Genome editing in zebrafish: a practical overview

Zebrafish is a powerfulmodel for the study of vertebrate development, being amenable to a wide range of genetic and other manipulations to probe themolecular basis of development and its perturbation in disease. Over recent years, genome editing approaches have become increasingly used as an efficient and sophisticated approach to precisely engineer the zebrafish genome, which has further enhanced the utility of this organism. This review provides a practical overview of genome editing and its application in zebrafish research, including alternate strategies for introducing and screening for specific genetic changes.

Plant-pathogen interactions: toward development of next-generation disease-resistant plants

Briskly evolving phytopathogens are dire threats to our food supplies and threaten global food security. From the recent advances made toward high-throughput sequencing technologies, understanding of pathogenesis and effector biology, and plant innate immunity, translation of these means into new control tools is being introduced to develop durable disease resistance. Effectoromics as a powerful genetic tool for uncovering effector-target genes, both susceptibility genes and executor resistance genes in effector-assisted breeding, open up new avenues to improve resistance. TALENs (Transcription Activator-Like Effector Nucleases), engineered nucleases and CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats)/Cas9 systems are breakthrough and powerful techniques for genome editing, providing efficient mechanisms for targeted crop protection strategies in disease resistance programs. In this review, major advances in plant disease management to confer durable disease resistance and novel strategies for boosting plant innate immunity are highlighted.

Genome sequencing: a grin without a cat

In some types of unicellular algae, the chloroplasts have their own nucleus — a legacy of the time when the chloroplast was a free-living cell. The sequence of the genome in one such nucleus is now revealed.

Dead, done for and dangerous: teaching editing students what not to do

The most difficult aspect of teaching editing at a university tutorial is imparting to students a sensitivity to the appropriate relationship between the editor and author and, more particularly, between the editor and the author's work. Students are tempted to see themselves as critics or assessors of the author's work rather than assistants in the writing process. This paper discusses where teaching editing is difficult in a classroom, arguing that such difficulty is a symptom of both problems experienced in the editing profession and limitations of university teaching.

A case for blended and collaborative learning as strategies for teaching editing and publishing within a postgraduate writing program

Several recent studies have called for the breakdown of' arbitrary distinctions between virtual and "face-to-face" classrooms' (Comeaux & McKenna-Byington 2003: 348; see also McDonald 2002; Rosset, Douglis & Frazee 2003; Morse 2003). In 2004 the Professional and Creative Writing discipline at Deakin University added Editing and Publishing (which had previously been available as on-campus-only units at our institution) to an established list of online postgraduate writing units taught via the auspices of the new (to our university) WebCT technology. This paper describes and evaluates our experience of challenging the 'arbitrary distinctions' between our two cohorts of students by incorporating blended and collaborative learning strategies into our course via two specific projects.

We must become gatekeepers : editing indigenous writing

With the proliferation of Indigenous texts currently published by specialist and mainstream publishers, non-Indigenous editors increasingly find themselves negotiating the uncomfortable territories of race, politics and power for which current training (in an Australian context) leaves them poorly prepared. Indigenous writer Anita Heiss advocates the employment of Indigenous editors as an 'ideal' solution, though few are currently working in the Australian industry. Margaret McDonell, an experienced non-Indigenous editor of Indigenous texts, suggests non-Indigenous editors need to 'undertake a journey of learning' during which 'assumptions, biases, tastes and preconceptions' are examined. Yet this presents a difficult task within a postcolonial society, when, as identified by Clare Bradford, even the classification of texts into genres such as fiction and the short story represents an entirely Eurocentric construct, 'not readily correspond[ing] with Aboriginal schemata'. The Australian Society of Authors' discussion paper 'Writing about Indigenous Australia: Some Issues to Consider and Protocols to Follow' provides practical guidelines that may be adapted for editorial use. This article canvasses these and other ideas with a focus on establishing an ethical and appropriately sensitive cross-cultural approach to editing Indigenous writing.

Genome - wide association study identifies novel breast cancer susceptibility loci

Breast cancer exhibits familial aggregation, consistent with variation in genetic susceptibility to the disease. Known susceptibility genes account for less than 25% of the familial risk of breast cancer, and the residual genetic variance is likely to be due to variants conferring more moderate risks. To identify further susceptibility alleles, we conducted a two-stage genome-wide association study in 4,398 breast cancer cases and 4,316 controls, followed by a third stage in which 30 single nucleotide polymorphisms (SNPs) were tested for confirmation in 21,860 cases and 22,578 controls from 22 studies. We used 227,876 SNPs that were estimated to correlate with 77% of known common SNPs in Europeans at r² > 0.5. SNPs in five novel independent loci exhibited strong and consistent evidence of association with breast cancer (P < 10^-7). Four of these contain plausible causative genes (FGFR2, TNRC9, MAP3K1 and LSP1). At the second stage, 1,792 SNPs were significant at the P < 0.05 level compared with an estimated 1,343 that would be expected by chance, indicating that many additional common susceptibility alleles may be identifiable by this approach.

Differential tumor necrosis factor receptor 2-mediated editing of virus-specific CD8+ effector T cells

Much of the CD8+ T cell response in H2b mice with influenza pneumonia is directed at the nucleoprotein366-374 (NP366) and acid polymerase224-233 (PA224) peptides presented by the H2Db MHC class I glycoprotein. These DbNP366- and DbPA224-specific T cell populations are readily analyzed by staining with tetrameric complexes of MHC+ peptide (tetramers) or by cytokine production subsequent to in vitro stimulation with the cognate peptides. The DbPA224-specific CD8+ effector T cells make more tumor necrosis factor (TNF) α than the comparable CD8+DbNP366+ set, a difference reflected in the greater sensitivity of the CD8+DbPA224+ population to TNF receptor (TNFR) 2-mediated apoptosis under conditions of in vitro culture. Freshly isolated CD8+DbNP366+ and CD8+DbPA224+ T cells from influenza-infected TNFR2-/- mice produce higher levels of IFN-γ and TNF-α after in vitro stimulation with peptide, although the avidity of the T cell receptor-epitope interaction does not change. Increased numbers of both CD8+DbPA224+ and CD8+DbNP366+ T cells were recovered from the lungs (but not the spleens) of secondarily challenged TNFR2-/- mice, a pattern that correlates with the profiles of TNFR expression in the TNFR2+/+ controls. Thus, it seems that TNFR2-mediated editing of influenza-specific CD8+ T cells functions to limit the numbers of effectors that have localized to the site of pathology in the lung but does not modify the size of the less activated responder T cell populations in the spleen. Therefore, the massive difference in magnitude for the secondary, although not the primary, response to these DbNP366 and DbPA224 epitopes cannot be considered to reflect differential TNFR2-mediated T cell editing.

Insights into bacterial genome composition through variable target GC content profiling

This study presents a new computational method for guanine (G) and cytosine (C), or GC, content profiling based on the idea of multiple resolution sampling (MRS). The benefit of our new approach over existing techniques follows from its ability to locate significant regions without prior knowledge of the sequence, nor the features being sought. The use of MRS has provided novel insights into bacterial genome composition. Key findings include those that are related to the core composition of bacterial genomes, to the identification of large genomic islands (in Enterobacterial genomes), and to the identification of surface protein determinants in human pathogenic organisms (e.g., Staphylococcus genomes). We observed that bacterial surface binding proteins maintain abnormal GC content, potentially pointing to a viral origin. This study has demonstrated that GC content holds a high informational worth and hints at many underlying evolutionary processes. For online Supplementary Material, see www.liebertonline.com.