Seasonal movements of northern pike in Minto Flats, Alaska

Thesis (M.S.) University of Alaska Fairbanks, 2016Northern pike (Esox lucius) is a large, long-lived piscivorous species that are harvested in sport and subsistence fisheries in Alaska. My study described the seasonal movements of northern pike that inhabit the Minto Lakes portion (Goldstream Creek drainage) of the Minto Flats wetland complex, Alaska, from May 2008 through January 2010. Very high frequency (VHF) radio tags (n = 220) were surgically implanted in northern pike in Minto Flats in May 2007, 2008, and 2009, and fish were relocated with fixed telemetry stations and aerial- and boat-based telemetry surveys. Radio-tagged northern pike displayed a distinct spring pre-spawning migration into the Minto Lakes study area, where they remained for the duration of the open-water season. A protracted out-migration occurred between late September and early December, with downstream movements peaking in November and October of 2008 and 2009, respectively. Radio-tagged fish present in the Minto Lakes study area during the open-water season overwintered exclusively in a 26-km reach of the Chatanika River from its confluence with Goldstream Creek upstream to the Murphy Dome Road access point. Daily movement rates were greatest during May and August. In addition to providing a better understanding of northern pike life history in Minto Flats, these results will aid managers and researchers by identifying critical habitats and providing information to better design future population assessment experiments

Antigen Cross-Priming of Cell-Associated Proteins is Enhanced by Macroautophagy within the Antigen Donor Cell

Phagocytosis of dying cells constitutes an important mechanism of antigen capture for the cross-priming of CD8+ T cells. This process has been shown to be critical for achieving tumor and viral immunity. While most studies have focused on the mechanisms inherent in the dendritic cell that account for exogenous antigen accessing MHC I, several recent reports have highlighted the important contribution made by the antigen donor cell. Specifically, the cell stress and cell death pathways that precede antigen transfer are now known to impact cross-presentation and cross-priming. Herein, we review the current literature regarding a role for macroautophagy within the antigen donor cell. Further examination of this point of immune regulation is warranted and may contribute to a better understanding of how to optimize immunotherapy for treatment of cancer and chronic infectious disease

Impurity transport in Alcator C-Mod in the presence of poloidal density variation induced by ion cyclotron resonance heating

Impurity particle transport in an ion cyclotron resonance heated Alcator C-Mod discharge is studied with local gyrokinetic simulations and a theoretical model including the effect of poloidal asymmetries and elongation. In spite of the strong minority temperature anisotropy in the deep core region, the poloidal asymmetries are found to have a negligible effect on the turbulent impurity transport due to low magnetic shear in this region, in agreement with the experimental observations. According to the theoretical model, in outer core regions poloidal asymmetries may contribute to the reduction of the impurity peaking, but uncertainties in atomic physics processes prevent quantitative comparison with experiments.Comment: 32 pages, 12 figure

Realistic atomistic structure of amorphous silicon from machine-learning-driven molecular dynamics

Amorphous silicon (a-Si) is a widely studied noncrystalline material, and yet the subtle details of its atomistic structure are still unclear. Here, we show that accurate structural models of a-Si can be obtained using a machine-learning-based interatomic potential. Our best a-Si network is obtained by simulated cooling from the melt at a rate of 1011 K/s (that is, on the 10 ns time scale), contains less than 2% defects, and agrees with experiments regarding excess energies, diffraction data, and 29Si NMR chemical shifts. We show that this level of quality is impossible to achieve with faster quench simulations. We then generate a 4096-atom system that correctly reproduces the magnitude of the first sharp diffraction peak (FSDP) in the structure factor, achieving the closest agreement with experiments to date. Our study demonstrates the broader impact of machine-learning potentials for elucidating structures and properties of technologically important amorphous materials

Inhibition of mTORC1 Enhances the Translation of Chikungunya Proteins via the Activation of the MnK/eIF4E Pathway

International audienceChikungunya virus (CHIKV), the causative agent of a major epidemic spanning five continents, is a positive stranded mRNA virus that replicates using the cell's cap-dependent translation machinery. Despite viral infection inhibiting mTOR, a metabolic sensor controls cap-dependent translation, viral proteins are efficiently translated. Rapalog treatment, silencing of mtor or raptor genes, but not rictor, further enhanced CHIKV infection in culture cells. Using biochemical assays and real time imaging, we demonstrate that this effect is independent of autophagy or type I interferon production. Providing in vivo evidence for the relevance of our findings, mice treated with mTORC1 inhibitors exhibited increased lethality and showed a higher sensitivity to CHIKV. A systematic evaluation of the viral life cycle indicated that inhibition of mTORC1 has a specific positive effect on viral proteins, enhancing viral replication by increasing the translation of both structural and nonstructural proteins. Molecular analysis defined a role for phosphatidylinositol-3 kinase (PI3K) and MAP kinase-activated protein kinase (MnKs) activation, leading to the hyper-phosphorylation of eIF4E. Finally, we demonstrated that in the context of CHIKV inhibition of mTORC1, viral replication is prioritized over host translation via a similar mechanism. Our study reveals an unexpected bypass pathway by which CHIKV protein translation overcomes viral induced mTORC1 inhibition

