Genome-wide analysis of transposon and retroviral insertions reveals preferential integrations in regions of DNA flexibility

DNA transposons and retroviruses are important transgenic tools for genome engineering. An important consideration affecting the choice of transgenic vector is their insertion site preferences. Previous large-scale analyses of Ds transposon integration sites in plants were done on the basis of reporter gene expression or germline transmission, making it difficult to discern vertebrate integration preferences. Here, we compare over 1300 Ds transposon integration sites in zebrafish, with Tol2 transposon and retroviral integration sites. Genome-wide analysis shows that Ds integration sites in the presence or absence of marker selection are remarkably similar and distributed throughout the genome. No strict motif was found, but a preference for structural features in the target DNA associated with DNA flexibility (Twist, Tilt, Rise, Roll, Shift and Slide) was observed. Remarkably, this feature is also found in transposon and retroviral integrations in maize and mouse cells. Our findings show that structural features influence integration of heterologous DNA in genomes, and have implications for targeted genome engineering

A 3D searchable database of transgenic zebrafish gal4 and cre lines for functional neuroanatomy studies

Citation: Marquart, G. D., Tabor, K. M., Brown, M., Strykowski, J. L., Varshney, G. K., LaFave, M. C., . . . Burgess, H. A. (2015). A 3D searchable database of transgenic zebrafish gal4 and cre lines for functional neuroanatomy studies. Frontiers in Neural Circuits, 9(November), 1-17. doi:10.3389/fncir.2015.00078Transgenic methods enable the selective manipulation of neurons for functional mapping of neuronal circuits. Using confocal microscopy, we have imaged the cellular-level expression of 109 transgenic lines in live 6 day post fertilization larvae, including 80 Gal4 enhancer trap lines, 9 Cre enhancer trap lines and 20 transgenic lines that express fluorescent proteins in defined gene-specific patterns. Image stacks were acquired at single micron resolution, together with a broadly expressed neural marker, which we used to align enhancer trap reporter patterns into a common 3-dimensional reference space. To facilitate use of this resource, we have written software that enables searching for transgenic lines that label cells within a selectable 3-dimensional region of interest (ROI) or neuroanatomical area. This software also enables the intersectional expression of transgenes to be predicted, a feature which we validated by detecting cells with co-expression of Cre and Gal4. Many of the imaged enhancer trap lines show intrinsic brain-specific expression. However, to increase the utility of lines that also drive expression in non-neuronal tissue we have designed a novel UAS reporter, that suppresses expression in heart, muscle, and skin through the incorporation of microRNA binding sites in a synthetic 3? untranslated region. Finally, we mapped the site of transgene integration, thus providing molecular identification of the expression pattern for most lines. Cumulatively, this library of enhancer trap lines provides genetic access to 70% of the larval brain and is therefore a powerful and broadly accessible tool for the dissection of neural circuits in larval zebrafish. © 2015 Marquart, Tabor, Brown, Strykowski, Varshney, LaFave, Mueller, Burgess, Higashijima and Burgess

A multifunctional mutagenesis system for analysis of gene function in zebrafish

Since the sequencing of the human reference genome, many human disease-related genes have been discovered. However, understanding the functions of all the genes in the genome remains a challenge. The biological activities of these genes are usually investigated in model organisms such as mice and zebrafish. Large-scale mutagenesis screens to generate disruptive mutations are useful for identifying and understanding the activities of genes. Here, we report a multifunctional mutagenesis system in zebrafish using the maize Ds transposon. Integration of the Ds transposable element containing an mCherry reporter for protein trap events and an EGFP reporter for enhancer trap events produced a collection of transgenic lines marking distinct cell and tissue types, and mutagenized genes in the zebrafish genome by trapping and prematurely terminating endogenous protein coding sequences. We obtained 642 zebrafish lines with dynamic reporter gene expression. The characterized fish lines with specific expression patterns will be made available through the European Zebrafish Resource Center (EZRC), and a database of reporter expression is available online (http://fishtrap.warwick.ac.uk/). Our approach complements other efforts using zebrafish to facilitate functional genomic studies in this model of human development and disease

