Discovery and characterization of a novel non-competitive inhibitor of the divalent metal transporter DMT1/SLC11A2

Divalent metal transporter-1 (SLC11A2/DMT1) uses the H+ electrochemical gradient as the driving force to transport divalent metal ions such as Fe2+, Mn2+ and others metals into mammalian cells. DMT1 is ubiquitously expressed, most notably in proximal duodenum, immature erythroid cells, brain and kidney. This transporter mediates H+-coupled transport of ferrous iron across the apical membrane of enterocytes. In addition, in cells such as to erythroid precursors, following transferrin receptor (TfR) mediated endocytosis; it mediates H+-coupled exit of ferrous iron from endocytic vesicles into the cytosol. Dysfunction of human DMT1 is associated with several pathologies such as iron deficiency anemia hemochromatosis, Parkinson's disease and Alzheimer's disease, as well as colorectal cancer and esophageal adenocarcinoma, making DMT1 an attractive target for drug discovery. In the present study, we performed a ligand-based virtual screening of the Princeton database (700,000 commercially available compounds) to search for pharmacophore shape analogs of recently reported DMT1 inhibitors. We discovered a new compound, named pyrimidinone 8, which mediates a reversible linear non-competitive inhibition of human DMT1 (hDMT1) transport activity with a Ki of ∼20 μM. This compound does not affect hDMT1 cell surface expression and shows no dependence on extracellular pH. To our knowledge, this is the first experimental evidence that hDMT1 can be allosterically modulated by pharmacological agents. Pyrimidinone 8 represents a novel versatile tool compound and it may serve as a lead structure for the development of therapeutic compounds for pre-clinical assessment.

First international external quality assessment of molecular diagnostics for Mers-CoV

BACKGROUND: Since the discovery of Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012, diagnostic protocols were quickly published and deployed globally. OBJECTIVES: We set out to assess the quality of MERS-CoV molecular diagnostics worldwide. STUDY DESIGN: Both sensitivity and specificity were assessed using 12 samples containing different viral loads of MERS-CoV or common coronaviruses (OC43, 229E, NL63, HKU1). RESULTS: The panel was sent to more than 106 participants, of which 99 laboratories from 6 continents returned 189 panel results.Scores ranged from 100% (84 laboratories) to 33% (1 laboratory). 15% of respondents reported quantitative results, 61% semi-quantitative (Ct-values or time to positivity) and 24% reported qualitative results. The major specific technique used was real-time RT-PCR using the WHO recommended targets upE, ORF1a and ORF1b. The evaluation confirmed that RT-PCRs targeting the ORF1b are less sensitive, and therefore not advised for primary diagnostics. CONCLUSIONS: The first external quality assessment MERS-CoV panel gives a good insight in molecular diagnostic techniques and their performances for sensitive and specific detection of MERS-CoV RNA globally. Overall, all laboratories were capable of detecting MERS-CoV with some differences in sensitivity. The observation that 8% of laboratories reported false MERS-CoV positive single assay results shows room for improvement, and the importance of using confirmatory targets.

Discovery of Novel Adenosine Receptor Agonists That Exhibit Subtype Selectivity

A series of N6-bicyclic and N6-(2-hydroxy)cyclopentyl derivatives of adenosine were synthesized as novel A1R agonists and their A1R/A2R selectivity assessed using a simple yeast screening platform. We observed that the most selective, high potency ligands were achieved through N6-adamantyl substitution in combination with 5′-N-ethylcarboxamido or 5′-hydroxymethyl groups. In addition, we determined that 5′-(2-fluoro)thiophenyl derivatives all failed to generate a signaling response despite showing an interaction with the A1R. Some selected compounds were also tested on A1R and A3R in mammalian cells revealing that four of them are entirely A1R-selective agonists. By using in silico homology modeling and ligand docking, we provide insight into their mechanisms of recognition and activation of the A1R. We believe that given the broad tissue distribution, but contrasting signaling profiles, of adenosine receptor subtypes, these compounds might have therapeutic potential.

False normal Lung Clearance Index in infants with cystic fibrosis due to software algorithms.

