Cas9 Cuts and Consequences; Detecting,Predicting, and Mitigating CRISPR/Cas9 On- and Off-Target Damage

Large deletions and genomic re-arrangements are increasingly recognized as common products of double-strand break repair at Clustered Regularly Interspaced, Short Palindromic Repeats - CRISPR associated protein 9 (CRISPR/Cas9) on-target sites. Together with well-known off-target editing products from Cas9 target misrecognition, these are important limitations, that need to be addressed. Rigorous assessment of Cas9-editing is necessary to ensure validity of observed phenotypes in Cas9-edited cell-lines and model organisms. Here the mechanisms of Cas9 specificity, and strategies to assess and mitigate unwanted effects of Cas9 editing are reviewed; covering guide-RNA design, RNA modifications, Cas9 modifications, control of Cas9 activity; computational prediction for off-targets, and experimental methods for detecting Cas9 cleavage. Although recognition of the prevalence of on- and off-target effects of Cas9 editing has increased in recent years, broader uptake across the gene editing community will be important in determining the specificity of Cas9 across diverse applications and organisms.     

From PMTCT to a more comprehensive AIDS response for women: a much-needed shift

Half of the 33.2 million people living with HIV today are women. Yet, responses to the epidemic are not adequately meeting the needs of women. This article critically evaluates how prevention of mother-to-child transmission (PMTCT) programs, the principal framework under which women's health is currently addressed in the global response to AIDS, have tended to focus on the prevention of HIV transmission from HIV-positive women to their infants. This paper concludes that more than ten years after their inception, PMTCT programs still do not successfully ensure the adequate treatment, care and support of HIV-infected women. Of particular concern is the continued widespread use of single-dose nevirapine despite World Health Organization recommendations to employ more effective combination therapies that do not potentially jeopardize women's future treatment outcomes. In response, the article calls for a more comprehensive approach that places women's health needs at the centre of AIDS responses. This is critical in settings where the pandemic is generalized and there is a push to greatly expand PMTCT programs, as a more effective and equitable way of meeting the needs of women in the context of HIV. Without such a comprehensive approach, women will continue to be impacted disproportionately by the pandemic, and current strategies for prevention, including PMTCT, and treatment will not be as effective and responsive as they need to be.     

Perceptions,paradigms and ethics: A perspective on the social context of environmental issues

The rapid evolution in public perceptions and understandings of environmental issues in Canada has evolved to the point where today such issues are beginning to be seen as cultural issues. The array of environmental and other societal problems is bringing into question the taken-for-granted assumptions or the worldview of cultural paradigm common to all industrialized countries. Many social analysts are suggesting that these problems are inherent in the industrial worldview and can therefore only be resolved by moving onward to another way of making sense of the world around us, and that elements of a new paradigm appear to be emerging. The major characteristics of the industrial worldview are described, and those of an emerging alternate worldview are sketched. Part of this societal questioning is evidenced in a resurgence of interest in environmental ethics but, except for deep ecology, this debate has yet to be linked to the broader discussion of shifting cultural paradigms. The changing social context suggests that there are opportunities to use different policy instruments than regulation that would prevent the occurence of environmental damage in the first place. It also suggests that the active involvement of thoughtful and responsible citizens is essential if the current period of questioning is to lead to a society that is sound and dynamic in ecological and human terms.     

Juvenile silver grunter Mesopristes argenteus shift benthic objects to access food

Juvenile silver grunter Mesopristes argenteus were observed, photographed and filmed manoeuvring objects with their snout and nape to expose benthic prey in two short steep coastal streams, including in the micro-estuary of one of these streams within the Australian Wet Tropics. Objects that were moved included leaves, sticks, bark, wood, seed pods, rainforest fruit, coral fragments and pebbles. Follower fish were sometimes associated with the foraging behaviour.     

Ontogeny of the pulmonary surfactant and antioxidant enzyme systems in the viviparous lizard,Tiliqua rugosa

The antioxidant enzyme (AOE) system protects the lung from oxidative damage. The pulmonary surfactant (PS) system lowers the interfacial pressure within the lung, improving lung compliance and aiding lung clearance. In mammals, the AOE and PS systems develop in tandem during the final 10%-20% of gestation. Here, we investigated the development of these systems in the viviparous skink, Tiliqua rugosa. The content of total phospholipid (PL), disaturated phospholipid (DSP), and cholesterol (Chol) increased in lung washings from foetal lizards with advancing gestational age. Similarly, the relative saturation of the PLs increased throughout gestation, with mid-stage 40 foetuses having a DSP/PL equivalent to newborns and adults. Maternal lizards had significantly less total PL, DSP, and Chol than nongravid and newborn lizards; however, the relative composition did not differ from nongravid animals. This presumably results from compression of the lungs under the bulk of the developing foetus. The Chol/PL and Chol/DSP ratios declined early in development such that mid-stage 40 embryos had comparable ratios to both newborns and adults. Thus, it appears that the PS system matures in a similar manner in skinks and in mammals. However, the composition of surfactant is complete some weeks before parturition, probably to enable improved survivorship of the precocial young in the event of premature birth. Unlike the surfactant lipids, the AOEs, catalase, superoxide dismutase, and glutathione peroxidase did not differ appreciably throughout gestation. It appears therefore that like the surfactant lipids the AOE system is in readiness for air breathing throughout the latter stages of gestation, possibly in preparation for premature birth. Unlike mammals, the PS and AOE systems develop independently from one another.     

All in the ears: unlocking the early life history biology and spatial ecology of fishes

Obtaining biological and spatial information of the early life history (ELH) phases of fishes has been problematic, such that larval and juvenile phases are often referred to as the ‘black box’ of fish population biology and ecology. However, a potent source of life‐history data has been mined from the earstones (otoliths) of bony fishes. We systematically reviewed 476 empirical papers published between 2005 and 2012 (inclusive) that used otoliths to examine fish ELH phases, which has been an area of increasing attention over this period. We found that otolith‐based research during this period could be split into two broad themes according to whether studies examined: (i) biological objectives related to intrinsic processes such as larval and juvenile age, growth and mortality, and/or (ii) spatial objectives, such as habitat use, dispersal and migration. Surprisingly, just 24 studies (5%) explored a combined biological–spatial objective by simultaneously exploiting biological and spatial information from otoliths, suggesting much more scope for such integrated research objectives to be answered via the use of multiple otolith‐based techniques in a single study. Mapping otolith analytical techniques across these two approaches revealed that otolith structural analysis was mainly used to investigate biological processes, while otolith chemical analyses were most often applied to spatial questions. Heavy skew in research effort was apparent across biomes, with most (62%) publications specific to marine species, despite comparable levels of species richness and the importance of freshwater taxa (just 15% of papers). Indeed, around 1% (380 species) of a possible 31400+ extant species were examined in our surveyed papers, with a strong emphasis on temperate marine species of commercial value. Potential model species for otolith‐based ELH ecology research are arising, with the eel genus Anguilla (24 studies) and the European anchovy Engraulis encrasicolis (14 studies) attracting more research effort than most other taxa. While there is a preponderance of common techniques (e.g. daily otolith increment counts, increment widths), novel techniques such as transgenerational marking and computed X‐ray tomography, are increasingly being applied in published studies. The application of an integrative approach based on a combination of emerging techniques and traditional methods holds promise for major advances in our understanding of ELH fish ecology and to shine light into the ‘black box’ of fish ecology.