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DOE OSTI2015

Virology: The Next Generation from Digital PCR to Single Virion Genomics

In the past 25 years, virology has had major technology breakthroughs stemming first from the introduction of nucleic acid amplification testing, but more recently from the use of next-generation sequencing, digital PCR, and the possibility of single virion genomics. These technologies have and will improve diagnosis and disease state monitoring in clinical settings, aid in environmental monitoring, and reveal the vast genetic potential of viruses. Using the principle of limiting dilution, digital PCR amplifies single molecules of DNA in highly partitioned endpoint reactions and reads each of those reactions as either positive or negative based on the presence or absence of target fluorophore. In this review, digital PCR will be highlighted along with current studies, advantages/disadvantages, and future perspectives with regard to digital PCR, viral load testing, and the possibility of single virion genomics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Designing for Big Area Additive Manufacturing

Additive manufacturing (AM), more commonly referred to as 3D printing, is revolutionizing the manufacturing industry. With any new technology comes new rules and guidelines for the optimal use of said technology. Big Area Additive Manufacturing (BAAM), developed by Cincinnati Incorporated and Oak Ridge National Laboratory’s Manufacturing Demonstration Facility, requires a host of new design parameters compared to small-scale 3D printing to create large-scale parts. However, BAAM also creates new possibilities in material testing and various applications in the manufacturing industry. Most of the design constraints of small-scale polymer 3D printers still apply to BAAM. Beyond those constraints, new rules and limitations exist because BAAM’s large-scale system significantly changes the thermal properties associated with small-scale AM. Here, this work details both physical and software-related design considerations for additive manufacturing. After reading this guide, one will have a better understanding of slicing software’s capabilities and limitations, different physical characteristics of design and how to apply them appropriately for AM, and how to take the inherent nature of AM into consideration during the design process.

36 MATERIALS SCIENCE↗

DOE OSTI2020

The state of algal genome quality and diversity

The genomic era of biology has created unprecedented opportunity to study how life works, including understanding evolutionary principles, bioprospecting for novel antibiotics, and genetic manipulation of bioeconomically-relevant species. While genome sequencing and genomic analysis was previously restricted to large-scale projects and consortia, sequencing has become democratized. However, as genomics has become commonplace, the cataloging of sequenced organisms has become challenging, and standardized practices for sequencing, assembly, and annotation have not been adopted. This is equally true in research fields such as algal biology, despite the growing importance of algae in a bio-based economy. Here, in this study, we provide a comprehensive review of the state of eukaryotic algal genomics, explore the quality of algal genome assemblies, and identify the biases and gaps in the current species distribution to inform the development of future genome projects. Overall, we find a trend of declining quality of genomic resources, including a reduction in assembly quality, gene annotation quality, and genome completeness. Potential solutions to improve genome quality include widespread utilization of long read and scaffolding technologies, implementation of standards for assembly quality, evidence-based gene annotation and requisite publication, and support of continued development of gene prediction and genome assessment software.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

ONIX: An open-source depletion code

Open Source software enables innovative, community-based software development. ONIX brings this concept to the field of depletion calculations. It is an open-source depletion software to be used for nuclear reactor simulations, for fissile material production analysis as well as for nuclear arms control applications. ONIX provides a module to solve the depletion equation using a Chebyshev Rational Approximation Method. For the generation of one-group cross sections, it includes a coupling interface for the open-source neutron transport code, OpenMC, as well as a module to read pre-computed values in a stand-alone mode. ONIX has special features to optimize nuclear data libraries, to update isomeric branching ratio during burnup, and to support automation of simulations for nuclear archaeology. In conclusion, ONIX has been validated against results from numerical and experimental benchmarks, and its results agree with other methods within expected error ranges.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2021

