Changes in the genetic requirements for microbial interactions with increasing community complexity.

Microbial community structure and function rely on complex interactions whose underlying molecular mechanisms are poorly understood. To investigate these interactions in a simple microbiome, we introduced E. coli into an experimental community based on a cheese rind and identified the differences in E. coli's genetic requirements for growth in interactive and non-interactive contexts using Random Barcode Transposon Sequencing (RB-TnSeq) and RNASeq. Genetic requirements varied among pairwise growth conditions and between pairwise and community conditions. Our analysis points to mechanisms by which growth conditions change as a result of increasing community complexity and suggests that growth within a community relies on a combination of pairwise and higher-order interactions. Our work provides a framework for using the model organism E. coli as a readout to investigate microbial interactions regardless of the genetic tractability of members of the studied ecosystem

Why People Are Not Willing to Let Their Children Ride in Driverless School Buses: A Gender and Nationality Comparison

As driverless vehicles proliferate, it is possible that this technology will be applied in mass transport vehicles. School buses may be suited for autonomous operations as they follow set routes and schedules. However, a research gap exists in whether or not parents would be willing to have their children ride in autonomously operated school buses. The purpose of this study was to examine parents’ willingness to allow their child to ride in an autonomous school bus. Participant gender and nationality were also two independent variables, along with affect measures as a possible mediating variable. The research used a two-study approach. In study one, it was found that participants were less willing to have their child ride in a driverless school bus than a traditional human-operated vehicle. In study two, findings suggest a significant interaction between the type of driver, participant gender, and nationality. In general, American females were less willing than Indian females and overall, Americans were less willing than Indians in the driverless conditions. Affect was found to be a mediating variable, which suggests that emotions were playing a role in the responses of participants. The paper concludes with theoretical contributions, practical applications, and suggestions for future research

Combining geometric morphometrics and finite element analysis with evolutionary modeling:towards a synthesis

<p>Geometric morphometrics (GM) and finite element analysis (FEA) are increasingly common techniques for the study of form and function. We show how principles of quantitative evolution in continuous phenotypic traits can link the two techniques, allowing hypotheses about the relative importance of different functions to be tested in a phylogenetic and evolutionary framework. Finite element analysis is used to derive quantitative surfaces that describe the comparative performance of different morphologies in a morphospace derived from GM. The combination of two or more performance surfaces describes a quantitative adaptive landscape that can be used to predict the direction morphological evolution would take if a combination of functions was selected for. Predicted paths of evolution also can be derived for hypotheses about the relative importance of multiple functions, which can be tested against evolutionary pathways that are documented by phylogenies or fossil sequences. Magnitudes of evolutionary trade-offs between functions can be estimated using maximum likelihood. We apply these methods to an earlier study of carapace strength and hydrodynamic efficiency in emydid turtles. We find that strength and hydrodynamic efficiency explain about 45% of the variance in shell shape; drift and other unidentified functional factors are necessary to explain the remaining variance. Measurement of the proportional trade-off between shell strength and hydrodynamic efficiency shows that throughout the Cenozoic aquatic turtles generally sacrificed strength for streamlining and terrestrial species favored stronger shells; this suggests that the selective regime operating on small to mid-sized emydids has remained relatively static.</p> <p>SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at <a href="http://www.tandfonline.com/UJVP" target="_blank">www.tandfonline.com/UJVP</a></p> <p>Citation for this article: Polly, P. D., C. T. Stayton, E. R. Dumont, S. E. Pierce, E. J. Rayfield, and K. D. Angielczyk. 2016. Combining geometric morphometrics and finite element analysis with evolutionary modeling: towards a synthesis. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1111225.</p

Constraining emissions of volatile organic compounds from western US wildfires with WE-CAN and FIREX-AQ airborne observations

The impact of biomass burning (BB) on the atmospheric burden of volatile organic compounds (VOCs) is highly uncertain. Here we apply the GEOS-Chem chemical transport model (CTM) to constrain BB emissions in the western US at ~25 km resolution. Across three BB emission inventories widely used in CTMs, the total of 14 modeled BB VOC emissions in the western US agree with each other within 30&ndash;40 %. However, emissions for individual VOC differ by up to a factor of 5 (i.e., lumped &ge; C4 alkanes), driven by the regionally averaged emission ratios (ERs) among inventories. We further evaluate GEOS-Chem simulations with aircraft observations made during WE-CAN (Western Wildfire Experiment for Cloud Chemistry, Aerosol Absorption, and Nitrogen) and FIREX-AQ (Fire Influence on Regional to Global Environments and Air Quality) field campaigns. Despite being driven by different global BB inventories or applying various injection height assumptions, GEOS-Chem simulations underpredict observed vertical profiles by a factor of 3&ndash;7. The model shows small-to-no bias for most species in low/no smoke conditions. We thus attribute the negative model biases mostly to underestimated BB emissions in these inventories. Tripling BB emissions in the model reproduces observed vertical profiles for primary compounds, i.e., CO, propane, benzene, and toluene. However, it shows no-to-less significant improvements for oxygenated VOCs, particularly formaldehyde, formic acid, acetic acid, and lumped &ge; C3 aldehydes, suggesting the model is missing secondary sources of these compounds in BB-impacted environments. The underestimation of primary BB emissions in inventories is likely attributable to underpredicted amounts of effective dry matter burned, rather than errors in fire detection, injection height, or ERs. We cannot rule out potential sub-grid uncertainties (i.e., not being able to fully resolve fire plumes) in the nested GEOS-Chem which could explain the model negative bias partially, though the back-of-the-envelope calculation and evaluation using longer-term ground measurements help increase the argument of the dry matter burned underestimation. The ERs of the 14 BB VOCs implemented in GEOS-Chem account for about half of the total 161 measured VOCs (~75 versus 150 ppb ppm-1). This reveals a significant amount of missing reactive organic carbon in widely-used BB emission inventories. Considering both uncertainties in effective dry matter burned and unmodeled VOCs, we infer that BB contributed up to 10 % in 2019 and 45 % in 2018 (240 and 2040 GgC) of the total VOC primary emission flux in the western US during these two fire seasons, compared to only 1&ndash;10 % in the standard GEOS-Chem.</p

Interim Report: Uranium Stabilization Through Polyphosphate Injection - 300 Area Uranium Plume Treatability Demonstration Project

This report presents results from bench-scale treatability studies conducted under site-specific conditions to optimize the polyphosphate amendment for implementation of a field-scale technology demonstration to treat aqueous uranium within the 300 Area aquifer of the Hanford site. The general treatability testing approach consists of conducting studies with site sediment and under site conditions, in order to develop an effective chemical formulation for the polyphosphate amendments and evaluate the transport properties of these amendments under site conditions. Phosphorus-31 (31P) NMR was utilized to determine the effects of Hanford groundwater and sediment on the degradation of inorganic phosphates. Static batch tests were conducted to optimize the composition of the polyphosphate formulation for the precipitation of apatite and autunite, as well as to quantify the kinetics, loading and stability of apatite as a long-term sorbent for uranium. Dynamic column tests were used to further optimize the polyphosphate formulation for emplacement within the subsurface and the formation of autunite and apatite. In addition, dynamic testing quantified the stability of autunite and apatite under relevant site conditions. Results of this investigation provide valuable information for designing a full-scale remediation of uranium in the 300 aquifer

Challenges in quantifying changes in the global water cycle

Human influences have likely already impacted the large-scale water cycle but natural variability and observational uncertainty are substantial. It is essential to maintain and improve observational capabilities to better characterize changes. Understanding observed changes to the global water cycle is key to predicting future climate changes and their impacts. While many datasets document crucial variables such as precipitation, ocean salinity, runoff, and humidity, most are uncertain for determining long-term changes. In situ networks provide long time-series over land but are sparse in many regions, particularly the tropics. Satellite and reanalysis datasets provide global coverage, but their long-term stability is lacking. However, comparisons of changes among related variables can give insights into the robustness of observed changes. For example, ocean salinity, interpreted with an understanding of ocean processes, can help cross-validate precipitation. Observational evidence for human influences on the water cycle is emerging, but uncertainties resulting from internal variability and observational errors are too large to determine whether the observed and simulated changes are consistent. Improvements to the in situ and satellite observing networks that monitor the changing water cycle are required, yet continued data coverage is threatened by funding reductions. Uncertainty both in the role of anthropogenic aerosols, and due to large climate variability presently limits confidence in attribution of observed changes

NMNAT1 Mutations Cause Leber Congenital Amaurosis

Leber congenital amaurosis (LCA) is an infantile-onset form of inherited retinal degeneration characterized by severe vision loss. Two-thirds of LCA cases are caused by mutations in 17 known disease genes (RetNet Retinal Information Network). Using exome sequencing, we identified a homozygous missense mutation (c.25G>A, p.Val9Met) in NMNAT1 as likely disease-causing in two siblings of a consanguineous Pakistani kindred affected by LCA. This mutation segregated with disease in their kindred, including in three other children with LCA. NMNAT1 resides in the previously identified LCA9 locus and encodes the nuclear isoform of nicotinamide mononucleotide adenylyltransferase, a rate-limiting enzyme in nicotinamide adenine dinucleotide $(NAD^+)$ biosynthesis. Functional studies showed the p.Val9Met mutation decreased NMNAT1 enzyme activity. Sequencing NMNAT1 in 284 unrelated LCA families identified 14 rare mutations in 13 additional affected individuals. These results are the first to link an NMNAT isoform to disease and indicate that NMNAT1 mutations cause LCA

Serial monitoring of genomic alterations in circulating tumor cells of ER-positive/HER2-negative advanced breast cancer: feasibility of precision oncology biomarker detection.

Nearly all estrogen receptor (ER)-positive (POS) metastatic breast cancers become refractory to endocrine (ET) and other therapies, leading to lethal disease presumably due to evolving genomic alterations. Timely monitoring of the molecular events associated with response/progression by serial tissue biopsies is logistically difficult. Use of liquid biopsies, including circulating tumor cells (CTC) and circulating tumor DNA (ctDNA), might provide highly informative, yet easily obtainable, evidence for better precision oncology care. Although ctDNA profiling has been well investigated, the CTC precision oncology genomic landscape and the advantages it may offer over ctDNA in ER-POS breast cancer remain largely unexplored. Whole-blood (WB) specimens were collected at serial time points from patients with advanced ER-POS/HER2-negative (NEG) advanced breast cancer in a phase I trial of AZD9496, an oral selective ER degrader (SERD) ET. Individual CTC were isolated from WB using tandem CellSearch® /DEPArray™ technologies and genomically profiled by targeted single-cell DNA next-generation sequencing (scNGS). High-quality CTC (n = 123) from 12 patients profiled by scNGS showed 100% concordance with ctDNA detection of driver estrogen receptor α (ESR1) mutations. We developed a novel CTC-based framework for precision medicine actionability reporting (MI-CTCseq) that incorporates novel features, such as clonal predominance and zygosity of targetable alterations, both unambiguously identifiable in CTC compared to ctDNA. Thus, we nominated opportunities for targeted therapies in 73% of patients, directed at alterations in phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), fibroblast growth factor receptor 2 (FGFR2), and KIT proto-oncogene, receptor tyrosine kinase (KIT). Intrapatient, inter-CTC genomic heterogeneity was observed, at times between time points, in subclonal alterations. Our analysis suggests that serial monitoring of the CTC genome is feasible and should enable real-time tracking of tumor evolution during progression, permitting more combination precision medicine interventions

How does the tobacco industry attempt to influence marketing regulations? A systematic review

BACKGROUND: The Framework Convention on Tobacco Control makes a number of recommendations aimed at restricting the marketing of tobacco products. Tobacco industry political activity has been identified as an obstacle to Parties' development and implementation of these provisions. This study systematically reviews the existing literature on tobacco industry efforts to influence marketing regulations and develops taxonomies of 1) industry strategies and tactics and 2) industry frames and arguments. METHODS: Searches were conducted between April-July 2011, and updated in March 2013. Articles were included if they made reference to tobacco industry efforts to influence marketing regulations; supported claims with verifiable evidence; were written in English; and concerned the period 1990-2013. 48 articles met the review criteria. Narrative synthesis was used to combine the evidence. RESULTS: 56% of articles focused on activity in North America, Europe or Australasia, the rest focusing on Asia (17%), South America, Africa or transnational activity. Six main political strategies and four main frames were identified. The tobacco industry frequently claims that the proposed policy will have negative unintended consequences, that there are legal barriers to regulation, and that the regulation is unnecessary because, for example, industry does not market to youth or adheres to a voluntary code. The industry primarily conveys these arguments through direct and indirect lobbying, the promotion of voluntary codes and alternative policies, and the formation of alliances with other industrial sectors. The majority of tactics and arguments were used in multiple jurisdictions. CONCLUSIONS: Tobacco industry political activity is far more diverse than suggested by existing taxonomies of corporate political activity. Tactics and arguments are repeated across jurisdictions, suggesting that the taxonomies of industry tactics and arguments developed in this paper are generalisable to multiple jurisdictions and can be used to predict industry activity

Regulator of G-Protein Signaling 14 (RGS14) Is a Selective H-Ras Effector

Background: Regulator of G-protein signaling (RGS) proteins have been well-described as accelerators of Ga-mediated GTP hydrolysis (‘‘GTPase-accelerating proteins’’ or GAPs). However, RGS proteins with complex domain architectures are now known to regulate much more than Ga GTPase activity. RGS14 contains tandem Ras-binding domains that have been reported to bind to Rap- but not Ras GTPases in vitro, leading to the suggestion that RGS14 is a Rap-specific effector. However, more recent data from mammals and Drosophila imply that, in vivo, RGS14 may instead be an effector of Ras.Methodology/Principal Findings: Full-length and truncated forms of purified RGS14 protein were found to bind indiscriminately in vitro to both Rap- and Ras-family GTPases, consistent with prior literature reports. In stark contrast, however, we found that in a cellular context RGS14 selectively binds to activated H-Ras and not to Rap isoforms. Co- transfection / co-immunoprecipitation experiments demonstrated the ability of full-length RGS14 to assemble a multiprotein complex with components of the ERK MAPK pathway in a manner dependent on activated H-Ras. Small interfering RNA-mediated knockdown of RGS14 inhibited both nerve growth factor- and basic fibrobast growth factor- mediated neuronal differentiation of PC12 cells, a process which is known to be dependent on Ras-ERK signaling.Conclusions/Significance: In cells, RGS14 facilitates the formation of a selective Ras?GTP-Raf-MEK-ERK multiprotein complex to promote sustained ERK activation and regulate H-Ras-dependent neuritogenesis. This cellular function for RGS14 is similar but distinct from that recently described for its closely-related paralogue, RGS12, which shares the tandem Ras- binding domain architecture with RGS14