Identity Foreclosure, Athletic Identity, and College Sport Participation

A study was conducted with 502 college students (246 non-athletes, 90 intramural athletes, and 166 intercollegiate athletes) to investigate the relationship between self-identity variables (i.e., identity foreclosure and athletic identity) and college sport participation. The researchers used two scales, the foreclosure subscale of the Objective Measure of Ego Identity Status (OM-EIS, Adams et al., 1979) and the Athletic Identity Measurement Scale (AIMS, Brewer et al., 1993). Results indicated that identity foreclosure and athletic identity increase with level of sport participation. Identity foreclosure was significantly lower for upperclass students than for underclass students among non-athletes, but not among intramural and intercollegiate student-athletes. No gender differences were found. These findings suggested that intercollegiate student-athletes may commit to the role of "athlete" without exploring alternative identities. Implications of the results for the academic and career development of student-athletes were discussed. "The results of this study imply that college student-athletes may identify strongly with the athlete role to the extent that they fail to explore alternative identities." - p.

Dissecting T Cell Contraction In Vivo Using a Genetically Encoded Reporter of Apoptosis

SummaryContraction is a critical phase of immunity whereby the vast majority of effector T cells die by apoptosis, sparing a population of long-lived memory cells. Where, when, and why contraction occurs has been difficult to address directly due in large part to the rapid clearance of apoptotic T cells in vivo. To circumvent this issue, we introduced a genetically encoded reporter for caspase-3 activity into naive T cells to identify cells entering the contraction phase. Using two-photon imaging, we found that caspase-3 activity in T cells was maximal at the peak of the response and was associated with loss of motility followed minutes later by cell death. We demonstrated that contraction is a widespread process occurring uniformly in all organs tested and targeting phenotypically diverse T cells. Importantly, we identified a critical window of time during which antigen encounters act to antagonize T cell apoptosis, supporting a causal link between antigen clearance and T cell contraction. Our results offer insight into a poorly explored phase of immunity and provide a versatile methodology to study apoptosis during the development or function of a variety of immune cells in vivo

Deconvolution of the Response to Bacillus Calmette–Guérin Reveals NF-κB-Induced Cytokines As Autocrine Mediators of Innate Immunity

Bacillus Calmette–Guérin (BCG) is used as a vaccine and diagnostic test for tuberculosis, as well as immunotherapy in the treatment of bladder cancer. While clinically useful, the response to mycobacterial stimulation is complex and the induced protein signature remains poorly defined. We characterized the cell types directly engaged by BCG, as well as the induced cytokine loops that transmit signal(s) to bystander cells. Standardized whole-blood stimulations and mechanistic studies on single and purified cell populations identified distinct patterns of activation in monocytes as compared to neutrophils and invariant lymphocyte populations. Deconvoluting the role of Toll-like receptor 2/4 and Dectin-1/2 in the inflammatory response to BCG, we revealed Dectin-1/2 as dominant in neutrophils as compared to monocytes, which equally engaged both pathways. Furthermore, we quantified the role of NF-κB and NADPH/reactive oxygen species (ROS)-dependent cytokines, which triggered a JAK1/2-dependent amplification loop and accounted for 40–50% of the induced response to BCG. In sum, this study provides new insight into the molecular and cellular pathways involved in the response to BCG, establishing the basis for a new generation of immunodiagnostic tools

Apoptotic Cells Deliver Processed Antigen to Dendritic Cells for Cross-Presentation

Antigen derived from engulfed apoptotic cells can be cross-presented by dendritic cells (DCs) for the generation of major histocompatibility class I/peptide complexes. While the early events of recognition and internalization of the dying cell have been characterized, the antigen-processing pathway or pathways remain unknown. We established a mouse model assaying for the activation of polyclonal T cells reactive to antigen derived from apoptotic cells, and demonstrated two distinct pathways for the trafficking of exogenous epitopes. In the first, exogenous antigen is dependent on the DC's expression of a functional transporter associated with antigen processing (TAP). Surprisingly, we found evidence that a second pathway exists in which transfer of processed antigen from the dying cell allows formation of major histocompatibility class I/peptide complexes in TAP-deficient DCs. In vivo data suggest that in situations of stress (e.g., viral infection), this latter pathway may be more efficient, illustrating that dying cells may preselect immunologically important antigenic determinants