ASU Scholarship Showcase

A structurally and compositionally well-defined and spectrally tunable artificial light-harvesting system has been constructed in which multiple organic dyes attached to a three-arm-DNA nanostructure serve as an antenna conjugated to a photosynthetic reaction center isolated from Rhodobacter sphaeroides 2.4.1. The light energy absorbed by the dye molecules is transferred to the reaction center, where charge separation takes place. The average number of DNA three-arm junctions per reaction center was tuned from 0.75 to 2.35. This DNA-templated multichromophore system serves as a modular light-harvesting antenna that is capable of being optimized for its spectral properties, energy transfer efficiency, and photostability, allowing one to adjust both the size and spectrum of the resulting structures. This may serve as a useful test bed for developing nanostructured photonic systems.

High-resolution, global quantification of fossil fuel CO[subscript 2] emissions is emerging as a critical need in carbon cycle science and climate policy. We build upon a previously developed fossil fuel data assimilation system (FFDAS) for estimating global high-resolution fossil fuel CO[subscript 2] emissions. We have improved the underlying observationally based data sources, expanded the approach through treatment of separate emitting sectors including a new pointwise database of global power plants, and extended the results to cover a 1997 to 2010 time series at a spatial resolution of 0.1°. Long-term trend analysis of the resulting global emissions shows subnational spatial structure in large active economies such as the United States, China, and India. These three countries, in particular, show different long-term trends and exploration of the trends in nighttime lights, and population reveal a decoupling of population and emissions at the subnational level. Analysis of shorter-term variations reveals the impact of the 2008–2009 global financial crisis with widespread negative emission anomalies across the U.S. and Europe. We have used a center of mass (CM) calculation as a compact metric to express the time evolution of spatial patterns in fossil fuel CO[subscript 2] emissions. The global emission CM has moved toward the east and somewhat south between 1997 and 2010, driven by the increase in emissions in China and South Asia over this time period. Analysis at the level of individual countries reveals per capita CO[subscript 2] emission migration in both Russia and India. The per capita emission CM holds potential as a way to succinctly analyze subnational shifts in carbon intensity over time. Uncertainties are generally lower than the previous version of FFDAS due mainly to an improved nightlight data set.

Time-resolved fluorescence spectroscopy was used to explore the pathway and kinetics of energy transfer in photosynthetic membrane vesicles (chromatophores) isolated from Rhodobacter (Rba.) sphaeroides cells harvested 2, 4, 6 or 24 hours after a transition from growth in high to low level illumination. As previously observed, this light intensity transition initiates the remodeling of the photosynthetic apparatus and an increase in the number of light harvesting 2 (LH2) complexes relative to light harvesting 1 (LH1) and reaction center (RC) complexes. It has generally been thought that the increase in LH2 complexes served the purpose of increasing the overall energy transmission to the RC. However, fluorescence lifetime measurements and analysis in terms of energy transfer within LH2 and between LH2 and LH1 indicate that, during the remodeling time period measured, only a portion of the additional LH2 generated are well connected to LH1 and the reaction center. The majority of the additional LH2 fluorescence decays with a lifetime comparable to that of free, unconnected LH2 complexes. The presence of large LH2-only domains has been observed by atomic force microscopy in Rba. sphaeroides chromatophores (Bahatyrova et al., Nature, 2004, 430, 1058), providing structural support for the existence of pools of partially connected LH2 complexes. These LH2-only domains represent the light-responsive antenna complement formed after a switch in growth conditions from high to low illumination, while the remaining LH2 complexes occupy membrane regions containing mixtures of LH2 and LH1–RC core complexes. The current study utilized a multi-parameter approach to explore the fluorescence spectroscopic properties related to the remodeling process, shedding light on the structure-function relationship of the photosynthetic assembles. Possible reasons for the accumulation of these largely disconnected LH2-only pools are discussed.

Background:
Ketogenic diets are high fat and low carbohydrate or very low carbohydrate diets, which render high production of ketones upon consumption known as nutritional ketosis (NK). Ketosis is also produced during fasting periods, which is known as fasting ketosis (FK). Recently, the combinations of NK and FK, as well as NK alone, have been used as resources for weight loss management and treatment of epilepsy.