Ductility of wide-beam RC frames as lateral resisting system

[EN] Some Mediterranean seismic codes consider wide-beam reinforced concrete moment resisting frames (WBF) as horizontal load carrying systems that cannot guarantee high ductility performances. Conversely, Eurocode 8 allows High Ductility Class (DCH) design for such structural systems. Code prescriptions related to WBF are systematically investigated. In particular, lesson learnt for previous earthquakes, historical reasons, and experimental and numerical studies underpinning specific prescriptions on wide beams in worldwide seismic codes are discussed. Local and global ductility of WBF are then analytically investigated through (1) a parametric study on chord rotations of wide beams with respect to that of deep beams, and (2) a spectral-based comparison of WBF with conventional reinforced concrete moment resisting frames (i.e. with deep beams). Results show that the set of prescriptions given by modern seismic codes provides sufficient ductility to WBF designed in DCH. In fact, global capacity of WBF relies more on the lateral stiffness of the frames and on the overstrength of columns rather than on the local ductility of wide beams, which is systematically lower with respect to that of deep beams.Gómez-Martínez, F.; Alonso Durá, A.; De Luca, F.; Verderame, GM. (2016). Ductility of wide-beam RC frames as lateral resisting system. Bulletin of Earthquake Engineering. 14(6):1545-1569. doi:10.1007/s10518-016-9891-xS15451569146ACI (1989) Building code requirements for reinforced concrete (ACI 318-89). ACI Committee 318, American Concrete Institute, Farmington Hills, Michigan, USAACI (2008) Building code requirements for structural concrete (ACI 318-08) and commentary (318-08). ACI Committee 318, American Concrete Institute, Farmington Hills, Michigan, USAACI-ASCE (1991) Recommendations for design of beam-column connections in monolithic reinforced concrete structures (ACI 352R-91). Joint ACI-ASCE Committee 352, American Concrete Institute, Farmington Hills, Michigan, USAACI-ASCE (2002) Recommendations for design of beam-column connections in monolithic reinforced concrete structures (ACI 352R-02). Joint ACI-ASCE Committee 352, American Concrete Institute, Farmington Hills, Michigan, USAArslan MH, Korkmaz HH (2007) What is to be learned from damage and failure of reinforced concrete structures during recent earthquakes in Turkey? Eng Fail Anal 14(1):1–22ASCE (2007) Seismic Rehabilitation of Existing Buildings, ASCE/SEI 41-06. American Society of Civil Engineers, RestonASCE (2010) Minimum Design Loads for Building and Other Structures, ASCE/SEI 7-10. American Society of Civil Engineers, RestonBenavent-Climent A (2007) Seismic behavior of RC side beam-column connections under dynamic loading. J Earthquake Eng 11:493–511Benavent-Climent A, Zahran R (2010) An energy-based procedure for the assessment of seismic capacity of existing frames: application to RC wide beam systems in Spain. Soil Dyn Earthq Eng 30:354–367Benavent-Climent A, Cahís X, Zahran R (2009) Exterior wide beam-column connections in existing RC frames subjected to lateral earthquake loads. Eng Struct 31:1414–1424Benavent-Climent A, Cahís X, Vico JM (2010) Interior wide beam-column connections in existing RC frames subjected to lateral earthquake loading. Bull Earthq Eng 8:401–420BHRC (2004) Iranian Code of Practice for Seismic Resistant Design of Buildings. Standard Nº 2800, 3rd edn. Building and Housing Research Center, TehranBorzi B, Elnashai AS (2000) Refined force reduction factors for seismic design. Eng Struct 22:1244–1260Borzi B, Pinho R, Crowley H (2008) Simplified pushover-based vulnerability analysis for large-scale assessment of RC buildings. Eng Struct 30:804–820BSI (2004) Eurocode 2: Design of concrete structures: Part 1-1: General rules and rules for buildings. British Standards Institutions, LondonCalvi GM (1999) A displacement-based approach for vulnerability evaluation of classes of buildings. J Earthquake Eng 3(3):411–438CDSC (1994) Seismic construction code, NCSR-94. Committee for the Development of Seismic Codes, Spanish Ministry of Construction, Madrid, Spain (in Spanish)CDSC (2002) Seismic construction code, NCSE-02. Committee for the Development of Seismic Codes, Spanish Ministry of Construction, Madrid, Spain (in Spanish)CEN (2004) Eurocode 8: design of structures for earthquake resistance—part 1: general rules, seismic actions and rules for buildings. European Standard EN 1998-1:2003—Comité Européen de Normalisation, Brussels, BelgiumCEN (2005) Eurocode 8: design of structures for earthquake resistance—part 3: assessment and retrofitting of buildings. European Standard EN 1998-1:2005—Comité Européen de Normalisation, Brussels, BelgiumCheung PC, Paulay T, Park R (1991) Mechanisms of slab contributions in beam-column subassemblages. ACI Spec Publ 123Cosenza E, Manfredi G, Polese M, Verderame GM (2005) A multilevel approach to the capacity assessment of existing RC buildings. J Earthquake Eng 9(1):1–22Crowley H, Pinho R (2010) Revisiting Eurocode 8 formulae for