Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides
Abstract not provided
Déjean, Guillaume↗
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Gut Commensal Bacteroidetes Encode a Novel Class of Vitamin B 12 -Binding Proteins
The gut microbiome is a complex microbial community with important impacts on human health. One of the major groups within the gut microbiome, the Bacteroidetes , rely on their ability to capture vitamin B 12 and related molecules for fitness in the gut.
59 BASIC BIOLOGICAL SCIENCES↗
Predicting Antimicrobial Resistance Using Partial Genome Alignments
Antimicrobial resistance (AMR) is an important global health threat that impacts millions of people worldwide each year. Developing methods that can detect and predict AMR phenotypes can help to mitigate the spread of AMR by informing clinical decision making and appropriate mitigation strategies. Many bioinformatic methods have been developed for predicting AMR phenotypes from whole-genome sequences and AMR genes, but recent studies have indicated that predictions can be made from incomplete genome sequence data. In order to more systematically understand this, we built random forest-based machine learning classifiers for predicting susceptible and resistant phenotypes for Klebsiella pneumoniae (1,640 strains), Mycobacterium tuberculosis (2,497 strains), and Salmonella enterica (1,981 strains). We started by building models from alignments that were based on a reference chromosome for each species. We then subsampled each chromosomal alignment and built models for the resulting subalignments, finding that very small regions, representing approximately 0.1 to 0.2% of the chromosome, are predictive. In K. pneumoniae, M. tuberculosis, and S. enterica, the subalignments are able to predict multiple AMR phenotypes with at least 70% accuracy, even though most do not encode an AMR-related function. We used these models to identify regions of the chromosome with high and low predictive signals. Finally, subalignments that retain high accuracy across larger phylogenetic distances were examined in greater detail, revealing genes and intergenic regions with potential links to AMR, virulence, transport, and survival under stress conditions. IMPORTANCE Antimicrobial resistance causes thousands of deaths annually worldwide. Understanding the regions of the genome that are involved in antimicrobial resistance is important for developing mitigation strategies and preventing transmission. Machine learning models are capable of predicting antimicrobial resistance phenotypes from bacterial genome sequence data by identifying resistance genes, mutations, and other correlated features. They are also capable of implicating regions of the genome that have not been previously characterized as being involved in resistance. In this study, we generated global chromosomal alignments for Klebsiella pneumoniae, Mycobacterium tuberculosis, and Salmonella enterica and systematically searched them for small conserved regions of the genome that enable the prediction of antimicrobial resistance phenotypes. In addition to known antimicrobial resistance genes, this analysis identified genes involved in virulence and transport functions, as well as many genes with no previous implication in antimicrobial resistance.
59 BASIC BIOLOGICAL SCIENCES↗
Seroprevalence of Brucella spp. and Rift Valley fever virus among slaughterhouse workers in Isiolo County, northern Kenya
Brucella spp. and Rift Valley fever virus (RVFV) are classified as priority zoonotic agents in Kenya, based on their public health and socioeconomic impact on the country. Data on the pathogen-specific and co-exposure levels is scarce due to limited active surveillance. This study investigated seroprevalence and co-exposure of Brucella spp. and RVFV and associated risk factors among slaughterhouse workers in Isiolo County, northern Kenya. A cross-sectional serosurvey was done in all 19 slaughterhouses in Isiolo County, enrolling 378 participants into the study. The overall seroprevalences for Brucella spp. and RVFV were 40.2% (95% CI: 35.2–45.4) and 18.3% (95% CI: 14.5–22.5), respectively while 10.3% (95% CI 7.4%-13.8%) of individuals were positive for antibodies against both Brucella spp. and RVFV. Virus neutralisation tests (VNT) confirmed anti-RVFV antibodies in 85% of ELISA-positive samples. Our seroprevalence results were comparable to community-level seroprevalences previously reported in the area. Since most of the study participants were not from livestock-keeping households, our findings attribute most of the detected infections to occupational exposure. The high exposure levels indicate slaughterhouse workers are the most at-risk population and there is need for infection, prevention, and control programs among this high-risk group. This is the first VNT confirmation of virus-neutralising antibodies among slaughterhouse workers in Isiolo County and corroborates reports of the area being a high-risk RVFV area as occasioned by previously reported outbreaks. This necessitates sensitization campaigns to enhance awareness of the risks involved and appropriate mitigation measures.
