We assess the detectability of city emissions via a tower-based greenhouse gas (GHG) network, as part of the Indianapolis Flux (INFLUX) experiment. By examining afternoon-averaged results from a network of carbon dioxide (CO₂), methane (CH₄), and carbon monoxide (CO) mole fraction measurements in Indianapolis, Indiana for 2011–2013, we quantify spatial and temporal patterns in urban atmospheric GHG dry mole fractions. The platform for these measurements is twelve communications towers spread across the metropolitan region, ranging in height from 39 to 136 m above ground level, and instrumented with cavity ring-down spectrometers. Nine of the sites were deployed as of January 2013 and data from these sites are the focus of this paper. A background site, chosen such that it is on the predominantly upwind side of the city, is utilized to quantify enhancements caused by urban emissions. Afternoon averaged mole fractions are studied because this is the time of day during which the height of the boundary layer is most steady in time and the area that influences the tower measurements is likely to be largest. Additionally, atmospheric transport models have better performance in simulating the daytime convective boundary layer compared to the nighttime boundary layer. Averaged from January through April of 2013, the mean urban dormant-season enhancements range from 0.3 ppm CO₂ at the site 24 km typically downwind of the edge of the city (Site 09) to 1.4 ppm at the site at the downwind edge of the city (Site 02) to 2.9 ppm at the downtown site (Site 03). When the wind is aligned such that the sites are downwind of the urban area, the enhancements are increased, to 1.6 ppm at Site 09, and 3.3 ppm at Site 02. Differences in sampling height affect the reported urban enhancement by up to 50%, but the overall spatial pattern remains similar. The time interval over which the afternoon data are averaged alters the calculated urban enhancement by an average of 0.4 ppm. The CO₂ observations are compared to CO₂ mole fractions simulated using a mesoscale atmospheric model and an emissions inventory for Indianapolis. The observed and modeled CO₂ enhancements are highly correlated (r² = 0.94), but the modeled enhancements prior to inversion average 53% of those measured at the towers. Following the inversion, the enhancements follow the observations closely, as expected. The CH₄ urban enhancement ranges from 5 ppb at the site 10 km predominantly downwind of the city (Site 13) to 21 ppb at the site near the landfill (Site 10), and for CO ranges from 6 ppb at the site 24 km downwind of the edge of the city (Site 09) to 29 ppb at the downtown site (Site 03). Overall, these observations show that a dense network of urban GHG measurements yield a detectable urban signal, well-suited as input to an urban inversion system given appropriate attention to sampling time, sampling altitude and quantification of background conditions.

The ‘Hestia Project’ uses a bottom-up approach to quantify fossil fuel CO₂(FFCO₂) emissions spatially at the building/street level and temporally at the hourly level. Hestia FFCO₂ emissions are provided in the form of a group of sector-specific vector layers with point, line, and polygon sources to support carbon cycle science and climate policy. Application to carbon cycle science, in particular, requires regular gridded data in order to link surface carbon fluxes to atmospheric transport models. However, the heterogeneity and complexity of FFCO₂ sources within regular grids is sensitive to spatial resolution. From the perspective of a data provider, we need to find a balance between resolution and data volume so that the gridded data product retains the maximum amount of information content while maintaining an efficient data volume.

The Shannon entropy determines the minimum bits that are needed to encode an information source and can serve as a metric for the effective information content. In this paper, we present an analysis of the Shannon entropy of gridded FFCO₂ emissions with varying resolutions in four Hestia study areas, and find: (1) the Shannon entropy increases with smaller grid resolution until it reaches a maximum value (the max-entropy resolution); (2) total emissions (the sum of several sector-specific emission fields) show a finer max-entropy resolution than each of the sector-specific fields; (3) the residential emissions show a finer max-entropy resolution than the commercial emissions; (4) the max-entropy resolution of the onroad emissions grid is closely correlated to the density of the road network. These findings suggest that the Shannon entropy can detect the information effectiveness of the spatial resolution of gridded FFCO₂ emissions. Hence, the resolution-entropy relationship can be used to assist in determining an appropriate spatial resolution for urban CO₂ flux studies. We conclude that the optimal spatial resolution for providing Hestia total FFCO₂ emissions products is centered around 100 m, at which the FFCO₂ emissions data can not only fully meet the requirement of urban flux integration, but also be effectively used in understanding the relationships between FFCO₂ emissions and various social-economic variables at the U.S. census block group level.