Serpent transient analyses of GIACINT geometrical change experiments

This paper simulates seven transient experiments with geometrical movements performed at the GIACINT facility of Belarus. These experiments include three slow control rods insertion in more than 25 s, one fast control rod insertion in less than 1 s, and three water moderator draining transients. In the fast control rod insertion experiment, the control rods are first pushed by a mechanical spring and then let fall by gravity in the assembly. In this experiment, the control rods speed varies because of the initial spring force, the gravitational acceleration, and the water buoyancy force. In all other transient experiments, the geometry change occurs with a constant speed. The Serpent computer program was utilized to simulate these transient experiments with geometrical changes by performing two separate computations. One time-independent computation is performed in criticality mode and the other time-dependent computation is performed in dynamic-source mode. The first computation writes the neutron population and delayed neutron precursors for starting the transient simulation. The second computation divides the transient time into several time bins, reads the two files from the first computation, and updates them at the end of each time bin. The Serpent simulation results obtained for this set of experiments are in good agreement with the time dependent experimental measurements. In addition, Serpent and MCNP simulations results show an excellent agreement for the water moderator transient

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2023

Direct Bayesian inference for fault severity assessment in Digital-Twin-Based fault diagnosis

For applications in condition-based maintenance of nuclear systems, the assessment of fault severity is crucial. In this work, we developed a framework that allows for direct inference of the probability distributions of possible faults in a system. Here, we employed a model-based approach with model residuals generated from analytical redundancy relations provided by physics-based models of the system components. From real-time sensor readings, the values of the model residuals can be calculated, and the posterior probability distributions of the faults can be computed directly using the methods of Bayesian networks. From the posterior distribution of each fault, one can estimate the fault probability based on a chosen threshold and assess the severity of the fault. By eliminating the discretization and simplifications in middle steps, this approach allows us to leverage the available computational resources to provide more accurate fault probability estimates and severity assessments.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2014

Supertwistors and massive particles

In the (super)twistor formulation of massless (super)particle mechanics, the mass-shell constraint is replaced by a “spin-shell” constraint from which the spin content can be read off. We extend this formalism to massive (super)particles (with N-extended space–time supersymmetry) in three and four space–time dimensions, explaining how the spin-shell constraints are related to spin, and we use it to prove equivalence of the massive N=1 and BPS-saturated N=2 superparticle actions. We also find the supertwistor form of the action for “spinning particles” with N-extended worldline supersymmetry, massless in four dimensions and massive in three dimensions, and we show how this simplifies special features of the N=2 case. -- Highlights: •Spin-shell constraints are related to Poincaré Casimirs. •Twistor form of 4D spinning particle for spin N/2. •Twistor proof of scalar/antisymmetric tensor equivalence for 4D spin 0. •Twistor form of 3D particle with arbitrary spin. •Proof of equivalence of N=1 and N=2 BPS massive 4D superparticles.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2014

Pairing in half-filled Landau level

Pairing of composite fermions in half-filled Landau level state is reexamined by solving the BCS gap equation with full frequency dependent current–current interactions. Our results show that there can be a continuous transition from the Halperin–Lee–Read state to a chiral odd angular momentum Cooper pair state for short-range contact interaction. This is at odds with the previously established conclusion of first order pairing transition, in which the low frequency effective interaction was assumed for the entire frequency range. We find that even if the low frequency effective interaction is repulsive, it is compensated by the high frequency regime, which is attractive. We construct the phase diagrams and show that ℓ=1 angular momentum channel is quite different from higher angular momenta ℓ≥3. Remarkably, the full frequency dependent analysis applied to the bilayer Hall system with a total filling fraction ν=1/2 +1/2 is quantitatively changed from the previously established results but not qualitatively.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2015

Infinitely many singular interactions on noncompact manifolds

We show that the ground state energy is bounded from below when there are infinitely many attractive delta function potentials placed in arbitrary locations, while all being separated at least by a minimum distance, on two dimensional non-compact manifold. To facilitate the reading of the paper, we first present the arguments in the setting of Cartan–Hadamard manifolds and then subsequently discuss the general case. For this purpose, we employ the heat kernel techniques as well as some comparison theorems of Riemannian geometry, thus generalizing the arguments in the flat case following the approach presented in Albeverio et al. (2004). - Highlights: • Schrödinger-operator for infinitely many singular interactions on noncompact manifolds. • Proof of the finiteness of the ground-state energy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2018

Determination of many-electron basis functions for a quantum Hall ground state using Schur polynomials

A method for determining the ground state of a planar interacting many-electron system in a magnetic field perpendicular to the plane is described. The ground state wave-function is expressed as a linear combination of a set of basis functions. Given only the flux and the number of electrons describing an incompressible state, we use the combinatorics of partitioning the flux among the electrons to derive the basis wave-functions as linear combinations of Schur polynomials. The procedure ensures that the basis wave-functions form representations of the angular momentum algebra. We exemplify the method by deriving the basis functions for the (5/2) quantum Hall state with a few particles. We find that one of the basis functions is precisely the Moore–Read Pfaffian wave function.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2018