60 APPLIED LIFE SCIENCES↗
Digital Biosecurity Pilot Project
Security models for the bioeconomy have largely been developed on risk profiles borrowed from the financial industry and, in some cases, industrial control systems. The bioeconomy, however, has unique characteristics that require domain-specific knowledge of the risks to environmental, health and economic impact from directly targeted attacks. Key questions need to be assessed and answered for any facility engaged in bioproduction. These include: how much technical information must the attacker possess in order to target a specific process or facility? Which processes cause the largest economic impact if disrupted? Can an attacker lead companies down the wrong path of research, leading to irrecoverable losses of time, resources and capital? Can attackers disrupt venture capital strategies and affect financial returns? What are the resources required to attack key workflows, and subsequently what is the cost of defense? What strategies are effective against such attackers, and what are their cost? Can government provide an active role in assurance of material, process and results for critical bioeconomic infrastructure?
59 BASIC BIOLOGICAL SCIENCES↗
Safety Functions and Features, Events and Processes for the E-Area Performance Assessment
The DOE Technical Standard, “Disposal Authorization Statement and Tank Closure Documentation,” (DOE 2017) recommends the use of safety functions and features, events and processes (FEPs) to support development of conceptual models and identification of scenarios to be considered in a performance assessment (PA). The FEP process provides a means to describe how a PA considers and addresses the factors that could influence the performance of key barriers. Understanding the roles of barriers in terms of limiting migration helps to focus on how changes in the system could lead to a situation where those roles cannot be fulfilled and there is the potential for compromised performance. The FEPs screening and review process was used to identify FEPs that are relevant for the EArea Low-Level Waste Facility (LLWF) and specifically those FEPs that could have a detrimental impact on the effectiveness of a given safety function. For this PA, a default list of FEPs developed at the International Atomic Energy Agency (IAEA 2004) and an approach implemented for PAs at the Hanford and Idaho sites (Mehta et al. 2016, DOE-ID 2019) are used to identify processes and events that could influence the effectiveness of a given safety function for the E-Area LLWF (e.g., subsidence can impact the safety function of the cover system and lead to increased infiltration). The Hanford and Idaho PAs represent two of the most recent applications of this approach. The PA evaluates the potential impacts of changes in performance of different features of the system and demonstrates that the safety functions represent multiple and redundant barriers. Barrier analyses, assuming a safety function is not present, also test the robustness of the system in the event of the loss of one or more safety functions. Such evaluations also support a qualitative illustration of the concept of defense in depth. The safety concept for closure of the E-Area LLWF (generically referred to as “E-Area”) encompasses a variety of different features (i.e., administrative controls, natural site features, and engineered barriers) that reduce the potential impacts on human health and the environment from the residual waste that will remain after closure. These features can be represented as a collection of safety functions acting independently and as a system to provide for overall safety. In some applications, there have been attempts to assign numerical expectations to specific safety functions, but that is not the intent in this case. The concept of safety functions is used more qualitatively in two ways for this PA: 1. To illustrate the robustness of the E-Area design, operational practices and closure approach by documenting features that are and are not credited in different modeling cases. 2. To identify the roles of the different features and potential processes and events that could compromise the performance of safety features and need to be considered when developing the modeling approach. This report addresses both safety functions and FEPs for the E-Area PA.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Bioscience COVID Rapid Response Report
The COVID-19 disease outbreak and its impact on global health and economies have highlighted the national security threat posed by pathogens with pandemic potential and the need for rapid development of effective diagnostics and medical countermeasures. The Bioscience IA selected for funding rapid COVID LDRD project proposals that addressed critical R&D gaps in pandemic response that could be accomplished in 1-3 months with the requested funding. In total, the Bioscience IA funded nine rapid projects that addressed 1) rapid and accurate methods for SARS-CoV-2 RNA detection, 2) modeling tools to help prioritize populations for diagnostic testing, 3) bioinformatic tools to track SARS-CoV-2 genomic sequence changes over time, 4) molecular inhibitors of SARS-CoV-2 cellular infection, and 5) method for rapid staging of COVID19 disease to enable administration of more effective treatments. In addition, LDRD funded one larger project to be completed in FY21 that leverages Sandia capabilities to address the need for platform diagnostics and therapeutics that can be rapidly tailored against emerging pathogen targets.
