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The Environmental Brand Guidelines have been prepared by the CEA-CAS Visual Design team for use primarily by IFPROG, but they apply to all LANL employees ordering signage for new and existing buildings. By adhering to this guidance, you will be a responsible steward of the “One Lab, one voice” mentality and successfully implement the Lab’s brand on all of your communications.
Physical protection of public buildings has long been a concern of police and security services where a balance of facility security and personnel safety is vital. Due to the nature of public spaces, the use of permanently installed and deploy-on-demand physical barrier systems must be safe for the legitimate occupants and visitors of that space. Such systems must seek to mitigate the personal and organizational consequences of unintentionally seriously injuring or killing an innocent bystander by slamming a heavy, rigid, and quick-deploying barrier into place. Consideration and implementation of less-than-lethal technologies is necessary to reduce risk to visitors and building personnel. One potential barrier solution is a fast-acting, high-strength, composite airbag barrier system for doorways and hallways to quickly deploy a less-than-lethal barrier at entry points as well as isolate intruders who have already gained access. This system is envisioned to be stored within an architecturally attractive selectively frangible shell that could be permanently installed at a facility or installed in remote or temporary locations as dictated by risk. The system would be designed to be activated remotely (hardwired or wireless) from a Central Alarm Station (CAS) or other secure location.
This report describes research conducted to use data science and machine learning methods to distinguish targeted genome editing versus natural mutation and sequencer machine noise. Genome editing capabilities have been around for more than 20 years, and the efficiencies of these techniques has improved dramatically in the last 5+ years, notably with the rise of CRISPR-Cas technology. Whether or not a specific genome has been the target of an edit is concern for U.S. national security. The research detailed in this report provides first steps to address this concern. A large amount of data is necessary in our research, thus we invested considerable time collecting and processing it. We use an ensemble of decision tree and deep neural network machine learning methods as well as anomaly detection to detect genome edits given either whole exome or genome DNA reads. The edit detection results we obtained with our algorithms tested against samples held out during training of our methods are significantly better than random guessing, achieving high F1 and recall scores as well as with precision overall.
This report includes visual inspection results, maintenance and repair activities, and recommendations for calendar year (CY) 2021 for use restrictions (URs) at corrective action sites (CASs) located on the Nevada National Security Site (NNSS) and on the Nevada Test and Training Range (NTTR) that are accessed through the NNSS Main Gate. This document is formatted by project activity (i.e., Industrial Sites, Soils, and Defense Threat Reduction Agency [DTRA]); then by corrective action unit (CAU); and then by CAS.
The Security Starts With You Campaign Guidelines have been prepared by the CEA-CAS Visual Design team for use primarily by DSOs, FODs, and/or any LANL employee who wishes to extend the messaging to new and existing buildings. By adhering to this guidance, you will be a responsible steward of the “One Lab, one voice” mentality and successfully implement the Lab’s brand and security messaging on all of your communications.
To mark the anniversary of LANSCE and its five decades of cutting-edge science, the National Security Research Center’s graphic designer Gabriella Smith (from CEA-CAS) illustrated a commemorative poster now available for display. The LANSCE (the Los Alamos Neutron Science Center) facility houses one of the nation’s most powerful linear accelerators, which are used to improve safety and security as well as advance technology in stockpile sustainment, modern materials and manufacturing, and threat mitigation, among other areas. Now-deceased Lab scientist Louis Rosen, who is featured prominently on the poster, first proposed creating this major experimental science facility, said NSRC Archivist-Historian Madeline Whitacre (WRS-NSRCMS)
In year 2 of this project (2017), our group focused on determining the causes of isotopic signatures in fentanyl. In order to better predict isotopic signatures in fentanyl, we analyzed the nitrogen isotope compositions of two key intermediates of fentanyl, NPP and ANPP. In addition, we analyzed additional fentanyl products produced using the Valdez route, along with five other alternative fentanyl routes. A new, more sensitive GC-C-IRMS method has been developed, which allows for compound specific isotope analysis of Chemical Attribution Signatures (CAS) in fentanyl.
The project aimed towards the construction of computational methods capable of modeling the global potential energy surface (PES) of small molecules, molecular ions, and radicals — including the parts of the PES which correspond to chemical reactions, and the reaction paths connecting reactants, intermediates, and reaction products. This goal may seem humble at first glance, but for chemical systems with more than about six atoms in total, at the time the project was proposed, there were no established theoretical methods capable of simulating such systems reliably, not even for small molecules in the gas phase which are electronically benign. This restriction severely hampers our ability to model and control chemical processes under harsh conditions. With the goal of constructing a method capable of modeling such chemical systems, we proposed to pursue a novel approach towards a Multi-Configuration (MC) DFT outside the traditional frameworks of Kohn-Sham theory and other methods of coupling wave function theory with DFT. Rather than being a complete active space (CAS) method, the proposed DOCI-DFT would employ a special restricted form of the active space wave function, called Doubly-Occupied CI (DOCI)—this wave function form is sufficient to describe not only heterolytic, but also homolytic bond dissociation processes at the zeroth order (i.e., as active space wave function). There are no other standard mean field methods which can do so. In the original proposal, we also outlined strong formal and practical arguments speaking for this method. The project proposal was accepted by the Department of Energy and provided two years of seed funding for one graduate student, as well as two years of two weeks PI summer-salary for the PI. However, ultimately the project could not be effectively pursued due to severe interferences outside the context scientific problems and was cancelled. Apart from two weeks of PI salary (and associated fringe & overhead costs issues by the performing institution), no costs were charged against the award, with the entire rest of funding returned to the Department of Energy. This report reiterates the primary background information regarding the project, its original goals, and outlines the preliminary work performed during the two weeks of DOE funding charged.
