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89 records · Page 5

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics

We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. We present several novel scientific discoveries, including the elucidation of the spike’s full glycan shield, the role of spike glycans in modulating the infectivity of the virus, and the characterization of the flexible interactions between the spike and the human ACE2 receptor. We also demonstrate how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems.

59 BASIC BIOLOGICAL SCIENCES↗

A Mobile Hot Cell for Conditioning Disused Sealed Radioactive Sources for Storage or Transportation

An innovative Mobile Hot Cell (MHC) has been developed for conditioning Disused Sealed Radioactive Sources (DSRS) category 1 and 2 for storage or transportation. The MHC is designed to provide both Radiological and Biological containment with a maximum capacity of 1000 Ci Co60 or 5000Ci Cs137 source and can be transported via standard cargo containers. This project has been supported through the National Nuclear Safety Administration (NNSA) Offsite Source Recovery Program (OSRP). The project is intended for the international community rather than domestic although domestic use is a possibility. Many countries have significant stockpiles of these devices that are often stored in less-than-optimal circumstances. This necessitates that these devices be addressed expeditiously, and the sources secured. The MHC utilizes robotics, automation, and other non-traditional methods for disassembling, characterizing, and packaging these sources that have reached end of life or are otherwise not needed. These innovative approaches are necessary to facilitate an expedited timeline to efficiently and safely secure these sources in a non-proliferation effort. Conditioning efforts include disassembling the device such as a teletherapy head used for cancer treatment, or blood/research irradiators such that the radioactive sources may be removed safely. The sources are then characterized. Leak checks are performed, dimensions are verified, and serial numbers are confirmed. Upon completion, the sources are typically placed into a Standard Forms Capsule which is seal welded closed. It is leak tested and placed into a Long-Term Storage Shield (LTSS) which can either be secured for storage directly or loaded into an appropriate cask for transportation. Further innovations include multiple deployment scenarios that include a full deployment of MHC components, deployment of the MHC automation internal components to an existing hot cell, deployment of minimally required MHC components and incorporation of sand for shielding, and integration of the MHC for Silo Storage, or Bore Hole Storage efforts. The MHC has evolved from a very specific use case to a “Swiss Army Knife” type of a tool in that it can be readily adapted to a large variety of situations. Innovative approaches such as the use of robotics, Computer Numeric Control (CNC) machining centers, automated welding equipment, HDMI Cameras, and LED lighting are some of the developed technologies incorporated into the MHC design. Shielding is accomplished with a steel walled Base Box which is surrounded by four nesting doll shield shells which when combined limits the external dose rate to 5mr/hr when a 1000 Ci Co60 source is exposed inside.

99 - GENERAL AND MISCELLANEOUS↗

Structure of a ribonucleotide reductase R2 protein radical

Aerobic ribonucleotide reductases (RNRs) initiate synthesis of DNA building blocks by generating a free radical within the R2 subunit; the radical is subsequently shuttled to the catalytic R1 subunit through proton-coupled electron transfer (PCET). Here we present a high-resolution room temperature structure of the class Ie R2 protein radical captured by x-ray free electron laser serial femtosecond crystallography. The structure reveals conformational reorganization to shield the radical and connect it to the translocation path, with structural changes propagating to the surface where the protein interacts with the catalytic R1 subunit. Restructuring of the hydrogen bond network, including a notably short O–O interaction of 2.41 angstroms, likely tunes and gates the radical during PCET. These structural results help explain radical handling and mobilization in RNR and have general implications for radical transfer in proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Deinococcus radiodurans UWO298 Dependence on Background Radiation for Optimal Growth