Quantum dynamics of a small symmetry breaking measurement device

Highlights: • Ferromagnetic measurement device exploits symmetry breaking to measure a spin. • Quantum interaction results in loss of phase coherence of test object. • Dynamics lead to sizeable correlation with, and enhancement of, microscopic object. • No reliable registration of pointer readings is observed after decoupling spin. - Abstract: A quantum measuring instrument is constructed that utilises symmetry breaking to enhance a microscopic signal. The entire quantum system consists of a system–apparatus–environment triad that is composed of a small set of spin-1/2 particles. The apparatus is a ferromagnet that measures the z-component of a single spin. A full quantum many-body calculation allows for a careful examination of the loss of phase coherence, the formation and amplification of system–apparatus correlations, the irreversibility of registration, the fault tolerance, and the bias of the device.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2019

Specific heat and pairing of Dirac composite fermions in the half-filled Landau level

A recent proposal argues that an alternate description of the half-filled Landau level is a theory of massless Dirac fermions. We examine the possibility of pairing of these Dirac fermions by numerically solving the coupled Eliashberg equations unlike our previous calculation (Wang and Chakravarty, 2016). In addition, vertex corrections are calculated to be zero from the Ward identity. We find that pairing is possible in non-zero angular momentum channels; only differences are minor numerical shifts. As before, the pairing leads to the gapped Pfaffian and anti-Pfaffian states. However, in our approximation scheme, pairing is not possible in the putative particle–hole symmetric state for ℓ=0 angular momentum. The specific heat at low temperatures of a system of massless Dirac fermions interacting with a transverse gauge field, expected to be relevant for the half-filled Landau level, is calculated. Using the Luttinger formula, it is found to be ∝TlnT in the leading low temperature limit, due to the exchange of transverse gauge bosons. The result agrees with the corresponding one in the nonrelativistic composite fermion theory of Halperin, Lee and Read of the half-filled Landau level.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2013

Constitutive expression of a salinity-induced wheat WRKY transcription factor enhances salinity and ionic stress tolerance in transgenic Arabidopsis thaliana

Highlights: •A class II WRKY transcription factor, TaWRKY79 was isolated and characterized. •TaWRKY79 was induced by NaCl or abscisic acid. •843 bp regulatory segment was sufficient to respond to ABA or NaCl treatment. •TaWRKY79 enhanced salinity and ionic tolerance while reduced sensitivity to ABA. •TaWRKY79 increased salinity and ionic tolerance in an ABA-dependent pathway. -- Abstract: The isolation and characterization of TaWRKY79, a wheat class II WRKY transcription factor, is described. Its 1297 bp coding region includes a 987 bp long open reading frame. TaWRKY79 was induced by stressing seedlings with either NaCl or abscisic acid (ABA). When a fusion between an 843 bp segment upstream of the TaWRKY79 coding sequence and GUS was introduced into Arabidopsis thaliana, GUS staining indicated that this upstream segment captured the sequence(s) required to respond to ABA or NaCl treatment. When TaWRKY79 was constitutively expressed as a transgene in A. thaliana, the transgenic plants showed an improved capacity to extend their primary root in the presence of either 100 mM NaCl, 10 mM LiCl or 2 μM ABA. The inference was that TaWRKY79 enhanced the level of tolerance to both salinity and ionic stress, while reducing the level of sensitivity to ABA. The ABA-related genes ABA1, ABA2 ABI1 and ABI5 were all up-regulated in the TaWRKY79 transgenic plants, suggesting that the transcription factor operates in an ABA-dependent pathway.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

Alternative splicing variants of human Fbx4 disturb cyclin D1 proteolysis in human cancer

