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Results for “Environmental assay”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Development and evaluation of an agar capture system (ACS) for high-throughput screening of insoluble particulate substrates with bacterial growth and enzyme activity assays

In this work, we describe a method for containing insoluble particulates for use as substrates in either bacterial growth or enzyme assays. This method was designed for high-throughput screening of environmental or engineered bacteria. Benchmarking this method with several model bacteria uncovered phenotypes not observable with the particulate substrates alone.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Real-time PCR assays that detect genes for botulinum neurotoxin A–G subtypes

The role of Real-Time PCR assays for surveillance and rapid screening for pathogens is garnering more and more attention because of its versatility and ease of adoption. The goal of this study was to design, test, and evaluate Real-Time TaqMan PCR assays for the detection of botulinum neurotoxin (bont/A-G) genes from currently recognized BoNT subtypes. Assays were computationally designed and then laboratory tested for sensitivity and specificity using DNA preparations containing bont genes from 82 target toxin subtypes, including nine bivalent toxin types; 31 strains representing other clostridial species; and an extensive panel that consisted of DNA from a diverse set of prokaryotic (bacterial) and eukaryotic (fungal, protozoan, plant, and animal) species. In addition to laboratory testing, the assays were computationally evaluated using in silico analysis for their ability to detect bont gene sequences from recently identified toxin subtypes. Seventeen specific assays (two for each of the bont/C, bont/D, bont/E, and bont/G subtypes and three for each of the bont/A, bont/B, and bont/F subtypes) were designed and evaluated for their ability to detect bont genes encoding multiple subtypes from all seven serotypes. These assays could provide an additional tool for the detection of botulinum neurotoxins in clinical, environmental and food samples that can complement other existing methods used in clinical diagnostics, regulatory, public health, and research laboratories.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Lead tolerance and bioremoval by four strains of green algae from Nigerian fish ponds

Heavy metals from industry pose threats to human and environmental health. Microalgae are prime candidates to remove heavy metals from water and soil due to their metal-binding affinities, high growth rates, and contamination tolerance. Strain selection and composition of resulting contaminated biomass must be considered for downstream processing. In this study, we assessed the ability of four microalgae strains (Chlorophyceae) that were isolated from contaminated Nigerian fish ponds to take up dissolved lead at environmentally relevant concentrations (<0.05 mg L -1 – WHO standard). In a microplate assay, all strains grew in the presence of lead, tolerating concentrations up to 60 ppm, though the addition of dissolved lead affected the growth of the four strains. In a photobioreactor assay, all strains demonstrated the ability to take up dissolved lead, with removal efficiencies ranging from 86 to 93%. The concentrations of lead in contaminated biomass, removal efficiencies, and bioconcentration factors were greatest in one of the isolates Chlorella sp. MOW 12. Our results reinforce the fact that live microalgae have a greater biosorption capacity. Lead recovery from freeze-dried biomass using five different reagents showed that a 0.1 M hydrochloric acid solution was the most effective, with 83.4% recovery. We also showed that presence of lead in the culture medium resulted in an increase in the quantity of protein in the biomass. Elemental analysis of lead-bound biomass showed an increase in elements including boron and copper and a decrease in cobalt and sodium. Synergystic and antagonystic effect in uptake of other elements was strain specific, suggesting the possibility of tailored wastewater treatments depending on specific requirements.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Knowledge Graph of RB-Tnseq Data from Fitness Browser (KP-DP1)

Motivation: Predicting microbial gene fitness across environmental conditions remains a central challenge for predictive phenomics and autonomous experimentation. Fitness assays generate large volumes of genotype–phenotype measurements difficult to integrate with experimental metadata and biological function in a form that supports mechanistic reasoning. Knowledge graphs offer a semantic framework for unifying modalities and enabling context-aware inference. Results: We build GIMME (Graph Inference for Microbial Metabolism Exploration), a semantically grounded knowledge graph that unifies gene fitness measurements spanning 10 Pseudomonas species with experimental metadata and biological context. Media are decomposed into chemical components and experiments carry structured links to natural-language descriptions. The resulting graph supports two inference modes: (1) symbolic graph traversal to surface candidate gene–environment and gene–chemical associations, and (2) learned inference using heterogeneous graph neural networks that propagate information across neighborhoods. We formulate link regression over (gene, media, experiment) triplets, combining learned gene embeddings with pretrained LLM sourced text embeddings of node descriptions to predict gene fitness. We then augment a baseline MLP with an auxiliary message-passing encoder (GraphSAGE/GAT) that propagates information over gene–protein–function and media–chemical subgraphs, and fuse the two pathways with a gated residual connection. This approach produces strong agreement with held-out fitness measurements (GraphSAGE Pearson r 0.74) while also highlighting inference challenges in extreme-fitness regimes. We aggregate GAT edge-attention weights by relation type and layer to estimate which biological and environmental relations most influence fitness predictions. Conclusion: This work explores using knowledge graphs as “context graphs” for microbial phenotype prediction. They provide a rich substrate which enables explainable retrieval of supporting evidence, and provides a natural bridge to autonomous workflows that prioritize the next experiment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Scale-dependent enhancement of productivity and stability in xenic Nannochloropsis cultures

