Characterisation of Drosophila Ubx CPTI000601 and hth CPTI000378 protein trap lines.

In Drosophila, protein trap strategies provide powerful approaches for the generation of tagged proteins expressed under endogenous control. Here, we describe expression and functional analysis to evaluate new Ubx and hth protein trap lines generated by the Cambridge Protein Trap project. Both protein traps exhibit spatial and temporal expression patterns consistent with the reported endogenous pattern in the embryo. In imaginal discs, Ubx-YFP is expressed throughout the haltere and 3rd leg imaginal discs, while Hth-YFP is expressed in the proximal regions of haltere and wing discs but not in the pouch region. The UbxCPTI000601 line is semilethal as a homozygote. No T3/A1 to T2 transformations were observed in the embryonic cuticle or the developing midgut. The homozygous survivors, however, exhibit a weak haltere phenotype with a few wing-like marginal bristles on the haltere capitellum. Although hthCPTI000378 is completely lethal as a homozygote, the hthCPTI000378/hthC1 genotype is viable. Using a hth deletion (Df(3R)BSC479) we show that hthCPTI000378/Df(3R)BSC479 adults are phenotypically normal. No transformations were observed in hthCPTI000378, hthCPTI000378/hthC1, or hthCPTI000378/Df(3R)BSC479 embryonic cuticles. We have successfully characterised the Ubx-YFP and Hth-YFP protein trap lines demonstrating that the tagged proteins show appropriate expression patterns and produce at least partially functional proteins

Roles of cofactors and chromatin accessibility in Hox protein target specificity.

BACKGROUND: The regulation of specific target genes by transcription factors is central to our understanding of gene network control in developmental and physiological processes yet how target specificity is achieved is still poorly understood. This is well illustrated by the Hox family of transcription factors as their limited in vitro DNA-binding specificity contrasts with their clear in vivo functional specificity. RESULTS: We generated genome-wide binding profiles for three Hox proteins, Ubx, Abd-A and Abd-B, following transient expression in Drosophila Kc167 cells, revealing clear target specificity and a striking influence of chromatin accessibility. In the absence of the TALE class homeodomain cofactors Exd and Hth, Ubx and Abd-A bind at a very similar set of target sites in accessible chromatin, whereas Abd-B binds at an additional specific set of targets. Provision of Hox cofactors Exd and Hth considerably modifies the Ubx genome-wide binding profile enabling Ubx to bind at an additional novel set of targets. Both the Abd-B specific targets and the cofactor-dependent Ubx targets are in chromatin that is relatively DNase1 inaccessible prior to the expression of Hox proteins/Hox cofactors. CONCLUSIONS: Our experiments demonstrate a strong role for chromatin accessibility in Hox protein binding and suggest that Hox protein competition with nucleosomes has a major role in Hox protein target specificity in vivo.This work was supported by University of Malaya High Impact Research Grant UM-HIR UM.C/625/HIR/MOHE/CHAN-08 from the Ministry of Higher Education Malaysia.This is the final version of the article. It was first available from BioMed Central via http://dx.doi.org/10.1186/s13072-015-0049-

Coping Skills Used by Nurses After the Death of a Pediatric Patient

abstract: As the complexity and severity of hospitalized patients increase, nurses working in an acute care setting will experience patient deaths. From novice to expert, nurses may utilize a range of coping strategies. When the patient is a pediatric patient, the coping strategies become critical. The purpose of this study is to explore the coping strategies used by novice and expert nurses when a pediatric patient dies. The second objective is to compare the coping strategies used by novice and expert nurses. The final objective is to determine if nurses feel nursing school and employee training prepared them for the death of a pediatric patient. Research has shown that nurses use many different coping strategies when faced with a patient's death (Abdullah, 2015; Kellogg, Baker, & McCune, 2014; Plante & Cry, 2011). Expert nurses who have years of experience should have more options for coping strategies than novice nurses, yet there is little evidence to support this. This qualitative descriptive study used structured in-depth interviews to explore the coping strategies of pediatric nurses when experiencing a patient's death. Using thematic analysis, transcripts of the interviews were coded such that themes emerged. Themes for novice nurses were compared to expert nurses. These themes were also placed into concepts that encompassed many similar themes. The findings help determine that there is a difference in the coping mechanisms used by novice and expert nurses, and there is a need for more education on coping strategies after the death of a pediatric patient

Whole genome shotgun sequencing of Mycobacterium abscessus M156, an emerging clinical pathogen in Malaysia

Mycobacterium abscessus is an emerging clinical pathogen commonly associated with non-tuberculous mycobacterial infections. We report herein the draft genome of M. abscessus strain M156

VibrioBase: A Model for Next-Generation Genome and Annotation Database Development

To facilitate the ongoing research of Vibrio spp., a dedicated platform for the Vibrio research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. We present VibrioBase, a useful resource platform, providing all basic features of a sequence database with the addition of unique analysis tools which could be valuable for the Vibrio research community. VibrioBase currently houses a total of 252 Vibrio genomes developed in a user-friendly manner and useful to enable the analysis of these genomic data, particularly in the field of comparative genomics. Besides general data browsing features, VibrioBase offers analysis tools such as BLAST interfaces and JBrowse genome browser. Other important features of this platform include our newly developed in-house tools, the pairwise genome comparison (PGC) tool, and pathogenomics profiling tool (PathoProT). The PGC tool is useful in the identification and comparative analysis of two genomes, whereas PathoProT is designed for comparative pathogenomics analysis of Vibrio strains. Both of these tools will enable researchers with little experience in bioinformatics to get meaningful information from Vibrio genomes with ease. We have tested the validity and suitability of these tools and features for use in the next-generation database development

Overview of MabsBase.

<p>(A) The database overview which displays the main list of all strains and information such as genome size, genome identity and coverage etc., organized in columns. (B) ORF list of a specific strain. (C) Detailed information of an ORF with visualization in JBrowse.</p