Ionizing radiation is a major environmental variable for cells on Earth, and so organisms have adapted to either prevent or to repair damages caused by it, primarily from the appearance and accumulation of reactive oxygen species (ROS). In this study, we measured the differential gene expression in Deinococcus radiodurans UWO298 cultures deprived of background ionizing radiation (IR) while growing 605 m underground at the Waste Isolation Pilot Plant (WIPP), reducing the dose rate from 72.1 to 0.9 nGy h –1 from control to treatment, respectively. This reduction in IR dose rate delayed the entry into the exponential phase of the IR-shielded cultures, resulting in a lower biomass accumulation for the duration of the experiment. The RNASeq-based transcriptome analysis showed the differential expression of 0.2 and 2.7% of the D. radiodurans genome after 24 and 34 h of growth in liquid culture, respectively. Gene expression regulation after 34 h was characterized by the downregulation of genes involved in folding newly synthesized and denatured/misfolded proteins, in the assimilation of nitrogen for amino acid synthesis and in the control of copper transport and homeostasis to prevent oxidative stress. We also observed the upregulation of genes coding for proteins with transport and cell wall assembly roles. These results show that D. radiodurans is sensitive to the absence of background levels of ionizing radiation and suggest that its transcriptional response is insufficient to maintain optimal growth.

59 BASIC BIOLOGICAL SCIENCES↗

Structural insights into the modulation of coronavirus spike tilting and infectivity by hinge glycans

Abstract Coronavirus spike glycoproteins presented on the virion surface mediate receptor binding, and membrane fusion during virus entry and constitute the primary target for vaccine and drug development. How the structure dynamics of the full-length spikes incorporated in viral lipid envelope correlates with the virus infectivity remains poorly understood. Here we present structures and distributions of native spike conformations on vitrified human coronavirus NL63 (HCoV-NL63) virions without chemical fixation by cryogenic electron tomography (cryoET) and subtomogram averaging, along with site-specific glycan composition and occupancy determined by mass spectrometry. The higher oligomannose glycan shield on HCoV-NL63 spikes than on SARS-CoV-2 spikes correlates with stronger immune evasion of HCoV-NL63. Incorporation of cryoET-derived native spike conformations into all-atom molecular dynamic simulations elucidate the conformational landscape of the glycosylated, full-length spike that reveals a role of hinge glycans in modulating spike bending. We show that glycosylation at N1242 at the upper portion of the stalk is responsible for the extensive orientational freedom of the spike crown. Subsequent infectivity assays implicated involvement of N1242-glyan in virus entry. Our results suggest a potential therapeutic target site for HCoV-NL63.

59 BASIC BIOLOGICAL SCIENCES↗

Efficient 15 N hyperpolarization of [ 15 N 3 ]metronidazole antibiotic via spin-relayed pulsed SABRE-SHEATH

Signal Amplification by Reversible Exchange in SHield Enables Alignment Transfer to Heteronuclei (SABRE-SHEATH) is an NMR hyperpolarization technique that relies of the simultaneous exchange of parahydrogen and a to-be-hyperpolarized molecule on the metal center of a polarization-transfer catalyst in a microtesla magnetic field. Until recently, this method has been understood to perform hyperpolarization by establishing level anti-crossings between the nuclear spins of the parahydrogen derived hydrides (acting as a source of hyperpolarization) and those of the substrate. Recently, the application of highly non-intuitive pulse sequences (comprising pulses of microtesla DC fields) was predicted to hyperpolarize nuclear spins more efficiently than the canonical (static-field) SABRE-SHEATH approach. Here we show that by employing a basic “on-off” pulse sequence of rectangular microtesla pulses, it is possible to improve the hyperpolarization efficiency for SABRE-SHEATH of [ 15 N 3 ]metronidazole, an FDA-approved antibiotic (in non-enriched and non-hyperpolarized form) and potential hypoxia sensing molecule. Specifically, we demonstrate that 15N polarization of 18.5 % can be obtained in 80 s of parahydrogen bubbling parahydrogen through a solution containing 20 mM [ 15 N 3 ]metronidazole. In practice, (1.32 ± 0.14)-fold improvements in P 15N was obtained with the pulsed method described here compared to static field technique variant. These results show that pulsed SABRE-SHEATH was successfully applied to 15 N-labeled biologically relevant molecule. Moreover, we also demonstrate that although the pulsed SABRE-SHEATH sequence was designed for polarization transfer from parahydrogen derived hydrides to the metronidazole’s 15 N catalyst-binding site, all three 15 N sites of [ 15 N 3 ]metronidazole attained the hyperpolarized state. This spin-relayed polarization transfer becomes possible due to the 15 N relay network established by their spin-spin J-couplings. The feasibility of the spin-relayed polarization transfer is demonstrated here for the first time for pulsed SABRE-SHEATH (as opposed to the static-field SABRE-SHEATH reported previously) and it paves the way to broad applicability of the technique.

