Development and Lipid Composition of the Harpacticoid Copepod Nitocra Spinipes Reared on Different Diets

We reared the harpacticoid copepod Nitocra spinipes on diets of bacteria, a diatom, or a macroalga, evaluating survivorship and growth in short-term (≤ 1 generation) experiments. Lipid content of the copepods and their diets was measured and used as an index of nutrition. Although growth, survivorship and lipid content of N. spinipes were significantly greater when fed the diatom, which had the highest lipid content of the 3 diets, the copepod was able to develop from egg to adult when fed a lipid- poor bacterial diet. Furthermore, this species was able to go through developmental molts without the addition of food (6 individuals from a starved cohort of 25 made it to at least copepodite stage I), suggesting the uptake of dissolved organic matter for growth. This widespread estuarine benthic copepod apparently has the ability to survive on diverse and nutritionally poor diets, a quality that is useful in a variable, detritus-dominated environment

Vortex fluidics-mediated DNA rescue from formalin-fixed museum specimens.

DNA from formalin-preserved tissue could unlock a vast repository of genetic information stored in museums worldwide. However, formaldehyde crosslinks proteins and DNA, and prevents ready amplification and DNA sequencing. Formaldehyde acylation also fragments the DNA. Treatment with proteinase K proteolyzes crosslinked proteins to rescue the DNA, though the process is quite slow. To reduce processing time and improve rescue efficiency, we applied the mechanical energy of a vortex fluidic device (VFD) to drive the catalytic activity of proteinase K and recover DNA from American lobster tissue (Homarus americanus) fixed in 3.7% formalin for >1-year. A scan of VFD rotational speeds identified the optimal rotational speed for recovery of PCR-amplifiable DNA and while 500+ base pairs were sequenced, shorter read lengths were more consistently obtained. This VFD-based method also effectively recovered DNA from formalin-preserved samples. The results provide a roadmap for exploring DNA from millions of historical and even extinct species

On the detection of Lorentzian profiles in a power spectrum: A Bayesian approach using ignorance priors

Aims. Deriving accurate frequencies, amplitudes, and mode lifetimes from stochastically driven pulsation is challenging, more so, if one demands that realistic error estimates be given for all model fitting parameters. As has been shown by other authors, the traditional method of fitting Lorentzian profiles to the power spectrum of time-resolved photometric or spectroscopic data via the Maximum Likelihood Estimation (MLE) procedure delivers good approximations for these quantities. We, however, show that a conservative Bayesian approach allows one to treat the detection of modes with minimal assumptions (i.e., about the existence and identity of the modes). Methods. We derive a conservative Bayesian treatment for the probability of Lorentzian profiles being present in a power spectrum and describe an efficient implementation that evaluates the probability density distribution of parameters by using a Markov-Chain Monte Carlo (MCMC) technique. Results. Potentially superior to "best-fit" procedure like MLE, which only provides formal uncertainties, our method samples and approximates the actual probability distributions for all parameters involved. Moreover, it avoids shortcomings that make the MLE treatment susceptible to the built-in assumptions of a model that is fitted to the data. This is especially relevant when analyzing solar-type pulsation in stars other than the Sun where the observations are of lower quality and can be over-interpreted. As an example, we apply our technique to CoRoT observations of the solar-type pulsator HD 49933.Comment: 12 pages, 11 figures, accepted for publication in Astronomy and Astrophysic

Three Super-Earths Orbiting HD 7924

We report the discovery of two super-Earth mass planets orbiting the nearby K0.5 dwarf HD 7924 which was previously known to host one small planet. The new companions have masses of 7.9 and 6.4 M$_\oplus$, and orbital periods of 15.3 and 24.5 days. We perform a joint analysis of high-precision radial velocity data from Keck/HIRES and the new Automated Planet Finder Telescope (APF) to robustly detect three total planets in the system. We refine the ephemeris of the previously known planet using five years of new Keck data and high-cadence observations over the last 1.3 years with the APF. With this new ephemeris, we show that a previous transit search for the inner-most planet would have covered 70% of the predicted ingress or egress times. Photometric data collected over the last eight years using the Automated Photometric Telescope shows no evidence for transits of any of the planets, which would be detectable if the planets transit and their compositions are hydrogen-dominated. We detect a long-period signal that we interpret as the stellar magnetic activity cycle since it is strongly correlated with the Ca II H and K activity index. We also detect two additional short-period signals that we attribute to rotationally-modulated starspots and a one month alias. The high-cadence APF data help to distinguish between the true orbital periods and aliases caused by the window function of the Keck data. The planets orbiting HD 7924 are a local example of the compact, multi-planet systems that the Kepler Mission found in great abundance.Comment: Accepted to ApJ on 4/7/201

