Biochemical Conversions of Lignocellulosic Biomass for Sustainable Fuel-Ethanol Production in the Upper Midwest

Biofuels are an increasingly important component of worldwide energy supply. This research aims to understand the pathways and impacts of biofuels production, and to improve these processes to make them more efficient. In Chapter 2, a life cycle assessment (LCA) is presented for cellulosic ethanol production from five potential feedstocks of regional importance to the upper Midwest - hybrid poplar, hybrid willow, switchgrass, diverse prairie grasses, and logging residues - according to the requirements of Renewable Fuel Standard (RFS). Direct land use change emissions are included for the conversion of abandoned agricultural land to feedstock production, and computer models of the conversion process are used in order to determine the effect of varying biomass composition on overall life cycle impacts. All scenarios analyzed here result in greater than 60% reduction in greenhouse gas emissions relative to petroleum gasoline. Land use change effects were found to contribute significantly to the overall emissions for the first 20 years after plantation establishment. Chapter 3 is an investigation of the effects of biomass mixtures on overall sugar recovery from the combined processes of dilute acid pretreatment and enzymatic hydrolysis. Biomass mixtures studied were aspen, a hardwood species well suited to biochemical processing; balsam, a high-lignin softwood species, and switchgrass, an herbaceous energy crop with high ash content. A matrix of three different dilute acid pretreatment severities and three different enzyme loading levels was used to characterize interactions between pretreatment and enzymatic hydrolysis. Maximum glucose yield for any species was 70% oftheoretical for switchgrass, and maximum xylose yield was 99.7% of theoretical for aspen. Supplemental β-glucosidase increased glucose yield from enzymatic hydrolysis by an average of 15%, and total sugar recoveries for mixtures could be predicted to within 4% by linear interpolation of the pure species results. Chapter 4 is an evaluation of the potential for producing Trichoderma reesei cellulose hydrolases in the Kluyveromyces lactis yeast expression system. The exoglucanases Cel6A and Cel7A, and the endoglucanase Cel7B were inserted separately into the K. lactis and the enzymes were analyzed for activity on various substrates. Recombinant Cel7B was found to be active on carboxymethyl cellulose and Avicel powdered cellulose substrates. Recombinant Cel6A was also found to be active on Avicel. Recombinant Cel7A was produced, but no enzymatic activity was detected on any substrate. Chapter 5 presents a new method for enzyme improvement studies using enzyme co-expression and yeast growth rate measurements as a potential high-throughput expression and screening system in K. lactis yeast. Two different K. lactis strains were evaluated for their usefulness in growth screening studies, one wild-type strain and one strain which has had the main galactose metabolic pathway disabled. Sequential transformation and co-expression of the exoglucanase Cel6A and endoglucanase Cel7B was performed, and improved hydrolysis rates on Avicel were detectable in the cell culture supernatant. Future work should focus on hydrolysis of natural substrates, developing the growth screening method, and utilizing the K. lactis expression system for directed evolution of enzymes

Evaluation of azlocillin in-vitro and in discriminative animal models of infection

