Five Questions to Understand Epistemology and Its Influence on Integrative Marine Research

Developing solutions to the complex and uncertain problems facing marine and coastal social-ecological ecosystems requires new forms of knowledge production and integration. While progress has been made both in terms of successfully producing integrated marine research and connecting that knowledge to decision-makers, a number of significant challenges remain that prevent the routine development and implementation of successful integrated research practice. Based on our own experiences as social researchers working within interdisciplinary research teams, we contend that one of the main barriers to successful integrative marine research relates to understanding, and where possible reconciling, the different epistemologies that unpin how knowledge is created or discovered in different disciplines. We therefore aim to provide an accessible introduction to the concept of epistemology, with a focus on its importance and influence to integrated marine research practice. Specifically, we present and discuss five questions of research design that relate to epistemology in integrative research practices: (1) What is the object of study we seek to create knowledge about; (2) how do we create knowledge; (3) who accepts knowledge as ‘true’ and how?; (4) how do we determine the epistemology underpinning marine science; and (5) what are the implications of epistemology for applied integrative marine science? We demonstrate the application of each question through a hypothetical case study of marine restoration, focusing on coral transplanting. Finally, we offer readers a simple heuristic to guide them, irrespective of career stage or discipline, to understand and account for epistemology when participating in integrative marine research practices.</jats:p

27 years of benthic and coral community dynamics on turbid, highly urbanised reefs off Singapore

Coral cover on reefs is declining globally due to coastal development, overfishing and climate change. Reefs isolated from direct human influence can recover from natural acute disturbances, but little is known about long term recovery of reefs experiencing chronic human disturbances. Here we investigate responses to acute bleaching disturbances on turbid reefs off Singapore, at two depths over a period of 27 years. Coral cover declined and there were marked changes in coral and benthic community structure during the first decade of monitoring at both depths. At shallower reef crest sites (3–4 m), benthic community structure recovered towards pre-disturbance states within a decade. In contrast, there was a net decline in coral cover and continuing shifts in community structure at deeper reef slope sites (6–7 m). There was no evidence of phase shifts to macroalgal dominance but coral habitats at deeper sites were replaced by unstable substrata such as fine sediments and rubble. The persistence of coral dominance at chronically disturbed shallow sites is likely due to an abundance of coral taxa which are tolerant to environmental stress. In addition, high turbidity may interact antagonistically with other disturbances to reduce the impact of thermal stress and limit macroalgal growth rates

Evolutionary adaptation of an AraC-like regulatory protein in Citrobacter rodentium and Escherichia species

© 2015, American Society for Microbiology. The evolution of pathogenic bacteria is a multifaceted and complex process, which is strongly influenced by the horizontal acquisition of genetic elements and their subsequent expression in their new hosts. A well-studied example is the RegA regulon of the enteric pathogen Citrobacter rodentium. The RegA regulatory protein is a member of the AraC/XylS superfamily, which coordinates the expression of a gene repertoire that is necessary for full pathogenicity of this murine pathogen. Upon stimulation by an exogenous, gut-associated signal, namely, bicarbonate ions, RegA activates the expression of a series of genes, including virulence factors, such as autotransporters, fimbriae, a dispersin-like protein, and the grlRA operon on the locus of enterocyte effacement pathogenicity island. Interestingly, the genes encoding RegA homologues are distributed across the genus Escherichia, encompassing pathogenic and nonpathogenic subtypes. In this study, we carried out a series of bioinformatic, transcriptional, and functional analyses of the RegA regulons of these bacteria. Our results demonstrated that regA has been horizontally transferred to Escherichia spp. and C. rodentium. Comparative studies of two RegA homologues, namely, those from C. rodentium and E. coli SMS-3-5, a multiresistant environmental strain of E. coli, showed that the two regulators acted similarly in vitro but differed in terms of their abilities to activate the virulence of C. rodentium in vivo, which evidently was due to their differential activation of grlRA. Our data indicate that RegA from C. rodentium has strain-specific adaptations that facilitate infection of its murine host. These findings shed new light on the development of virulence by C. rodentium and on the evolution of virulence- regulatory genes of bacterial pathogens in general

Different Modes of Retrovirus Restriction by Human APOBEC3A and APOBEC3G In Vivo

The apolipoprotein B editing complex 3 (A3) cytidine deaminases are among the most highly evolutionarily selected retroviral restriction factors, both in terms of gene copy number and sequence diversity. Primate genomes encode seven A3 genes, and while A3F and 3G are widely recognized as important in the restriction of HIV, the role of the other genes, particularly A3A, is not as clear. Indeed, since human cells can express multiple A3 genes, and because of the lack of an experimentally tractable model, it is difficult to dissect the individual contribution of each gene to virus restriction in vivo. To overcome this problem, we generated human A3A and A3G transgenic mice on a mouse A3 knockout background. Using these mice, we demonstrate that both A3A and A3G restrict infection by murine retroviruses but by different mechanisms: A3G was packaged into virions and caused extensive deamination of the retrovirus genomes while A3A was not packaged and instead restricted infection when expressed in target cells. Additionally, we show that a murine leukemia virus engineered to express HIV Vif overcame the A3G-mediated restriction, thereby creating a novel model for studying the interaction between these proteins. We have thus developed an in vivo system for understanding how human A3 proteins use different modes of restriction, as well as a means for testing therapies that disrupt HIV Vif-A3G interactions.United States. Public Health Service (Grant R01-AI-085015)United States. Public Health Service (Grant T32-CA115299 )United States. Public Health Service (Grant F32-AI100512