Hyperpolarization↗

Challenges and Solutions in Operation and Lay-Up of the Modular Caustic- Side Solvent Extraction Unit - 20078

The Modular Caustic-Side Solvent Extraction (CSSX) Unit (MCU) was designed and constructed to provide interim salt waste processing so that the Liquid Waste Disposition Program (LWDP) could continue waste removal and tank closure until start-up of the Salt Waste Processing Facility (SWPF). MCU processes Clarified Salt Solution (CSS), or salt solution (SS) that has undergone actinide removal/filtration, to produce two waste streams: the cesium laden Strip Effluent (SE), which is incorporated into glass at the Defense Waste Processing Facility (DWPF), and the cesium depleted Decontaminated SS (DSS), which is incorporated into grout at the Saltstone Production Facility (SPF). MCU completed start-up in 2008 with an initial operating life of 3 years and design life of 5 years. Prior to reaching the end of the design life, multiple critical components were upgraded and/or replaced to mitigate risks associated with any delays in SWPF start-up. During the remainder of operation (until June 2019), MCU was challenged to maximize processing with minimal additional modifications to repair/improve aging infrastructure, while maintaining low levels of risk to workers and the environment. Notable challenges during the extended operating life of the facility involved both mechanical and operational issues. Two of the most significant issues were the increased frequency of Process Vessel Ventilation (PVV) High Efficiency Particulate Air (HEPA) filter change-outs and the biofouling of the SE coalescer (SEC). The major impacts of both issues were that replacement of these components 1) resulted in high exposure to workers, and 2) required substantial downtime, thus hindering achievement of processing goals. PVV HEPA filter replacements are required based on dose rate and differential pressure (dP) limits. After introducing a higher-curie feed to MCU, the operating time between change outs was reduced by approximately half. SEC replacements are required based on dP limits. After restarting from an extended outage, the operating life of the SEC was significantly reduced by more than half due to biofouling. As a result of extensive troubleshooting and process improvements, the facility was able to recover performance and extend the operating life of the PVV HEPA filters and the SEC media. Through troubleshooting both of these issues, the facility was also able to learn from prior experience and adapt in order to minimize down time and maintain throughput. Although the facility took advantage of short periods of downtime to perform nonintrusive troubleshooting and minor corrective/preventative maintenance activities, longer outages were periodically required for corrective maintenance involving process cell entry. During these outages, remote tools and specialized shield plates were employed to minimize dose to workers. Mock-ups of non-routine maintenance activities were critical to early identification of potential issues and improvements, which shortened outage duration. Consistent with the facility's operational strategy, evolutions needed for MCU layup were identified and sequenced to ensure safe conditions within the facility, meet pre-defined criteria for lay-up configuration, and protect workers, while minimizing the impact to SWPF integration. De-inventory and flushing of process areas was prioritized so that the total residual inventory was reduced as efficiently as possible. This paper discusses lessons learned and best practices from troubleshooting unique issues, performing complex maintenance activities, and implementing a layup strategy that best supports the overall system mission. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Selective consolidation of learning and memory via recall-gated plasticity