Although bacterial amendments can enhance algal productivity and stability, the development of algal-bacteria consortia for commercial-scale utilization is limited. Here, for this work, we used an established high-throughput approach to generate algal-bacteria consortia, and tested consortia performance at spatial scales from microplates to 320 L raceway ponds. We used both lab and field-reared strains of Nannochloropsis oceanica to build consortia. In some experiments, we imposed environmental perturbations to test the ability of bacteria to enhance algal culture stability. In repeated assays at the scale of well plates, flasks, and bioreactors, strong effects of bacterial amendments on N. oceanica were observed. These effects were most dramatic when cultures experienced stressors such as temperature perturbations or removal of CO 2 augmentation. Isolates that were advanced for field testing included species in the genera Algoriphagus, Oceanicaulis, and Marinobacter. When consortia were generated in the field, positive effects of bacterial amendments were not observed. The amended bacteria were outcompeted, and bacterial community composition across treatments converged after the first grow out. These results highlight the complexity of using consortia in open systems, where interactions between the existing bacterial community, inoculated bacteria, and changing environmental conditions are layered upon other differences in scale and cultivation regimes. Moreover, functionally redundant bacteria are likely present in the field. Following this work, we hypothesize that tight interactions (e.g., obligate relationships between partners) will scale more predictably to outdoor systems. We suggest relying on true synthetic ecological approaches in which the relationships between bacteria and algae partners are well understood, or synthetic ecological approaches coupled with high throughput approaches to design and test consortia. We also recommend future work to examine the effect of algae-bacteria inoculation ratios on productivity and stability, track dynamics of partners through time, and manage ponds to retain beneficial symbioses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Chemical Imaging for In Situ Detection and Discrimination of Aquatic Toxins Targeting Voltage Gated Sodium Channels

Biologically derived neurotoxins from cyanobacteria and algae impact environmental resources in addition to being considered a potential biological threat to human and animal health. Activity based assays are essential to detecting and responding to toxic neurotoxin events either naturally occurring or deliberate. Two toxins of interest include saxitoxin and brevetoxin. These toxins bind to and alter the function of voltage-gated sodium channels (NaV channels) which are essential for generating cell membrane action potential. We report the development and refinement of a System for Analysis at Liquid Vacuum Interface (SALVI) to assess the functional activity of saxitoxin and brevetoxin. This approach utilizes a vacuum-compatible microfluidic reactor that permits analysis at the liquid vacuum interface of human derived cells with a neurotoxin of interest in a biologically relevant environment.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

A triton X-100 assisted PMAxx-qPCR assay for rapid assessment of infectious African swine fever virus

Introduction African Swine Fever (ASF) is a highly infectious disease of pigs, caused by African swine fever virus (ASFV). The lack of vaccines and drugs makes strict disinfection practices to be one of the main measurements to curb the transmission of ASF. Therefore, it is important to assess if all viruses are inactivated after disinfection or after long time exposure in their natural conditions. Currently, the infectivity of ASFV is determined by virus isolation and culture in a biosafety level 3 (BSL-3) laboratory. However, BSL-3 laboratories are not readily available, need skilled expertise and may be time consuming. Methods In this study, a Triton X-100 assisted PMAxx-qPCR method was developed for rapid assessment of infectious ASFV in samples. PMAxx, an improved version of propidium monoazide (PMA), can covalently cross-link with naked ASFV-DNA or DNA inside inactivated ASFV virions under assistance of 0.1% (v/v) TritonX-100, but not with ASFV-DNA inside live virions. Formation of PMAxx-DNA conjugates prevents PCR amplification, leaving only infectious virions to be detected. Under optimum conditions, the limit of detection of the PMAxx-qPCR assay was 2.32log 10 HAD 50 /mL of infectious ASFV. Testing different samples showed that the PMAxx-qPCR assay was effective to evaluate intact ASFV virions after treatment by heat or chemical disinfectants and in simulated samples such as swine tissue homogenate, swine saliva swabs, and environmental swabs. However, whole-blood and saliva need to be diluted before testing because they may inhibit the PCR reaction or the cross-linking of PMAxx with DNA. Conclusion The Triton X-100 assisted PMAxx-qPCR assay took less than 3 h from sample to result, offering an easier and faster way for assessing infectious ASFV in samples from places like pig farms and pork markets.