Temporal regularity of the environment drives time perception

It’s reasonable to assume that a regularly paced sequence should be perceived as regular, but here we show that perceived regularity depends on the context in which the sequence is embedded. We presented one group of participants with perceptually regularly paced sequences, and another group of participants with mostly irregularly paced sequences (75% irregular, 25% regular). The timing of the final stimulus in each sequence could be varied. In one experiment, we asked whether the last stimulus was regular or not. We found that participants exposed to an irregular environment frequently reported perfectly regularly paced stimuli to be irregular. In a second experiment, we asked participants to judge whether the final stimulus was presented before or after a flash. In this way, we were able to determine distortions in temporal perception as changes in the timing necessary for the sound and the flash to be perceived synchronous. We found that within a regular context, the perceived timing of deviant last stimuli changed so that the relative anisochrony appeared to be perceptually decreased. In the irregular context, the perceived timing of irregular stimuli following a regular sequence was not affected. These observations suggest that humans use temporal expectations to evaluate the regularity of sequences and that expectations are combined with sensory stimuli to adapt perceived timing to follow the statistics of the environment. Expectations can be seen as a-priori probabilities on which perceived timing of stimuli depend

Impacts of Sediments on Coral Energetics: Partitioning the Effects of Turbidity and Settling Particles

Sediment loads have long been known to be deleterious to corals, but the effects of turbidity and settling particles have not previously been partitioned. This study provides a novel approach using inert silicon carbide powder to partition and quantify the mechanical effects of sediment settling versus reduced light under a chronically high sedimentary regime on two turbid water corals commonly found in Singapore (Galaxea fascicularis and Goniopora somaliensis). Coral fragmentswere evenly distributed among three treatments: an open control (30% ambient PAR), a shaded control (15% ambient PAR) and sediment treatment (15% ambient PAR; 26.4 mg cm22 day21). The rate of photosynthesis and respiration, and the dark-adapted quantum yield were measured once a week for four weeks. By week four, the photosynthesis to respiration ratio (P/R ratio) and the photosynthetic yield (Fv/Fm) had fallen by 14% and 3–17% respectively in the shaded control,contrasting with corals exposed to sediments whose P/R ratio and yield had declined by 21% and 18–34% respectively. The differences in rates between the shaded control and the sediment treatment were attributed to the mechanical effects of sediment deposition. The physiological response to sediment stress differed between species with G. fascicularis experiencing a greater decline in the net photosynthetic yield (13%) than G. somaliensis (9.5%), but a smaller increase in the respiration rates (G. fascicularis = 9.9%, G. somaliensis = 14.2%). These different physiological responses were attributed, in part, to coral morphology and highlighted key physiological processes that drive species distribution along high to low turbidity and depositional gradients

The neighbourhood social environment and alcohol use among urban and rural Scottish adolescents

Funding for the Scottish Health Behaviour in School-aged Children was provided by NHS Scotland. This work was also supported by the 600th Anniversary Ph.D. Scholarship which was awarded to Gina Martin by the University of St Andrews.Objectives This research examined the relationship between neighbourhood social environmental characteristics and drinking outcomes among a sample of urban and rural adolescents. Methods From a sample of 1558 Scottish secondary schoolchildren, surveyed as part of the 2010 Health Behaviour in School-aged Children study, we modelled three drinking outcomes on a variety of neighbourhood conditions, including social cohesion, disorder, alcohol outlet density, deprivation, and urban/rurality. Nested and cross-classified multilevel logistic regressions were specified. Results An urban-to-rural gradient was found with non-urban adolescents exhibiting higher odds of having ever drank. Neighbourhood social cohesion related to having ever drank. Among drinkers, those living in accessible small towns had higher odds of weekly drinking and drunkenness compared to urban areas. Higher odds of drunkenness were also found in remote rural areas. Those residing in the least deprived areas had lower odds of weekly drinking. Conclusions In Scotland, inequalities exist in adolescent alcohol use by urban/rurality and neighbourhood social conditions. Findings support regional targeting of public health efforts to address inequalities. Future work is needed to develop and evaluate intervention and prevention approaches for neighbourhoods at risk.Publisher PDFPeer reviewe

