Meeting in the Middle: Towards Successful Multidisciplinary Bioimage Analysis Collaboration

With an increase in subject knowledge expertise required to solve specific biological questions, experts from different fields need to collaborate to address increasingly complex issues. To successfully collaborate, everyone involved in the collaboration must take steps to "meet in the middle". We thus present a guide on truly cross-disciplinary work using bioimage analysis as a showcase, where it is required that the expertise of biologists, microscopists, data analysts, clinicians, engineers, and physicists meet. We discuss considerations and best practices from the perspective of both users and technology developers, while offering suggestions for working together productively and how this can be supported by institutes and funders. Although this guide uses bioimage analysis as an example, the guiding principles of these perspectives are widely applicable to other cross-disciplinary work

Genetic dissection of MHC-associated susceptibility to Lepeophtheirus salmonis in Atlantic salmon

Background: Genetic variation has been shown to play a significant role in determining susceptibility to the salmon louse, Lepeophtheirus salmonis. However, the mechanisms involved in differential response to infection remain poorly understood. Recent findings in Atlantic salmon (Salmo salar) have provided evidence for a potential link between marker variation at the major histocompatibility complex (MHC) and differences in lice abundance among infected siblings, suggesting that MHC genes can modulate susceptibility to the parasite. In this study, we used quantitative trait locus (QTL) analysis to test the effect of genomic regions linked to MHC class I and II on linkage groups (LG) 15 and 6, respectively. Results: Significant QTL effects were detected on both LG 6 and LG 15 in sire-based analysis but the QTL regions remained unresolved due to a lack of recombination between markers. In dam-based analysis, a significant QTL was identified on LG 6, which accounted for 12.9% of within-family variance in lice abundance. However, the QTL was located at the opposite end of DAA, with no significant overlap with the MHC class II region. Interestingly, QTL modelling also revealed evidence of sex-linked differences in lice abundance, indicating that males and females may have different susceptibility to infection. Conclusion: Overall, QTL analysis provided relatively weak support for a proximal effect of classical MHC regions on lice abundance, which can partly be explained by linkage to other genes controlling susceptibility to L. salmonis on the same chromosom

Cell wall glycans and soluble factors determine the interactions between the hyphae of Candida albicans and Pseudomonas aeruginosa

The fungus, Candida albicans, and the bacterium, Pseudomonas aeruginosa, are opportunistic human pathogens that have been coisolated from diverse body sites. Pseudomonas aeruginosa suppresses C. albicans proliferation in vitro and potentially in vivo but it is the C. albicans hyphae that are killed while yeast cells are not. We show that hyphal killing involves both contact-mediated and soluble factors. Bacterial culture filtrates contained heat-labile soluble factors that killed C. albicans hyphae. In cocultures, localized points of hyphal lysis were observed, suggesting that adhesion and subsequent bacteria-mediated cell wall lysis is involved in the killing of C. albicans hyphae. The glycosylation status of the C. albicans cell wall affected the rate of contact-dependent killing because mutants with severely truncated O-linked, but not N-linked, glycans were hypersensitive to Pseudomonas-mediated killing. Deletion of HWP1, ALS3 or HYR1, which encode major hypha-associated cell wall proteins, had no effect on fungal susceptibility

Understanding uncertainty in temperature effects on vector-borne disease: A Bayesian approach

Extrinsic environmental factors influence the distribution and population dynamics of many organisms, including insects that are of concern for human health and agriculture. This is particularly true for vector-borne infectious diseases, like malaria, which is a major source of morbidity and mortality in humans. Understanding the mechanistic links between environment and population processes for these diseases is key to predicting the consequences of climate change on transmission and for developing effective interventions. An important measure of the intensity of disease transmission is the reproductive number $R_0$. However, understanding the mechanisms linking $R_0$ and temperature, an environmental factor driving disease risk, can be challenging because the data available for parameterization are often poor. To address this we show how a Bayesian approach can help identify critical uncertainties in components of $R_0$ and how this uncertainty is propagated into the estimate of $R_0$. Most notably, we find that different parameters dominate the uncertainty at different temperature regimes: bite rate from 15-25$^\circ$ C; fecundity across all temperatures, but especially $\sim$25-32$^\circ$ C; mortality from 20-30$^\circ$ C; parasite development rate at $\sim$15-16$^\circ$C and again at $\sim$33-35$^\circ$C. Focusing empirical studies on these parameters and corresponding temperature ranges would be the most efficient way to improve estimates of $R_0$. While we focus on malaria, our methods apply to improving process-based models more generally, including epidemiological, physiological niche, and species distribution models.Comment: 27 pages, including 1 table and 3 figure