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.

Salmonella enterica serovar Typhimurium genome encodes 13 fimbrial operons. Most of the fimbriae encoded by these operons are not produced under laboratory conditions but are likely to be synthesized in vivo. We used an in vivo expression technology (IVET) strategy to identify four fimbrial operons, agf, saf, sti, and stc that are expressed in the spleen. When any three of these operons were deleted, the strain retained wild-type virulence. However, when all four operons were deleted, the resulting strain was completely attenuated, indicating that these four fimbriae play functionally redundant roles critical for virulence. In mice, oral doses of as low as 1 × 10[superscript 5] CFU of the strain with four fimbrial operons deleted provided 100% protection against challenge with 1 × 10[superscript 9] CFU of wild-type S. Typhimurium. We also examined the possible effect of these fimbriae on the ability of a Salmonella vaccine strain to deliver a guest antigen. We modified one of our established attenuated vaccine strains, χ9088, to delete three fimbrial operons while the fourth operon was constitutively expressed. Each derivative was modified to express the Streptococcus pneumoniae antigen PspA. Strains that constitutively expressed saf or stc elicited a strong Th1 response with significantly greater levels of anti-PspA serum IgG and greater protective efficacy than strains carrying saf or stc deletions. The isogenic strain in which all four operons were deleted generated the lowest anti-PspA levels and did not protect against challenge with virulent S. pneumoniae. Our results indicate that these fimbriae play important roles, as yet not understood, in Salmonella virulence and immunogenicity.

Several Zika virus (ZIKV) vaccine candidates have recently been described which use inactivated whole virus, DNA or RNA that express the virus’ Envelope (E) glycoprotein as the antigen. These were successful in stimulating production of virus-targeted antibodies that protected animals against ZIKV challenges, but their use potentially will predispose vaccinated individuals to infection by the related Dengue virus (DENV). We have devised a virus like particle (VLP) carrier based on the hepatitis B core antigen (HBcAg) that displays the ZIKV E protein domain III (zDIII), and shown that it can be produced quickly and easily purified in large quantities from Nicotiana benthamiana plants. HBcAg-zDIII VLPs are shown to be highly immunogenic, as two doses elicited potent humoral and cellular responses in mice that exceed the threshold correlated with protective immunity against multiple strains of Zika virus. Notably, HBcAg-zDIII VLPs-elicited antibodies did not enhance the infection of DENV in Fc gamma receptor-expressing cells, offsetting the concern of ZIKV vaccines inducing cross-reactive antibodies and sensitizing people to subsequent DENV infection. Thus, our zDIII-based vaccine offers improved safety and lower cost production than other current alternatives, with equivalent effectiveness.

Quantifying greenhouse gas (GHG) emissions from cities is a key challenge towards effective emissions management. An inversion analysis from the INdianapolis FLUX experiment (INFLUX) project, as the first of its kind, has achieved a top-down emission estimate for a single city using CO₂ data collected by the dense tower network deployed across the city. However, city-level emission data, used as a priori emissions, are also a key component in the atmospheric inversion framework. Currently, fine-grained emission inventories (EIs) able to resolve GHG city emissions at high spatial resolution, are only available for few major cities across the globe. Following the INFLUX inversion case with a global 1.1 km ODIAC fossil fuel CO₂ emission dataset, we further improved the ODIAC emission field and examined its utility as a prior for the city scale inversion. We disaggregated the 1.1 km ODIAC non-point source emissions using geospatial datasets such as the global road network data and satellite-data driven surface imperviousness data to a 30 . 30 m resolution. We assessed the impact of the improved emission field on the inversion result, relative to priors in previous studies (Hestia and ODIAC). The posterior total emission estimate (5.1 MtC/yr) remains statistically similar to the previous estimate with ODIAC (5.3 MtC/yr). However, the distribution of the flux corrections was very close to those of Hestia inversion and the model-observation mismatches were significantly reduced both in forward and inverse runs, even without hourly temporal changes in emissions. EIs reported by cities often do not have estimates of spatial extents. Thus, emission disaggregation is a required step when verifying those reported emissions using atmospheric models. Our approach offers gridded emission estimates for global cities that could serves as a prior for inversion, even without locally reported EIs in a systematic way to support city-level Measuring, Reporting and Verification (MRV) practice implementation.

