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This report compiles Wetlab training slides for DTRA sponsored training and has presentations titled: 1) Library Validation Step 2: Bioanalyzer DNA HS Assay, 2) Library Validation Step 3: qPCR, 3) Setting up a MiSeq Run, 4) Sample Prep & Initial QC, 5) Detailed Illumina MiSeq Sequencing, 6) AmpliSeq for Illumina: Best Practices, and 7) Sample/Data Management for SARS-CoV-2 Samples.
Abstract not provided.
This publication highlights achievements in nuclear security, science, technology and engineering, mission operations, and community relations at Los Alamos National Laboratory.
This publication highlights achievements in nuclear security, science, technology and engineering, mission operations, and community relations at Los Alamos National Laboratory.
Abstract not provided.
A monthly summary of top achievements at Los Alamos National Laboratory for July 2021 in the areas of Nuclear Security; Science, Technology, and Engineering; Mission Operations; Community Relations, and Selected Media Coverage.
Carbon dioxide (CO 2 ) is considered the sole culprit for global warming; however, nitrous oxide (N 2 O), a greenhouse gas (GHG) with approximately 300 times more global warming potential than CO 2 , accounts for 6% of the GHG emissions in the United States. Seventy five percent of N 2 O emissions come from synthetic nitrogen (N) fertilizer usage in the agriculture sector primarily due to excess fertilization. Numerous studies have shown that changes in soil management practices, specifically optimizing N fertilizer use and amending soil with organic and humate materials can reverse soil damage and improve a farmer's or land reclamation company's balance sheet. Soil restoration is internationally recognized as one of the lowest cost GHG abatement opportunities available. Profitability improves in two ways: (1) lower operating costs resulting from lower input costs (water and fertilizer); and (2) increased revenue by participation in emerging GHG offsets markets, and water quality trading markets.
The NVBL Viral Fate and Transport Team includes researchers from eleven DOE national laboratories and is utilizing unique experimental facilities combined with physics-based and data-driven modeling and simulation to study the transmission, transport, and fate of SARSCoV-2. The team was focused on understanding and ultimately predicting SARS-CoV-2 viability in varied environments with the goal of rapidly informing strategies that guide the nation’s resumption of normal activities. The primary goals of this project include prioritizing administrative and engineering controls that reduce the risk of SARS-CoV-2 transmission within an enclosed environment; identifying the chemical and physical properties that influence binding of SARS-CoV-2 to common surfaces; and understanding the contribution of environmental reservoirs and conditions on transmission and resurgence of SARS-CoV-2.
The University of Texas (UT), Genesis of Methane Hydrate in Coarse-Grained Systems: Northern Gulf of Mexico Slope Project (GOM2), will perform the UT-GOM2-2 drilling and coring expedition in the Terrebonne Basin, Gulf of Mexico outer continental shelf. This is the scientific plan for the acquisition, storage, analysis, and distribution of core and other collected samples for UT-GOM2-2.
Switchgrass (Panicum virgatum) has great potential as a sustainable bioenergy and bioproducts feedstock. However, there are a number of challenges that must be overcome to achieve this goal. One of the most significant challenges to switchgrass productivity are fungal pathogens, especially rusts and smuts. The primary goals of our project were to characterize the distribution of fungal pathogens on switchgrass across central North America and to identify genetic loci that control resistance to those pathogens. The research was primarily conducted with large common garden plantings of a switchgrass, distributed along a latitudinal gradient from South Texas to South Dakota. By conducting this research simultaneously at 10 field locations, we were able establish the relative contributions of genes and the environment to pathogen resistance. Through this research, we identified multiple genomic regions (loci) that contribute to rust resistance and found that the effects of these loci on resistance were highly influenced by field site location. Our research revealed that most of the rust damage to switchgrass from Texas to the northern United States is caused by a single fungal species, Puccinia novopanici. Therefore, genetic variation within this species and/or local environmental conditions are responsible for the inconsistent efficacy of pathogen resistance loci. We are currently investigating these two non-mutually exclusive hypotheses. In addition to our studies of rust pathogens, we were able to identify resistance loci for the head smut fungal pathogen Tilletia maclaganii. The funding from this grant facilitated a collaboration with the DOE Joint Genome Institute to develop a reference genome for T. maclaganii. A reference genome will make population genetic studies of this smut fungus possible, which in turn will facilitate the development of strategies to mitigate its impact. Overall, the funded research has greatly advanced our understanding of the genetic basis of fungal pathogen resistance switchgrass. This knowledge will help facilitate the breeding of more resistant cultivars and thus, increase the productivity of swichgrass generally.
In the early weeks of the COVID-19 pandemic, Lawrence Livermore researchers mobilized to address emerging challenges and develop capabilities for detecting the SARS-CoV-2 virus and fighting COVID-19, the diseased caused by the virus. As described in the article beginning on p. 4, the Laboratory’s Innovation and Partnerships Office provided technology transfer expertise to deploy existing, in-development, and new technologies to help detect SARS-CoV-2 and treat COVID-19.