Homonegativity, Substance Use, Sexual Risk Behaviors, and HIV Status in Poor and Ethnic Men Who Have Sex with Men in Los Angeles

This study evaluates associations between internalized homonegativity and demographic factors, drug use behaviors, sexual risk behaviors, and HIV status among men who have sex with men (MSM) and with men and women (MSM/W). Participants were recruited in Los Angeles County using respondent-driven sampling (RDS) and completed the Internalized Homonegativity Inventory (IHNI) and questionnaires on demographic and behavioral factors. Biological samples were tested for HIV and for recent cocaine, methamphetamine, and heroin use. The 722 MSM and MSM/W participants were predominantly African American (44%) and Hispanic (28%), unemployed (82%), homeless (50%), and HIV positive (48%) who used drugs in the past 6 months (79.5%). Total and Personal Homonegativity, Gay Affirmation, and Morality of Homosexuality IHNI scores were significantly higher for African American men than for other ethnicities, for MSM/W than for MSM, for recent cocaine users than for recent methamphetamine users, and for HIV-seronegative men than for HIV-seropositive men. Linear regression showed the Gay Affirmation scale significantly and inversely correlated with the number of sexual partners when controlling for effects of ethnicity/race and sexual identification, particularly for men who self-identified as straight. Highest IHNI scores were observed in a small group of MSM/W (n = 62) who never tested for HIV. Of these, 26% tested HIV positive. Findings describe ways in which internalized homophobia is a barrier to HIV testing and associated HIV infection and signal distinctions among participants in this sample that can inform targeted HIV prevention efforts aimed at increasing HIV testing

Non-detection of previously reported transits of HD 97658b with MOST photometry

The radial velocity-discovered exoplanet HD 97658b was recently announced to transit, with a derived planetary radius of 2.93 \pm 0.28 R_{Earth}. As a transiting super-Earth orbiting a bright star, this planet would make an attractive candidate for additional observations, including studies of its atmospheric properties. We present and analyze follow-up photometric observations of the HD 97658 system acquired with the MOST space telescope. Our results show no transit with the depth and ephemeris reported in the announcement paper. For the same ephemeris, we rule out transits for a planet with radius larger than 2.09 R_{Earth}, corresponding to the reported 3\sigma lower limit. We also report new radial velocity measurements which continue to support the existence of an exoplanet with a period of 9.5 days, and obtain improved orbital parameters.Comment: 16 pages, 4 figures; 1 Table; accepted for publication in ApJL, includes changes made in response to the referee repor

Common ADRB2 Haplotypes Derived from 26 Polymorphic Sites Direct β2-Adrenergic Receptor Expression and Regulation Phenotypes

Background: The β2-adrenergic receptor (β2AR) is expressed on numerous cell-types including airway smooth muscle cells and cardiomyocytes. Drugs (agonists or antagonists) acting at these receptors for treatment of asthma, chronic obstructive pulmonary disease, and heart failure show substantial interindividual variability in response. The ADRB2 gene is polymorphic in noncoding and coding regions, but virtually all ADRB2 association studies have utilized the two common nonsynonymous coding SNPs, often reaching discrepant conclusions. Methodology/Principal Findings: We constructed the 8 common ADRB2 haplotypes derived from 26 polymorphisms in the promoter, 5′UTR, coding, and 3′UTR of the intronless ADRB2 gene. These were cloned into an expression construct lacking a vector-based promoter, so that β2AR expression was driven by its promoter, and steady state expression could be modified by polymorphisms throughout ADRB2 within a haplotype. “Whole-gene” transfections were performed with COS-7 cells and revealed 4 haplotypes with increased cell surface β2AR protein expression compared to the others. Agonist-promoted downregulation of β2AR protein expression was also haplotype-dependent, and was found to be increased for 2 haplotypes. A phylogenetic tree of the haplotypes was derived and annotated by cellular phenotypes, revealing a pattern potentially driven by expression. Conclusions/Significance: Thus for obstructive lung disease, the initial bronchodilator response from intermittent administration of β-agonist may be influenced by certain β2AR haplotypes (expression phenotypes), while other haplotypes may influence tachyphylaxis during the response to chronic therapy (downregulation phenotypes). An ideal clinical outcome of high expression and less downregulation was found for two haplotypes. Haplotypes may also affect heart failure antagonist therapy, where β2AR increase inotropy and are anti-apoptotic. The haplotype-specific expression and regulation phenotypes found in this transfection-based system suggest that the density of genetic information in the form of these haplotypes, or haplotype-clusters with similar phenotypes can potentially provide greater discrimination of phenotype in human disease and pharmacogenomic association studies

