Toothed whale interactions with longline fisheries in Alaska

Thesis (Ph.D.) University of Alaska Fairbanks, 2014Killer whale (Orcinus orca) and sperm whale (Physeter macrocephalus) depredation occurs when whales damage or remove fish caught on longline gear. This project used a mixed methods approach incorporating Generalized Linear and Additive Modeling techniques and social research methods, such as semi-directed interviews and written questionnaires, to evaluate: 1) spatio-temporal depredation trends, 2) depredation effects on groundfish catch rates, and 3) socio-economic implications of depredation avoidance and changing fishing practices due to whale interactions. The occurrence of killer whale depredation varied by target species and area based on National Marine Fisheries Service longline survey data and observer commercial fishery data collected from 1998 to 2012 in the Bering Sea, Aleutian Islands, and Western Gulf of Alaska. The percentage of commercial fishery sets affected by killer whales was highest in Bering Sea fisheries for: sablefish (Anoplopomafimbria; 21.4%), Greenland turbot (Reinhardtius hippoglossoides; 9.9%), and Pacific halibut (Hippogolossus stenolepis; 6.9%). Killer whale depredation was more common on the standardized longline survey (9.2-34.6% skates impacted) than the commercial sablefish fishery (1.0-21.4% sets impacted) in all three management areas. Catch reductions were consistent across data sets. Average commercial fleet catch reductions ranged from 35-69% for sablefish, Pacific halibut and Greenland turbot (p<0.001); survey catch reductions ranged from 51-73% (p<0.001). Sablefish catch per unit effort, gear haul time and location significantly impacted the proportion of sets depredated. Fishermen reported changing their fishing practices in response to depredating whales by soaking gear longer to "wait the whales out" or moving to different fishing sites. These avoidance measures resulted in increased operation costs and opportunity costs in lost time. In a follow-up analysis based on data collected by fishermen in 2011 and 2012, it was found that killer whale depredation avoidance measures resulted in an average additional cost of $494 per vessel-day for fuel and crew food. Opportunity costs of time lost by fishermen averaged$486 per additional vessel-day on the grounds. These results provide insight into the potential impacts of whale depredation on fish stock abundance indices and commercially important fisheries in Alaska and will inform future research on apex predator-fisheries interactions

Comparative Performance of Three Length-Based Mortality Estimators

Length‐based methods provide alternatives for estimating the instantaneous total mortality rate (Z) in exploited marine populations when data are not available for age‐based methods. We compared the performance of three equilibrium length‐based methods: the length‐converted catch curve (LCCC), the Beverton–Holt equation (BHE), and the length‐based spawning potential ratio (LB‐SPR) method. The LCCC and BHE are two historically common procedures that use length as a proxy for age. From a truncated length‐frequency distribution of fully selected animals, the LCCC estimates Z with a regression of the logarithm of catch at length by the midpoint of the length‐bins, while the BHE estimates Z as a function of the mean length. The LB‐SPR method is a likelihood‐based population dynamics model, which—unlike the LCCC and BHE—does not require data truncation. Using Monte Carlo simulations across a range of scenarios with varying mortality and life history characteristics, our study showed that neither the LCCC nor the BHE was uniformly superior in terms of bias or root mean square error across simulations, but these estimators performed better than LB‐SPR, which had the largest bias in most cases. Generally, if the ratio of natural mortality (M) to the von Bertalanffy growth rate parameter (K) is low, then the BHE is most preferred, although there is likely to be high bias and low precision. If M/K is high, then the LCCC and BHE performed better and similarly to each other. Differences in performance among commonly used truncation methods for the LCCC and BHE were small. The LB‐SPR method did not perform as well as the classical methods but may still be of interest because it provides estimates of a logistic selectivity curve. The M/K ratio provided the most contrast in the performance of the three methods, suggesting that it should be considered for predicting the likely performance of length‐based mortality estimators

Transferrable protection by gut microbes against STING-associated lung disease

STING modulates immunity by responding to bacterial and endogenous cyclic dinucleotides (CDNs). Humans and mice with STING gain-of-function mutations develop a syndrome known as STING-associated vasculopathy with onset in infancy (SAVI), which is characterized by inflammatory or fibrosing lung disease. We hypothesized that hyperresponsiveness of gain-of-function STING to bacterial CDNs might explain autoinflammatory lung disease in SAVI mice. We report that depletion of gut microbes with oral antibiotics (vancomycin, neomycin, and ampicillin [VNA]) nearly eliminates lung disease in SAVI mice, implying that gut microbes might promote STING-associated autoinflammation. However, we show that germ-free SAVI mice still develop severe autoinflammatory disease and that transferring gut microbiota from antibiotics-treated mice to germ-free animals eliminates lung inflammation. Depletion of anaerobes with metronidazole abolishes the protective effect of the VNA antibiotics cocktail, and recolonization with the metronidazole-sensitive anaerobe Bacteroides thetaiotaomicron prevents disease, confirming a protective role of a metronidazole-sensitive microbe in a model of SAVI