59 BASIC BIOLOGICAL SCIENCES↗
Human Factors Considerations for Automating Microreactors
The U.S. Nuclear Regulatory Commission (NRC) has interacted with vendors pursuing the commercialization of microreactors ( <10 MW th ). It is envisioned that microreactors could be assembled and fueled in a factory and shipped to a site. Many of the sites are expected to be remote locations requiring off-grid power or in some cases military bases. However, before this new class of nuclear reactor can be fully developed and implemented by designers, an effort must be made to explore the technical issues and provide reasonable assurance to the public regarding health and safety impacts centered on various technical issues. Prior works have examined many of these issues. One issue not yet fully explored is the possible change in role of the operations and support personnel. Due to the passive safety features of microreactors and their low level of nuclear material, the microreactor facilities may automate more functions and rely on inherent safety features more than its predecessor nuclear power plants. In some instances, human operators may not be located onsite and may instead be operating or monitoring the facility from a remote location. Some designs also call for operators to supervise and control multiple microreactors from the control room. This report explores the issues around reduced staffing of microreactors, highlights the historical safety functions associated with human operators, assesses current licensing requirements for appropriateness to varying levels of personnel support, and describes a recommended regulatory approach for reviewing the impact of reduced staff to the operation of microreactors. The report evaluates these issues through an extensive literature survey and Subject Matter Expert interviews. The literature covers research topics related to Human Factors Engineering as well as regulatory guidance given by the Nuclear Regulatory Commission.
22 GENERAL STUDIES OF NUCLEAR REACTORS↗
Emission Inventories from Natural Gas Storage Facilities using Regional Frequency Comb Laser Monitoring and Aircraft Flyovers. Final Report
The project centers around a ground-based regional methane sensor developed by the CU/NIST team members under the DOE ARPA-E MONITOR program, and sophisticated aircraft measurement techniques developed by the UCD/Scientific Aviation team (responsible for a recent Science publication quantifying the Aliso Canyon storage field release). The dual frequency-comb spectrometer is an invisible, eye-safe laser capable of measuring atmospheric methane concentrations along beam paths 1+ miles in length with high precision and stability (<1 ppb methane over 1 mile). The CU/NIST team has developed a unique approach to using a single, central spectrometer to locate and size methane emissions as small as 6 scfh from specific gas field structures within the 1+ mile range of the laser. Deployment involves the stationing of small cubic mirrors at strategic locations across the gas storage site. The mirrors direct light from the spectrometer back to a detector, where methane concentrations are recorded based on light absorption at specific wavelengths. The measurements are coupled with high resolution gas transport models based on meteorological measurements (wind, etc.) to determine the precise location and emission rate of methane sources. The calibration-free and continuous nature of dual frequency-comb spectrometer measurements means that a large area can be monitored continuously for temporal variability of emissions over long periods of time. The aircraft measurements involve spiral flights around storage facilities with a sensitive ethane/methane measurement package. Upwind/downwind concentration comparisons and wind data provide total facility emissions data. During this project, a new micrometeorological package was integrated onto the Scientific Aviation aircraft to provide even greater emissions quantification capability. In this project, the ground-based measurement system was deployed for 11 months (to capture seasonal variability) at a West Coast storage facility, together with a campaign of twice monthly aircraft total facility emissions flights. The data from these two modalities was combined to quantify the methane emissions from the facility with first-of-its-kind temporal and spatial detail. Concurrent with this deployment, the aircraft team performed flights to quantify emissions at a wider array of previously un-surveyed storage sites. The ground-based measurement system was then moved to an additional site of differing total storage