Breaking Barriers with Bread: Using the Sourdough Starter Microbiome to Teach High-Throughput Sequencing Techniques.

Widespread usage of high-throughput sequencing (HTS) in the LIFE SCIENCES has produced a demand for undergraduate and graduate institutions to offer classes exposing students to all aspects of HTS (sample acquisition, laboratory work, sequencing technologies, bioinformatics, and statistical analyses). Despite the increase in demand, many challenges exist for these types of classes. We advocate for the usage of the sourdough starter microbiome for implementing meta-amplicon sequencing. The relatively small community, dominated by a few taxa, enables potential contaminants to be easily identified, while between-sample differences can be quickly statistically assessed. Finally, bioinformatic pipelines and statistical analyses can be carried out on personal student laptops or in a teaching computer lab. In two semesters adopting this system, 12 of 14 students were able to effectively capture the sourdough starter microbiome, using the instructor's paired sample as reference.

Turbidity and fecal indicator bacteria in recreational marine waters increase following the 2018 Woolsey Fire.

Wildfires increase runoff and sediment yields that impact downstream ecosystems. While the effects of wildfire on stream water quality are well documented, oceanic responses to wildfire remain poorly understood. Therefore, this study investigated oceanic responses to the 2018 Woolsey Fire using satellite remote sensing and in situ data analyses. We examined 2016-2020 turbidity plume (n = 192) and 2008-2020 fecal indicator bacteria (FIB, n = 15,015) measurements at variable proximity to the Woolsey Fire. Shifts in coastal water quality were more pronounced in the "inside" region, which drained the burn area. The inside region experienced 2018-2019 plume surface area monthly means that were 10 and 9 times greater than 2016-2017 and 2017-2018 monthly means, respectively. Further, linear regressions showed that 2018-2019 three-day precipitation totals produced plumes of greater surface area. We also noted statistically significant increases in the inside region in 2018-2019 total coliform and Enterococcus monthly means that were 9 and 53 times greater than 2008-2018 monthly means, respectively. These results indicate that sediment and microbial inputs to coastal ecosystems can increase substantially post-wildfire at levels relevant to public and environmental health, and underscore the benefit of considering remote sensing and in situ measurements for water quality monitoring.

Experimental L-Band Airborne SAR for Oil Spill Response at Sea and in Coastal Waters.

Satellite synthetic aperture radar (SAR) is frequently used during oil spill response efforts to identify oil slick extent, but suffers from the major disadvantages of potential long latency between when a spill occurs and when a satellite can image the site and an inability to continuously track the spill as it develops. We show using data acquired with the Uninhabited Aerial Vehicle SAR (UAVSAR) instrument how a low noise, high resolution, L-band SAR could be used for oil spill response, with specific examples of tracking slick extent, position and weathering; determining zones of relatively thicker or more emulsified oil within a slick; and identifying oil slicks in coastal areas where look-alikes such as calm waters or biogenic slicks can confound the identification of mineral oil spills. From these key points, the essential features of an airborne SAR system for operational oil spill response are described, and further research needed to determine SAR's capabilities and limitations in quantifying slick thickness is discussed.

Stormwater runoff plumes in the Southern California Bight: A comparison study with SAR and MODIS imagery.

Stormwater runoff is the largest source of pollution in the Southern California Bight (SCB), resulting from untreated runoff and pollutants from urban watersheds entering the coastal waters after rainstorms. We make use of both satellite SAR and MODIS-Aqua ocean color imagery to examine two different components of runoff plumes, the surface slick and the sediment discharge. We expand on earlier satellite SAR studies by examining an extensive collection of multi-platform SAR imagery, spanning from 1992 to 2014, that provides a more comprehensive view of the plume surface slick characteristics, illustrated with distribution maps of the extent and flow direction of the plumes. The SAR-detected surface plumes are compared with coincident rain and runoff measurements, and with available measured shoreline fecal bacteria loads. We illustrate differences in the detection of SAR surface plumes with the sediment-related discharge plumes derived from MODIS imagery. A conceptual satellite stormwater runoff monitoring approach is presented.