periods of vibration and their employment in linear seismic analysis. Earthquake Eng Struct Dynam 39:223–235CS.LL.PP (2009) Instructions for the application of the technique code for the Constructions. Official Gazette of the Italian Republic, 47, Regular Supplement no. 27 (in Italian)De Luca F, Vamvatsikos D, Iervolino I (2013) Near-optimal piecewise linear fits of static pushover capacity curves for equivalent SDOF analysis. Earthquake Eng Struct Dynam 42(4):523–543De Luca F, Verderame GM, Gómez-Martínez F, Pérez-García A (2014) The structural role played by masonry infills on RC building performances after the 2011 Lorca, Spain, earthquake. Bull Earthq Eng 12(5):1999–2026Decanini LD, Mollaioli F (2000) Analisi di vulnerabilità sismica di edifici in cemento armato pre-normativa. In: Cosenza E (ed) Comportamento sismico di edifici in cemento armato progettati per carichi verticali. CNR—Gruppo Nazionale per la Difesa dei Terremoti, Rome (in Italian)Dolšek M, Fajfar P (2004) IN2—a simple alternative for IDA. In: Proceedings of the 13th World conference on Earthquake Engineering. August 1–6, Vancouver, Canada. Paper 3353Domínguez D, López-Almansa F, Benavent-Climent A (2014) Comportamiento para el terremoto de Lorca de 11-05-2011, de edificios de vigas planas proyectados sin tener en cuenta la acción sísmica. Informes de la Construcción 66(533):e008 (in Spanish)Domínguez D, López-Almansa F, Benavent-Climent A (2016) Would RC wide-beam buildings in Spain have survived Lorca earthquake (11-05-2011)? Eng Struct 108:134–154Dönmez C (2013) Seismic Performance of Wide-Beam Infill-Joist Block RC Frames in Turkey. J Perform Constr Facil 29(1):04014026Fadwa I, Ali TA, Nazih E, Sara M (2014) Reinforced concrete wide and conventional beam-column connections subjected to lateral load. Eng Struct 76:34–48Fardis MN (2009) Seismic design, assessment and retrofitting of concrete, Buildings edn. Springer, LondonGentry TR, Wight JK (1992) Reinforced concrete wide beam-column connections under earthquake-type loading. Report no. UMCEE 92-12. Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USAGómez-Martínez F (2015) FAST simplified vulnerability approach for seismic assessment of infilled RC MRF buildings and its application to the 2011 Lorca (Spain) earthquake. Ph.D. Thesis, Polytechnic University of Valencia, SpainGómez-Martínez F, Pérez García A, De Luca F, Verderame GM (2015a) Comportamiento de los edificios de HA con tabiquería durante el sismo de Lorca de 2011: aplicación del método FAST. Informes de la Construcción 67(537):e065 (in Spanish)Gómez-Martínez F, Pérez-García A, Alonso Durá A, Martínez Boquera A, Verderame GM (2015b) Eficacia de la norma NCSE-02 a la luz de los daños e intervenciones tras el sismo de Lorca de 2011. In: Proceedings of Congreso Internacional sobre Intervención en Obras Arquitectónicas tras Sismo: L’Aquila (2009), Lorca (2011) y Emilia Romagna (2012), May 13–14, Murcia, Spain (in Spanish)Gómez-Martínez F, Verderame GM, De Luca F, Pérez-García A, Alonso-Durá, A (2015c). High ductility seismic performances of wide-beam RC frames. In; XVI Convegno ANIDIS. September 13–17, L'Aquila, ItalyHawkins NM, Mitchell D (1979) Progressive collapse of flat plate structures. ACI J 76(7):775–808Iervolino I, Manfredi G, Polese M, Verderame GM, Fabbrocino G (2007) Seismic risk of RC building classes. Eng Struct 29(5):813–820Inel M, Ozmen HB, Akyol E (2013) Observations on the building damages after 19 May 2011 Simav (Turkey) earthquake. Bull Earthq Eng 11(1):255–283Kurose Y, Guimaraes GN, Zuhua L, Kreger ME, Jirsa JO (1991) Evaluation of slab-beam-column connections subjected to bidirectional loading. ACI Spec Publ 123:39–67LaFave JM, Wight JK (1997) Behavior of reinforced exterior wide beam-column-slab connections subjected to lateral earthquake loading. Report no. UMCEE 97-01. Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USALaFave JM, Wight JK (1999) Reinforced concrete exterior wide beam-column-slab connections subjected to lateral earthquake loading. ACI Struct J 96(4):577–586LaFave JM, Wight JK (2001) Reinforced concrete wide-beam construction vs. conventional construction: resistance to lateral earthquake loads. Earthq Spectra 17(3):479–505Li B, Kulkarni SA (2010) Seismic behavior of reinforced concrete exterior wide beam-column joints. J Struct Eng (ASCE) 136(1):26–36López-Almansa F, Domínguez D, Benavent-Climent A (2013) Vulnerability analysis of RC buildings with wide beams located in moderate seismicity regions. Eng Struct 46:687–702Masi A, Santarsiero G, Nigro D (2013a) Cyclic tests on external RC beam-column joints: role of seismic design level and axial load value on the ultimate capacity. J Earthquake Eng 17(1):110–136Masi A, Santarsiero G, Mossucca A, Nigro D (2013b) Seismic behaviour of RC beam-column subassemblages with flat beam. In: Proceedings of XV Convegno della Associazione Nazionale Italiana di Ingegneria Sismica, ANIDIS. 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ASXL2 is essential for haematopoiesis and acts as a haploinsufficient tumour suppressor in leukemia