Low fluid shear force, including that encountered in microgravity models, induces bacterial responses, but the range of bacteria capable of responding to this signal remains poorly characterized. We systematically analyzed a range of Gram negative Enterobacteriaceae for conservation of the low-shear modeled microgravity (LSMMG) response using phenotypic assays, qPCR, and targeted mutations. Our results indicate LSMMG response conservation across Enterobacteriacae with potential variance in up- or down-regulation of a given response depending on genus. Based on the data, we analyzed the role of the trp operon genes and the TrpR regulator in the LSMMG response using targeted mutations in these genes in S. Typhimurium and E. coli. We found no alteration of the LSMMG response compared to WT in these mutant strains under the conditions tested here. To our knowledge, this study is first-of-kind for Citrobacter, Enterobacter, and Serratia, presents novel data for Escherichia, and provides the first analysis of trp genes in LSMMG responses. This impacts our understanding of how LSMMG affects bacteria and our ability to modify bacteria with this condition in the future.

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.

We previously reported a recombinant protein production system based on a geminivirus replicon that yields high levels of vaccine antigens and monoclonal antibodies in plants. The bean yellow dwarf virus (BeYDV) replicon generates massive amounts of DNA copies, which engage the plant transcription machinery. However, we noticed a disparity between transcript level and protein production, suggesting that mRNAs could be more efficiently utilized. In this study, we systematically evaluated genetic elements from human, viral, and plant sources for their potential to improve the BeYDV system. The tobacco extensin terminator enhanced transcript accumulation and protein production compared to other commonly used terminators, indicating that efficient transcript processing plays an important role in recombinant protein production.

Evaluation of human-derived 5′ untranslated regions (UTRs) indicated that many provided high levels of protein production, supporting their cross-kingdom function. Among the viral 5′ UTRs tested, we found the greatest enhancement with the tobacco mosaic virus omega leader. An analysis of the 5′ UTRs from the Arabidopsis thaliana and Nicotinana benthamiana photosystem I K genes found that they were highly active when truncated to include only the near upstream region, providing a dramatic enhancement of transgene production that exceeded that of the tobacco mosaic virus omega leader. The tobacco Rb7 matrix attachment region inserted downstream from the gene of interest provided significant enhancement, which was correlated with a reduction in plant cell death. Evaluation of Agrobacterium strains found that EHA105 enhanced protein production and reduced cell death compared to LBA4301 and GV3101. We used these improvements to produce Norwalk virus capsid protein at >20% total soluble protein, corresponding to 1.8 mg/g leaf fresh weight, more than twice the highest level ever reported in a plant system. We also produced the monoclonal antibody rituximab at 1 mg/g leaf fresh weight.

The botanical, Astragalus membranaceus, is a therapeutic in traditional Chinese medicine. Limited literature exists on the overall in vivo effects of A. membranaceus on the human body. This study evaluates the physiological responses to A. membranaceus by measuring leukocyte, platelet, and cytokine responses as well as body temperature and blood pressure in healthy individuals after the in vivo administration of A. membranaceus. A dose-dependent increase in monocytes, neutrophils, and lymphocytes was measured 8–12 hours after administration and an increase in the number of circulating platelets was seen as early as 4 hours. A dynamic change in the levels of circulating cytokines was observed, especially in interferon-γ and tumor necrosis factor-α, IL-13, IL-6, and soluble IL-2R. Subjective symptoms reported by participants were similar to those typically experienced in viral type immune responses and included fatigue, malaise, and headache. Systolic and diastolic blood pressure were reduced within 4 hours after administration, while body temperature mildly increased within 8 hours after administration. In general, all responses returned to baseline values by 24 hours. Collectively, these results support the role of A. membranaceus in priming for a potential immune response as well as its effect on blood flow and wound healing.