Homeostatic interferon-lambda response to bacterial microbiota stimulates preemptive antiviral defense within discrete pockets of intestinal epithelium

Interferon-lambda (IFN-λ) protects intestinal epithelial cells (IECs) from enteric viruses by inducing expression of antiviral IFN-stimulated genes (ISGs). Here, we find that bacterial microbiota stimulate a homeostatic ISG signature in the intestine of specific pathogen-free mice. This homeostatic ISG expression is restricted to IECs, depends on IEC-intrinsic expression of IFN-λ receptor

Optimism/pessimism and health-related quality of life during pregnancy across three continents: a matched cohort study in China, Ghana, and the United States

<p>Abstract</p> <p>Background</p> <p>Little is known about how optimism/pessimism and health-related quality of life compare across cultures.</p> <p>Methods</p> <p>Three samples of pregnant women in their final trimester were recruited from China, Ghana, and the United States (U.S.). Participants completed a survey that included the Life Orientation Test - Revised (LOT-R, an optimism/pessimism measure), the Short Form 12 (SF-12, a quality of life measure), and questions addressing health and demographic factors. A three-country set was created for analysis by matching women on age, gestational age at enrollment, and number of previous pregnancies. Anovas with post-hoc pairwise comparisons were used to compare results across the cohorts. Multivariate regression analysis was used to create a model to identify those variables most strongly associated with optimism/pessimism.</p> <p>Results</p> <p>LOT-R scores varied significantly across cultures in these samples, with Ghanaian pregnant women being the most optimistic and least pessimistic and Chinese pregnant women being the least optimistic overall and the least pessimistic in subscale analysis. Four key variables predicted approximately 20% of the variance in overall optimism scores: country of origin (p = .006), working for money (p = .05); level of education (p = .002), and ever being treated for emotional issues with medication (p < .001). Quality of life scores also varied by country in these samples, with the most pronounced difference occurring in the vitality measure. U.S. pregnant women reported far lower vitality scores than both Chinese and Ghanaian pregnant women in our sample.</p> <p>Conclusion</p> <p>This research raises important questions regarding what it is about country of origin that so strongly influences optimism/pessimism among pregnant women. Further research is warranted exploring underlying conceptualization of optimism/pessimism and health related quality of life across countries.</p

Pahs, Ionized Gas, and Molecular Hydrogen in Brightest Cluster Galaxies of Cool Core Clusters of Galaxies

We present measurements of 5-25 {\mu}m emission features of brightest cluster galaxies (BCGs) with strong optical emission lines in a sample of 9 cool-core clusters of galaxies observed with the Infrared Spectrograph on board the Spitzer Space Telescope. These systems provide a view of dusty molecular gas and star formation, surrounded by dense, X-ray emitting intracluster gas. Past work has shown that BCGs in cool-core clusters may host powerful radio sources, luminous optical emission line systems, and excess UV, while BCGs in other clusters never show this activity. In this sample, we detect polycyclic aromatic hydrocarbons (PAHs), extremely luminous, rotationally-excited molecular hydrogen line emission, forbidden line emission from ionized gas ([Ne II] and [Ne III]), and infrared continuum emission from warm dust and cool stars. We show here that these BCGs exhibit more luminous forbidden neon and H2 rotational line emission than star-forming galaxies with similar total infrared luminosities, as well as somewhat higher ratios of 70 {\mu}m / 24 {\mu}m luminosities. Our analysis suggests that while star formation processes dominate the heating of the dust and PAHs, a heating process consistent with suprathermal electron heating from the hot gas, distinct from star formation, is heating the molecular gas and contributing to the heating of the ionized gas in the galaxies. The survival of PAHs and dust suggests that dusty gas is somehow shielded from significant interaction with the X-ray gas.Comment: 27 preprint pages, 18 figures, accepted by Astrophysical Journa

Synthesis and reductive chemistry of bimetallic and trimetallic rare-earth metallocene hydrides with (C5H4SiMe3)1− ligands