BACKGROUND Lung clearance index (LCI), a marker of ventilation inhomogeneity, is elevated early in children with cystic fibrosis (CF). However, in infants with CF, LCI values are found to be normal, although structural lung abnormalities are often detectable. We hypothesized that this discrepancy is due to inadequate algorithms of the available software package. AIM Our aim was to challenge the validity of these software algorithms. METHODS We compared multiple breath washout (MBW) results of current software algorithms (automatic modus) to refined algorithms (manual modus) in 17 asymptomatic infants with CF, and 24 matched healthy term-born infants. The main difference between these two analysis methods lies in the calculation of the molar mass differences that the system uses to define the completion of the measurement. RESULTS In infants with CF the refined manual modus revealed clearly elevated LCI above 9 in 8 out of 35 measurements (23%), all showing LCI values below 8.3 using the automatic modus (paired t-test comparing the means, P < 0.001). Healthy infants showed normal LCI values using both analysis methods (n = 47, paired t-test, P = 0.79). The most relevant reason for false normal LCI values in infants with CF using the automatic modus was the incorrect recognition of the end-of-test too early during the washout. CONCLUSION We recommend the use of the manual modus for the analysis of MBW outcomes in infants in order to obtain more accurate results. This will allow appropriate use of infant lung function results for clinical and scientific purposes.

Schriftliche Prüfungen: Vorteile von Multiple True-False Fragen gegenüber Typ-A Fragen

Fragestellung/Einleitung: Prüfungen sind essentieller Bestandteil in der ärztlichen Ausbildung. Sie liefern wertvolle Informationen über den Entwicklungsprozess der Studierenden und wirken lernbegleitend und lernmodulierend [1], [2]. Bei schriftlichen Prüfungen dominieren derzeit Multiple Choice Fragen, die in verschiedenen Typen verwendet werden. Zumeist werden Typ-A Fragen genutzt, bei denen genau eine Antwort richtig ist. Multiple True-False (MTF) Fragen hingegen lassen mehrere richtige Antworten zu: es muss für jede Antwortmöglichkeit entschieden werden, ob diese richtig oder falsch ist. Durch die Mehrfachantwort scheinen MTF Fragen bestimmte klinische Sachverhalte besser widerspiegeln zu können. Auch bezüglich Reliabilität und dem Informationsgewinn pro Testzeit scheinen MTF Fragen den Typ-A Fragen überlegen zu sein [3]. Dennoch werden MTF Fragen bislang selten genutzt und es gibt wenig Literatur zu diesem Fragenformat. In dieser Studie soll untersucht werden, inwiefern die Verwendung von MTF Fragen die Nutzbarkeit (Utility) nach van der Vleuten (Reliabilität, Validität, Kostenaufwand, Effekt auf den Lernprozess und Akzeptanz der Teilnehmer) [4] schriftlicher Prüfungen erhöhen kann. Um die Testreliabilität zu steigern, sowie den Kostenaufwand für Prüfungen zu senken, möchten wir das optimale Bewertungssystem (Scoring) für MTF Fragen ermitteln. Methoden: Wir analysieren die Daten summativer Prüfungen der Medizinischen Fakultät der Universität Bern. Unsere Daten beinhalten Prüfungen vom ersten bis zum sechsten Studienjahr, sowie eine Facharztprüfung. Alle Prüfungen umfassen sowohl MTF als auch Typ-A Fragen. Für diese Prüfungen vergleichen wir die Viertel-, Halb- und Ganzpunktbewertung für MTF Fragen. Bei der Viertelpunktbewertung bekommen Kandidaten für jede richtige Teilantwort ¼ Punkt. Bei der Halbpunktbewertung wird ½ Punkt vergeben, wenn mehr als die Hälfte der Antwortmöglichkeiten richtig ist, einen ganzen Punkt erhalten die Kandidaten wenn alle Antworten richtig beantwortet wurden. Bei der Ganzpunktbewertung erhalten Kandidaten lediglich einen Punkt wenn die komplette Frage richtig beantwortet wurde. Diese unterschiedlichen Bewertungsschemata werden hinsichtlich Fragencharakteristika wie Trennschärfe und Schwierigkeit sowie hinsichtlich Testcharakteristika wie der Reliabilität einander gegenübergestellt. Die Ergebnisse werden ausserdem mit denen für Typ A Fragen verglichen. Ergebnisse: Vorläufige Ergebnisse deuten darauf hin, dass eine Halbpunktbewertung optimal zu sein scheint. Eine Halbpunktbewertung führt zu mittleren Item-Schwierigkeiten und daraus resultierend zu hohen Trennschärfen. Dies trägt zu einer hohen Testreliabilität bei. Diskussion/Schlussfolgerung: MTF Fragen scheinen in Verbindung mit einem optimalen Bewertungssystem, zu höheren Testreliabilitäten im Vergleich zu Typ A Fragen zu führen. In Abhängigkeit des zu prüfenden Inhalts könnten MTF Fragen einen wertvolle Ergänzung zu Typ-A Fragen darstellen. Durch die geeignete Kombination von MTF und Typ A Fragen könnte die Nutzbarkeit (Utility) schriftlicher Prüfungen verbessert werden.

