Gill transcriptome response to changes in environmental calcium in the green spotted puffer fish

Abstract Background Calcium ion is tightly regulated in body fluids and for euryhaline fish, which are exposed to rapid changes in environmental [Ca2+], homeostasis is especially challenging. The gill is the main organ of active calcium uptake and therefore plays a crucial role in the maintenance of calcium ion homeostasis. To study the molecular basis of the short-term responses to changing calcium availability, the whole gill transcriptome obtained by Super Serial Analysis of Gene Expression (SuperSAGE) of the euryhaline teleost green spotted puffer fish, Tetraodon nigroviridis, exposed to water with altered [Ca2+] was analysed. Results Transfer of T. nigroviridis from 10 ppt water salinity containing 2.9 mM Ca2+ to high (10 mM Ca2+ ) and low (0.01 mM Ca2+) calcium water of similar salinity for 2-12 h resulted in 1,339 differentially expressed SuperSAGE tags (26-bp transcript identifiers) in gills. Of these 869 tags (65%) were mapped to T. nigroviridis cDNAs or genomic DNA and 497 (57%) were assigned to known proteins. Thirteen percent of the genes matched multiple tags indicating alternative RNA transcripts. The main enriched gene ontology groups belong to Ca2+ signaling/homeostasis but also muscle contraction, cytoskeleton, energy production/homeostasis and tissue remodeling. K-means clustering identified co-expressed transcripts with distinct patterns in response to water [Ca2+] and exposure time. Conclusions The generated transcript expression patterns provide a framework of novel water calcium-responsive genes in the gill during the initial response after transfer to different [Ca2+]. This molecular response entails initial perception of alterations, activation of signaling networks and effectors and suggests active remodeling of cytoskeletal proteins during the initial acclimation process. Genes related to energy production and energy homeostasis are also up-regulated, probably reflecting the increased energetic needs of the acclimation response. This study is the first genome-wide transcriptome analysis of fish gills and is an important resource for future research on the short-term mechanisms involved in the gill acclimation responses to environmental Ca2+ changes and osmoregulation.Peer Reviewe

PTHrP-induced modifications of the sea bream (Sparus auratus) vertebral bone proteome

Endocrine factors play an essential role in the formation and turnover of the skeleton in vertebrates. In the present study sea bream vertebral bone transcripts for PTH1R and PTH3R were identified and the action of intermittent administration of parathyroid hormone related protein (PTHrP) on the proteome of vertebral bone was analysed. Treatment of immature sea bream (Sparus auratus, n = 6) for 5 days with homologous recombinant PTHrP(1–125; 150 ng/g body weight) modified bone metabolism and caused a significant (p < 0.05) reduction in both tartrate resistant acid phosphatase (TRACP) and alkaline phosphatase (ALP) in relation to control fish. However, the ratio of TRACP: ALP in PTHrP treated fish (1.3 to 2.2 cf. control) suggested it had an anabolic response. A sea bream vertebral bone proteome of 157 protein spots was generated and putative identity assigned to 118 (75.2%) proteins of which 72% had homology to proteins/transcripts from teleosts many of which have not previously been reported in teleost bone. Classification of bone proteins using gene ontology revealed those with protein or metal/ion (e.g., calcium, magnesium, zinc) binding (∼53%) activities were most abundant. The expression of eight proteins was significantly (p < 0.05) modified in the vertebra of PTHrP treated compared to control fish; three were up-regulated, betainehomocystein S-methyltransferase, glial fibrillary acidic protein, parvalbumin beta and five were down-regulated, annexin A5, apolipoprotein A1, myosin light chain 2, fast skeletal myosin light chain 3, troponin C. In conclusion, intermittent administration of PTHrP to sea bream is associated with an anabolic response in vertebral bone metabolism and modifies calcium binding proteins in the proteome

Characterization and refinement of growth related quantitative trait loci in European sea bass (Dicentrarchus labrax) using a comparative approach