Methods:
A crossover study design was applied to 11 healthy individuals, who maintained moderately sedentary lifestyle, and consumed three types of diet randomly assigned over a three-week period. All participants completed the diets in a randomized and counterbalanced fashion. Each weekly diet protocol included three phases: Phase 1 - A mixed diet with ratio of fat: (carbohydrate + protein) by mass of 0.18 or the equivalence of 29% energy from fat from Day 1 to Day 5. Phase 2- A mixed or a high-fat diet with ratio of fat: (carbohydrate + protein) by mass of approximately 0.18, 1.63, or 3.80 on Day 6 or the equivalence of 29%, 79%, or 90% energy from fat, respectively. Phase 3 - A fasting diet with no calorie intake on Day 7. Caloric intake from diets on Day 1 to Day 6 was equal to each individual’s energy expenditure. On Day 7, ketone buildup from FK was measured.

Results:
A statistically significant effect of Phase 2 (Day 6) diet was found on FK of Day 7, as indicated by repeated analysis of variance (ANOVA), F(2,20) = 6.73, p < 0.0058. Using a Fisher LDS pair-wise comparison, higher significant levels of acetone buildup were found for diets with 79% fat content and 90% fat content vs. 29% fat content (with p = 0.00159**, and 0.04435**, respectively), with no significant difference between diets with 79% fat content and 90% fat content. In addition, independent of the diet, a significantly higher ketone buildup capability of subjects with higher resting energy expenditure (R[superscript 2] = 0.92), and lower body mass index (R[superscript 2] = 0.71) was observed during FK.

Many drugs are effective in the early stage of treatment, but patients develop drug resistance after a certain period of treatment, causing failure of the therapy. An important example is Herceptin, a popular monoclonal antibody drug for breast cancer by specifically targeting human epidermal growth factor receptor 2 (Her2). Here we demonstrate a quantitative binding kinetics analysis of drug-target interactions to investigate the molecular scale origin of drug resistance. Using a surface plasmon resonance imaging, we measured the in situ Herceptin-Her2 binding kinetics in single intact cancer cells for the first time, and observed significantly weakened Herceptin-Her2 interactions in Herceptin-resistant cells, compared to those in Herceptin-sensitive cells. We further showed that the steric hindrance of Mucin-4, a membrane protein, was responsible for the altered drug-receptor binding. This effect of a third molecule on drug-receptor interactions cannot be studied using traditional purified protein methods, demonstrating the importance of the present intact cell-based binding kinetics analysis.

Large urban emissions of greenhouse gases result in large atmospheric enhancements relative to background that are easily measured. Using CO₂ mole fractions and Δ¹⁴C and δ¹³C values of CO₂ in the Los Angeles megacity observed in inland Pasadena (2006–2013) and coastal Palos Verdes peninsula (autumn 2009–2013), we have determined time series for CO₂ contributions from fossil fuel combustion (C_ff) for both sites and broken those down into contributions from petroleum and/or gasoline and natural gas burning for Pasadena. We find a 10 % reduction in Pasadena C_ff during the Great Recession of 2008–2010, which is consistent with the bottom-up inventory determined by the California Air Resources Board. The isotopic variations and total atmospheric CO₂ from our observations are used to infer seasonality of natural gas and petroleum combustion. The trend of CO₂ contributions to the atmosphere from natural gas combustion is out of phase with the seasonal cycle of total natural gas combustion seasonal patterns in bottom-up inventories but is consistent with the seasonality of natural gas usage by the area's electricity generating power plants. For petroleum, the inferred seasonality of CO₂ contributions from burning petroleum is delayed by several months relative to usage indicated by statewide gasoline taxes. Using the high-resolution Hestia-LA data product to compare C_ff from parts of the basin sampled by winds at different times of year, we find that variations in observed fossil fuel CO₂ reflect seasonal variations in wind direction. The seasonality of the local CO₂ excess from fossil fuel combustion along the coast, on Palos Verdes peninsula, is higher in autumn and winter than spring and summer, almost completely out of phase with that from Pasadena, also because of the annual variations of winds in the region. Variations in fossil fuel CO₂ signals are consistent with sampling the bottom-up Hestia-LA fossil CO₂ emissions product for sub-city source regions in the LA megacity domain when wind directions are considered.