Do multiple true-false items beat the commonly used one-best-answers questions regarding to the Ottawa Criteria for Good Assessment? Results of a literature review

Background: Multiple True-False-Items (MTF-Items) might offer some advantages compared to one-best-answer-questions (TypeA) as they allow more than one correct answer and may better represent clinical decisions. However, in medical education assessment MTF-Items are seldom used. Summary of Work: With this literature review existing findings on MTF-items and on TypeA were compared along the Ottawa Criteria for Good Assessment, i.e. (1) reproducibility, (2) feasibility, (3) validity, (4) acceptance, (5) educational effect, (6) catalytic effects, and (7) equivalence. We conducted a literature research on ERIC and Google Scholar including papers from the years 1935 to 2014. We used the search terms “multiple true-false”, “true-false”, “true/false”, and “Kprim” combined with “exam”, “test”, and “assessment”. Summary of Results: We included 29 out of 33 studies. Four of them were carried out in the medical field Compared to TypeA, MTF-Items are associated with (1) higher reproducibility (2) lower feasibility (3) similar validity (4) higher acceptance (5) higher educational effect (6) no studies on catalytic effects or (7) equivalence. Discussion and Conclusions: While studies show overall good characteristics of MTF items according to the Ottawa criteria, this type of question seems to be rather seldom used. One reason might be the reported lower feasibility. Overall the literature base is still weak. Furthermore, only 14 % of literature is from the medical domain. Further studies to better understand the characteristics of MTF-Items in the medical domain are warranted. Take-home messages: Overall the literature base is weak and therefore further studies are needed. Existing studies show that: MTF-Items show higher reliability, acceptance and educational effect; MTF-Items are more difficult to produce

Charge exchange in cometary coma: Discovery of H- ions in the solar wind close to comet 67P/Churyumov-Gerasimenko

As Rosetta was orbiting comet 67P/Churyumov-Gerasimenko, the Ion and Electron Sensor detected negative particles with angular distributions like those of the concurrently measured solar wind protons but with fluxes of only about 10% of the proton fluxes and energies of about 90% of the proton energies. Using well-known cross sections and energy-loss data, it is determined that the fluxes and energies of the negative particles are consistent with the production of H- ions in the solar wind by double charge exchange with molecules in the coma.

Search, Seizure and (False?) Arrest: An Analysis of Fourth Amendment Remedies when Police can Plant Evidence

The Fourth Amendment prohibits unreasonable searches and seizures in criminal investigations. The Supreme Court has interpreted this to require that police obtain a warrant prior to search and that illegally seized evidence be excluded from trial. A consensus has developed in the law and economics literature that tort liability for police officers is a superior means of deterring unreasonable searches. We argue that this conclusion depends on the assumption of truth-seeking police, and develop a game-theoretic model to compare the two remedies when some police officers (the bad type) are willing to plant evidence in order to obtain convictions, even though other police (the good type) are not (where this type is private information). We characterize the perfect Bayesian equilibria of the asymmetric-information game between the police and a court that seeks to minimize error costs in deciding whether to convict or acquit suspects. In this framework, we show that the exclusionary rule with a warrant requirement leads to superior outcomes (relative to tort liability) in terms of truth-finding function of courts, because the warrant requirement can reduce the scope for bad types of police to plant evidence

The Effect of Direct Instruction versus Discovery Learning on the Understanding of Science Lessons by Second Grade Students

This study examined the effectiveness of discovery learning and direct instruction in a diverse second grade classroom. An assessment test and transfer task were given to students to examine which method of instruction enabled the students to grasp the content of a science lesson to a greater extent. Results demonstrated that students in the direct instruction group scored higher on the assessment test and completed the transfer task at a faster pace; however, this was not statistically significant. Results also suggest that a mixture of instructional styles would serve to effectively disseminate information, as well as motivate students to learn.