This report includes visual inspection results, descriptions of maintenance and repair activities, and recommendations for calendar year (CY) 2022 for use restrictions (URs) at corrective action sites (CASs) located on the Nevada National Security Site (NNSS) and on the Nevada Test and Training Range (NTTR) that are accessed through the NNSS Main Gate. This document is formatted by project activity (i.e., Industrial Sites, Soils, and Defense Threat Reduction Agency [DTRA]); then by corrective action unit (CAU); and then by CAS.
This report includes visual inspection results, descriptions of maintenance and repair activities, and recommendations for CY 2023 for URs at CASs located on the NNSS and on the NTTR that are accessed through the NNSS Main Gate. This document is formatted by project activity (i.e., Industrial Sites, Soils, and DTRA]; then by CAU; and then by CAS.
Evolve CAPP Basinal Resource Assessment presentation at SME-CAS Annual Meeting 2022
The overall objective of this proposal was to develop technologies to alter the composition and function of important members of microbial communities. In particular, the overall objective of the microbial community editing portion of the proposal focuses on developing foundational tools and understanding required to predict, alter and design grass rhizosphere communities impacting DOE missions. Specifically, the project is centered on the Microbial Community Analysis & Functional Evaluation in Soils (m-CAFES) to manipulate microbial consortia associated with plants of interest for the bioenergy sector, under the presumption that bacterial communities can be manipulated to enhance plant health. For tasks of specific interest to us, we are focusing on developing novel Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) based technologies (primarily focusing on Aim 1) and their delivery modalities (notably subaim 1.2) to edit specific bacterial genomes of interest to enhance their functionalities, and programmably ablate specific undesirable members of bacterial communities for plant health. We are focusing on engineering bacteriophages (bacterial viruses, for subaim 1.2) to carry programmable CRISPR-Cas systems (subaim 1.1) to target (ablate) or alter (edit) genomes of interest. This will enable us to carry out microbial perturbations that will impact community composition and function and ultimately plant growth and health, to enable the next phase of the project by deploying them in situ (subaims 1.3 and 1.4).
This project focused on developing and analyzing a method that could be employed by operational nuclear facilities to evaluate their CAS operators and determine a probability of assessment for each operator. This method is agnostic of alarm communication and display system (AC&D), sensors and cameras in place in the field, and any other technical security measures. This security-measure-agnostic method enables operational facilities to adopt it to determine the effectiveness of their alarm station operators.
This report includes visual inspection results, descriptions of maintenance and repair activities, and recommendations for CY 2025 for use restrictions (URs) at corrective action sites (CASs) located on the Nevada National Security Site and on the Nevada Test and Training Range (NTTR) that are accessed through the NNSS Main Gate. This document is arranged by project activity (i.e., Industrial Sites, Soils, and Defense Threat Reduction Agency [DTRA]); then by corrective action unit (CAU); and then by CAS. Post-closure UR inspections are performed on an annual basis, unless as noted in text. Post-closure UR inspections verify the condition of physical controls required by each UR, which may include the following activities: • Visual verification of the legibility of signs • Visual inspection of fencing, signs, monuments, and/or markers for indications of wear • Visual inspection of soil covers for indications of subsidence, erosion, or unauthorized use Deficiencies in UR requirements that were identified during CY 2024 inspections and not addressed in the CY 2024 report are addressed in this CY 2025 report.
CRISPR technology has revolutionized fungal genetic engineering by accelerating the pace and expanding the feasible scope of experiments in this field. Among various CRISPR-Cas systems, Cas9 and Cas12a are widely used in genetic and metabolic engineering. In filamentous fungi, both Cas9 and Cas12a have been utilized as CRISPR nucleases. In this work we first compared efficacies and types of genetic edits for CRISPR-Cas9 and -Cas12a systems at the polyketide synthase (albA) gene locus in Aspergillus niger. By employing a tRNA-based gRNA polycistronic cassette, both Cas9 and Cas12a have demonstrated equally remarkable editing efficacy. Cas12a showed potential superiority over Cas9 protein when one gRNA was used for targeting, achieving an editing efficiency of 86.5% compared to 31.7% for Cas9. Moreover, when employing two gRNAs for targeting, both systems achieved up to 100% editing efficiency for single gene editing. In addition, the CRISPR-Cas9 system has been reported to induce large genomic deletions in various species. However, its use for engineering large chromosomal segments deletions in filamentous fungi still requires optimization. Here, we engineered Cas9 and -Cas12a-induced large genomic fragment deletions by targeting various genomic regions of A. niger ranging from 3.5 kb to 40 kb. Our findings demonstrate that targeted engineering of large chromosomal segments can be achieved, with deletions of up to 69.1% efficiency. Furthermore, by targeting a secondary metabolite gene cluster, we show that fragments over 100 kb can be efficiently and specifically deleted using the CRISPR-Cas9 or -Cas12a system. Overall, in this paper, we present an efficient multi-gRNA genome editing system utilizing Cas9 or Cas12a that enables highly efficient targeted editing of genes and large chromosomal regions in A. niger.
