viability assay. After primary screening, 641 compounds were identified that inhibited RVFV infection by ≥80%, with ≥50% cell viability at 50 µM concentration. These compounds were subjected to a second screening regarding dose-response profiles, and 63 compounds with ≥60% inhibition of RVFV infection at 3.12 µM compound concentration and ≥50% cell viability at 25 µM were considered hits. Of these, six compounds with high inhibitory activity were identified. In conclusion, the high-throughput assay could efficiently and safely identify several promising compounds that inhibited RVFV infection. © 2016 Society for Laboratory Automation and Screening.

Child and teacher acceptability of school-based echocardiographic screening for rheumatic heart disease in Uganda.

PubMed

Ploutz, Michelle; Aliku, Twalib; Bradley-Hewitt, Tyler; Dantin, Andrea; Lemley, Bethan; Gillespie, Catherine W; Lwabi, Peter; Sable, Craig; Beaton, Andrea

2017-01-01

Introduction Rheumatic heart disease causes substantial morbidity in children in low-income countries. School-based echocardiographic screening has been suggested as a means to identify children with latent disease; however, little is known about the experience of children and teachers participating in screenings. The aim of our study was to assess students' and teachers' experience of school-based echocardiographic screening and identify areas for improvement. Materials and methods A school-based echocardiographic screening programme was conducted in five schools in Northern Uganda in 2013. After 8 months, an age- and gender-stratified population that included 5% of the participating students and teachers completed a questionnaire via an in-person interview. Responses were reviewed by question and coded to identify key themes. A total of 255 students (mean 10.7 years; 48% male) and 35 teachers participated in our study. In total, 95% of the students and 100% of the teachers were happy to have participated in the screening; however, students reported feeling scared (35%) and nervous (48%) during the screening process. Programmatic strengths included the following: knowing one's health status, opportunity to receive treatment, and staff interactions. Although 43% of the patients did not suggest a change with open-ended questioning, concerns regarding privacy, fear of the screening process, and a desire to include others in the community were noted. Discussion School-based echocardiographic rheumatic heart disease screening was well received by students and teachers. Future programmes would likely benefit from improved pre-screening education regarding the screening process and diagnosis of rheumatic heart disease. Furthermore, education of teachers and students could improve screening perception and establish realistic expectations regarding the scope of screening.

Patterns of colorectal cancer screening uptake in newly-eligible men and women

PubMed Central

Wernli, Karen J.; Hubbard, Rebecca A.; Johnson, Eric; Chubak, Jessica; Kamineni, Aruna; Green, Beverly B.; Rutter, Carolyn M.

2014-01-01

Background We describe patterns of colorectal cancer screening uptake in a U.S. insured population as individuals become newly-eligible for screening at age 50 and assess temporal trends and patient characteristics with screening uptake. Methods We identified a cohort of 81,223 men and women who were members of Group Health and turned 50 years old from 1996 – 2010. We ascertained receipt of colorectal cancer screening within five years. Time to screening was estimated by year of cohort entry using cumulative incidence curves and Cox proportional hazards models estimated patient characteristics associated with screening uptake. Results Stool-based screening tests were the most common, 72% of first screening tests. The proportion of individuals initiating colorectal cancer screening via colonoscopy increased from 8% in 1996–98 to 33% in 2008–10. Patient factors associated with increased colorectal cancer screening were: turning 50 more recently (2008–10) (p-trend<0.0001) or Asian race (HR=1.14, 95% CI 1.10–1.19). Patient factors associated with decreased screening were: being a woman (HR=0.70, 95% CI 0.68–0.72), Native American (HR=0.68, 95% CI 0.60–0.78) or Pacific Islander race (HR=0.82, 95% CI 0.72–0.95), and having prevalent diabetes (HR=0.78, 95% CI 0.75–0.82) and higher body mass index (p-trend<0.0001). Conclusions Patient characteristics associated with initiation of colorectal cancer screening in a newly-eligible population are similar to characteristics associated with overall screening participation in all age-eligible adults. Our results identify patient populations to target in outreach programs. Impact Disparities in receipt of colorectal cancer screening are evident from onset of an age-eligible cohort, identifying key groups for future interventions for screening. PMID:24793956