Azlocillin was more active in vitro than ticarcillin or carbenicillin against 561 aminoglycoside-resistant strains of Pseudomonas aeruginosa collected from 74 hospitals distributed over a wide geographic area in the eastern United States. Azlocillin was compared with various other antimicrobial agents in discriminative animal models of Ps. aeruginosa pyelonephritis, osteomyelitis, endocarditis, and meningitis in a variety of mammalian species. Cefsulodin was more effective than azlocillin in reducing Ps. aeruginosa kidney concentrations in rat pyelonephritis induced by intrarenal inoculation. The mean±s.d. logl0 cfu/g kidney after three days of therapy were as follows: controls = 5.4±1.5, azlocillin = 4.4±1.8, cefsulodin = 2.6±0.9 (P < 0.01) but the MBC for the test strain was eight-fold higher for azlocillin (8 vs. 1 mg/l) and effective concentrations were maintained longer in rat serum for cefsulodin as against azlocillin. In addition, ticarcillin reduced kidney bacterial concentrations faster than azlocillin in a mouse pyelonephritis model induced by intravenous Ps. aeruginosa inoculation with subsequent iron loading. Azlocillin was less effective than tobramycin in experimental chronic Ps. aeruginosa osteomyelitis induced in rabbits by direct injection into the tibia. An azlocillin-tobramycin regimen was not more effective than tobramycin alone. After 28 days of therapy, the percentages of positive bone cultures after death were as follows: no antibiotic (controls) = 92%, azlocillin = 95%, tobramycin = 76%, azlocillin plus tobramycin = 60%. Both ticarcillin and azlocillin were less active than tobramycin in experimental Ps. aeruginosa endocarditis induced in rabbits by intravenous inoculation of 108 cfu following 1 h of catheter induced aortic valve trauma. The best results were noted with an azlocillin-tobramycin regimen. The mean±s.d. log10 cfu Ps. aeruginosa/g vegetation after five days of therapy were as follows: no antibiotic controls = 8.1 ± 1.1, tobramycin = 4.5 ±0.8, ticarcillin = 6.9 ± 0.8, azlocillin = 5.7 ± 1.5, ticarcillin phis tobramycin = 4.9 ± 1.0, azlocillin plus tobramycin = 3.3 ± 1.6. Sterile vegetations were rarely attained with any regimen. The mean percentage penetration into purulent cerebrospinal fluid (CSF) in experimental Ps. aeruginosa meningitis for azlocillin was 13.3%, comparable to many other β-lactam antibiotics. Azlocillin was the single most active (P < 0.01) agent evaluated after 8 h intravenous infusions in this model. An azlocillin-amikacin regimen was more rapidly bactericidal (P < 0.01) than either agent alone in vivo. None of the agents evaluated alone or in combination, however, produced a sterile CSF after 8 h of therapy in any anima

Analysis of Energy Flow in US GLOBEC Ecosystems Using End-to-End Models

End-to-end models were constructed to examine and compare the trophic structure and energy flow in coastal shelf ecosystems of four US Global Ocean Ecosystem Dynamics (GLOBEC) study regions: the Northern California Current, the Central Gulf of Alaska, Georges Bank, and the Southwestern Antarctic Peninsula. High-quality data collected on system components and processes over the life of the program were used as input to the models. Although the US GLOBEC program was species-centric, focused on the study of a selected set of target species of ecological or economic importance, we took a broader community-level approach to describe end-to-end energy flow, from nutrient input to fishery production. We built four end-to-end models that were structured similarly in terms of functional group composition and time scale. The models were used to identify the mid-trophic level groups that place the greatest demand on lower trophic level production while providing the greatest support to higher trophic level production. In general, euphausiids and planktivorous forage fishes were the critical energy-transfer nodes; however, some differences between ecosystems are apparent. For example, squid provide an important alternative energy pathway to forage fish, moderating the effects of changes to forage fish abundance in scenario analyses in the Central Gulf of Alaska. In the Northern California Current, large scyphozoan jellyfish are important consumers of plankton production, but can divert energy from the rest of the food web when abundant

Seasonal food web models for the Oregon inner-shelf ecosystem : investigating the role of large jellyfish

Previously published in California Cooperative Oceanic Fisheries Investigations Progress Report, 2007, Vol.48; access courtesy of publisher and authors.We developed two seasonal food-web models, spring and summer, within the Ecopath framework for the Oregon upwelling ecosystem to investigate the role of large jellyfish as competitors for zooplankton prey. We used information about fish and jellyfish biomass, distribution, and diet derived from pelagic trawl survey data. Information about lower trophic-level production was acquired from zooplankton survey data. The models indicate that in spring, jellyfish are a modest consumer of zooplankton, and forage fishes dominate the system in terms of biomass and consumption. By late summer, jellyfish become the major zooplankton consumers, and they consume 17% of the summer zooplankton production while forage fish consume 9%. Jellyfish appear to divert zooplankton production away from upper trophic levels. Only 2% of the energy consumed by jellyfish is passed to higher trophic levels. However, the role of jellyfish as competitors may be moderate; a large proportion of zooplankton production (40%–44%) is not consumed but lost to detritus.Keywords: food-web models, Jellyfis

Unclear associations between small pelagic fish and jellyfish in several major marine ecosystems