HEX-P is a probe-class mission concept that will combine high spatial resolution X-ray imaging (< 10" full width at half maximum) and broad spectral coverage (0.2–80 keV) with an effective area far superior to current facilities (including XMM-Newton and NuSTAR) to enable revolutionary new insights into a variety of important astrophysical problems. HEX-P is ideally suited to address important problems in the physics and astrophysics of supernova remnants (SNRs) and pulsar wind nebulae (PWNe). For shell SNRs, HEX-P can greatly improve our understanding via more accurate spectral characterization and localization of non-thermal X-ray emission from both non-thermal-dominated SNRs and those containing both thermal and non-thermal components, and can discover previously unknown non-thermal components in SNRs. Multi-epoch HEX-P observations of several young SNRs (e.g., Cas A and Tycho) are expected to detect year-scale variabilities of X-ray filaments and knots, thus enabling us to determine fundamental parameters related to diffusive shock acceleration, such as local magnetic field strengths and maximum electron energies. For PWNe, HEX-P will provide spatially-resolved, broadband X-ray spectral data separately from their pulsar emission, allowing us to study how particle acceleration, cooling, and propagation operate in different evolution stages of PWNe. HEX-P is also poised to make unique and significant contributions to nuclear astrophysics of Galactic radioactive sources by improving detections of, or limits on, 44Ti in the youngest SNRs and by potentially discovering rare nuclear lines as evidence of double neutron star mergers. Throughout the paper, we present simulations of each class of objects, demonstrating the power of both the imaging and spectral capabilities of HEX-P to advance our knowledge of SNRs, PWNe, and nuclear astrophysics.
Although CRISPR/Cas-based genome editing has been widely used for plant genetic engineering, its application in the genetic improvement of trees has been limited, partly because of challenges in Agrobacterium-mediated transformation. As an important model for poplar genomics and biotechnology research, eastern cottonwood (Populus deltoides) clone WV94 can be transformed by A. tumefaciens, but several challenges remain unresolved, including the relatively low transformation efficiency and the relatively high rate of false positives from antibiotic-based selection of transgenic events. Moreover, the efficacy of CRISPR-Cas system has not been explored in P. deltoides yet. Here, we first optimized the protocol for Agrobacterium-mediated stable transformation in P. deltoides WV94 and applied a UV-visible reporter called eYGFPuv in transformation. Our results showed that the transgenic events in the early stage of transformation could be easily recognized and counted in a non-invasive manner to narrow down the number of regenerated shoots for further molecular characterization (at the DNA or mRNA level) using PCR. We found that approximately 8.7% of explants regenerated transgenic shoots with green fluorescence within two months. Next, we examined the efficacy of multiplex CRISPR-based genome editing in the protoplasts derived from P. deltoides WV94 and hybrid poplar clone ‘52-225’ (P. trichocarpa × P. deltoides clone ‘52-225’). The two constructs expressing the Trex2-Cas9 system resulted in mutation efficiency ranging from 31% to 57% in hybrid poplar clone 52-225, but no editing events were observed in P. deltoides WV94 transient assay. The eYGFPuv-assisted plant transformation and genome editing approach demonstrated in this study has great potential for accelerating the genome editing-based breeding process in poplar and other non-model plants species and point to the need for additional CRISPR work in P. deltoides.
Many applications in plant biology requires editing genomes accurately including correcting point mutations, incorporation of single-nucleotide polymorphisms (SNPs), and introduction of multinucleotide insertion/deletions (indels) into a predetermined position in the genome. These types of modifications are possible using existing genome-editing technologies such as the CRISPR-Cas systems, which require induction of double-stranded breaks in the target DNA site and the supply of a donor DNA molecule that contains the desired edit sequence. However, low frequency of homologous recombination in plants and difficulty of delivering the donor DNA molecules make this process extremely inefficient. Another kind of technology known as base editing can perform precise editing; however, only certain types of modifications can be obtained, e.g., C/G-to-T/A and A/T-to-G/C. Recently, a new type of genome-editing technology, referred to as “prime editing,” has been developed, which can achieve various types of editing such as any base-to-base conversion, including both transitions (C→T, G→A, A→G, and T→C) and transversion mutations (C→A, C→G, G→C, G→T, A→C, A→T, T→A, and T→G), as well as small indels without the requirement for inducing double-stranded break in the DNA. Because prime editing has wide flexibility to achieve different types of edits in the genome, it holds a great potential for developing superior crops for various purposes, such as increasing yield, providing resistance to various abiotic and biotic stresses, and improving quality of plant product. In this review, we describe the prime editing technology and discuss its limitations and potential applications in plant biology research.