In a variety of species and behavioral contexts, learning and memory formation recruits two neural systems, with initial plasticity in one system being consolidated into the other over time. Moreover, consolidation is known to be selective; that is, some experiences are more likely to be consolidated into long-term memory than others. Here, we propose and analyze a model that captures common computational principles underlying such phenomena. The key component of this model is a mechanism by which a long-term learning and memory system prioritizes the storage of synaptic changes that are consistent with prior updates to the short-term system. This mechanism, which we refer to as recall-gated consolidation, has the effect of shielding long-term memory from spurious synaptic changes, enabling it to focus on reliable signals in the environment. We describe neural circuit implementations of this model for different types of learning problems, including supervised learning, reinforcement learning, and autoassociative memory storage. These implementations involve synaptic plasticity rules modulated by factors such as prediction accuracy, decision confidence, or familiarity. We then develop an analytical theory of the learning and memory performance of the model, in comparison to alternatives relying only on synapse-local consolidation mechanisms. We find that recall-gated consolidation provides significant advantages, substantially amplifying the signal-to-noise ratio with which memories can be stored in noisy environments. We show that recall-gated consolidation gives rise to a number of phenomena that are present in behavioral learning paradigms, including spaced learning effects, task-dependent rates of consolidation, and differing neural representations in short- and long-term pathways.

59 BASIC BIOLOGICAL SCIENCES↗

Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre

Scientific exploration of phototrophic bacteria over nearly 200 years has revealed large phylogenetic gaps between known phototrophic groups that limit understanding of how phototrophy evolved and diversified. Here, through Boreal Shield lake water incubations, we cultivated an anoxygenic phototrophic bacterium from a previously unknown order within the Chloroflexota phylum that represents a highly novel transition form in the evolution of photosynthesis. Unlike all other known phototrophs, this bacterium uses a type I reaction centre (RCI) for light energy conversion yet belongs to the same bacterial phylum as organisms that use a type II reaction centre (RCII) for phototrophy. Using physiological, phylogenomic and environmental metatranscriptomic data, we demonstrate active RCI-utilizing metabolism by the strain alongside usage of chlorosomes and bacteriochlorophylls related to those of RCII-utilizing Chloroflexota members. Despite using different reaction centres, our phylogenomic data provide strong evidence that RCI-utilizing and RCII-utilizing Chloroflexia members inherited phototrophy from a most recent common phototrophic ancestor. The Chloroflexota phylum preserves an evolutionary record of the use of contrasting phototrophic modes among genetically related bacteria, giving new context for exploring the diversification of phototrophy on Earth.

59 BASIC BIOLOGICAL SCIENCES↗

Development of an immersion fiber optic Raman probe for real-time analysis of molten materials

This study presents an advancement in high-temperature Raman spectroscopy, specifically for analyzing molten materials. It introduces an approach by integrating a fiber-optic Raman probe with a copper block protection system designed to endure extreme thermal conditions. The copper block features an open port designed to accommodate an external telescope with a 3 cm focal length, enabling Raman spectra collection in challenging high-temperature environments. A built-in gas channel ensures a continuous flow of argon gas to prevent flux intrusion. The robust copper block acts as a reliable shield, safeguarding the fiber-optic Raman probe within molten materials. This enhancement maintains the probe's integrity and significantly improves its resilience, making it ideal for rigorous investigations of molten substances. This advancement is particularly relevant in metallurgy, where flux materials impact production quality and efficiency. The ability to acquire Raman signals under elevated thermal conditions offers opportunities for studying molecular dynamics, compositional changes, and chemical interactions within molten substances. This introduced direct immersion probing technique has implications, benefiting both scientific and industrial fields. It holds promise for advancing research and exploration in various contexts, from fundamental scientific inquiries to practical applications in metallurgical processes, where flux materials are critical for optimizing production quality and efficiency. Furthermore, this approach enhances the capabilities of high-temperature Raman spectroscopy, making it a valuable tool for investigating molten materials and their properties in diverse settings.