and delivery capacity. Aircraft mass balance flights continued, repeatedly surveying (twice monthly) this site, as well as surveying a large number of previously un-assessed sites spanning a variety of size, reservoir type and age. Assessment of ground-based, temporally and spatially detailed methane emissions information alongside aircraft-derived methane total facility emissions information led to an improved understanding of emissions, relevant for inventories of the natural gas storage sector. In particular, this work provided temporal detail (seasonal of emissions and frequency of leaks) to stakeholders and personnel responsible for updates to the EPA’s GHGI. The impact of the proposed work has been a dramatic improvement in the temporal, spatial, and site- and type- specific detail and quantification of emissions inventories for the natural gas storage sector. This work directly benefits the EPA’s GHGI, directly ameliorates the environmental impacts and public health and safety of the natural gas storage sector, and aids policymakers and industry to make sound choices with respect to management and regulation.
03 NATURAL GAS↗
Disease Precognition [Slides]
How can we reduce the health and economic impacts future epidemics and pandemics? Global Real-Time Disease Forecasting is not just for weather anymore! Disease precognition technology is discussed.
59 BASIC BIOLOGICAL SCIENCES↗
The Electron-Ion Collider - A machine that will unlock the secrets of the strongest force in nature!
The computers and smartphones we use every day depend on what we learned about the atom in the last century. All information technology – and much of our economy today – relies on understanding the electromagnetic force between the atomic nucleus and the electrons that orbit it. The science of that force is well understood, but we still know little about the microcosm within the protons and neutrons that make up the atomic nucleus. That’s where Brookhaven National Laboratory (BNL) comes in. Brookhaven National Laboratory (located in Suffolk County, NY, about 60 miles east of midtown Manhattan) was recently chosen as the building site for an Electron-Ion Collider (EIC), a one-of-a-kind nuclear physics research facility. The EIC will be a discovery machine for unlocking the secrets of the “glue” that binds the building blocks of visible matter in the universe. The machine design will take advantage of the existing and highly optimized Relativistic Heavy Ion Collider (RHIC) that’s been operating at Brookhaven Lab since 2000. Beyond sparking scientific discoveries in a new frontier of fundamental physics, the Electron-Ion Collider will trigger technological breakthroughs that have broad-ranging impact on human health and national challenges.
43 PARTICLE ACCELERATORS↗
The Net Zero World Initiative’s Preliminary Analysis of Decarbonization Pathways for Five Countries
Under the Net Zero World Initiative, the United States is mobilizing the capabilities of nine U.S. government agencies, led by the U.S. Department of Energy (DOE), to partner with philanthropies and multiple countries to cocreate and implement tailored technical and investment pathways to accelerate the decarbonization of global energy systems. In addition, 10 of the DOE national laboratories have built a consortium housed in the Net Zero World Action Center to implement this vision by providing the deep analysis and modeling required to carry out the vision. As a whole-of-government program, the Net Zero World Initiative partners with countries committed to raising their climate ambitions by creating and implementing highly tailored, actionable technical and investment strategies that put a net-zero world within reach. The initiative enables country partners to harness the convening power and technical expertise of U.S. agencies and laboratories, international industry, and technical institutions while providing the United States an opportunity to learn from and deepen U.S. technical cooperation with key countries. This report is the first of a series, with future Phase II work being informed by ongoing consultations with the partner countries to address country pathway analysis priorities. This future work will likely include evaluating detailed technological, policy, and investment options for key sectors and for energy systems holistically. This analysis may examine in greater detail the economic and social benefits of net-zero energy transitions, including quality jobs and health outcomes, the impacts of price and supply volatility on energy investments and decisions, the risk of stranded assets, and related issues.