During the last 20 years, a series of studies has suggested trends of increasing jellyfish (Cnidaria and Ctenophora) biomass in several major ecosystems worldwide. Some of these systems have been heavily fished, causing a decline among their historically dominant small pelagic fish stocks, or have experienced environmental shifts favouring jellyfish proliferation. Apparent reduction in fish abundance alongside increasing jellyfish abundance has led to hypotheses suggesting that jellyfish in these areas could be replacing small planktivorous fish through resource competition and/or through predation on early life stages of fish. In this study, we test these hypotheses using extended and published data of jellyfish, small pelagic fish and crustacean zooplankton biomass from four major ecosystems within the period of 1960 to 2014: the Southeastern Bering Sea, the Black Sea, the Northern California Current and the Northern Benguela. Except for a negative association between jellyfish and crustacean zooplankton in the Black Sea, we found no evidence of jellyfish biomass being related to the biomass of small pelagic fish nor to a common crustacean zooplankton resource. Calculations of the energy requirements of small pelagic fish and jellyfish stocks in the most recent years suggest that fish predation on crustacean zooplankton is 2–30 times higher than jellyfish predation, depending on ecosystem. However, compared with available historical data in the Southeastern Bering Sea and the Black Sea, it is evident that jellyfish have increased their share of the common resource, and that jellyfish can account for up to 30% of the combined fish-jellyfish energy consumption. We conclude that the best available time-series data do not suggest that jellyfish are outcompeting, or have replaced, small pelagic fish on a regional scale in any of the four investigated ecosystems. However, further clarification of the role of jellyfish requires higher-resolution spatial, temporal and taxonomic sampling of the pelagic community.publishedVersio

Evidence that summer jellyfish blooms impact Pacific Northwest salmon production

Interannual variability in salmon (Oncorhynchus spp.) production in the northeast Pacific is understood to be driven by oceanographic variability and bottom-up processes affecting prey availability to juvenile salmon. Scyphozoan jellyfish have an important role in shaping the pathways of energy flow through pelagic food webs. While jellyfish obtain high production rates and biomasses as major consumers of zooplankton production, they have few predators and may divert plankton production away from higher trophic levels. Although jellyfish are planktivorous and juvenile coho (O. kisutch) and Chinook (O. tshawytscha) salmon are mainly piscivorous, they may be indirect competitors for plankton production. Ecosystem model simulations suggested that among all trophic interactions within the Pacific Northwest coastal food web, juvenile salmon are particularly sensitive to jellyfish blooms, and that salmon production will be suppressed in years of high summer jellyfish biomass. Pelagic surveys off Oregon and Washington (1999–2012) were used to examine the interannual relationship between salmon production and the dominant jellyfish species, the sea nettle Chrysaora fuscescens, off the Pacific Northwest coast. There was a significant, negative correlation between sea nettle biomass and the strength of adult coho and Chinook salmon returns to the Columbia River. Examination of spatial distributions across years showed a positive association between sea nettles and salmon. Within individual years, significant differences between the distribution of sea nettles and yearling coho and Chinook salmon generally occurred during cooler ocean summers, perhaps due to the greater expanse of optimal salmon habitat resulting from more upwelling. Whether the association is behavioral or a product of oceanographic processes, association enhances the opportunity for indirect competition. Examination of feeding incidence in September showed that salmon stomachs were less full at locations with higher sea nettle biomass

Jellyfish, Forage Fish, and the World\u27s Major Fisheries

A majority of the world’s largest net-based fisheries target planktivorous forage fish that serve as a critical trophic link between the plankton and upper-level consumers such as large predatory fishes, seabirds, and marine mammals. Because the plankton production that drives forage fish also drives jellyfish production, these taxa often overlap in space, time, and diet in coastal ecosystems. This overlap likely leads to predatory and competitive interactions, as jellyfish are effective predators of fish early life stages and zooplankton. The trophic interplay between these groups is made more complex by the harvest of forage fish, which presumably releases jellyfish from competition and is hypothesized to lead to an increase in their production. To understand the role forage fish and jellyfish play as alternate energy transfer pathways in coastal ecosystems, we explore how functional group productivity is altered in three oceanographically distinct ecosystems when jellyfish are abundant and when fish harvest rates are reduced using ecosystem modeling. We propose that ecosystem-based fishery management approaches to forage fish stocks include the use of jellyfish as an independent, empirical “ecosystem health” indicator