Argon↗

High-resolution ultra-low field magnetic resonance imaging with a high-sensitivity sensing coil

We present high-resolution magnetic resonance imaging (MRI) at ultra-low field (ULF) with a proton Larmor frequency of around 120 kHz. The key element is a specially designed high-sensitivity sensing coil in the shape of a solenoid with a few millimeter gap between windings to decrease the proximity effect and, hence, increase the coil’s quality ([Formula: see text]) factor and sensitivity. External noise is strongly suppressed by enclosing the sensing coil in a copper cylindrical shield, large enough not to negatively affect the coil’s [Formula: see text] factor and sensitivity, measured to be 217 and 0.47 fT/Hz[Formula: see text], respectively. To enhance small polarization of proton spins at ULF, a strong pulsed 0.1 T prepolarization field is applied, making the signal-to-noise ratio (SNR) of ULF MRI sufficient for high-quality imaging in a short time. We demonstrate ULF MRI of a copper sulfate solution phantom with a resolution of [Formula: see text] and SNR of 10. The acquisition time is 6.3 min without averaging. The sensing coil size in the current realization can accommodate imaging objects of 9 cm in size, sufficient for hand, and it can be further increased for human head imaging in the future. Since the in-plane resolution of [Formula: see text] is typical in anatomical medical imaging, this ULF MRI method can be an alternative low-cost, rapid, portable method for anatomical medical imaging of the human body or animals. This ULF MRI method can supplement other MRI methods, especially when such methods are restricted due to high cost, portability requirement, imaging artifacts, and other factors.

59 BASIC BIOLOGICAL SCIENCES↗

High foliar K and P resorption efficiencies in old-growth tropical forests growing on nutrient-poor soils

Resorption is the active withdrawal of nutrients before leaf abscission. This mechanism represents an important strategy to maintain efficient nutrient cycling; however, resorption is poorly characterized in old-growth tropical forests growing in nutrientpoor soils. We investigated nutrient resorption from leaves in 39 tree species in two tropical forests on the Guiana Shield, French Guiana, to investigate whether resorption efficiencies varied with soil nutrient, seasonality, and species traits. The stocks of P in leaves, litter, and soil were low at both sites, indicating potential P limitation of the forests. Accordingly, mean resorption efficiencies were higher for P (35.9%) and potassium (K; 44.6%) than for nitrogen (N; 10.3%). K resorption was higher in the wet (70.2%) than in the dry (41.7%) season. P resorption increased slightly with decreasing total soil P; and N and P resorptions were positively related to their foliar concentrations. We conclude that nutrient resorption is a key plant nutrition strategy in these old-growth tropical forests, that trees with high foliar nutrient concentration reabsorb more nutrient, and that nutrients resorption in leaves, except P, are quite decoupled from nutrients in the soil. Seasonality and biochemical limitation played a role in the resorption of nutrients in leaves, but species-specific requirements obscured general tendencies at stand and ecosystem level.

59 BASIC BIOLOGICAL SCIENCES↗

Active anaerobic methane oxidation and sulfur disproportionation in the deep terrestrial subsurface

Abstract Microbial life is widespread in the terrestrial subsurface and present down to several kilometers depth, but the energy sources that fuel metabolism in deep oligotrophic and anoxic environments remain unclear. In the deep crystalline bedrock of the Fennoscandian Shield at Olkiluoto, Finland, opposing gradients of abiotic methane and ancient seawater-derived sulfate create a terrestrial sulfate-methane transition zone (SMTZ). We used chemical and isotopic data coupled to genome-resolved metaproteogenomics to demonstrate active life and, for the first time, provide direct evidence of active anaerobic oxidation of methane (AOM) in a deep terrestrial bedrock. Proteins from Methanoperedens (formerly ANME-2d) are readily identifiable despite the low abundance (≤1%) of this genus and confirm the occurrence of AOM. This finding is supported by 13C-depleted dissolved inorganic carbon. Proteins from Desulfocapsaceae and Desulfurivibrionaceae, in addition to 34S-enriched sulfate, suggest that these organisms use inorganic sulfur compounds as both electron donor and acceptor. Zerovalent sulfur in the groundwater may derive from abiotic rock interactions, or from a non-obligate syntrophy with Methanoperedens, potentially linking methane and sulfur cycles in Olkiluoto groundwater. Finally, putative episymbionts from the candidate phyla radiation (CPR) and DPANN archaea represented a significant diversity in the groundwater (26/84 genomes) with roles in sulfur and carbon cycling. Our results highlight AOM and sulfur disproportionation as active metabolisms and show that methane and sulfur fuel microbial activity in the deep terrestrial subsurface.