Bryozoans are Major Modern Builders of South Atlantic Oddly Shaped Reefs

Supplementary information accompanies this paper at https://doi.org/10.1038/s41598-018-27961-6.In major modern reef regions, either in the Indo-Pacific or the Caribbean, scleractinian corals are described as the main reef framework builders, often associated with crustose coralline algae. We used underwater cores to investigate Late Holocene reef growth and characterise the main framework builders in the Abrolhos Shelf, the largest and richest modern tropical reef complex in the South Western Atlantic, a scientifically underexplored reef province. Rather than a typical coralgal reef, our results show a complex framework building system dominated by bryozoans. Bryozoans were major components in all cores and age intervals (2,000 yrs BP), accounting for up to 44% of the reef framework, while crustose coralline algae and coral accounted for less than 28 and 23%, respectively. Reef accretion rates varied from 2.7 to 0.9 mm yr−1, which are similar to typical coralgal reefs. Bryozoan functional groups encompassed 20 taxa and Celleporaria atlantica (Busk, 1884) dominated the framework at all cores. While the prevalent mesotrophic conditions may have driven suspensionfeeders’ dominance over photoautotrophs and mixotrophs, we propose that a combination of historical factors with the low storm-disturbance regime of the tropical South Atlantic also contributed to the region’s low diversity, and underlies the unique mushroom shape of the Abrolhos pinnacles.We thank CNPq/FAPES-Sisbiota/PELD, CAPES/IODP, CAPES/Ciências do Mar, and ANP/Brasoil for long term project funding. We also thank ICMBio for research permits and field logistic support, and Conservation International for providing and authorizing the use of the IKONOS image. JMW and JCB are International Visiting Researcher at UFES and JBRJ, supported by the Science Without Borders program. Zá Cajueiro provided invaluable field support and Ronaldo Francini, Carlos Janovitch and Lucio Engler helped in the drilling operations. This is a contribution from the Rede Abrolhos (abrolhos.org)

Substance abuse, treatment needs and access among female sex workers and non-sex workers in Pretoria, South Africa

<p>Abstract</p> <p>Background</p> <p>This study examined cross-sectional data collected from substance-using female sex workers (FSW) and non-sex workers (non-SW) in Pretoria, South Africa, who entered a randomized controlled trial.</p> <p>Methods</p> <p>Women who reported alcohol use and recently engaging in sex work or unprotected sex were recruited for a randomized study. The study sample (N = 506) comprised 335 FSW and 171 female non-SW from Pretoria and surrounding areas. Self-reported data about alcohol and other drug use as well as treatment needs and access were collected from participants before they entered a brief intervention.</p> <p>Results</p> <p>As compared with female non-SW, FSW were found to have a greater likelihood of having a past year diagnosis of alcohol or other drug abuse or dependence, having a family member with a history of alcohol or other drug abuse, having been physically abused, having used alcohol before age 18, and having a history of marijuana use. In addition, the FSW were more likely to perceive that they had alcohol or other drug problems, and that they had a need for treatment and a desire to go for treatment. Less than 20% of participants in either group had any awareness of alcohol and drug treatment programs, with only 3% of the FSW and 2% of the non-SW reporting that they tried but were unable to enter treatment in the past year.</p> <p>Conclusion</p> <p>FSW need and want substance abuse treatment services but they often have difficulty accessing services. The study findings suggest that barriers within the South African treatment system need to be addressed to facilitate access for substance-using FSW. Ongoing research is needed to inform policy change that fosters widespread educational efforts and sustainable, accessible, woman-sensitive services to ultimately break the cycle for current and future generations of at-risk South African women.</p

Coral Colonisation of an Artificial Reef in a Turbid Nearshore Environment, Dampier Harbour, Western Australia

A 0.6 hectare artificial reef of local rock and recycled concrete sleepers was constructed in December 2006 at Parker Point in the industrial port of Dampier, western Australia, with the aim of providing an environmental offset for a nearshore coral community lost to land reclamation. Corals successfully colonised the artificial reef, despite the relatively harsh environmental conditions at the site (annual water temperature range 18-32°C, intermittent high turbidity, frequent cyclones, frequent nearby ship movements). Coral settlement to the artificial reef was examined by terracotta tile deployments, and later stages of coral community development were examined by in-situ visual surveys within fixed 25 x 25 cm quadrats on the rock and concrete substrates. Mean coral density on the tiles varied from 113 ± 17 SE to 909 ± 85 SE per m2 over five deployments, whereas mean coral density in the quadrats was only 6.0 ± 1.0 SE per m2 at eight months post construction, increasing to 24.0 ± 2.1 SE per m2 at 62 months post construction. Coral taxa colonising the artificial reef were a subset of those on the surrounding natural reef, but occurred in different proportions-Pseudosiderastrea tayami, Mycedium elephantotus and Leptastrea purpurea being disproportionately abundant on the artificial reef. Coral cover increased rapidly in the later stages of the study, reaching 2.3 ± 0.7 SE % at 62 months post construction. This study indicates that simple materials of opportunity can provide a suitable substrate for coral recruitment in Dampier Harbour, and that natural colonisation at the study site remains sufficient to initiate a coral community on artificial substrate despite ongoing natural and anthropogenic perturbations. © 2013 Blakeway et al