The Infrared Imaging Spectrograph (IRIS) for TMT: Data Reduction System

IRIS (InfraRed Imaging Spectrograph) is the diffraction-limited first light instrument for the Thirty Meter Telescope (TMT) that consists of a near-infrared (0.84 to 2.4 $\mu$m) imager and integral field spectrograph (IFS). The IFS makes use of a lenslet array and slicer for spatial sampling, which will be able to operate in 100's of different modes, including a combination of four plate scales from 4 milliarcseconds (mas) to 50 mas with a large range of filters and gratings. The imager will have a field of view of 34$\times$34 arcsec$^{2}$ with a plate scale of 4 mas with many selectable filters. We present the preliminary design of the data reduction system (DRS) for IRIS that need to address all of these observing modes. Reduction of IRIS data will have unique challenges since it will provide real-time reduction and analysis of the imaging and spectroscopic data during observational sequences, as well as advanced post-processing algorithms. The DRS will support three basic modes of operation of IRIS; reducing data from the imager, the lenslet IFS, and slicer IFS. The DRS will be written in Python, making use of open-source astronomical packages available. In addition to real-time data reduction, the DRS will utilize real-time visualization tools, providing astronomers with up-to-date evaluation of the target acquisition and data quality. The quicklook suite will include visualization tools for 1D, 2D, and 3D raw and reduced images. We discuss the overall requirements of the DRS and visualization tools, as well as necessary calibration data to achieve optimal data quality in order to exploit science cases across all cosmic distance scales.Comment: 13 pages, 2 figures, 6 tables, Proceeding 9913-165 of the SPIE Astronomical Telescopes + Instrumentation 201

Satellite detection of dinoflagellate blooms off California by UV reflectance ratios

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kahru, M., Anderson, C., Barton, A. D., Carter, M. L., Catlett, D., Send, U., Sosik, H. M., Weiss, E. L., & Mitchell, B. G. Satellite detection of dinoflagellate blooms off California by UV reflectance ratios. Elementa: Science of the Anthropocene, 9(1), (2021): 00157, https://doi.org/10.1525/elementa.2020.00157.As harmful algae blooms are increasing in frequency and magnitude, one goal of a new generation of higher spectral resolution satellite missions is to improve the potential of satellite optical data to monitor these events. A satellite-based algorithm proposed over two decades ago was used for the first time to monitor the extent and temporal evolution of a massive bloom of the dinoflagellate Lingulodinium polyedra off Southern California during April and May 2020. The algorithm uses ultraviolet (UV) data that have only recently become available from the single ocean color sensor on the Japanese GCOM-C satellite. Dinoflagellates contain high concentrations of mycosporine-like amino acids and release colored dissolved organic matter, both of which absorb strongly in the UV part of the spectrum. Ratios 1, consistent with historical observations showing a sharp transition from dinoflagellate- to diatom-dominated waters in these areas. UV bands are thus potentially useful in the remote sensing of phytoplankton blooms but are currently available only from a single ocean color sensor. As several new satellites such as the NASA Plankton, Aerosol, Cloud, and marine Ecosystem mission will include UV bands, new algorithms using these bands are needed to enable better monitoring of blooms, especially potentially harmful algal blooms, across large spatiotemporal scales.Part of this work was funded by National Science Foundation (NSF) grants to the CCE-LTER Program, most recently OCE-1637632. Processing of Second-Generation Global Imager satellite data was funded by Japan Aerospace Exploration Agency. Data shown in Figure 1 were collected by BGM and MK with support from the NASA SIMBIOS project. DC was supported by the NASA Biodiversity and Ecological Forecasting Program (Grant NNX14AR62A), the Bureau of Ocean and Energy Management Ecosystem Studies Program (BOEM award MC15AC00006), and the NOAA through the Santa Barbara Channel Marine Biodiversity Observation Network. HMS was supported by NSF (Grant OCE-1810927) and the Simons Foundation (Grant 561126). ELW was supported by NSF GRFP (Grant DGE-1650112). Funding for Scripps and Santa Monica Piers sampling was through the Southern California Coastal Ocean Observing Harmful Algal Bloom Monitoring Program by NOAA NA16NOS0120022