Additional sex combs-like (ASXL) proteins are mammalian homologues of additional sex combs (Asx), a regulator of trithorax and polycomb function in Drosophila. While there has been great interest in ASXL1 due to its frequent mutation in leukemia, little is known about its paralog ASXL2, which is frequently mutated in acute myeloid leukemia patients bearing the RUNX1-RUNX1T1 (AML1-ETO) fusion. Here we report that ASXL2 is required for normal haematopoiesis with distinct, non-overlapping effects from ASXL1 and acts as a haploinsufficient tumour suppressor. While Asxl2 was required for normal haematopoietic stem cell self-renewal, Asxl2 loss promoted AML1-ETO leukemogenesis. Moreover, ASXL2 target genes strongly overlapped with those of RUNX1 and AML1-ETO and ASXL2 loss was associated with increased chromatin accessibility at putative enhancers of key leukemogenic loci. These data reveal that Asxl2 is a critical regulator of haematopoiesis and mediates transcriptional effects that promote leukemogenesis driven by AML1-ETO

Use of SMS texts for facilitating access to online alcohol interventions: a feasibility study

A41 Use of SMS texts for facilitating access to online alcohol interventions: a feasibility study In: Addiction Science & Clinical Practice 2017, 12(Suppl 1): A4

Punishing Terrorists: A Re-Examination of U.S. Federal Sentencing in the Postguidelines Era

The empirical literature on the theory and practice of sentencing politically motivated offenders such as terrorists in U.S. federal courts is limited. Thus, we know relatively little about the dealings between terrorist offenders and the criminal justice system or how these interactions may be influenced by changes in American legal or political context. This study summarizes previous findings relative to sentencing disparity among terrorists and nonterrorists in U.S. federal courts prior to the imposition of the U.S. Sentencing Guidelines. We then identify events occurring after the advent of the guidelines, including the early acts of terrorism on American soil. We evaluate the sentencing of terrorists versus nonterrorists following the confluence imposition of the guidelines and these events. We determine whether and how the sentencing disparity between terrorist and nonterrorist has changed since the implementation of the U.S. Sentencing Guidelines and the terrorist events of the early 1990s. Based on our findings, we put forth suggestions as to the possible ways these conditions may have affected sentencing outcomes.Yeshttps://us.sagepub.com/en-us/nam/manuscript-submission-guideline