Atmospheric CO₂ inversions estimate surface carbon fluxes from an optimal fit to atmospheric CO₂ measurements, usually including prior constraints on the flux estimates. Eleven sets of carbon flux estimates are compared, generated by different inversions systems that vary in their inversions methods, choice of atmospheric data, transport model and prior information. The inversions were run for at least 5 yr in the period between 1990 and 2010. Mean fluxes for 2001–2004, seasonal cycles, interannual variability and trends are compared for the tropics and northern and southern extra-tropics, and separately for land and ocean. Some continental/basin-scale subdivisions are also considered where the atmospheric network is denser. Four-year mean fluxes are reasonably consistent across inversions at global/latitudinal scale, with a large total (land plus ocean) carbon uptake in the north (−3.4 Pg C yr^-1 (±0.5 Pg C yr^-1 standard deviation), with slightly more uptake over land than over ocean), a significant although more variable source over the tropics (1.6 ± 0.9 Pg C yr^-1) and a compensatory sink of similar magnitude in the south (−1.4 ± 0.5 Pg C yr^-1) corresponding mainly to an ocean sink. Largest differences across inversions occur in the balance between tropical land sources and southern land sinks. Interannual variability (IAV) in carbon fluxes is larger for land than ocean regions (standard deviation around 1.06 versus 0.33 Pg C yr[superscript −1] for the 1996–2007 period), with much higher consistency among the inversions for the land. While the tropical land explains most of the IAV (standard deviation ~ 0.65 Pg C yr^-1), the northern and southern land also contribute (standard deviation ~ 0.39 Pg C yr^-1). Most inversions tend to indicate an increase of the northern land carbon uptake from late 1990s to 2008 (around 0.1 Pg C yr^-1, predominantly in North Asia. The mean seasonal cycle appears to be well constrained by the atmospheric data over the northern land (at the continental scale), but still highly dependent on the prior flux seasonality over the ocean. Finally we provide recommendations to interpret the regional fluxes, along with the uncertainty estimates.

This paper presents an analysis of methane emissions from the Los Angeles Basin at monthly timescales across a 4-year time period – from September 2011 to August 2015. Using observations acquired by a ground-based near-infrared remote sensing instrument on Mount Wilson, California, combined with atmospheric CH₄–CO₂ tracer–tracer correlations, we observed −18 to +22 % monthly variability in CH₄ : CO₂ from the annual mean in the Los Angeles Basin. Top-down estimates of methane emissions for the basin also exhibit significant monthly variability (−19 to +31 % from annual mean and a maximum month-to-month change of 47 %). During this period, methane emissions consistently peaked in the late summer/early fall and winter. The estimated annual methane emissions did not show a statistically significant trend over the 2011 to 2015 time period.

There are an increasing variety of applications in which peptides are both synthesized and used attached to solid surfaces. This has created a need for high throughput sequence analysis directly on surfaces. However, common sequencing approaches that can be adapted to surface bound peptides lack the throughput often needed in library-based applications. Here we describe a simple approach for sequence analysis directly on solid surfaces that is both high speed and high throughput, utilizing equipment available in most protein analysis facilities. In this approach, surface bound peptides, selectively labeled at their N-termini with a positive charge-bearing group, are subjected to controlled degradation in ammonia gas, resulting in a set of fragments differing by a single amino acid that remain spatially confined on the surface they were bound to. These fragments can then be analyzed by MALDI mass spectrometry, and the peptide sequences read directly from the resulting spectra.

Exposure to fine particles can cause various diseases, and an easily accessible method to monitor the particles can help raise public awareness and reduce harmful exposures. Here we report a method to estimate PM air pollution based on analysis of a large number of outdoor images available for Beijing, Shanghai (China) and Phoenix (US). Six image features were extracted from the images, which were used, together with other relevant data, such as the position of the sun, date, time, geographic information and weather conditions, to predict PM_2.5 index. The results demonstrate that the image analysis method provides good prediction of PM_2.5 indexes, and different features have different significance levels in the prediction.