Liu, Huan↗
DOE OSTI2024

SPRUCE Quantitative PCR (qPCR) of Microbial Gene Copy Numbers, 2021-2022

This dataset provides the results for quantitative polymerase chain reaction (qPCR) of peat samples collected from ambient and experimental plots in the Spruce and Peatland Responses Under Climatic and Environmental Change (SPRUCE) experiment site in June and August of 2021, and June of 2022. SPRUCE is located within the Marcell Experimental Forest in northern Minnesota, USA. The dataset includes bacterial, archaeal, fungal gene copy numbers, along with corresponding logarithmic values, at 11 depth increments of two-meter deep peat cores taken from 12 sampling sites locations inside SPRUCE plots (10 chambered and 2 ambient plots). The sampling, sample prep and analysis followed standard methods outlined in prior publications (Wilson et al. 2016; Kluber et al. 2020) except that a higher yielding Omega Bio-Tek Mag-Bind Environmental DNA 96 Kit was used for extractions and DNA was quantified using Qubit dsDNA High Sensitivity Assay Kit. qPCR subsamples of peat cores from the SPRUCE plots characterize changes in the abundance and composition of microbial communities of peat seasonally showing how composition varies under multiple levels of experimental peat warming and atmospheric CO2 concentrations. This dataset contains one data file in comma-separated values (.csv) format. Additional metadata are provided: one data dictionary and a file-level metadata file in comma-separated values (.csv) format and a user guide in PDF (*.pdf) format. On 2026-07-07 this dataset was updated to add three columns to the data file: ‘Fungal_copy_dry’, ‘Log_fungal_copy_dry’, ‘Fungal_copy_wet’. No previously released data values were altered. Additionally, the abstract, data dictionary, and user guide were updated, and a file-level metadata file was added.

Archaea↗
DOE OSTI2024

Nonparametric Multiparticle Set Methods for Interpreting Environmental Samples

Collection and analysis of environmental samples is commonly used by a range of stakeholders in nuclear safeguards and security contexts. While the ubiquity of samples and their transport in the environment allow regular collection, developing and demonstrating methods for analyzing these samples is difficult. In this work, an environmental sample consists of a set of one or more individual particles. Recent advances in reactor simulation have allowed us to generate data that are more representative of real-world environmental samples, enabling statistically defensible method development and testing. The most notable of these advances is a drastic increase in the number of material depletion regions, which allows our simulations to capture the variation in isotopic composition seen at length scales consistent with environmental samples. Traditional approaches for handling multiparticle samples treat each particle in the sample individually, estimating the quantity of interest (e.g., core-average burnup) resulting from measurement and analysis of signatures (e.g., nuclide assays) from each individual particle. Individual estimates are then averaged to generate a single estimate of the quantity of interest over the entire sample. In this presentation, we introduce two novel approaches for interpreting environmental samples that comprise of multiple particles: (1) the Quantile-Quantile Comparator, which uses a multivariate generalization of quantile-quantile plots for comparing unknown statistical distributions, and (2) the Set Transformer, an attention-based neural network module designed to model interactions among elements (particles) in the input set (sample). Statistically representative sampling cannot be guaranteed as samples are passively collected and are beholden to what particles are available in the environment. These new analysis methods for set-input problems are expected to be more robust than traditional approaches to issues of sampling bias where particles are not uniformly distributed throughout regions of interest, as well as generally outperform traditional approaches by jointly considering all elements in the set. We will present results comparing the performance of traditional single particle approaches and the novel Quantile-Quantile Comparator and Set Transformer for interpretation of simulated environmental samples.

Phathanapirom, Birdy↗
DOE OSTI2025

An elastin-like polymer targeting vascular endothelial growth factor receptor-1 reduces survival in serum-starved endothelial cells

Peptides often exhibit biological activity that depends on the context in which they are displayed and delivered. Understanding and controlling these contextual effects on peptide function is critical for designing targeted and responsive peptide-based biomaterials and therapeutics. Genetically engineered protein polymers such as elastin-like polypeptides (ELPs) can incorporate bioactive peptide motifs and are attractive candidates for biomaterials used in tissue engineering and targeted drug delivery. They also present an opportunity for investigating and modulating cell signaling pathways by presenting a peptide ligand in various defined chemical and physical environments. Vascular endothelial growth factor receptor-1 (VEGFR1) signaling plays important and complex roles in cell survival and angiogenesis, but polymeric materials that interact with this signaling axis are scarce. In this study, a novel genetically engineered elastin-like polymer that targets VEGFR1 is characterized. This polymer, termed R1B-ELP, binds to human endothelial cells in a manner dependent on its VEGFR1-targeting motif and, based on cell proliferation and cytotoxicity assays, demonstrates activity consistent with disrupting pro-survival signaling necessary for endothelial cell function under conditions of environmental stress. Notably, these findings indicate that ELP fusion alters the functional behavior of the targeting peptide. Modulators of VEGFR1 signaling have potential applications in basic studies of angiogenesis as well as in therapeutic applications targeting vascular or inflammatory diseases.

36 MATERIALS SCIENCE↗
DOE OSTI2023

JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom

Abstract Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mercury immunotoxicity in the brown watersnake ( Nerodia taxispilota ): An in vitro study

Mercury (Hg) is a heavy metal that enters the environment through natural and anthropogenic means. Once in the environment, Hg can biomagnify in food webs and is known to cause immunotoxic effects to wildlife. Compared with other vertebrates, knowledge of the reptilian immune system is lacking, especially in snakes. Further, even less is known about the impact of environmental contaminants on snake immunity. This gap in knowledge is largely due to an absence of established immune-based assays or specific reagents for these species. In this study, brown watersnakes (Nerodia taxispilota; n = 23) were captured on the Savannah River (Augusta, Georgia, USA), weighed, measured, bled, and released. Peripheral blood leukocytes (24 h old) were enriched and evaluated with an established mammalian in vitro lymphocyte proliferation assay. Enriched leukocytes were then exposed to mercury chloride (HgCl2) at 3.75, 37.5, and 75 μM. Total mercury (THg) in whole blood was also quantified. Snake peripheral blood leukocyte enrichment yielded >90% lymphocytes with viabilities averaging >70%. Exposure to HgCl 2 resulted in significant dose-dependent suppression of proliferative responses relative to spontaneous proliferation at 37.5 and 75 μM (both p ≤ 0.01) but not 3.75 μM (p = 0.99). Mean ± 1 SE concentration of THg in whole blood was 0.127 ± 0.027 mg/kg (wet weight). Based on the in vitro findings with HgCl 2 , snakes in systems with heavy Hg pollution may be at risk of immunosuppression, but N. taxispilota at the site in this study appear to be at low risk.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Activity assays of NnlA homologs suggest the natural product N -nitroglycine is degraded by diverse bacteria

Linear nitramines (R–N(R′)NO 2 ; R′ = H or alkyl) are toxic compounds, some with environmental relevance, while others are rare natural product nitramines. One of these natural product nitramines is N -nitroglycine (NNG), which is produced by some Streptomyces strains and exhibits antibiotic activity towards Gram-negative bacteria. An NNG degrading heme enzyme, called NnlA, has recently been discovered in the genome of Variovorax sp. strain JS1663 ( Vs NnlA). Evidence is presented that NnlA and therefore, NNG degradation activity is widespread. To achieve this objective, we characterized and tested the NNG degradation activity of five Vs NnlA homologs originating from bacteria spanning several classes and isolated from geographically distinct locations. E. coli transformants containing all five homologs converted NNG to nitrite. Four of these five homologs were isolated and characterized. Each isolated homolog exhibited similar oligomerization and heme occupancy as Vs NnlA. Reduction of this heme was shown to be required for NnlA activity in each homolog, and each homolog degraded NNG to glyoxylate, NO 2 − and NH 4 + in accordance with observations of Vs NnlA. It was also shown that NnlA cannot degrade the NNG analog 2-nitroaminoethanol. The combined data strongly suggest that NnlA enzymes specifically degrade NNG and are found in diverse bacteria and environments. These results imply that NNG is also produced in diverse environments and NnlA may act as a detoxification enzyme to protect bacteria from exposure to NNG.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Feedback on Forty-year Long Clean-up Operations of a Contaminated Soil for Environmental Purpose - 20026

One of the CEA facilities in France is the place of miscellaneous mapping and clean-up operations since the 1980's. The final purpose of the conducted work deals with the environmental remediation of the building. In France, the absence of a regulatory framework for the management of sites polluted by radioactive substances, especially as the lack of release thresholds, has led to develop different approaches of soil radiological characterization. The geostatistical approach is part of them. Preliminary investigations are an unavoidable step prior to clearance and remediation. First, historical analysis enables to define site perimeters to investigate as well as to precisely locate expected contaminated parts. For radioactive pollutants, the media (water, soil, air) and transfer routes participate in the definition of the investigation perimeter and thus also need to be identified through a geological study. At the same time, functional analysis leads to choose the best measurement means which could provide useful information when combined with visual inspection. An equipment well adapted to easy-to-measure radionuclides as gamma emitters, such as gamma probe or on-site gamma spectrometry, is usually selected as a non-destructive assay. Coupled with spatial positions, processed on-site radiological data can be mapped. Data processing consists in mapping and kriging before a geostatistical analysis in order to identify the zones of interest to be targeted. Selected zones are not only linked to high level count rates but also to low level ones so that a pollution-free reference is known in the area. This data processing also enables to categorize waste types according to their origin and contamination levels. An expected volume of different waste then follows as well as the waste characterization equipments. In-depth investigations, e.g. core drillings and samplings, naturally ensue to aim at remediation optimization through the assessment of environmental impact. After clean-up operations, non-destructive assays as well as destructive samplings enable to check the effective clearance. Following this methodology in the present remediation work, results of the first non-destructive assay campaign highlighted a long-lived transuranic radionuclides contamination in the concrete flagstone. Successive non-destructive assays were then performed in the defined zones of interest. Count rates measured with a surface probe were first mapped. The best localization of destructive assays, i.e. core drillings at a 1 meter depth, came from this surface mapping followed by a geostatistical analysis. The concrete flagstone was totally removed. Then, the depth of soil to remove under the flagstone was optimized from the results of radiological activities measured in core drillings samples. A new surface mapping was then drawn after this partial soil excavation. The sand and demolition rubble samples, homogeneously constituted from the flagstone fragments, were analyzed by gamma spectrometry. Meanwhile, waste drums and other containers were also measured by gamma spectrometry and passive neutron measurement devices. All these results have brought miscellaneous pieces of information. In this context, major issues appear in terms of physical constraints such as the premises tininess as well as of soil sampling techniques and in terms of measurement performances assessment and the representativeness of homogeneous samples. The choice of radiological soil and waste characterization devices is described in the light of enhanced performances by keeping in mind radiation protection requirements and a willing to always optimize waste categories (very low level waste) and volume. The improvement of the characterization methods appears through this forty-year long work while sharing the feedback of encountered difficulties. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2026

Enzymatic Biocontrol of Fire Blight ( Erwinia amylovora ) Using an Engineered Glycosyl Hydrolase

Current management of fire blight, caused by Erwinia amylovora , relies heavily on streptomycin a practice that has contributed to the emergence of antibiotic-resistant strains and raised environmental and regulatory concerns. Enzyme-based biocontrol agents offer a promising antibiotic-free approach that combines target specificity with environmental compatibility. This study evaluates CAase, a bacteriophage-derived glycosyl hydrolase, for its ability to disrupt E. amylovora biofilms and reduce disease severity. Biochemical assays and scanning electron microscopy confirmed that CAase efficiently degraded the extracellular polysaccharide (EPS) matrix, releasing cells from biofilms. Gas chromatography–mass spectrometry (GC–MS) linkage analysis of EPS isolated from two Erwinia amylovora strains demonstrated that CAase preferentially cleaves galactan-rich amylovoran produced by strain EA273, while exhibiting only limited activity toward the levan-rich EPS from strain EA1430. Functional assays revealed that CAase reduced bacterial viability by nearly 2 orders of magnitude at higher enzyme concentrations, strongly suppressed surface motility, and induced ultrastructural damage visible by transmission electron microscopy. Importantly, field trials showed that CAase significantly lowered blossom and shoot blight incidence under orchard conditions. These results highlight CAase as a potent enzyme-based strategy for reducing the virulence of E. amylovora and demonstrate its potential as a sustainable alternative to antibiotics in fire blight management.

antibiotic resistance↗
DOE OSTI2024

Untargeted Spatial Metabolomics and Spatial Proteomics on the Same Tissue Section

An increasing number of spatial multiomic workflows have been recently developed. Some of these approaches have leveraged initial mass spectrometry imaging (MSI)-based spatial metabolomics to inform region of interest (ROI) selection for downstream spatial proteomics. However, these workflows have been limited by varied substrate requirements between modalities or have required analyzing serial sections (i.e., one section per modality). To mitigate these issues, we present a novel multiomic workflow that uses desorption electrospray ionization (DESI)-MSI to identify representative spatial metabolite patterns on-tissue prior to spatial proteomic analyses on the same tissue section. Further, this workflow is demonstrated here with a model mammalian tissue (coronal rat brain section) mounted on a polyethylene naphthalate-membrane slide. Initial DESI-MSI resulted in 160 annotations (SwissLipids) within to the METASPACE platform (≤20% false discovery rate). A segmentation map from the annotated ion images informed downstream ROI selection for spatial proteomics characterization from the same sample. The unspecific substrate requirements and minimal sample disruption inherent to DESI-MSI allowed for an optimized, downstream spatial proteomics assay, resulting in 3888 ± 240 to 4717 ± 48 proteins being confidently directed per ROI (200 µm x 200 µm). Finally, we demonstrate the integration of multiomic information, where we found ceramide localization to be correlated with SMPD3 abundance (ceramide synthesis protein), and we also utilized protein abundance to resolve metabolite isomeric ambiguity. Overall, the integration of DESI-MSI into the multiomic workflow allows for complementary spatial and molecular-level information to be achieved from optimized implementations of each MS assay inherent to the workflow itself.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

An integrated multi-omics approach identifies the landscape of interferon-α-mediated responses of human pancreatic beta cells

Proinflammatory cytokines are important mediators of pancreatic beta cell dysfunction and demise in the early stages of type 1 diabetes (T1D). Interferon-a (IFNa), a type I interferon member, is expressed in the islets of T1D individuals and it is expression and signaling is regulated by both genetic (T1D risk variants) and environmental factors (viral infections) associated to T1D. We presently characterized human beta cells responses to IFNa by combining ATAC-seq, RNA-seq and proteomics assays. The initial beta cell response to IFNa was characterized by major chromatin remodeling, followed by marked changes in transcriptional and translational regulation. IFNa-induced changes in alternative splicing (AS) and first exon usage increased the diversity of transcripts expressed by beta cells. This, combined with changes observed on protein modification/degradation, ER stress and MHC class I, may significantly expand the peptide repertoire presented by beta cells to the immune system. On the other hand, beta cells up-regulated checkpoint proteins, such as PDL1 and HLA-E, that may protect them against the autoimmune assault. Data mining of the present multi-omics analysis led to the identification of two compound classes that revert IFNa effects on human beta cells and may be translated to clinical trials.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

A Rapid and High Throughput MIC Determination Method to Screen Uranium Resistant Microorganisms

The assessment of minimum inhibitory concentration (MIC) is a conventional technique used for the screening of microbial resistance against antibiotics, biocides, and contaminants such as heavy metals. However, as part of our ongoing work, we have observed biases associated with using traditional liquid MIC method to screen microbial heavy metal resistance, including both bacterial and fungal strains. Specifically, the addition of uranium into synthetic media causes immediate precipitation prior to the initiation of microbial growth, thus hampering the optical density measurements, and the obtained MIC values are thus flawed and inaccurate. To address this discrepancy, we report the optimization and development of a serial-dilution-based MIC method conducted on solid growth media supplemented with uranium, which is more accurate, relative to the testing of MICs performed in liquid cultures. Notably, we report on the efficacy of this method to screen not only bacteria that are resistant to uranium but also demonstrate the successful application to yeast and fungal isolates, for their ability to resist uranium, is more accurate and sensitive relative to the liquid method. We believe that this newly developed method to screen heavy metal resistance, such as uranium, is far superior to the existing liquid MIC method and propose replacing the liquid assay with the solid plate MIC reported herein.

54 ENVIRONMENTAL SCIENCES↗