Sandia provided technical assistance to Energy Cloud to support the assessment of Energy Cloud’s technology for air filtration of the SARS-CoV-2 virus. The Energy Cloud system was developed to filter the SARS-CoV-2 virus from commercial HVAC systems, ducts, and enclosed rooms without generating ozone. The project included a 3-week experimental series with aerosolized SARS-CoV-2 virus at the University of Southern California’s biosafety level 3 (BSL-3) laboratory. USC provided the facility as well as experimentally derived measurements and assessment of the Energy Cloud system efficacy for SARSCoV-2 filtration from air handling systems.
A bibliography of COVID-19 or SARS-COV-2 Works Published and Presentations 2020-2021.
The current study made a comprehensive literature review of the structure activity relationship (SAR) for microcidal and virucidal influence of ionic liquids. It summarized the key structure parameters that have close correlation to the antimicrobial and antiviral properties of the ILs. It proposed an experimental plan on developing and testing an effective ionic liquid from renewable lignocellulosic biomass. The goal is to understand the structure activity relationship (SAR) for virucidal influence of ionic liquids through comprehensive literature search and data analysis. A full experimental plan will be drafted based on the literature summary. Perform a comprehensive literature search to aid the development of an effective and easily deployable method to inactivate SARS-CoV-2 and decontaminate surfaces based on low-cost functional ionic liquids. These designer solvents have the potential to be a compelling and environmentally friendly alternative to common chemical disinfectants. Literature summary report including reported ionic liquid structures, synthesis and testing methods, and the structure activity relationship. Experimental plan on developing a low cost effective antiviral ionic liquid.
In this issue of Physical Sciences Vistas we highlight examples of “excellence in nuclear security.” In this issue, highlights of our outstanding work supporting the Laboratory’s nuclear security enterprise include the following: The complete refurbishment of Sigma’s surface finishing lab. Pride in the lab’s revitalized condition on the part of the operations and R&D staff responsible for this complex operation is well justified. Development of advanced materials and processes enabling next-generation weapons designs, much of which has been facilitated by projects supported by the Laboratory Directed Research and Development Program. The use of proton radiography in illuminating elements important to validating high explosive burn models. The experimental series was a collaboration between Los Alamos researchers and staff at Lawrence Livermore and Sandia national laboratories and the United Kingdom’s Atomic Weapons Establishment. Deployment of a sophisticated remote handling unit to safely transfer highly radioactive materials required to support mission-critical projects. The skillful swap of an electrical transformer at the Los Alamos Neutron Science Center (LANSCE). The deliberate operation restored power to the accelerator in less than estimated time. A look at George Goff ’s role in translating fundamental science into applied solutions essential to the Lab’s nuclear security mission.
Abstract not provided.
Low temperature plasmas (LTPs) are the plasmas of electron-volt (eV) physics and eV technologies. LTPs have characteristic electron temperatures of a few eV and fractional ionizations that are typically small. Since LTPs have electron temperatures commensurate with the threshold energies of excited states in neutral atoms and molecules, power transfer from electrons to these atoms and molecules efficiently produces activated species (e.g., radicals, excited states, photons). Acceleration of ions in the sheaths of LTPs to energies of tens to hundreds of eV enable activation of surface modifying processes – sputtering, etching, deposition. With such properties, LTPs are often and beneficially used in technological devices, ranging from etching and deposition in microelectronics and solar cell fabrication, to hardening of surgical instruments. LTPs harbor fundamental science issues that are intellectually challenging and rewarding. At the same time, there are enormous societal benefits that are enabled by LTPs. The entire present-day and future information technology infrastructure owes its very existence to LTPs. Renewable energy sources, such as solar cell arrays, could not be economically produced in the absence of deposition and etching by LTPs. In acknowledgment of the importance of LTPs, the DOE Office of Fusion Energy Sciences supported the Plasma Science Center for Predictive Control of Plasma Kinetics: Multi-Phase and Bounded Systems from August 2009 to July 2021, consisting of an initial 5-year grant, 3 funded extensions and 2 no-cost extensions. This is the final report of the Center in which the productivity of the Center is discussed in terms of publications, impact and personnel. High-lights of the research performed in the Center are provided.
Highly dense carbohydrates located on the surface of the HIV Env protein play a key role in immune evasion. Such evolutionary adaptation hampers any attempt to obtain a full mechanistic understanding of the role played by the glycans in protecting the virus against an effective immune response. Moreover, and due to their chemical variability, an accurate molecular understanding of the so called “glycan shield” is still limited by the lack of effective resolution of state-of-the-art experimental technics. Here, we have used extensive computational modelling in order to fill this gap, addressing the presence of a large glycan variability as observed experimentally. Based on an automated pipeline, we were able to assemble, set-up and simulate via Molecular dynamics hundreds of different glycosylated Env variants at nearly atomic resolution, recapitulating the glycosylation distributions observed experimentally. Results from these simulations were subjected to machine learning and very accurate prediction of simulation derived glycan shielding areas of each glycan as a function of static sequence features. Such predictive models of per-glycan shielding, incorporating both glycan dynamics and heterogeneity, were used to develop a novel sequence-based glycan shield mapping strategy. Parallel to these studies, we also developed an accurate machine learning approach to predict glycan heterogeneity data using sequence features and found good prediction accuracy.