59 BASIC BIOLOGICAL SCIENCES↗

Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation

Abstract Single-stranded DNA (ssDNA) intermediates which emerge during DNA metabolic processes are shielded by replication protein A (RPA). RPA binds to ssDNA and acts as a gatekeeper to direct the ssDNA towards downstream DNA metabolic pathways with exceptional specificity. Understanding the mechanistic basis for such RPA-dependent functional specificity requires knowledge of the structural conformation of ssDNA when RPA-bound. Previous studies suggested a stretching of ssDNA by RPA. However, structural investigations uncovered a partial wrapping of ssDNA around RPA. Therefore, to reconcile the models, in this study, we measured the end-to-end distances of free ssDNA and RPA–ssDNA complexes using single-molecule FRET and double electron–electron resonance (DEER) spectroscopy and found only a small systematic increase in the end-to-end distance of ssDNA upon RPA binding. This change does not align with a linear stretching model but rather supports partial wrapping of ssDNA around the contour of DNA binding domains of RPA. Furthermore, we reveal how phosphorylation at the key Ser-384 site in the RPA70 subunit provides access to the wrapped ssDNA by remodeling the DNA-binding domains. These findings establish a precise structural model for RPA-bound ssDNA, providing valuable insights into how RPA facilitates the remodeling of ssDNA for subsequent downstream processes.

Biochemistry & Molecular Biology↗

Influence of ion-pairing reagents on the separation of intact glycoproteins using hydrophilic-interaction liquid chromatography - high-resolution mass spectrometry

Hydrophilic-interaction liquid chromatography (HILIC) of intact proteins offers high-resolution separations of glycoforms of glycoproteins differing in the number of (neutral) glycans. However, to obtain efficient separations it is essential that the positively charged sites of the proteins are shielded by acidic (negative) ion-pair reagents (IPRs), so as to enhance the contribution of the hydroxyl groups of the (neutral) sugars in the glycoprotein. Here, we studied the influence of various IPRs that differ in physico-chemical properties, such as hydrophobicity and acidity, on the capillary-scale HILIC separation of intact (glyco)proteins. We evaluated the use of fluoroacetic acid (MFA), difluoroacetic acid (DFA), trifluoroacetic acid (TFA), and heptafluorobutyric acid (HFBA) as diluents for sample preparation, as solvents for sample loading on a reversed-phase trap prior to the HILIC separation, and as mobile-phase components for HILIC and HILIC-MS. To reduce the contribution of ion-exchange interaction with the (silica-based) stationary phase, we used an acrylamide-based monolithic column. We studied the influence of the different IPRs on each step of the separation of a mixture of proteins of different size and hydrophilicity and on the separation of the five glycoforms of ribonuclease B. The content of IPR in the sample was shown not to affect the separation and the MS detection. However, a low content of TFA and DFA in the mobile phase is favourable, as it reduces adduct formation and leads to higher signal intensity. The optimized HILIC conditions successfully resolved nine major glycoforms groups of a ~40 kDa glycoprotein horseradish peroxidase (HRP), as an example of a complex glycoprotein.

