A decade of monitoring Atlantic cod Gadus morhua spawning aggregations in Massachusetts Bay using passive acoustics

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Caiger, P. E., Dean, M. J., DeAngelis, A. I., Hatch, L. T., Rice, A. N., Stanley, J. A., Tholke, C., Zemeckis, D. R., & Van Parijs, S. M. A decade of monitoring Atlantic cod Gadus morhua spawning aggregations in Massachusetts Bay using passive acoustics. Marine Ecology Progress Series, 635, (2020): 89-103, doi:10.3354/meps13219.Atlantic cod Gadus morhua populations in the northeast USA have failed to recover since major declines in the 1970s and 1990s. To rebuild these stocks, managers need reliable information on spawning dynamics in order to design and implement control measures; discovering cost-effective and non-invasive monitoring techniques is also favorable. Atlantic cod form dense, site-fidelic spawning aggregations during which they vocalize, permitting acoustic detection of their presence at such times. The objective of this study was to detect spawning activity of Atlantic cod using multiple fixed-station passive acoustic recorders to sample across Massachusetts Bay during the winter spawning period. A generalized linear modeling approach was used to investigate spatio-temporal trends of cod vocalizing over 10 consecutive winter spawning seasons (2007-2016), the longest such timeline of any passive acoustic monitoring of a fish species. The vocal activity of Atlantic cod was associated with diel, lunar, and seasonal cycles, with a higher probability of occurrence at night, during the full moon, and near the end of November. Following 2009 and 2010, there was a general decline in acoustic activity. Furthermore, the northwest corner of Stellwagen Bank was identified as an important spawning location. This project demonstrated the utility of passive acoustic monitoring in determining the presence of an acoustically active fish species, and provides valuable data for informing the management of this commercially, culturally, and ecologically important species.Thanks to Eli Bonnell, Genevieve Davis, Julianne Bonell, Samara Haver, and Eric Matzen for assistance in MARU deployments, Dana Gerlach and Heather Heenehan for help in passive acoustic data analysis, and the NEFSC passive acoustics group for useful discussions. Funding for 2007−2012 passive acoustic surveys was provided by Excelerate Energy and Neptune LNG to Cornell University. Fieldwork for 2013−2015 was funded through the 2013−2014 NOAA Saltonstall-Kennedy grant program (Award No. NA14NMF4270027), and jointly funded by The Nature Conservancy, Massachusetts Division of Marine Fisheries, and the Cabot Family Charitable Foundation. Funding for 2016 SoundTrap data was provided by NOAA’s Ocean Acoustics Program (4 Sanctuaries Project)

Digital Holography Experiments with Degraded Temporal Coherence

To simulate the effects of multiple-longitudinal modes and rapid fluctuations in center frequency, we use sinusoidal phase modulation and linewidth broadening, respectively. These effects allow us to degrade the temporal coherence of our master-oscillator laser, which we then use to conduct digital holography experiments. In turn, our results show that the coherence efficiency decreases quadratically with fringe visibility and that our measurements agree with our models to within 1.8% for sinusoidal phase modulation and 6.9% for linewidth broadening

Behavioral Changes in Aging but Not Young Mice after Neonatal Exposure to the Polybrominated Flame Retardant DecaBDE

BACKGROUND: After several decades of commercial use, the flame-retardant chemicals polybrominated diphenyl ethers (PBDEs) and their metabolites are pervasive environmental contaminants and are detected in the human body. Decabrominated diphenyl ether (decaBDE) is currently the only PBDE in production in the United States. OBJECTIVES: Little is known about the health effects of decaBDE. In the present study we examined the effects of neonatal decaBDE exposure on behavior in mice at two ages. METHODS: Neonatal male and female C57BL6/J mice were exposed to a daily oral dose of 0, 6, or 20 mg/kg decaBDE from postnatal days 2 through 15. Two age groups were examined: a cohort that began training during young adulthood and an aging cohort of littermates that began training at 16 months of age. Both cohorts were tested on a series of operant procedures that included a fixed-ratio I schedule of reinforcement, a fixed-interval (FI) 2-min schedule, and a light-dark visual discrimination. RESULTS: We observed minimal effects on the light-dark discrimination in the young cohort, with no effects on the other tasks. The performance of the aging cohort was significantly affected by decaBDE. On the FI schedule, decaBDE exposure increased the overall response rate. On the light-dark discrimination, older treated mice learned the task more slowly, made fewer errors on the first-response choice of a trial but more perseverative errors after an initial error, and had lower latencies to respond compared with controls. Effects were observed in both dose groups and sexes on various measures. CONCLUSIONS: These findings suggest that neonatal decaBDE exposure produces effects on behavioral tasks in older but not younger animals. The behavioral mechanisms responsible for the pattern of observed effects may include increased impulsivity, although further research is required