Selective retardation of perfume oil evaporation from oil-in-water emulsions stabilized by either surfactant or nanoparticles.

We have used dynamic headspace analysis to investigate the evaporation rates of perfume oils from stirred oil-in-water emulsions into a flowing gas stream. We compare the behavior of an oil of low water solubility (limonene) and one of high water solubility (benzyl acetate). It is shown how the evaporation of an oil of low water solubility is selectively retarded and how the retardation effect depends on the oil volume fraction in the emulsion. We compare how the evaporation retardation depends on the nature of the adsorbed film stabilizing the emulsion. Surfactant films are less effective than adsorbed films of nanoparticles, and the retardation can be further enhanced by compression of the adsorbed nanoparticle films by preshrinking the emulsion drops.

p66(shc)'s role as an essential mitophagic molecule in controlling neuronal redox and energetic tone.

Stroke is the leading cause of adult disability in the U.S. and is now recognized as a global epidemic. There are currently no FDA-approved drugs to block the cell death that results from oxygen and glucose deprivation. This void in clinical medicine has sparked an intense interest in understanding endogenous cellular protective pathways that might be exploited for therapeutic development. The work highlighted here describes the critical role between redox tone and energetic stress signaling in mediating mitophagy and determining neuronal cell fate following acute oxygen glucose deprivation.

Phase inversion of particle-stabilised perfume oil-water emulsions: experiment and theory.

Phase inversion of fumed silica particle-stabilised emulsions of water and perfume oil can be effected in three ways. The transitional inversion from water-in-oil (w/o) to oil-in-water (o/w) occurs upon increasing the particle hydrophilicity for 9 oils of different polarity and structure. Results are compared for systems in which particles are pre-dispersed in one of the bulk phases and for those in which a novel powdered particle method is used. Using a simple theory involving the surface energies of the various interfaces, the contact angle θ of a particle with the oil-water interface is calculated as a function of the particle hydrophilicity. Assuming phase inversion occurs at θ = 90°, very good agreement is obtained for all oils between the calculated and experimental particle hydrophilicity required for inversion in the case of the powdered particle method. Inversion from o/w to w/o induced by simply increasing the particle concentration is shown to be as a result of changes in the aggregation state of the particles influencing their wettability. Finally, catastrophic phase inversion from w/o to o/w is achieved by increasing the volume fraction of water, and multiple emulsions form around inversion in a system containing only one particle type. Results of the latter two inversion routes are combined to develop an emulsion compositional map allowing a variety of emulsions with different characteristics to be described by varying the relative amounts of the three components.

Drop sizes and particle coverage in emulsions stabilised solely by silica nanoparticles of irregular shape.

We have investigated emulsions stabilised solely by partially-hydrophobised fumed silica particles which consist of a mixture of primary particles and irregularly-shaped fused aggregates and larger agglomerates. The particle wettability is controlled by varying the extent of hydrophobisation of their surfaces. This, in turn, controls the contact angle between the oil-water interface and the particle surface (θ(ow)) which affects the particle adsorption energy and the type of emulsion formed (oil-in-water, o/w or water-in-oil, w/o). Progressive particle hydrophobisation causes transitional phase inversion of the emulsions from o/w to w/o which occurs when θ(ow) = 90° and the energy of particle adsorption to the oil-water interface is maximally favourable. The key problem addressed here is to understand why the emulsion drop size passes through a minimum at the point of emulsion phase inversion. In principle, this effect could be the result of particle desorption, changes in the extent of close-packing of the adsorbed particle film (at constant particle orientation), particle re-orientation or a combination of these processes. Using measurements of emulsion drop size and the extent of particle desorption, we have derived adsorbed particle surface concentrations as a function of the energy of desorption of the particles from the oil-water interface for a range of particle concentrations and different oil-water systems. The main conclusion is that the minimum in emulsion drop size through phase inversion is mainly caused by re-orientation of the particles from a high surface area orientation when the energy of desorption is high to a low surface area orientation when the energy of desorption is low. Some particle desorption occurs but this is a secondary effect.