Highlights: • The expression of Fbx4 was significantly lower in HCC tissues. • Novel splicing variants of Fbx4 were identified. • These novel variants are much more abundant in human cancer tissues and cells. • The novel Fbx4 isoforms could promote cell proliferation and migration in vitro. • These isoforms showed less capability for cyclin D1 binding and degradation. - Abstract: Fbx4 is a specific substrate recognition component of SCF ubiquitin ligases that catalyzes the ubiquitination and subsequent degradation of cyclin D1 and Trx1. Two isoforms of human Fbx4 protein, the full length Fbx4α and the C-terminal truncated Fbx4β have been identified, but their functions remain elusive. In this study, we demonstrated that the mRNA level of Fbx4 was significantly lower in hepatocellular carcinoma tissues than that in the corresponding non-tumor tissues. More importantly, we identified three novel splicing variants of Fbx4: Fbx4γ (missing 168–245nt of exon1), Fbx4δ (missing exon6) and a N-terminal reading frame shift variant (missing exon2). Using cloning sequencing and RT-PCR, we demonstrated these novel splice variants are much more abundant in human cancer tissues and cell lines than that in normal tissues. When expressed in Sk-Hep1 and NIH3T3 cell lines, Fbx4β, Fbx4γ and Fbx4δ could promote cell proliferation and migration in vitro. Concordantly, these isoforms could disrupt cyclin D1 degradation and therefore increase cyclin D1 expression. Moreover, unlike the full-length isoform Fbx4α that mainly exists in cytoplasm, Fbx4β, Fbx4γ, and Fbx4δ locate in both cytoplasm and nucleus. Since cyclin D1 degradation takes place in cytoplasm, the nuclear distribution of these Fbx4 isoforms may not be involved in the down-regulation of cytoplasmic cyclin D1. These results define the impact of alternative splicing on Fbx4 function, and suggest that the attenuated cyclin D1 degradation by these novel Fbx4 isoforms provides a new insight for aberrant cyclin D1 expression in human cancers.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

Transcriptome sequencing and differential gene expression analysis in Viola yedoensis Makino (Fam. Violaceae) responsive to cadmium (Cd) pollution

Viola yedoensis Makino is an important Chinese traditional medicine plant adapted to cadmium (Cd) pollution regions. Illumina sequencing technology was used to sequence the transcriptome of V. yedoensis Makino. We sequenced Cd-treated (VIYCd) and untreated (VIYCK) samples of V. yedoensis, and obtained 100,410,834 and 83,587,676 high quality reads, respectively. After de novo assembly and quantitative assessment, 109,800 unigenes were finally generated with an average length of 661 bp. We then obtained functional annotations by aligning unigenes with public protein databases including NR, NT, SwissProt, KEGG and COG. In addition, 892 differentially expressed genes (DEGs) were investigated between the two libraries of untreated (VIYCK) and Cd-treated (VIYCd) plants. Moreover, 15 randomly selected DEGs were further validated with qRT-PCR and the results were highly accordant with the Solexa analysis. This study firstly generated a successful global analysis of the V. yedoensis transcriptome and it will provide for further studies on gene expression, genomics, and functional genomics in Violaceae. - Highlights: • A de novo assembly generated 109,800 unigenes and 5,4479 of them were annotated. • 31,285 could be classified into 26 COG categories. • 263 biosynthesis pathways were predicted and classified into five categories. • 892 DEGs were detected and 15 of them were validated by qRT-PCR.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

Characterization of the fusion core in zebrafish endogenous retroviral envelope protein

Zebrafish endogenous retrovirus (ZFERV) is the unique endogenous retrovirus in zebrafish, as yet, containing intact open reading frames of its envelope protein gene in zebrafish genome. Similarly, several envelope proteins of endogenous retroviruses in human and other mammalian animal genomes (such as syncytin-1 and 2 in human, syncytin-A and B in mouse) were identified and shown to be functional in induction of cell–cell fusion involved in placental development. ZFERV envelope protein (Env) gene appears to be also functional in vivo because it is expressible. After sequence alignment, we found ZFERV Env shares similar structural profiles with syncytin and other type I viral envelopes, especially in the regions of N- and C-terminal heptad repeats (NHR and CHR) which were crucial for membrane fusion. We expressed the regions of N + C protein in the ZFERV Env (residues 459–567, including predicted NHR and CHR) to characterize the fusion core structure. We found N + C protein could form a stable coiled-coil trimer that consists of three helical NHR regions forming a central trimeric core, and three helical CHR regions packing into the grooves on the surface of the central core. The structural characterization of the fusion core revealed the possible mechanism of fusion mediated by ZFERV Env. These results gave comprehensive explanation of how the ancient virus infects the zebrafish and integrates into the genome million years ago, and showed a rational clue for discovery of physiological significance (e.g., medicate cell–cell fusion). - Highlights: • ZFERV Env shares similar structural profiles with syncytin and other type I viral envelopes. • The fusion core of ZFERV Env forms stable coiled-coil trimer including three NHRs and three CHRs. • The structural mechanism of viral entry mediated by ZFERV Env is disclosed. • The results are helpful for further discovery of physiological function of ZFERV Env in zebrafish.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