Radio Polarimetry of the ELAIS N1 Field: Polarized Compact Sources

We present deep polarimetric observations at 1420 MHz of the European Large Area ISO Survey North 1 region (ELAIS N1) as part of the Dominion Radio Astrophysical Observatory Planck Deep Fields project. By combining closely spaced aperture synthesis fields, we image a region of 7.43 square degrees to a maximum sensitivity in Stokes Q and U of 78 microJy/beam, and detect 786 compact sources in Stokes I. Of these, 83 exhibit polarized emission. We find that the differential source counts (log N - log p) for polarized sources are nearly constant down to p > 500 microJy, and that these faint polarized radio sources are more highly polarized than the strong source population. The median fractional polarization is (4.8 +/- 0.7)% for polarized sources with Stokes I flux density between 1 and 30 mJy; approximately three times larger than sources with I > 100 mJy. The majority of the polarized sources have been identified with galaxies in the Spitzer Wide Area Infrared Extragalactic Survey (SWIRE) image of ELAIS N1. Most of the galaxies occupy regions in the IRAC 5.8/3.6 micron vs. 8.0/4.5 micron color-color diagram associated with dusty AGNs, or with ellipticals with an aging stellar population. A few host galaxies have colors that suggests significant PAH emission in the near-infrared. A small fraction, 12%, of the polarized sources are not detected in the SWIRE data. None of the polarized sources in our sample appears to be associated with an actively star-forming galaxy.Comment: 28 pages, 8 Figures. Figures 2 and 3 as separate gif images. Accepted for publication in the Astrophysical Journa

Spectral Typing of Late Type Stellar Companions to Young Stars from Low Dispersion Near-Infrared Integral Field Unit Data

We used the Project 1640 near-infrared coronagraph and integral field spectrograph to observe 19 young solar type stars. Five of these stars are known binary stars and we detected the late-type secondaries and were able to measure their JH spectra with a resolution of R\sim30. The reduced, extracted, and calibrated spectra were compared to template spectra from the IRTF spectral library. With this comparison we test the accuracy and consistency of spectral type determination with the low-resolution near-infrared spectra from P1640. Additionally, we determine effective temperature and surface gravity of the companions by fitting synthetic spectra calculated with the PHOENIX model atmosphere code. We also present several new epochs of astrometry of each of the systems. Together these data increase our knowledge and understanding of the stellar make up of these systems. In addition to the astronomical results, the analysis presented helps validate the Project 1640 data reduction and spectral extraction processes and the utility of low-resolution, near-infrared spectra for characterizing late-type companions in multiple systems.Comment: Accepted to Astronomical Journal, 25 pages, 8 figure

Investigation of the biophysical and cell biological properties of ferroportin, a multipass integral membrane protein iron exporter

Ferroportin is a multipass membrane protein that serves as an iron exporter in many vertebrate cell types. Ferroportin-mediated iron export is controlled by the hormone hepcidin, which binds ferroportin, causing its internalization and degradation. Mutations in ferroportin cause a form of the iron overload hereditary disease hemochromatosis. Relatively little is known about ferroportin's properties or the mechanism by which mutations cause disease. In this study, we expressed and purified human ferroportin to characterize its biochemical/biophysical properties in solution and conducted cell biological studies in mammalian cells. We found that purified detergent-solubilized ferroportin is a well-folded monomer that binds hepcidin. In cell membranes, the N- and C-termini were both cytosolic, implying an even number of transmembrane regions, and ferroportin was mainly localized to the plasma membrane. Hepcidin addition resulted in a redistribution of ferroportin to intracellular compartments that labeled with early endosomal and lysosomal, but not Golgi, markers and that trafficked along microtubules. An analysis of 16 disease-related ferroportin mutants revealed that all were expressed and trafficked to the plasma membrane but that some were resistant to hepcidin-induced internalization. The characterizations reported here form a basis upon which models for ferroportin's role in regulating iron homeostasis in health and disease can be interpreted

miRNA independent hepacivirus variants suggest a strong evolutionary pressure to maintain miR-122 dependence

Hepatitis C virus (HCV) requires the liver specific micro-RNA (miRNA), miR-122, to replicate. This was considered unique among RNA viruses until recent discoveries of HCV-related hepaciviruses prompting the question of a more general miR-122 dependence. Among hepaciviruses, the closest known HCV relative is the equine non-primate hepacivirus (NPHV). Here, we used Argonaute cross-linking immunoprecipitation (AGO-CLIP) to confirm AGO binding to the single predicted miR-122 site in the NPHV 5’UTR in vivo. To study miR-122 requirements in the absence of NPHV-permissive cell culture systems, we generated infectious NPHV/HCV chimeric viruses with the 5’ end of NPHV replacing orthologous HCV sequences. These chimeras were viable even in cells lacking miR-122, although miR-122 presence enhanced virus production. No other miRNAs bound this region. By random mutagenesis, we isolated HCV variants partially dependent on miR-122 as well as robustly replicating NPHV/HCV variants completely independent of any miRNAs. These miRNA independent variants even replicate and produce infectious particles in non-hepatic cells after exogenous delivery of apolipoprotein E (ApoE). Our findings suggest that miR-122 independent HCV and NPHV variants have arisen and been sampled during evolution, yet miR-122 dependence has prevailed. We propose that hepaciviruses may use this mechanism to guarantee liver tropism and exploit the tolerogenic liver environment to avoid clearance and promote chronicity