De novo transcriptome assembly of the Southern Ocean copepod Rhincalanus gigas sheds light on developmental changes in gene expression

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Berger, C. A., Steinberg, D. K., Copley, N. J., & Tarrant, A. M. De novo transcriptome assembly of the Southern Ocean copepod Rhincalanus gigas sheds light on developmental changes in gene expression. Marine Genomics, (2021): 100835, https://doi.org/10.1016/j.margen.2021.100835.Copepods are small crustaceans that dominate most zooplankton communities in terms of both abundance and biomass. In the polar oceans, a subset of large lipid-storing copepods occupy central positions in the food web because of their important role in linking phytoplankton and microzooplankton with higher trophic levels. In this paper, we generated a high-quality de novo transcriptome for Rhincalanus gigas, the largest—and among the most abundant—of the Southern Ocean copepods. We then conducted transcriptional profiling to characterize the developmental transition between late-stage juveniles and adult females. We found that juvenile R. gigas substantially upregulate lipid synthesis and glycolysis pathways relative to females, as part of a developmental gene expression program that also implicates processes such as muscle growth, chitin formation, and ion transport. This study provides the first transcriptional profile of a developmental transition within Rhincalanus gigas or any endemic Southern Ocean copepod, thereby extending our understanding of copepod molecular physiology.Funding for this project was provided by the National Science Foundation (Grants OPP-1746087 to AMT and OPP-1440435 to DKS)

Creating psychological connections between intervention recipients: development and focus group evaluation of a group singing session for people with aphasia

This is the final version of the article. Available from BMJ Publishing Group via the DOI in this record.Objectives The study sought to identify key design features that could be used to create a new framework for group-based health interventions. We designed and tested the first session of a group intervention for stroke survivors with aphasia which was aimed at nurturing new psychological connections between group members. Setting The intervention session, a participant focus group and interviews with intervention facilitators were held in a local community music centre in the South West of England. Participants A convenience sample of 10 community-dwelling people with poststroke aphasia participated in the session. Severity of aphasia was not considered for inclusion. Intervention Participants took part in a 90-min group singing session which involved singing songs from a specially prepared song book. Musical accompaniment was provided by the facilitators. Primary and secondary outcome measures Participants and group facilitators reported their experiences of participating in the session, with a focus on activities within the session related to the intervention aims. Researcher observations of the session were also made. Results Two themes emerged from the analysis, concerning experiences of the session (‘developing a sense of group belonging’) and perceptions of its design and delivery (‘creating the conditions for engagement’). Participants described an emerging sense of shared social identity as a member of the intervention group and identified fixed (eg, group size, session breaks) and flexible (eg, facilitator responsiveness) features of the session which contributed to this emergence. Facilitator interviews and researcher observations corroborated and expanded participant reports. Conclusions Engagement with health intervention content may be enhanced in group settings when intervention participants begin to establish positive and meaningful psychological connections with other group members. Understanding and actively nurturing these connections should be a core feature of a general framework for the design and delivery of group interventions.This research was funded by the National Institute for Health Research (NIHR) Collaboration for Leadership in Applied Health Research and Care South West Peninsula. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health

Stress Induced Degradation Modes in CIGS Mini-Modules: Preprint

This study demonstrates that the method of encapsulation can affect the long-term stability of CIGS modules, principally through interactions with the ZnO

Stress Induced Degradation Modes in CIGSS Minimodules

The experimental objectives of this report are: (1) compare the performance of modules exposed to high temperature and humidity; (2) determine the effects of different encapsulants on long term stability of CIGSS modules; and (3) analyze failure modes to determine areas in need of improvement

Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lenz, P. H., Roncalli, V., Cieslak, M. C., Tarrant, A. M., Castelfranco, A. M., & Hartline, D. K. Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod. Communications Biology, 4(1), (2021): 426, https://doi.org/10.1038/s42003-021-01946-0.Many arthropods undergo a seasonal dormancy termed “diapause” to optimize timing of reproduction in highly seasonal environments. In the North Atlantic, the copepod Calanus finmarchicus completes one to three generations annually with some individuals maturing into adults, while others interrupt their development to enter diapause. It is unknown which, why and when individuals enter the diapause program. Transcriptomic data from copepods on known programs were analyzed using dimensionality reduction of gene expression and functional analyses to identify program-specific genes and biological processes. These analyses elucidated physiological differences and established protocols that distinguish between programs. Differences in gene expression were associated with maturation of individuals on the reproductive program, while those on the diapause program showed little change over time. Only two of six filters effectively separated copepods by developmental program. The first one included all genes annotated to RNA metabolism and this was confirmed using differential gene expression analysis. The second filter identified 54 differentially expressed genes that were consistently up-regulated in individuals on the diapause program in comparison with those on the reproductive program. Annotated to oogenesis, RNA metabolism and fatty acid biosynthesis, these genes are both indicators for diapause preparation and good candidates for functional studies.This work was supported by National Science Foundation Grants (NSF) OCE-1459235 and OCE-1756767 to P.H.L., D.K.H. and AE Christie and OPP-1746087 to A.M.T