Orientifolds and the Refined Topological String

We study refined topological string theory in the presence of orientifolds by counting second-quantized BPS states in M-theory. This leads us to propose a new integrality condition for both refined and unrefined topological strings when orientifolds are present. We define the SO(2N) refined Chern-Simons theory which computes refined open string amplitudes for branes wrapping Seifert three-manifolds. We use the SO(2N) refined Chern-Simons theory to compute new invariants of torus knots that generalize the Kauffman polynomials. At large N, the SO(2N) refined Chern-Simons theory on the three-sphere is dual to refined topological strings on an orientifold of the resolved conifold, generalizing the Gopakumar-Sinha-Vafa duality. Finally, we use the (2,0) theory to define and solve refined Chern-Simons theory for all ADE gauge groups

Revisiting Consumer Ethnocentrism: Review, Reconceptualization, and Empirical Testing

Prior research has suggested that many consumers prefer domestic to foreign products, even when the quality is lower and the price is higher. Such bias is attributed to consumer ethnocentrism. This study critically examines the current conceptualizations of consumer ethnocentrism and proposes an extension of its conceptual boundaries and measurement. It determines that consumer ethnocentrism is a multidimensional construct that encompasses five dimensions: prosociality, cognition, insecurity, reflexiveness, and habituation. Empirical evidence from the United Kingdom and the United States demonstrates that the extended measurement instrument better predicts consumers' preferences for local brands at the expense of foreign brands

Pacific anthropogenic carbon between 1991 and 2017

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Carter, B. R., Feely, R. A., Wanninkhof, R., Kouketsu, S., Sonnerup, R. E., Pardo, P. C., Sabine, C. L., Johnson, G. C., Sloyan, B. M., Murata, A., Mecking, S., Tilbrook, B., Speer, K., Talley, L. D., Millero, F. J., Wijffels, S. E., Macdonald, A. M., Gruber, N., & Bullister, J. L. Pacific anthropogenic carbon between 1991 and 2017. Global Biogeochemical Cycles, 33(5), (2019):597-617, doi:10.1029/2018GB006154.We estimate anthropogenic carbon (Canth) accumulation rates in the Pacific Ocean between 1991 and 2017 from 14 hydrographic sections that have been occupied two to four times over the past few decades, with most sections having been recently measured as part of the Global Ocean Ship‐based Hydrographic Investigations Program. The rate of change of Canth is estimated using a new method that combines the extended multiple linear regression method with improvements to address the challenges of analyzing multiple occupations of sections spaced irregularly in time. The Canth accumulation rate over the top 1,500 m of the Pacific increased from 8.8 (±1.1, 1σ) Pg of carbon per decade between 1995 and 2005 to 11.7 (±1.1) PgC per decade between 2005 and 2015. For the entire Pacific, about half of this decadal increase in the accumulation rate is attributable to the increase in atmospheric CO2, while in the South Pacific subtropical gyre this fraction is closer to one fifth. This suggests a substantial enhancement of the accumulation of Canth in the South Pacific by circulation variability and implies that a meaningful portion of the reinvigoration of the global CO2 sink that occurred between ~2000 and ~2010 could be driven by enhanced ocean Canth uptake and advection into this gyre. Our assessment suggests that the accuracy of Canth accumulation rate reconstructions along survey lines is limited by the accuracy of the full suite of hydrographic data and that a continuation of repeated surveys is a critical component of future carbon cycle monitoring.The data we use can be accessed at CCHDO website (https://cchdo.ucsd.edu/) and GLODAP website (https://www.glodap.info/). This research would not be possible without the hard work of the scientists and crew aboard the many repeated hydrographic cruises coordinated by GO‐SHIP, which is funded by NSF OCE and NOAA OAR. We thank funding agencies and program managers as follows: U.S., Australian, Japanese national science funding agencies that support data collection, data QA/QC, and data centers. Contributions from B. R. C., R. A. F., and R. W. are supported by the National Oceanic and Atmospheric Administration Global Ocean Monitoring and Observing Program (Data Management and Synthesis Grant: N8R3CEA‐PDM managed by Kathy Tedesco and David Legler). G. C. J. is supported by the Climate Observation Division, Climate Program Office, National Oceanic and Atmospheric Administration (NOAA), U.S. Department of Commerce and NOAA Research (fund reference 100007298), grant (N8R1SE3‐PGC). B. M. S was supported by the Australian Government Department of the Environment and CSIRO through the Australian Climate Change Science Programme and by the National Environmental Science Program. N. G. acknowledges support by ETH Zurich. This is JISAO contribution 2018‐0149 and PMEL contribution 4786. We fondly remember John Bullister as a treasured friend, valued colleague, and dedicated mentor, and we thank him for sharing his days with us. He is and will be dearly missed