The reductive chemistry of [Cp\u272Ln(μ–H)(THF)x]y [Ln = Y, Dy, Tb; Cp\u27 = (C5H4SiMe3)1−; x = 2, 0 and y = 2, 3] was examined to determine if these hydrides would be viable precursors for 4fn5d1 Ln2+ ions that could form 5d1-5d1 metal–metal bonded complexes. The hydrides were prepared by reaction of the chlorides, [Cp\u272Ln(μ–Cl)]2, 1-Ln, with allylmagnesium chloride to form the allyl complexes, [Cp\u272Y(η3–C3H5)(THF)], 2-Ln, which were hydrogenolyzed. The solvent-free reaction of solid 2-Ln with 60 psi of H2 gas in a Fischer-Porter apparatus produced, in the Y case, the trimetallic species, [Cp\u272Y(μ–H)]3, 3-Y, and in the Dy and Tb cases, the bimetallic complexes [Cp\u272Ln(μ–H)(THF)]2, 4-Ln (Ln = Dy, Tb). The latter complexes could be converted to 3-Dy and 3-Tb by heating under vacuum. Isopiestic data indicate that 3-Y solvates to 4-Y in THF. Reductions of 4-Y, 4-Dy, and 4-Tb with KC8 in the presence of a chelate such as 2.2.2-cryptand or 18-crown-6 all gave reaction products with intense dark colors characteristic of Ln2+ ions. In the yttrium case, with either chelating agent, the dark green product gives a rhombic EPR spectrum (g1 = 2.01, g2 = 1.99, g3 = 1.98, A = 24.1 G) at 77 K. However, the only crystallographically-characterizable products obtainable from these solutions were Ln3+polyhydride anion complexes of composition, [K(chelate)]{[Cp\u272Ln(μ–H)]3(μ–H)}

The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies

Reproducibility is a fundamental requirement in scientific experiments and clinical contexts. Recent publications raise concerns about the reliability of microarray technology because of the apparent lack of agreement between lists of differentially expressed genes (DEGs). In this study we demonstrate that (1) such discordance may stem from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion, the lists become much more reproducible, especially when fewer genes are selected; and (3) the instability of short DEG lists based on P cutoffs is an expected mathematical consequence of the high variability of the t-values. We recommend the use of FC ranking plus a non-stringent P cutoff as a baseline practice in order to generate more reproducible DEG lists. The FC criterion enhances reproducibility while the P criterion balances sensitivity and specificity

A Giant Metrewave Radio Telescope/Chandra view of IRAS 09104+4109: A type 2 QSO in a cooling flow

IRAS 09104+4109 is a rare example of a dust enshrouded type 2 QSO in the centre of a cool-core galaxy cluster. Previous observations of this z=0.44 system showed that as well as powering the hyper-luminous infrared emission of the cluster-central galaxy, the QSO is associated with a double-lobed radio source. However, the steep radio spectral index and misalignment between the jets and ionised optical emission suggested that the orientation of the QSO had recently changed. We use a combination of new, multi-band Giant Metrewave Radio Telescope observations and archival radio data to confirm that the jets are no longer powered by the QSO, and estimate their age to be 120-160 Myr. This is in agreement with the ~70-200 Myr age previously estimated for star-formation in the galaxy. Previously unpublished Very Long Baseline Array data reveal a 200 pc scale double radio source in the galaxy core which is more closely aligned with the current QSO axis and may represent a more recent period of jet activity. These results suggest that the realignment of the QSO, the cessation of jet activity, and the onset of rapid star-formation may have been caused by a gas-rich galaxy merger. A Chandra X-ray observation confirms the presence of cavities associated with the radio jets, and we estimate the energy required to inflate them to be ~7.7x10^60 erg. The mechanical power of the jets is sufficient to balance radiative cooling in the cluster, provided they are efficiently coupled to the intra-cluster medium (ICM). We find no evidence of direct radiative heating and conclude that the QSO either lacks the radiative luminosity to heat the ICM, or that it requires longer than 100-200 Myr to significantly impact its environment. [Abridged]Comment: 23 pages, 18 figures and 7 tables. Accepted for publication in MNRA

(p)ppGpp and c-di-AMP Homeostasis Is Controlled by CbpB in Listeria monocytogenes

The facultative intracellular pathogen Listeria monocytogenes, like many related Firmicutes, uses the nucleotide second messenger cyclic di-AMP (c-di-AMP) to adapt to changes in nutrient availability, osmotic stress, and the presence of cell wall-acting antibiotics. In rich medium, c-di-AMP is essential; however, mutations in cbpB, the gene encoding c-di-AMP binding protein B, suppress essentiality. In this study, we identified that the reason for cbpB-dependent essentiality is through induction of the stringent response by RelA. RelA is a bifunctional RelA/SpoT homolog (RSH) that modulates levels of (p)ppGpp, a secondary messenger that orchestrates the stringent response through multiple allosteric interactions. We performed a forward genetic suppressor screen on bacteria lacking c-di-AMP to identify genomic mutations that rescued growth while cbpB was constitutively expressed and identified mutations in the synthetase domain of RelA. The synthetase domain of RelA was also identified as an interacting partner of CbpB in a yeast-2-hybrid screen. Biochemical analyses confirmed that free CbpB activates RelA while c-di-AMP inhibits its activation. We solved the crystal structure of CbpB bound and unbound to c-di-AMP and provide insight into the region important for c-di-AMP binding and RelA activation. The results of this study show that CbpB completes a homeostatic regulatory circuit between c-di-AMP and (p)ppGpp in Listeria monocytogenes.</div