Using cloud infrastructure to facilitate data collection and conversion of HLA diagnostic data for the 18th International HLA and Immunogenetics Workshop

The International HLA and Immunogenetics Workshop (IHIW) is a recurring gathering of researchers, technologists and clinicians where participants contribute to collaborative projects with a variety of goals, and come to consensus on definitions and standards for representing HLA and immunogenic determinants. The collaborative and international nature of these workshops, combined with the multifaceted goals of several specific workshop components, necessitates the collection and curation of a wide assortment of data, as well as an adaptable platform for export and analysis. With the aim of ensuring data quality and creation of reusable datasets, specific standards and nomenclature conventions are continuously being developed, and are an integral part of IHIW. Here we present the 18th IHIW Database, a purpose-built and extensible cloud-based file repository and web application for collecting and analyzing project-specific data. This platform is based on open-source software and uses established HLA data standards and web technologies to facilitate de-centralized data repository ownership, reduce duplicated efforts, and promote continuity for future IHIWs

Mikrohärte der Kavitätenwände nach Fluoreszenz-unterstützter Kariesexkavation (FACE) in vitro

Bis zum heutigen Tag ist eine eindeutige Unterscheidung von gesunder und erkrankter Zahnhartsubstanz während der Kariestherapie schwer. Aufgabe der vorliegenden Arbeit war es eines der Verfahren zur Kariesdiagnostik auf seine Zuverlässigkeit zu prüfen: die Fluoreszenzdiagnostik. Ziel der Studie war es, die konventionelle Methode eine Karies zu behandeln der Fluoreszenz-unterstützten Behandlung gegenüberzustellen. Zu diesem Zweck wurden insgesamt 44 kariöse menschliche Zähne gesammelt und in vitro die Mikrohärte des Dentins nach erfolgter Kariesexkavation untersucht. Die Versuchszähne wurden dazu randomisiert in Gruppen unterteilt, von denen die eine Hälfte konventionell und die andere Fluoreszenz-unterstützt behandelt wurde. Die Karies wurde bei jedem Zahn unter standardisierten Bedingungen exkaviert. Bei den Zähnen der konventionellen Gruppe wurde der Endpunkt der Kariesexkavation durch die Überprüfung des Dentins auf Sondenhärte festgelegt. Bei den Zähnen der Fluoreszenz-unterstützten Gruppe wurde exkaviert, bis keine Fluoreszenz-typisch roten Fluoreszenzerscheinungen mehr erkennbar waren. Im Anschluss wurden die Zähne inmitten der vorhandenen Kavitäten halbiert und auf Objektträger aufgebracht. Nun konnte eine Härtemessung des Dentins mit einem entsprechenden Härteprüfgerät erfolgen. Jede Messreihe begann am Kavitärenrand und erstreckte sich in Abständen von 120 μm bis zu einem Gesamtabstand von 630 μm in das Dentin. Dabei zeigte sich eine signifikanter Unterschied der konventionell und Laserfluoreszenz-unterstützt behandelten Zähne. Im unmittelbaren Kavitätenrandbereich zeigten die Fluoreszenz-Zähne eine deutlich geringere Dentinhärte als die konventionell behandelten, während sich die Dentinhärten in der Peripherie einander annäherten. Es kann davon ausgegangen werden, dass die Fluoreszenz-unterstütze Kariestherapie eine Überexkavation verhindert. Bei tiefen Läsionen sollte dennoch nicht auf die Zuhilfenahme einer zahnärztlichen Sonde verzichtet werden, da pulpanahes Dentin eigene Fluoreszenzerscheinungen aufweisen kann. Zudem zeigte sich eine deutliche Zeitersparnis bei der Fluoreszenz-unterstützten Kariesexkavation in vitro, der allerdings noch in der Praxis bestätigt werden muss

Alba-domain proteins of Trypanosoma brucei are cytoplasmic RNA-binding proteins that interact with the translation machinery

International audienceTrypanosoma brucei and related pathogens transcribe most genes as polycistronic arrays that are subsequently processed into monocistronic mRNAs. Expression is frequently regulated post-transcriptionally by cis-acting elements in the untranslated regions (UTRs). GPEET and EP procyclins are the major surface proteins of procyclic (insect midgut) forms of T. brucei. Three regulatory elements common to the 3' UTRs of both mRNAs regulate mRNA turnover and translation. The glycerol-responsive element (GRE) is unique to the GPEET 3' UTR and regulates its expression independently from EP. A synthetic RNA encompassing the GRE showed robust sequence-specific interactions with cytoplasmic proteins in electromobility shift assays. This, combined with column chromatography, led to the identification of 3 Alba-domain proteins. RNAi against Alba3 caused a growth phenotype and reduced the levels of Alba1 and Alba2 proteins, indicative of interactions between family members. Tandem-affinity purification and co-immunoprecipitation verified these interactions and also identified Alba4 in sub-stoichiometric amounts. Alba proteins are cytoplasmic and are recruited to starvation granules together with poly(A) RNA. Concomitant depletion of all four Alba proteins by RNAi specifically reduced translation of a reporter transcript flanked by the GPEET 3' UTR. Pulldown of tagged Alba proteins confirmed interactions with poly(A) binding proteins, ribosomal protein P0 and, in the case of Alba3, the cap-binding protein eIF4E4. In addition, Alba2 and Alba3 partially cosediment with polyribosomes in sucrose gradients. Alba-domain proteins seem to have exhibited great functional plasticity in the course of evolution. First identified as DNA-binding proteins in Archaea, then in association with nuclear RNase MRP/P in yeast and mammalian cells, they were recently described as components of a translationally silent complex containing stage-regulated mRNAs in Plasmodium. Our results are also consistent with stage-specific regulation of translation in trypanosomes, but most likely in the context of initiation

Implementation of formalin-fixed, paraffin-embedded cell line pellets as high-quality process controls in quality assessment programs for KRAS mutation analysis.

Contains fulltext : 108255.pdf (publisher's version ) (Closed access)In recent years, the mutational status of the KRAS oncogene has become incorporated into standard medical care as a predictive marker for therapeutic decisions related to patients with metastasized colorectal cancer. This is necessary, because these patients benefit from epidermal growth factor receptor (EGFR)-targeted therapy with increased progression-free survival only if the tumor does not carry a mutation in KRAS. Many different analytical platforms, both those commercially available and those developed in house, have been used within pathology laboratories to assess KRAS mutational status. For a testing laboratory to become accredited to perform such tests, it is essential that they perform reliability testing, but it has not previously been possible to perform this kind of testing on the complete workflow on a large scale without compromising reproducibility or the mimicry of the control sample. We assessed a novel synthetic control for formalin-fixed, paraffin-embedded (FFPE) tumor samples in a blind study conducted within nine laboratories across Europe. We show that FFPE material can, at least in part, mimic clinical samples and we demonstrate this control to be a valuable tool in the assessment of platforms used in testing for KRAS mutational status