59 BASIC BIOLOGICAL SCIENCES↗

Domestic Supply Chain of Medical Consumables Needed During COVID-19 Pandemic

This report is an assessment of the availability, demand, and production capability of medical consumables needed to combat the COVID-19 pandemic. We focus here on the ability of the supply chain to increase production to meet demand during peak pandemic conditions. In addition, we report on domestic production efforts and supply chain issues, as well as the propensity of other countries to limit export of needed medical supplies to the United States. In brief, the domestic supply chain and production capability vary greatly depending on the consumable. Some consumables, such as N95 masks or face shields, can likely be nearly fully supplied by domestic production, while other consumables, such as gloves or surgical masks, have little domestic production and thus will depend on imports to meet demand. The assessment pulls primarily from published news sources and company press releases. As such, the demand and production numbers are not precisely known, and some degree of uncertainty exists in them. The total production capability is also often difficult to ascertain from these reports especially as other industries have begun to supplement existing supply chains. In addition, local conditions (including company financial decisions, local public health issues, and political aspects) can vary throughout the pandemic which will affect future production. The report also pulls from estimates of demand and domestic production of some consumables compiled by the White House COVID-19 Supply Chain Taskforce (SCTF) presented by Rear Admiral John Polowczyk before a June 9, 2020 hearing of the Senate Homeland Security and Governmental Affairs Committee. These numbers, where applicable, are likely to be more accurate than those found in public news sources since they are more directly tied to private companies’ actual orders and actual production estimates, as opposed to publicly released estimates. Finally, we note that other issues with the supply chain, including the production of raw materials, increase demand due to industries that have not previously used PPE now using it, and increased domestic production from non-traditional suppliers, make complete picture of a rapidly changing supply chain difficult to obtain. This report attempts to produce an accurate image of the supply and estimated demand, as understood by the authors who are not experts in the medical supply chain.

42 ENGINEERING↗

A transcriptome software comparison for the analyses of treatments expected to give subtle gene expression responses

Background: In this comparative study we evaluate the performance of four software tools: DNAstar-D (DESeq2), DNAstar-E (edgeR), CLC Genomics and Partek Flow for identification of differentially expressed genes (DEGs) using a transcriptome of E. coli. The RNA-seq data are from the effect of below-background radiation 5.5 nGy total dose (0.2nGy/hr) on E. coli grown shielded from natural radiation 655 m below ground in a pre-World War II steel vault. The gene expression response to three supplemented sources of radiation designed to mimic natural background, 1952 – 5720 nGy in total dose (71–208 nGy/hr), are compared to this “radiation-deprived” treatment. In addition, RNA-seq data of Caenorhabditis elegans nematode from similar radiation treatments was analyzed by three of the software packages. Results: In E. coli, the four software programs identified one of the supplementary sources of radiation (KCl) to evoke about 5 times more transcribed genes than the minus-radiation treatment (69–114 differentially expressed genes, DEGs), and so the rest of the analyses used this KCl vs “Minus” comparison. After imposing a 30-read minimum cutoff, one of the DNAStar options shared two of the three steps (mapping, normalization, and statistic) with Partek Flow (they both used median of ratios to normalize and the DESeq2 statistical package), and these two programs identified the highest number of DEGs in common with each other (53). In contrast, when the programs used different approaches in each of the three steps, between 31 and 40 DEGs were found in common. Regarding the extent of expression differences, three of the four programs gave high fold-change results (15–178 fold), but one (DNAstar’s DESeq2) resulted in more conservative fold-changes (1.5–3.5). In a parallel study comparing three qPCR commercial validation software programs, these programs also gave variable results as to which genes were significantly regulated. Similarly, the C. elegans analysis showed exaggerated fold-changes in CLC and DNAstar’s edgeR while DNAstar-D was more conservative. Conclusions: Regarding the extent of expression (fold-change), and considering the subtlety of the very low level radiation treatments, in E. coli three of the four programs gave what we consider exaggerated fold-change results (15 – 178 fold), but one (DNAstar’s DESeq2) gave more realistic fold-changes (1.5–3.5). When RT-qPCR validation comparisons to transcriptome results were carried out, they supported the more conservative DNAstar-D’s expression results. When another model organism’s (nematode) response to these radiation differences was similarly analyzed, DNAstar-D also resulted in the most conservative expression patterns. Therefore, we would propose DESeq2 (“DNAstar-D”) as an appropriate software tool for differential gene expression studies for treatments expected to give subtle transcriptome responses.

59 BASIC BIOLOGICAL SCIENCES↗