The climate of the coastal US West coast is characterized by cool, alongshore, northerly wind from the Oregon border to the Southern California Bight, south of Point Conception. New datasets, including surface wind estimates derived from satellite scatterometer and North American Regional Reanalysis fields allow for a more detailed exploration than has heretofore been possible. This thesis examines episodes of enhanced northerly surface wind to determine the spatial and temporal character of the surface wind along and offshore of the California coast and the 3-D structure and seasonality of the atmosphere associated with the wind episodes. A deterministic approach is employed to enhance understanding of fundamental processes rather than improve predictability. The methodology includes diagnostic spatial and temporal analysis and numerical sensitivity experiments. Processes known to affect coastal wind are investigated to gain a better understanding of the role of possible mechanisms driving northerly wind events. It is found that the spatial and temporal structure of wind offshore of California is characterized by episodes of enhance equatorward surface wind that often extend from Cape Mendocino to Hawaii. Wind events typically last four days and are present 20% of the time during January-August. The summer circulation structure associated with wind events is fundamentally different than winter and spring. For instance the surface and upper-air circulation patterns associated with wind events are co-located in winter and 90⁰ out-of-phase in summer. Wind events are nearly always accompanied by a strong trough in the upper-air circulation that is directly above or just east of the coast. The analysis concludes that troughs are a nearly universal forcing mechanism for wind events, while the low -level atmospheric thermal gradient across the coast also plays an important, but less consistent role in wind events. A hypothesis is developed suggesting that southeastward movement of the North Pacific High may be a sufficient forcing mechanism for wind events in summer, but a trough along the coast is a necessary ingredient in winter. Other forcing mechanisms, feedbacks, and processes may also be important in reinforcing the circulation associated with wind events

Soil microbial fuel cells (SMFCs) function as bioelectrochemical energy harvesters that convert electrons stored in soil organic matter into useful electrical energy. Broadly, an SMFC comprises three essential components: an anode buried in the soil (the negative terminal), a colony of exoelectrogenic microorganisms residing on this anode, and a cathode (the positive terminal). As the exoelectrogens respire, they release electrons to the anode, which acts as an external receptor. These released electrons then flow through a load (e.g. a resistor), connecting the anode and cathode. Though minuscule, the electrical power produced by SMFCs has a number of potential applications such as sustaining low-power embedded electronics, pollutant remediation, or as a bio-sensing proxy for soil qualities and microbial activity. This discussion aims to emphasize the potential of SMFCs in addressing real-world environmental issues and to generate interest in the larger scientific community for broad interdisciplinary research efforts, particularly in field deployments.

AbstractThe complement system, a major component of the innate immune system, is becoming increasingly recognised as a key participant in physiology and disease. The awareness that immunological mediators support various aspects of both normal central nervous system (CNS) function and pathology has led to a renaissance of complement research in neuroscience. Various studies have revealed particularly novel findings on the wide-ranging involvement of complement in neural development, synapse elimination and maturation of neural networks, as well as the progression of pathology in a range of chronic neurodegenerative disorders, and more recently, neurotraumatic events, where rapid disruption of neuronal homeostasis potently triggers complement activation. The purpose of this review is to summarise recent findings on complement activation and acquired brain or spinal cord injury, i.e. ischaemic-reperfusion injury or stroke, traumatic brain injury (TBI) and spinal cord injury (SCI), highlighting the potential for complement-targeted therapeutics to alleviate the devastating consequences of these neurological conditions.

Taxol and other antimitotic agents are frontline chemotherapy agents but the mechanisms responsible for patient benefit remain unclear. Following a genome-wide siRNA screen, we identified the oncogenic transcription factor Myc as a taxol sensitizer. Using time-lapse imaging to correlate mitotic behavior with cell fate, we show that Myc sensitizes cells to mitotic blockers and agents that accelerate mitotic progression. Myc achieves this by upregulating a cluster of redundant pro-apoptotic BH3-only proteins and suppressing pro-survival Bcl-xL. Gene expression analysis of breast cancers indicates that taxane responses correlate positively with Myc and negatively with Bcl-xL. Accordingly, pharmacological inhibition of Bcl-xL restores apoptosis in Myc-deficient cells. These results open up opportunities for biomarkers and combination therapies that could enhance traditional and second-generation antimitotic agents.

Precision medicine in immune-mediated inflammatory diseases (IMIDs) requires a cellular understanding of treatment response. We describe a therapeutic atlas for Crohns disease (CD) and ulcerative colitis (UC) following adalimumab, an anti-tumour necrosis factor (anti-TNF) treatment. We generated ~1 million single-cell transcriptomes, organised into 109 cell states, from 216 gut biopsies (41 subjects), revealing disease-specific differences. A systems biology-spatial analysis identified granuloma signatures in CD and interferon (IFN)-response signatures localising to T cell aggregates and epithelial damage in CD and UC. Pretreatment differences in epithelial and myeloid compartments were associated with remission outcomes in both diseases. Longitudinal comparisons demonstrated disease progression in nonremission: myeloid and T cell perturbations in CD and increased multi-cellular IFN signalling in UC. IFN signalling was also observed in rheumatoid arthritis (RA) synovium with a lymphoid pathotype. Our therapeutic atlas represents the largest cellular census of perturbation with the most common biologic treatment, anti-TNF, across multiple inflammatory diseases.

We present BVRI and unfiltered (Clear) light curves of 70 stripped-envelope supernovae (SESNe), observed between 2003 and 2020, from the Lick Observatory Supernova Search follow-up program. Our SESN sample consists of 19 spectroscopically normal SNe Ib, 2 peculiar SNe Ib, six SNe Ibn, 14 normal SNe Ic, 1 peculiar SN Ic, 10 SNe Ic-BL, 15 SNe IIb, 1 ambiguous SN IIb/Ib/c, and 2 superluminous SNe. Our follow-up photometry has (on a per-SN basis) a mean coverage of 81 photometric points (median of 58 points) and a mean cadence of 3.6 d (median of 1.2 d). From our full sample, a subset of 38 SNe have pre-maximum coverage in at least one passband, allowing for the peak brightness of each SN in this subset to be quantitatively determined. We describe our data collection and processing techniques, with emphasis toward our automated photometry pipeline, from which we derive publicly available data products to enable and encourage further study by the community. Using these data products, we derive host-galaxy extinction values through the empirical colour evolution relationship and, for the first time, produce accurate rise-time measurements for a large sample of SESNe in both optical and infrared passbands. By modelling multiband light curves, we find that SNe Ic tend to have lower ejecta masses and lower ejecta velocities than SNe Ib and IIb, but higher 56Ni masses.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists.