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ABSTRACT The overuse and misuse of antibiotics in clinical settings and in food production have been linked to the increased prevalence and spread of antimicrobial resistance (AR). Consequently, public health and consumer concerns have resulted in a remarkable reduction in antibiotics used for food animal production. However, there are no data on the effectiveness of antibiotic removal in reducing AR shared through horizontal gene transfer (HGT). In this study, we used neonatal broiler chicks and Salmonella enterica serovar Heidelberg, a model food pathogen, to test if chicks raised antibiotic free harbor transferable AR. We challenged chicks with an antibiotic-susceptible S. Heidelberg strain using various routes of inoculation and determined if S. Heidelberg isolates recovered carried plasmids conferring AR. We used antimicrobial susceptibility testing and whole-genome sequencing (WGS) to show that chicks grown without antibiotics harbored an antimicrobial resistant S. Heidelberg population at 14 days after challenge and chicks challenged orally acquired AR at a higher rate than chicks inoculated via the cloaca. Using 16S rRNA gene sequencing, we found that S. Heidelberg infection perturbed the microbiota of broiler chicks, and we used metagenomics and WGS to confirm that a commensal Escherichia coli population was the main reservoir of an IncI1 plasmid acquired by S. Heidelberg. The carriage of this IncI1 plasmid posed no fitness cost to S. Heidelberg but increased its fitness when exposed to acidic pH in vitro. These results suggest that HGT of plasmids carrying AR shaped the evolution of S. Heidelberg and that antibiotic use reduction alone is insufficient to limit antibiotic resistance transfer from commensal bacteria to Salmonella enterica. IMPORTANCE The reported increase in antibiotic-resistant bacteria in humans has resulted in a major shift away from antibiotic use in food animal production. This shift has been driven by the assumption that removing antibiotics will select for antibiotic susceptible bacterial taxa, which in turn will allow the currently available antibiotic arsenal to be more effective. This change in practice has highlighted new questions that need to be answered to assess the effectiveness of antibiotic removal in reducing the spread of antibiotic resistance bacteria. This research demonstrates that antibiotic-susceptible Salmonella enterica serovar Heidelberg strains can acquire multidrug resistance from commensal bacteria present in the gut of neonatal broiler chicks, even in the absence of antibiotic selection. We demonstrate that exposure to acidic pH drove the horizontal transfer of antimicrobial resistance plasmids and suggest that simply removing antibiotics from food animal production might not be sufficient to limit the spread of antimicrobial resistance.

Abstract Background Acute cellular rejection (ACR) is associated with complications after kidney transplantation, such as graft dysfunction and graft loss. Early risk assessment is therefore critical for the improvement of transplantation outcomes. In this work, we retrospectively analyzed a pre-transplant HLA antigen bead assay data set that was acquired by the e:KID consortium as part of a systems medicine approach. Results The data set included single antigen bead (SAB) reactivity profiles of 52 low-risk graft recipients (negative complement dependent cytotoxicity crossmatch, PRA

Lysyl oxidase (LOX) is a copper-binding enzyme that cross-links elastin and collagen. The dominant LOX variation contributes to familial thoracic aortic aneurysm. Previously reported murine Lox mutants had a mild phenotype and did not dilate without drug-induced provocation. Here, we present a new, more severe mutant, Loxb2b370.2Clo (c.G854T; p.Cys285Phe), whose mutation falls just N-terminal to the copper-binding domain. Unlike the other mutants, the C285F Lox protein was stably produced/secreted, and male C57Bl/6J Lox+/C285F mice exhibit increased systolic blood pressure (BP; p < 0.05) and reduced caliber aortas (p < 0.01 at 100mmHg) at 3 months that independently dilate by 6 months (p < 0.0001). Multimodal imaging reveals markedly irregular elastic sheets in the mutant (p = 2.8 × 10−8 for breaks by histology) that become increasingly disrupted with age (p < 0.05) and breeding into a high BP background (p = 6.8 × 10−4). Aortic dilation was amplified in males vs. females (p < 0.0001 at 100mmHg) and ameliorated by castration. The transcriptome of young Lox mutants showed alteration in dexamethasone (p = 9.83 × 10−30) and TGFβ-responsive genes (p = 7.42 × 10−29), and aortas from older C57Bl/6J Lox+/C285F mice showed both enhanced susceptibility to elastase (p < 0.01 by ANOVA) and increased deposition of aggrecan (p < 0.05). These findings suggest that the secreted Lox+/C285F mutants produce dysfunctional elastic fibers that show increased susceptibility to proteolytic damage. Over time, the progressive weakening of the connective tissue, modified by sex and blood pressure, leads to worsening aortic disease.

Abstract Protein acetylation is a highly frequent protein modification. However, comparatively little is known about its enzymatic machinery. N‐α‐acetylation (NTA) and ε‐lysine acetylation (KA) are known to be catalyzed by distinct families of enzymes (NATs and KATs, respectively), although the possibility that the same GCN5‐related N‐acetyltransferase (GNAT) can perform both functions has been debated. Here, we discovered a new family of plastid‐localized GNATs, which possess a dual specificity. All characterized GNAT family members display a number of unique features. Quantitative mass spectrometry analyses revealed that these enzymes exhibit both distinct KA and relaxed NTA specificities. Furthermore, inactivation of GNAT2 leads to significant NTA or KA decreases of several plastid proteins, while proteins of other compartments were unaffected. The data indicate that these enzymes have specific protein targets and likely display partly redundant selectivity, increasing the robustness of the acetylation process in vivo. In summary, this study revealed a new layer of complexity in the machinery controlling this prevalent modification and suggests that other eukaryotic GNATs may also possess these previously underappreciated broader enzymatic activities.

Bioluminescence resonance energy transfer (BRET) has been mostly employed in imaging applications. Here the authors use BRET to activate a ruthenium-based photocatalyst and perform a bioorthogonal chemical reaction, which can be used to uncage small molecule drugs in a cellular context.

Abstract Euclid is a European Space Agency medium-class mission selected for launch in 2020 within the cosmic vision 2015–2025 program. The main goal of Euclid is to understand the origin of the accelerated expansion of the universe. Euclid will explore the expansion history of the universe and the evolution of cosmic structures by measuring shapes and red-shifts of galaxies as well as the distribution of clusters of galaxies over a large fraction of the sky. Although the main driver for Euclid is the nature of dark energy, Euclid science covers a vast range of topics, from cosmology to galaxy evolution to planetary research. In this review we focus on cosmology and fundamental physics, with a strong emphasis on science beyond the current standard models. We discuss five broad topics: dark energy and modified gravity, dark matter, initial conditions, basic assumptions and questions of methodology in the data analysis. This review has been planned and carried out within Euclid’s Theory Working Group and is meant to provide a guide to the scientific themes that will underlie the activity of the group during the preparation of the Euclid mission.

The Brazilian Atlantic Forest has undergone adverse land-use change due to deforestation for urbanization and agriculture. Numerous restoration initiatives have been taken to restore its ecosystem services. Deforested areas have been restored through active intervention or natural regeneration. Understanding the impact of those different reforestation approaches on soil quality should provide important scientific and practical conclusions on increasing forest cover in the Brazilian Atlantic Forest biome. However, studies evaluating active planting versus natural regeneration in terms of soil recovery are scarce. We evaluate soil dynamics under those two contrasting strategies at an early stage (

Abstract Growth of eukaryotic cells is regulated by the target of rapamycin (TOR). The strongest activator of TOR in metazoa is amino acid availability. The established transducers of amino acid sensing to TOR in metazoa are absent in plants. Hence, a fundamental question is how amino acid sensing is achieved in photo-autotrophic organisms. Here we demonstrate that the plant Arabidopsis does not sense the sulfur-containing amino acid cysteine itself, but its biosynthetic precursors. We identify the kinase GCN2 as a sensor of the carbon/nitrogen precursor availability, whereas limitation of the sulfur precursor is transduced to TOR by downregulation of glucose metabolism. The downregulated TOR activity caused decreased translation, lowered meristematic activity, and elevated autophagy. Our results uncover a plant-specific adaptation of TOR function. In concert with GCN2, TOR allows photo-autotrophic eukaryotes to coordinate the fluxes of carbon, nitrogen, and sulfur for efficient cysteine biosynthesis under varying external nutrient supply.

The Global Ocean Observing System (GOOS) and its partners have worked together over the past decade to break down barriers between open-ocean and coastal observing, between scientific disciplines, and between operational and research institutions. Here we discuss some GOOS successes and challenges from the past decade, and present ideas for moving forward, including highlights of the GOOS 2030 Strategy, published in 2019. The OceanObs’09 meeting in Venice in 2009 resulted in a remarkable consensus on the need for a common set of guidelines for the global ocean observing community. Work following the meeting led to development of the Framework for Ocean Observing (FOO) published in 2012 and adopted by GOOS as a foundational document that same year. The FOO provides guidelines for the setting of requirements, assessing technology readiness, and assessing the usefulness of data and products for users. Here we evaluate successes and challenges in FOO implementation and consider ways to ensure broader use of the FOO principles. The proliferation of ocean observing activities around the world is extremely diverse and not managed, or even overseen by, any one entity. The lack of coherent governance has resulted in duplication and varying degrees of clarity, responsibility, coordination and data sharing. GOOS has had considerable success over the past decade in encouraging voluntary collaboration across much of this broad community, including increased use of the FOO guidelines and partly effective governance, but much remains to be done. Here we outline and discuss several approaches for GOOS to deliver more effective governance to achieve our collective vision of fully meeting society’s needs. What would a more effective and well-structured governance arrangement look like? Can the existing system be modified? Do we need to rebuild it from scratch? We consider the case for evolution versus revolution. Community-wide consideration of these governance issues will be timely and important before, during and following the OceanObs’19 meeting in September 2019.

The air–sea interface is a key gateway in the Earth system. It is where the atmosphere sets the ocean in motion, climate/weather-relevant air–sea processes occur, and pollutants (i.e., plastic, anthropogenic carbon dioxide, radioactive/chemical waste) enter the sea. Hence, accurate estimates and forecasts of physical and biogeochemical processes at this interface are critical for sustainable blue economy planning, growth, and disaster mitigation. Such estimates and forecasts rely on accurate and integrated in situ and satellite surface observations. High-impact uses of ocean surface observations of essential ocean/climate variables (EOVs/ECVs) include (1) assimilation into/validation of weather, ocean, and climate forecast models to improve their skill, impact, and value; (2) ocean physics studies (i.e., heat, momentum, freshwater, and biogeochemical air–sea fluxes) to further our understanding and parameterization of air–sea processes; and (3) calibration and validation of satellite ocean products (i.e., currents, temperature, salinity, sea level, ocean color, wind, and waves). We review strengths and limitations, impacts, and sustainability of in situ ocean surface observations of several ECVs and EOVs. We draw a 10-year vision of the global ocean surface observing network for improved synergy and integration with other observing systems (e.g., satellites), for modeling/forecast efforts, and for a better ocean observing governance. The context is both the applications listed above and the guidelines of frameworks such as the Global Ocean Observing System (GOOS) and Global Climate Observing System (GCOS) (both co-sponsored by the Intergovernmental Oceanographic Commission of UNESCO, IOC–UNESCO; the World Meteorological Organization, WMO; the United Nations Environment Programme, UNEP; and the International Science Council, ISC). Networks of multiparametric platforms, such as the global drifter array, offer opportunities for new and improved in situ observations. Advances in sensor technology (e.g., low-cost wave sensors), high-throughput communications, evolving cyberinfrastructures, and data information systems with potential to improve the scope, efficiency, integration, and sustainability of the ocean surface observing system are explored.

The importance of stakeholder engagement in ocean observation and in particular the realization of economic and societal benefits is discussed, introducing a number of overarching principles such as the convergence on common goals, effective communication, co-production of information and knowledge and the need for innovation. A series of case studies examine the role of coordinating frameworks such as the United States’ Interagency Ocean Observing System (IOOS®), and the European Ocean Observing System (EOOS), public–private partnerships such as Project Azul and the Coastal Data Information Program (CDIP) and finally the role of the “third” or voluntary sector. The paper explores the value that stakeholder engagement can bring as well as making recommendations for the future.

Advances in L-band microwave satellite radiometry in the past decade, pioneered by ESA’s SMOS and NASA’s Aquarius and SMAP missions, have demonstrated an unprecedented capability to observe global sea surface salinity (SSS) from space. Measurements from these missions are the only means to probe the very-near surface salinity (top cm), providing a unique monitoring capability for the interfacial exchanges of water between the atmosphere and the upper-ocean, and delivering a wealth of information on various salinity processes in the ocean, linkages with the climate and water cycle, including land-sea connections, and providing constraints for ocean prediction models. The satellite SSS data are complimentary to the existing in situ systems such as Argo that provide accurate depiction of large-scale salinity variability in the open ocean but under-sample mesoscale variability, coastal oceans and marginal seas, and energetic regions such as boundary currents and fronts. In particular, salinity remote sensing has proven valuable to systematically monitor the open oceans as well as coastal regions up to approximately 40 km from the coasts. This is critical to addressing societally relevant topics, such as land-sea linkages, coastal-open ocean exchanges, research in the carbon cycle, near-surface mixing, and air-sea exchange of gas and mass. In this paper, we provide a community perspective on the major achievements of satellite SSS for the aforementioned topics, the unique capability of satellite salinity observing system and its complementarity with other platforms, uncertainty characteristics of satellite SSS, and measurement versus sampling errors in relation to in situ salinity measurements. We also discuss the need for technological innovations to improve the accuracy, resolution, and coverage of satellite SSS, and the way forward to both continue and enhance salinity remote sensing as part of the integrated Earth Observing System in order to address societal needs.

This data article contains the dynamic mechanical thermal analysis (DMTA) results for sheets made from cellulose fibers partially converted to dialcohol cellulose as presented in “Advanced Three-Dimensional Paper Structures: Mechanical Characterization and Forming of Sheets Made from Modified Cellulose Fibers” by Linvill et al. [1]. See Larsson and Wågberg [2] for a description and characterization of the material as well as how the material is produced. The DMTA tests were conducted at four different relative humidity levels: 0, 50, 60, and 70% RH, and the temperature was swept between 10 and 113 °C. The DMTA results enable the understanding of the elastic, viscoelastic, and viscoplastic mechanical properties of this material at a wide range of temperature and relative humidity combinations.

The impact of polypropylene and high-density polyethylene backbone binders on the structure of organic matrix, feedstock, and ceramic parts is investigated in terms of morphology in this paper. The miscibility of wax with polyethylene and polypropylene is investigated in the molten state via a rheological study, revealing wax full miscibility with high-density polyethylene and restricted miscibility with polypropylene. Mercury porosimetry measurements realized after wax extraction allow the characterization of wax dispersion in both neat organic blends and zirconia filled feedstocks. Miscibility differences in the molten state highly impact wax dispersion in backbone polymers after cooling: wax is preferentially located in polyethylene phase, while it is easily segregated from polypropylene phase, leading to the creation of large cracks during solvent debinding. The use of a polyethylene/polypropylene ratio higher than 70/30 hinders wax segregation and favors its homogeneous dispersion in organic binder. As zirconia is added to organic blends containing polyethylene, polypropylene, and wax, the pore size distribution created by wax extraction is shifted towards smaller pores. Above zirconia percolation at 40 vol%, the pore size distribution becomes sharp attesting of wax homogeneous dispersion. As the PP content in the organic binder decreases from 100% to 0%, the pore size distribution is reduced of 30%, leading to higher densification ability. In order to ensure a maximal densification of the final ceramic, polyethylene/polypropylene ratios with a minimum content of 70% of high-density polyethylene should be employed.

The end of 2016 is an uneasy moment for climate science in the United States. With a new Administration and a new Congress arriving in January 2017, future support for climate science and observing systems is uncertain. Against this backdrop, this special issue of Oceanography on ocean-ice interaction is timely. Although it was not our intent to highlight climate change, the fragile nature of Earth’s cryosphere and how it is responding to a warming world are essential parts of each article. Many aspects of the shrinking cryosphere are not yet understood, but the research described in these pages points to larger-​than-​anticipated—and alarming—changes to the planet’s large ice sheets, with associated future increases in global sea levels. Importantly, the articles in this special issue demonstrate the value to society of continuing vigorous scientific research that will enable us to better understand our planet’s rapidly changing polar environments.

Recent experiences with avian influenza outbreaks in poultry in the United States have tested biosecurity protocols and outbreak management strategies. During an outbreak, regulatory officials managing the emergency response need to make timely decisions in order to achieve disease control and eradication goals while simultaneously decreasing the unintended consequences of the response. To move susceptible animals or animal products out of a disease Control Area via a secure food supply continuity of business (COB) permit without the risk of expanding a disease outbreak, premises must be designated as Monitored Premises (MP) by regulatory officials. The experience of and lessons learned from the 2014 to 2015 highly pathogenic avian influenza (HPAI) outbreak have resulted in defined criteria necessary to establish MP status during an HPAI outbreak and highlighted the need for a clear method to determine that those criteria have been met. Establishing MP status is different from an epidemiologic investigation, though they both require analyses of how avian influenza virus may enter poultry premises and can take significant staff time. MP status of premises seeking to move animals or animal products must be continuously re-evaluated as Infected Premises status, and resulting epidemiologic contacts, can rapidly change during an outbreak. We present here a questionnaire to establish MP status, designed to be initially completed by industry representatives in an attempt to streamline processes and conserve resources. During an outbreak, the MP status questionnaire is an essential risk-based management tool used to establish premises status, as part of operationalizing permitted movement to support COB.

Templated reactions proceed by bringing reagents in close proximity through their interaction with a template thus raising their effective concentrations. Templated reactions empower chemists to perform reactions at low concentrations in complex environments. Herein, we discuss our work on templated reactions leveraged on ruthenium photocatalysis. Over the past five years, we have used this reaction to uncage reporter molecules and sense or image nucleic acids or proteins of interest. The ruthenium photocatalysis chemistry has proven to be extremely robust and compatible with complex biological environments.

Garbage management represents a potential pathway of HPAI-virus infection for commercial poultry operations as multiple poultry premises may share a common trash collection service provider, trash collection site (e.g., shared dumpster for multiple premises) or disposal site (e.g., landfill). The types of potentially infectious or contaminated material disposed of in the garbage has not been previously described but is suspected to vary by poultry industry sector. A survey of representatives from the broiler, turkey, and layer sectors in the United States revealed that many potentially contaminated or infectious items are routinely disposed of in the trash on commercial poultry premises. On-farm garbage management practices, along with trash hauling and disposal practices are thus key components that must be considered to evaluate the risk of commercial poultry becoming infected with HPAI virus.

In this special issue of Oceanography, we explore the results of SPURS-1, the first part of the ocean process study Salinity Processes in the Upper-ocean Regional Study (SPURS). The experiment was conducted between August 2012 and October 2013 in the subtropical North Atlantic and was the first of two experiments (SPURS come in pairs!). SPURS-2 is planned for 2016–2017 in the tropical eastern Pacific Ocean. The scientific motivation behind SPURS arises from the desire to understand the patterns and variations of salinity at the ocean’s surface. To first order, surface salinity patterns reflect the overlying patterns of evaporation and precipitation that force the freshwater balance in the upper ocean (Wüst, 1936). Maps of the net difference between evaporation and precipitation (E–P) appear to be quite similar in pattern to surface salinity. If the surface salinity is determined only by (E–P), then the ocean itself might serve as crude “rain gauge.” In fact, it is already known that ocean circulation in the form of wind-driven surface currents must be accounted for in understanding surface salinity patterns (surface salinity maxima are offset poleward of subtropical E–P maxima due to Ekman currents induced by the trade winds). In addition, ocean mixing processes also affect the temporal evolution of surface salinity. SPURS was designed to examine the salinity balance in the upper ocean through observation of salinity and ocean circulation on a variety of scales

In the current precision medicine era, more and more samples get genotyped and sequenced. Both researchers and commercial companies expend significant time and resources to reduce the error rate. However, it has been reported that there is a sample mix-up rate of between 0.1% and 1%, not to mention the possibly higher mix-up rate during the down-stream genetic reporting processes. Even on the low end of this estimate, this translates to a significant number of mislabeled samples, especially over the projected one billion people that will be sequenced within the next decade. Here, we first describe a method to identify a small set of Single nucleotide polymorphisms (SNPs) that can uniquely identify a personal genome, which utilizes allele frequencies of five major continental populations reported in the 1000 genomes project and the ExAC Consortium. To make this panel more informative, we added four SNPs that are commonly used to predict ABO blood type, and another two SNPs that are capable of predicting sex. We then implement a web interface (http://qrcme.tech), nicknamed QRC (for QR code based Concordance check), which is capable of extracting the relevant ID SNPs from a raw genetic data, coding its genotype as a quick response (QR) code, and comparing QR codes to report the concordance of underlying genetic datasets. The resulting 80 fingerprinting SNPs represent a significant decrease in complexity and the number of markers used for genetic data labelling and tracking. Our method and web tool is easily accessible to both researchers and the general public who consider the accuracy of complex genetic data as a prerequisite towards precision medicine.

The distribution of flowering across the growing season is governed by each species' evolutionary history and climatic variability. However, global change factors, such as eutrophication and invasion, can alter plant community composition and thus change the distribution of flowering across the growing season. We examined three ecoregions (tall-, mixed, and short-grass prairie) across the U.S. Central Plains to determine how nutrient (nitrogen (N), phosphorus, and potassium (+micronutrient)) addition alters the temporal patterns of plant flowering traits. We calculated total community flowering potential (FP) by distributing peak-season plant cover values across the growing season, allocating each species' cover to only those months in which it typically flowers. We also generated separate FP profiles for exotic and native species and functional group. We compared the ability of the added nutrients to shift the distribution of these FP profiles (total and sub-groups) across the growing season. In all ecoregions, N increased the relative cover of both exotic species and C3 graminoids that flower in May through August. The cover of C4 graminoids decreased with added N, but the response varied by ecoregion and month. However, these functional changes only aggregated to shift the entire community's FP profile in the tall-grass prairie, where the relative cover of plants expected to flower in May and June increased and those that flower in September and October decreased with added N. The relatively low native cover in May and June may leave this ecoregion vulnerable to disturbance-induced invasion by exotic species that occupy this temporal niche. There was no change in the FP profile of the mixed and short-grass prairies with N addition as increased abundance of exotic species and C3 graminoids replaced other species that flower at the same time. In these communities a disturbance other than nutrient addition may be required to disrupt phenological patterns.

The Newborn Screening Technical assistance and Evaluation Program (NewSTEPs) conducts non-regulatory site reviews of state newborn screening programs in the US with the goal of providing comprehensive reports and recommendations to support quality improvements within the system. A detailed coding and qualitative analysis of data extracted from reports of seven programs visited between 2012 and 2017, of thirteen pre-site visit surveys completed by state newborn screening programs, and of information from interviews conducted with three site review experts revealed four common themes that exist across states within the national newborn screening system. These themes include opportunities to implement improvements in: (1) communications inside and outside of the state newborn screening program, (2) education, (3) information technology, and (4) operations. The cross-cutting recommendations provided by NewSTEPs within the comprehensive site review reports may prove valuable for all state programs to consider and to incorporate as quality improvement measures in the absence of a full site review. The analysis of the site review process and recommendations identified important opportunities for improvement, many of which were previously unknown to be common across programs, and also provided affirmation of known challenges.