From protein microarray to biology: The discovery of epigenetic regulatory molecules

Chromatin, composed of repeating nucleosome units, is the genetic polymer of life. To aid in DNA compaction and organized storage, the double helix wraps around a core complex of histone proteins to form the nucleosome, and is therefore no longer freely accessible to cellular proteins for the processes of transcription, replication and DNA repair. Over the course of evolution, DNA-based applications have developed routes to access DNA bound up in chromatin, and further, have actually utilized the chromatin structure to create another level of complexity and information storage. The histone molecules that DNA surrounds have free-floating tails that extend out of the nucleosome. These tails are post-translationally modified to create docking sites for the proteins involved in transcription, replication and repair, thus providing one prominent way that specific genomic sequences are accessed and manipulated. Adding another degree of information storage, histone tail-modifications paint the genome in precise manners to influence a state of transcriptional activity or repression, to generate euchromatin, containing gene-dense regions, or heterochromatin, containing repeat sequences and low-density gene regions. The work presented here is the study of histone tail modifications, how they are written and how they are read, divided into two projects. Both begin with protein microarray experiments where we discover the protein domains that can bind modified histone tails, and how multiple tail modifications can influence this binding. Project one then looks deeper into the enzymes that lay down the tail modifications. Specifically, we studied histone-tail arginine methylation by PRMT6. We found that methylation of a specific histone residue by PRMT6, arginine 2 of H3, can antagonize the binding of protein domains to the H3 tail and therefore affect transcription of genes regulated by the H3-tail binding proteins. Project two focuses on a protein we identified to bind modified histone tails, PHF20, and was an endeavor to discover the biological role of this protein. Thus, in total, we are looking at a complete process: (1) histone tail modification by an enzyme (here, PRMT6), (2) how this and other modifications are bound by conserved protein domains, and (3) by using PHF20 as an example, the functional outcome of binding through investigating the biological role of a chromatin reader. ^

Advanced Protein Modeling Method: Benchmarking and Applications in Computer-Aided Drug Discovery

Development of homology modeling methods will remain an area of active research. These methods aim to develop and model increasingly accurate three-dimensional structures of yet uncrystallized therapeutically relevant proteins e.g. Class A G-Protein Coupled Receptors. Incorporating protein flexibility is one way to achieve this goal. Here, I will discuss the enhancement and validation of the ligand-steered modeling, originally developed by Dr. Claudio Cavasotto, via cross modeling of the newly crystallized GPCR structures. This method uses known ligands and known experimental information to optimize relevant protein binding sites by incorporating protein flexibility. The ligand-steered models were able to model, reasonably reproduce binding sites and the co-crystallized native ligand poses of the β2 adrenergic and Adenosine 2A receptors using a single template structure. They also performed better than the choice of template, and crude models in a small scale high-throughput docking experiments and compound selectivity studies. Next, the application of this method to develop high-quality homology models of Cannabinoid Receptor 2, an emerging non-psychotic pain management target, is discussed. These models were validated by their ability to rationalize structure activity relationship data of two, inverse agonist and agonist, series of compounds. The method was also applied to improve the virtual screening performance of the β2 adrenergic crystal structure by optimizing the binding site using β2 specific compounds. These results show the feasibility of optimizing only the pharmacologically relevant protein binding sites and applicability to structure-based drug design projects.

False -positives and false-negatives in tests for trend

False-positive and false-negative values were calculated for five different designs of the trend test and it was demonstrated that a design suggested by Portier and Hoel in 1984 for a different problem produced the lowest false-positive and false-negative rates when applied to historical spontaneous tumor rate data for Fischer Rats. ^