Jellyfish, Forage Fish, and the World\u27s Major Fisheries

A majority of the world’s largest net-based fisheries target planktivorous forage fish that serve as a critical trophic link between the plankton and upper-level consumers such as large predatory fishes, seabirds, and marine mammals. Because the plankton production that drives forage fish also drives jellyfish production, these taxa often overlap in space, time, and diet in coastal ecosystems. This overlap likely leads to predatory and competitive interactions, as jellyfish are effective predators of fish early life stages and zooplankton. The trophic interplay between these groups is made more complex by the harvest of forage fish, which presumably releases jellyfish from competition and is hypothesized to lead to an increase in their production. To understand the role forage fish and jellyfish play as alternate energy transfer pathways in coastal ecosystems, we explore how functional group productivity is altered in three oceanographically distinct ecosystems when jellyfish are abundant and when fish harvest rates are reduced using ecosystem modeling. We propose that ecosystem-based fishery management approaches to forage fish stocks include the use of jellyfish as an independent, empirical “ecosystem health” indicator

Impaired DNA replication within progenitor cell pools promotes leukemogenesis.

Impaired cell cycle progression can be paradoxically associated with increased rates of malignancies. Using retroviral transduction of bone marrow progenitors followed by transplantation into mice, we demonstrate that inhibition of hematopoietic progenitor cell proliferation impairs competition, promoting the expansion of progenitors that acquire oncogenic mutations which restore cell cycle progression. Conditions that impair DNA replication dramatically enhance the proliferative advantage provided by the expression of Bcr-Abl or mutant p53, which provide no apparent competitive advantage under conditions of healthy replication. Furthermore, for the Bcr-Abl oncogene the competitive advantage in contexts of impaired DNA replication dramatically increases leukemogenesis. Impaired replication within hematopoietic progenitor cell pools can select for oncogenic events and thereby promote leukemia, demonstrating the importance of replicative competence in the prevention of tumorigenesis. The demonstration that replication-impaired, poorly competitive progenitor cell pools can promote tumorigenesis provides a new rationale for links between tumorigenesis and common human conditions of impaired DNA replication such as dietary folate deficiency, chemotherapeutics targeting dNTP synthesis, and polymorphisms in genes important for DNA metabolism

Jellyfish Support High Energy Intake of Leatherback Sea Turtles (Dermochelys coriacea): Video Evidence from Animal-Borne Cameras

The endangered leatherback turtle is a large, highly migratory marine predator that inexplicably relies upon a diet of low-energy gelatinous zooplankton. The location of these prey may be predictable at large oceanographic scales, given that leatherback turtles perform long distance migrations (1000s of km) from nesting beaches to high latitude foraging grounds. However, little is known about the profitability of this migration and foraging strategy. We used GPS location data and video from animal-borne cameras to examine how prey characteristics (i.e., prey size, prey type, prey encounter rate) correlate with the daytime foraging behavior of leatherbacks (n = 19) in shelf waters off Cape Breton Island, NS, Canada, during August and September. Video was recorded continuously, averaged 1:53 h per turtle (range 0:08–3:38 h), and documented a total of 601 prey captures. Lion's mane jellyfish (Cyanea capillata) was the dominant prey (83–100%), but moon jellyfish (Aurelia aurita) were also consumed. Turtles approached and attacked most jellyfish within the camera's field of view and appeared to consume prey completely. There was no significant relationship between encounter rate and dive duration (p = 0.74, linear mixed-effects models). Handling time increased with prey size regardless of prey species (p = 0.0001). Estimates of energy intake averaged 66,018 kJ•d−1 but were as high as 167,797 kJ•d−1 corresponding to turtles consuming an average of 330 kg wet mass•d−1 (up to 840 kg•d−1) or approximately 261 (up to 664) jellyfish•d-1. Assuming our turtles averaged 455 kg body mass, they consumed an average of 73% of their body mass•d−1 equating to an average energy intake of 3–7 times their daily metabolic requirements, depending on estimates used. This study provides evidence that feeding tactics used by leatherbacks in Atlantic Canadian waters are highly profitable and our results are consistent with estimates of mass gain prior to southward migration