Essential role of the redox-sensitive kinase p66shc in determining energetic and oxidative status and cell fate in neuronal preconditioning.

Ischemic preconditioning is a phenomenon in which low-level stressful stimuli upregulate endogenous defensive programs, resulting in subsequent resistance to otherwise lethal injuries. We previously observed that signal transduction systems typically associated with neurodegeneration such as caspase activation are requisite events for the expression of tolerance and induction of HSP70. In this work, we sought to determine the extent and duration of oxidative and energetic dysfunction as well as the role of effector kinases on metabolic function in preconditioned cells. Using an in vitro neuronal culture model, we observed a robust increase in Raf and p66(Shc) activation within 1 h of preconditioning. Total ATP content decreased by 25% 3 h after preconditioning but returned to baseline by 24 h. Use of a free radical spin trap or p66(shc) inhibitor increased ATP content whereas a Raf inhibitor had no effect. Phosphorylated p66(shc) rapidly relocalized to the mitochondria and in the absence of activated p66(shc), autophagic processing increased. The constitutively expressed chaperone HSC70 relocalized to autophagosomes. Preconditioned cells experience significant total oxidative stress measured by F(2)-isoprostanes and neuronal stress evaluated by F(4)-neuroprostane measurement. Neuroprostane levels were enhanced in the presence of Shc inhibitors. Finally, we found that inhibiting either p66(shc) or Raf blocked neuroprotection afforded by preconditioning as well as upregulation of HSP70, suggesting both kinases are critical for preconditioning but function in fundamentally different ways. This is the first work to demonstrate the essential role of p66(shc) in mediating requisite mitochondrial and energetic compensation after preconditioning and suggests a mechanism by which protein and organelle damage mediated by ROS can increase HSP70.

Compositional ripening of particle- and surfactant-stabilised emulsions: a comparison.

When beta-ionone-in-water emulsions are mixed with squalane-in-water emulsions, the slightly water-soluble, mobile beta-ionone undergoes mass transfer to the drops of highly water-insoluble, immobile oil squalane. We have investigated this compositional ripening process for emulsions stabilised either by particles or by surfactant molecules. For particle-stabilised emulsions, the swelling of the squalane-containing drops triggers droplet coalescence which causes the final swollen droplet radius to be proportional to the swelling ratio to the power of 1. Surfactant-stabilised emulsions swell without coalescence which causes the final droplet radius to be proportional to the swelling ratio to the power 1/3. Addition of excess, non-adsorbed particles to the particle-stabilised emulsions suppresses the swelling-triggered coalescence and causes a switchover from particle to surfactant behaviour.

Anisotropic nano-papier mache microcapsules.

We report the fabrication of anisotropic microcapsules produced by using alternating layers of nano-cotton fibres and oppositely charged polyelectrolytes over anisotropic inorganic templates with needle-like and rhombohedral morphology.

Coastal pollution hazards in southern California observed by SAR imagery: stormwater plumes, wastewater plumes, and natural hydrocarbon seeps.

Stormwater runoff plumes, municipal wastewater plumes, and natural hydrocarbon seeps are important pollution hazards for the heavily populated Southern California Bight (SCB). Due to their small size, dynamic and episodic nature, these hazards are difficult to sample adequately using traditional in situ oceanographic methods. Complex coastal circulation and persistent cloud cover can further complicate detection and monitoring of these hazards. We use imagery from space-borne synthetic aperture radar (SAR), complemented by field measurements, to examine these hazards in the SCB. The hazards are detectable in SAR imagery because they deposit surfactants on the sea surface, smoothing capillary and small gravity waves to produce areas of reduced backscatter compared with the surrounding ocean. We suggest that high-resolution SAR, which obtains useful data regardless of darkness or cloud cover, could be an important observational tool for assessment and monitoring of coastal marine pollution hazards in the SCB and other urbanized coastal regions.