The identification of genetic markers for traits of interest for aquaculture, such as growth, is an important step for the establishment of breeding programmes. As more genomic information becomes available the possibility of applying comparative genomics to identify and refine quantitative trait locus (QTLs) and potentially identify candidate genes responsible for the QTL effect may accelerate genetic improvement in established and new aquaculture species. Here we report such an approach on growth related traits in the European sea bass (Dicentrarchus labrax), an important species for European aquaculture. A genetic map was generated with markers targeted to previously identified QTL for growth which reduced distance and improved resolution in these regions. A total of 36 significant QTLs were identified when morphometric traits were considered individually in maternal half sibs, paternal half sibs and sib-pair analysis. Twenty seven new markers targeted to the growth QTLs, obtained by comparative mapping, reduced the average distance between markers from 23.4, 9.1, and 5.8 cM in the previous map to 3.4, 2.2, and 5.2 cM, on linkage group (LG) LG4, LG6 and LG15 respectively. Lists of genes embedded in the QTL - 591 genes in LG4, 234 genes in LG6 and 450 genes in LG15 - were obtained from the European sea bass genome. Comparative mapping revealed conserved gene synteny across teleost fishes. Functional protein association network analysis with the gene products of the 3 linkage groups revealed a large global association network including 42 gene products. Strikingly the association network was populated with genes of known biological importance for growth and body weight in terrestrial farm animals, such as elements of the signaling pathways for Jak-STAT, MAPK, adipocytokine and insulin, growth hormone, IGFI and II. This study demonstrates the feasibility of a comparative genomics combined with functional gene annotation to refine the resolution of QTL and the establishment of hypothesis to accelerate discovery of putative responsible genes.Statement of relevance: This study demonstrates the feasibility of a comparative genomics approach, combined with functional annotation to refine the resolution of QTL and establishment of hypothesis to accelerate discovery of candidate genes. As production of genomic data is becoming more accessible, the implementation of this strategy will rapidly and efficiently provide the tools required for genetic selection in new candidate aquaculture species. (C) 2016 Elsevier B.V. All rights reserved

Assessing the Safety of Stem Cell Therapeutics

Unprecedented developments in stem cell research herald a new era of hope and expectation for novel therapies. However, they also present a major challenge for regulators since safety assessment criteria, designed for conventional agents, are largely inappropriate for cell-based therapies. This article aims to set out the safety issues pertaining to novel stem cell-derived treatments, to identify knowledge gaps that require further research, and to suggest a roadmap for developing safety assessment criteria. It is essential that regulators, pharmaceutical providers, and safety scientists work together to frame new safety guidelines, based on “acceptable risk,” so that patients are adequately protected but the safety “bar” is not set so high that exciting new treatments are lost

Feed, food and fuel: Competition and potential impacts on small-scale crop-livestock-energy farming systems

CGIAR System-wide Livestock Programm

JAK1/2 inhibition with baricitinib in the treatment of autoinflammatory interferonopathies

BACKGROUND. Monogenic IFN-mediated autoinflammatory diseases present in infancy with systemic inflammation, an IFN response gene signature, inflammatory organ damage, and high mortality. We used the JAK inhibitor baricitinib, with IFN-blocking activity in vitro, to ameliorate disease. METHODS. Between October 2011 and February 2017, 10 patients with CANDLE (chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperatures), 4 patients with SAVI (stimulator of IFN genes-associated [STING-associated] vasculopathy with onset in infancy), and 4 patients with other interferonopathies were enrolled in an expanded access program. The patients underwent dose escalation, and the benefit was assessed by reductions in daily disease symptoms and corticosteroid requirement. Quality of life, organ inflammation, changes in IFN-induced biomarkers, and safety were longitudinally assessed. RESULTS. Eighteen patients were treated for a mean duration of 3.0 years (1.5-4.9 years). The median daily symptom score decreased from 1.3 (interquartile range [IQR], 0.93-1.78) to 0.25 (IQR, 0.1-0.63) (P < 0.0001). In 14 patients receiving corticosteroids at baseline, daily prednisone doses decreased from 0.44 mg/kg/day (IQR, 0.31-1.09) to 0.11 mg/kg/day (IQR, 0.02-0.24) (P < 0.01), and 5 of 10 patients with CANDLE achieved lasting clinical remission. The patients' quality of life and height and bone mineral density Z-scores significantly improved, and their IFN biomarkers decreased. Three patients, two of whom had genetically undefined conditions, discontinued treatment because of lack of efficacy, and one CANDLE patient discontinued treatment because of BK viremia and azotemia. The most common adverse events were upper respiratory infections, gastroenteritis, and BK viruria and viremia. CONCLUSION. Upon baricitinib treatment, clinical manifestations and inflammatory and IFN biomarkers improved in patients with the monogenic interferonopathies CANDLE, SAVI, and other interferonopathies. Monitoring safety and efficacy is important in benefit-risk assessment