Cosmology of Axions and Moduli: A Dynamical Systems Approach

This paper is concerned with string cosmology and the dynamics of multiple scalar fields in potentials that can become negative, and their features as (Early) Dark Energy models. Our point of departure is the "String Axiverse", a scenario that motivates the existence of cosmologically light axion fields as a generic consequence of string theory. We couple such an axion to its corresponding modulus. We give a detailed presentation of the rich cosmology of such a model, ranging from the setting of initial conditions on the fields during inflation, to the asymptotic future. We present some simplifying assumptions based on the fixing of the axion decay constant $f_a$, and on the effective field theory when the modulus trajectory is adiabatic, and find the conditions under which these assumptions break down. As a by-product of our analysis, we find that relaxing the assumption of fixed $f_a$ leads to the appearance of a new meta-stable de-Sitter region for the modulus without the need for uplifting by an additional constant. A dynamical systems analysis reveals the existence of many fixed point attractors, repellers and saddle points, which we analyse in detail. We also provide geometric interpretations of the phase space. The fixed points can be used to bound the couplings in the model. A systematic scan of certain regions of parameter space reveals that the future evolution of the universe in this model can be rich, containing multiple epochs of accelerated expansion.Comment: 27 pages, 12 figures, comments welcome, v2 minor correction

Targeting the molecular and cellular interactions of the bone marrow niche in immunologic disease topical collection on autoimmunity

Recent investigations have expanded our knowledge of the regulatory bone marrow (BM) niche, which is critical in maintaining and directing hematopoietic stem cell (HSC) self-renewal and differentiation. Osteoblasts, mesenchymal stem cells (MSCs), and CXCL12-abundant reticular (CAR) cells are niche components in close association with HSCs and have been more clearly defined in immune cell function and homeostasis. Importantly, cellular inhabitants of the BM niche signal through G protein-coupled surface receptors (GPCRs) for various appropriate immune functions. In this article, recent literature on BM niche inhabitants (HSCs, osteoblasts, MSCs, CAR cells) and their GPCR mechanistic interactions are reviewed for better understanding of the BM cells involved in immune development, immunologic disease, and current immune reconstitution therapies

Neutrophils self-limit swarming to contain bacterial growth in vivo

Neutrophils communicate with each other to form swarms in infected organs. Coordination of this population response is critical for the elimination of bacteria and fungi. Using transgenic mice, we found that neutrophils have evolved an intrinsic mechanism to self-limit swarming and avoid uncontrolled aggregation during inflammation. G protein–coupled receptor (GPCR) desensitization acts as a negative feedback control to stop migration of neutrophils when they sense high concentrations of self-secreted attractants that initially amplify swarming. Interference with this process allows neutrophils to scan larger tissue areas for microbes. Unexpectedly, this does not benefit bacterial clearance as containment of proliferating bacteria by neutrophil clusters becomes impeded. Our data reveal how autosignaling stops self-organized swarming behavior and how the finely tuned balance of neutrophil chemotaxis and arrest counteracts bacterial escape

Nova light curves from the Solar Mass Ejection Imager (SMEI) - II. The extended catalogue

We present the results from observing nine Galactic novae in eruption with the Solar Mass Ejection Imager (SMEI) between 2004 and 2009. While many of these novae reached peak magnitudes that were either at or approaching the detection limits of SMEI, we were still able to produce light curves that in many cases contained more data at and around the initial rise, peak, and decline than those found in other variable star catalogs. For each nova, we obtained a peak time, maximum magnitude, and for several an estimate of the decline time (t2). Interestingly, although of lower quality than those found in Hounsell et al. (2010a), two of the light curves may indicate the presence of a pre-maximum halt. In addition the high cadence of the SMEI instrument has allowed the detection of low amplitude variations in at least one of the nova light curves