Cloning and characterization of HbMT2a, a metallothionein gene from Hevea brasiliensis Muell. Arg differently responds to abiotic stress and heavy metals

Metallothioneins (MTs) are of low molecular mass, cysteine-rich proteins. They play an important role in the detoxification of heavy metals and homeostasis of intracellular metal ions, and protecting against intracellular oxidative damages. In this study a full-length cDNA of type 2 plant metallothioneins, HbMT2a, was isolated from 25 mM Polyethyleneglycol (PEG) stressed leaves of Hevea brasiliensis by RACE. The HbMT2a was 372 bp in length and had a 237 bp open reading frame (ORF) encoding for a protein of 78 amino acid residues with molecular mass of 7.772 kDa. The expression of HbMT2a in the detached leaves of rubber tree clone RY7-33-97 was up-regulated by Me-JA, ABA, PEG, H{sub 2}O{sub 2}, Cu{sup 2+} and Zn{sup 2+}, but down-regulated by water. The role of HbMT2a protein in protecting against metal toxicity was demonstrated in vitro. PET-28a-HbMT2-beared Escherichia coli. Differential expression of HbMT2a upon treatment with 10 °C was observed in the detached leaves of rubber tree clone 93-114 which is cold-resistant and Reken501 which is cold-sensitive. The expression patterns of HbMT2a in the two rubber tree clones may be ascribed to a change in the level of endogenous H{sub 2}O{sub 2}. - Highlights: • Cloning an HbMT2a gene from rubber tree. • Analyzing expression patterns of HbMT2a upon abiotic stress and heavy metal stress. • Finding different expression patterns of HbMT2a among two Hevea germplasm. • The expressed protein of HbMT2a enhances copper and zinc tolerance in Escherichia coli.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Inhibition of the acetyl lysine-binding pocket of bromodomain and extraterminal domain proteins interferes with adipogenesis

The bromodomain and extraterminal (BET) domain family proteins are epigenetic modulators involved in the reading of acetylated lysine residues. The first BET protein inhibitor to be identified, (+)-JQ1, a thienotriazolo-1, 4-diazapine, binds selectively to the acetyl lysine-binding pocket of BET proteins. We evaluated the impact on adipogenesis of this druggable targeting of chromatin epigenetic readers, by investigating the physiological consequences of epigenetic modifications through targeting proteins binding to chromatin. JQ1 significantly inhibited the differentiation of 3T3-L1 preadipocytes into white and brown adipocytes by down-regulating the expression of genes involved in adipogenesis, particularly those encoding the peroxisome proliferator-activated receptor (PPAR-γ), the CCAAT/enhancer-binding protein (C/EBPα) and, STAT5A and B. The expression of a constitutively activated STAT5B mutant did not prevent inhibition by JQ1. Thus, the association of BET/STAT5 is required for adipogenesis but STAT5 transcription activity is not the only target of JQ1. Treatment with JQ1 did not lead to the conversion of white adipose tissue into brown adipose tissue (BAT). BET protein inhibition thus interferes with generation of adipose tissue from progenitors, confirming the importance of the connections between epigenetic mechanisms and specific adipogenic transcription factors. - Highlights: • JQ1 prevented the differentiation of 3T3-L1 preadipocytes into white adipocytes. • JQ1 affected clonal cell expansion and abolished lipid accumulation. • JQ1 prevented the differentiation of 3T3-L1 preadipocytes into brown adipocytes. • JQ1 treatment did not lead to the conversion of white adipose tissue into brown adipose tissue. • JQ1 decreased STAT5 expression, but STAT5B{sup ca} expression did not restore adipogenesis.

60 APPLIED LIFE SCIENCES↗