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
Electrochemical hydrogen isotope fractionation - fundamental insights leading to process scale up
Introduction Deuterium and tritium, the two isotopes of hydrogen besides protium, are utilized in many industries. Deuterium is routinely used as a nuclear reactor moderator and molecular labeling agent, while tritium is used as an autoradiography label in medical imaging, and in an emerging market for self-powered lighting for watches, exit signs, firearm night-sights and future fusion fuel. Tritium is produced naturally at very low steady-state levels due to cosmic rays, natural nuclear decay reactions, as well as commercial nuclear fission reactors, and terrestrial nuclear testing conducted primarily in the mid-twentieth century. Tritium often accumulates in the heavy water used in nuclear fission reactors and sometimes appears in groundwater near nuclear reactors due to slight leakage from water sources in the reactor. Because of the health and environmental impacts from tritium leaking into the water sources, as well as the value of this precious material, it is desirable to remove and recover as much tritium as reasonably possible from contaminated water.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
PNNL Superfund Research Program Analytics (srpAnalytics Data Release v.1.0)
The OSU/PNNL superfund Research Program represents a longstanding collaboration to quantify Polycyclic Aromatic Hydrocarbons at various superfund sites in the Pacific Northwest and assess their potential impact on human health. To link the chemical measurements to biological activity, we describe the use of the zebrafish as a high-throughput developmental model of human exposure that provides quantitative measurements of the biological ramifications of exposure to toxicants. The PNNL Superfund have implemented a dose-response modelling pipeline to calculate benchmark dose parameters that enable the comparison of potency across chemicals and phenotypes. Our portal provides public access to this dataset and an interactive web site designed to enable exploration and re-use of this data by the scientific community at http://srp.pnnl.gov.
59 BASIC BIOLOGICAL SCIENCES↗
PNNL Superfund Research Program Analytics (srpAnalytics Data Release v.1.0)
The OSU/PNNL superfund Research Program represents a longstanding collaboration to quantify Polycyclic Aromatic Hydrocarbons at various superfund sites in the Pacific Northwest and assess their potential impact on human health. To link the chemical measurements to biological activity, we describe the use of the zebrafish as a high-throughput developmental model of human exposure that provides quantitative measurements of the biological ramifications of exposure to toxicants. The PNNL Superfund have implemented a dose-response modelling pipeline to calculate benchmark dose parameters that enable the comparison of potency across chemicals and phenotypes. Our portal provides public access to this dataset and an interactive web site designed to enable exploration and re-use of this data by the scientific community at http://srp.pnnl.gov.
OSU-PNNL Superfund Research Program Center SRP↗
Whole-Genome Sequencing and Bioinformatic Analysis of Environmental, Agricultural, and Human Campylobacter jejuni Isolates From East Tennessee
As a leading cause of bacterial-derived gastroenteritis worldwide, Campylobacter jejuni has a significant impact on human health in both the developed and developing worlds. Despite its prevalence as a human pathogen, the source of these infections remains poorly understood due to the mutation frequency of the organism and past limitations of whole genome analysis. Recent advances in both whole genome sequencing and computational methods have allowed for the high-resolution analysis of intraspecies diversity, leading multiple groups to postulate that these approaches may be used to identify the sources of Campylobacter jejuni infection. To address this hypothesis, our group conducted a regionally and temporally restricted sampling of agricultural and environmental Campylobacter sources and compared isolated C. jejuni genomes to those that caused human infections in the same region during the same time period. Through a network analysis comparing genomes from various sources, we found that human C. jejuni isolates clustered with those isolated from cattle and chickens, indicating these as potential sources of human infection in the region.