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Hausaufgabenhilfe in Öffentlichen Bibliotheken : Entwicklungsstand und Perspektiven

Die vorliegende Bachelorarbeit befasst sich mit dem Entwicklungsstand von Hausaufgabenhilfe in Öffentlichen Bibliotheken in Deutschland gemessen am US-amerikanischen Vorbild. Hierfür werden die rechtlichen, schulischen sowie gesellschaftlichen Rahmenbedingungen betrachtet und der Ist-Zustand in Deutschland mithilfe einer Onlinebefragung von zehn Bibliotheken ermittelt. In einem zweiten Schritt werden die vorliegenden Ergebnisse diskutiert und Empfehlungen für Hausaufgabenhilfe in Öffentlichen Bibliotheken in Deutschland erarbeitet.The present bachelor thesis deals with the stage of development of homework help in public libraries in Germany measured to the American role model. For this purpose the legal, educational so as the social frame conditions will be considered and the actual state in Germany determined by using an online survey of ten libraries. In a second step the present results will be discussed and recommendations for homework help in public libraries in Germany will be developed

A disturbance analysis of the comparative student self-assessment for the evaluation of lectures in the study of human medicine

2011 führten wir eine Studie zur vergleichenden Selbsteinschätzung als Methode der Lehrevaluation durch. Die Studie bestand aus zwei Anteilen – Fokusgruppengesprächen als qualitativem und Befragungen der Studenten als quantitativem Anteil. Die Befragungen beinhalteten sowohl Selbsteinschätzungen als auch formative Testate vor und nach Absolvierung der Lehrveranstaltungen. Zunächst wurde untersucht welchen Stellenwert die Evaluation für die Studierenden hat. Es stellte sich außerdem die Frage ob ein paarweiser Vergleich studentischer Selbsteinschätzungen andere Ergebnisse als die Kalkulation des Lernzuwachses aus den Mittelwerten einer gesamten Studentenkohorte liefert. Weiterhin sollte gezeigt werden ob sich die Ergebnisse bei prospektiver Datenerhebung im Gegensatz zu retrospektiver Erhebung des initialen Leistungsstands ändern. Die Anzahl der pro Modul abzufragenden Lernziele, mit denen reliable Berechnungen möglich sind, sollten ermittelt werden. Außerdem war unklar ob das Ergebnis der vergleichenden Selbsteinschätzung durch psychometrische Größen wie das Selbstwertgefühl beeinflusst wird. Es stellte sich die Frage nach einer akzeptablen Kriteriumsvalidität. Zuletzt sollte, wenn möglich, ein Cut-Off-Wert für die Unterscheidung erfolgreich und erfolglos gelehrter Inhalte definiert werden. Der Stellenwert der Evaluation wurde von den Studierenden, die an den Fokusgruppengesprächen teilgenommen haben, als sehr hoch eingestuft. Zudem wurde der Lernzuwachs als wichtiges Kriterium in der Lehrevaluation identifiziert. Die group-level-Analyse bot gegenüber der individual-level-Analyse deutliche Vorteile. Die breite Streuung der Korrelationskoeffizienten zwischen subjektiven und objektiven individuellen Lernzuwachsberechnungen wies auf die Nachteile der individuellen Berechnung hin. Der Vergleich der prospektiven mit der retrospektiven Erhebung des Leistungsstandes zu Modulbeginn zeigte keine relevanten Unterschiede. Bei Einschluss von 39 Lernzielen lag die Schwankungsbreite bei unter 10%. Ein Einfluss des Selbstwertgefühls auf die vergleichende Selbsteinschätzung konnte nicht bestätigt werden. Die Studie gab Hinweise auf eine akzeptable Kriteriumsvalidität des Evaluationsinstruments. Der Cut-Off-Wert für die Unterscheidung von erfolglos und erfolgreich gelehrten Inhalten konnte für die aggregierten Selbsteinschätzungen (sALZ) bei 54,7% ermittelt werden