59 BASIC BIOLOGICAL SCIENCES↗
Acute Exposure to Aerosolized Nanoplastics Modulates Redox-Linked Immune Responses in Human Airway Epithelium
Micro- and nanoplastics (MPs and NPs) are pervasive environmental pollutants detected in aquatic ecosystems, with emerging evidence suggesting their presence in airborne particles generated by water body motion. Inhalation exposure to airborne MPs and NPs remains understudied despite documented links between occupational exposure to these particles and adverse respiratory outcomes, including airway inflammation, oxidative stress, and chronic respiratory diseases. This study explored the effects of acute NP exposure on a fully differentiated 3D human airway epithelial model derived from 14 healthy donors. Airway epithelium was exposed to aerosolized 50 nm polystyrene NPs at concentrations ranging from 2.5 to 2500 µg/mL for three minutes per day over three days. Functional assays revealed no significant alterations in tissue integrity, cell survival, mucociliary clearance, or cilia beat frequency, suggesting intact epithelial function post-exposure. However, cytokine and chemokine profiling identified a significant five-fold increase in CCL3 (MIP-1α), a neutrophilic chemoattractant, in NP-exposed samples compared to controls. This was corroborated by increased neutrophil chemotaxis in response to conditioned media from NP-exposed tissues, indicating a pro-inflammatory neutrophilic response. Conversely, levels of interleukins (IL-21, IL-2, IL-15), CXCL10, and TGF-β were significantly reduced, suggesting immunomodulatory effects that may impair adaptive immune responses and tissue repair mechanisms. These findings demonstrate that short-term exposure to NP-containing aerosols induces a distinct pro-inflammatory response in airway epithelium, characterized by enhanced neutrophil recruitment and reduced secretion of key immune modulators. These findings underscore the potential for aerosolized NPs to induce oxidative and inflammatory stress, raising concerns about their long-term impact on respiratory health and redox regulation.
Biochemistry & Molecular Biology↗
Physical Education Teachers’ Representations of Their Training to Promote the Inclusion of Students with Disabilities
School inclusion is based on the need to adopt and implement a holistic view of education, training, and human development embodied in the idea of everyone, for everyone. In the context of Physical Education (PE), there are still several constraints to the realization of this universal desideratum. Among these, teacher training and qualification for the inclusion of students with Specific Health Needs (SHNs) stands out. That is, students with physical and mental health problems whose impact is significantly manifested in the learning process. Thus, the objective of this study was to identify the representations of PE teachers about their training to develop inclusive processes with students with SES. Participants in this study were 151 PE teachers from different regions and districts of Portugal (Algarve, Aveiro, Castelo Branco, Lisbon, Porto, and Viseu) who had 23.6 ± 8.1 years of teaching service. Teachers answered an online questionnaire, on the Google Forms platform, with open and closed questions about their education and training to develop inclusive processes in PE. The results indicate two significant dimensions: (1) initial training for teaching inclusive PE and (2) continuous training for inclusion. Regarding initial training, a large majority of the teachers under study, at the end of their initial training, did not have the essential skills to teach PE to students with SES. It was also identified that a large majority reported not having had any contact with students with SES throughout their training process for teaching. It was also recognized that this training was not adjusted to the development of intervention skills with students with SHN. Regarding continuous training, it was identified that attendance at this training increased their skills to teach PE to students with SHN. Workshops/actions/training courses are the main training models adopted. However, it is recognized that the training provided does not respond concretely to their training needs to intervene with students with SHN, since teachers essentially seek to improve intervention in the context of inclusive physical education. We conclude that teacher training for inclusion is not yet fully adjusted to the reality of the inclusive school paradigm. In this sense, in practical terms, the following are suggested: (1) the need for reinforcement in study plans with specific and long-term curricular units; (2) the introduction of real practice components in context; and (3) supervised pedagogical practice in diverse contexts.
Celestino, Tadeu (ORCID:0000000163087981)↗