Multiscale Investigation of Deformation Around a Triple Point Using Microstructure Clones
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Fitzgerald, Kaitlynn [United States Naval Academy]↗
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Article including Gene lists, and clone information
Supplementary information includes genelists and strain ids
cbi↗
SIMULATION CLONING FOR DIGITAL TWINS: A SCALABLE APPROACH
Digital Twin (DT) methods represent an important technology in which a simulated model of the operations of a physical system uses real-time sensor data to simulate, monitor, and consequently, improve its operations. One of the primary objectives of such a DT is to inform the physical system of measures to be taken in response to one or multiple intervening events that can change the state of the physical system. As such, a capability that is able to carry out multiple scenario assessments in real time in readiness for such events is a very effective tool in the use of simulations as DTs. However, continuous evaluation with highly probable event simulation scenarios are challenging due to the constraints of finite memory and a large exploration space. This paper reports a novel methodology for the continuous evaluation of $k$ probabilistic \textit{what-if} event scenarios under finite resource constraints and demonstrates its use as a digital-twin for a real-world application.
Yoginath, Srikanth↗
Probing Quantum Telecloning on Superconducting Quantum Processors
Quantum information cannot be perfectly cloned, but approximate copies of quantum information can be generated. Quantum telecloning combines approximate quantum cloning, more typically referred to as quantum cloning, and quantum teleportation. Quantum telecloning allows approximate copies of quantum information to be constructed by separate parties, using the classical results of a Bell measurement made on a prepared quantum telecloning state. Quantum telecloning can be implemented as a circuit on quantum computers using a classical coprocessor to compute classical feedforward instructions using if statements based on the results of a midcircuit Bell measurement in real time. We present universal symmetric optimal 1 → M telecloning circuits and experimentally demonstrate these quantum telecloning circuits for M = 2 up to M = 10, natively executed with real-time classical control systems on IBM Quantum superconducting processors, known as dynamic circuits. We perform the cloning procedure on many different message states across the Bloch sphere, on seven IBM Quantum processors, optionally using the error suppression technique X–X sequence digital dynamical decoupling. Two circuit optimizations are utilized: one that removes ancilla qubits for M = 2,3 , and one that reduces the total number of gates in the circuit but still uses ancilla qubits. Parallel single-qubit tomography with maximum likelihood estimation density matrix reconstruction is used in order to compute the mixed-state density matrices of the clone qubits, and clone quality is measured using quantum fidelity. These results present one of the largest and most comprehensive noisy intermediate-scale quantum computer experimental analyses on (single qubit) quantum telecloning to date. The clone fidelity sharply decreases to 0.5 for M > 5 , but for M = 2 , we are able to achieve a mean clone fidelity of up to 0.79 using dynamical decoupling.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Vectors of Efficiency in Hybrid Poplar Genotype Testing
Abstract The Natural Resources Research Institute Hybrid Poplar Program breeds and tests genetically improved clones for bio-mass production and environmental services. The testing process progresses from Nursery Progeny Tests (NPT) to Family Field Trials (FFT) to Clone Trials (CT) to Yield Blocks (YB), with limited replication of many clones in FFT and CT and a limited number of highly selected clones set out in monoclonal blocks (YB) to approximate the conditions of commercial plantations. We used correlation vectors, R 2 (coefficient of determination) and r s (Spearman’s Coefficient) for growth (DBH 2 ) and McFadden’s Pseudo R 2 for canker severity score, to determine where testing times could be altered (age – age correlations) and whole testing steps eliminated. FFT can be shortened from 5 years to 4 years. In CT, rank correlations between age 5 (half-rotation) and age 9/10 (full rotation) were significant (R 2 = 0.39 – 0.72), but age 5 selection missed 44 % of the top ten clones at age 9/10. Clone rank in CT at full, but not half, rotation was correlated with rank at full rotation in YB. Choosing clones at 9 years in CT adds 4 years but allows possible elimination of YB for clone selection. Both FFT and CT are necessary. Canker abundance and severity in CT at full rotation cannot be determined at earlier ages. An aggressive strategy saves 6 years of testing.
Forestry↗
Functional but not taxonomic diversity increases productivity of Populus in the southeastern United States
Plant interactions like competition and facilitation impact ecosystem function and resilience. Improving our understanding of the relationships between these interactions and community productivity has important implications for managers of production systems in forestry and agriculture as well as conservation science. Populus spp. are an excellent model system for exploring how inter‐ and intraspecific interactions impact ecosystem functions, such as productivity, in forest plantations. In this study, we compared aboveground productivity of six Populus clones from three different taxa grown in monoclonal and mixed‐clonal plots. The different mixture treatments were intended to experimentally test aboveground biomass response to contrasting levels of taxonomic diversity and functional diversity based on nitrogen use characteristics of Populus clones. We hypothesize that functional diversity would be more important than taxonomic diversity in increasing aboveground productivity of mixed‐clonal plantings compared to monocultures. In addition, a subset of treatments was carried out on additional sites representing a productivity gradient in order to determine if the relationship between biodiversity and productivity in these systems diminished at more productive sites as suggested by the stress‐gradient hypothesis. We found that functionally diverse mixtures of clones had greater yield of aboveground biomass than the average of their constituent monocultures, while more taxonomically diverse mixes of clones did not differ from the average of their constituent monocultures. However, when reestablished on sites with extremely high or low productivity, the best performing clone mixture also did not differ from the average of its constituent monocultures. Our results suggest that intimate clone mixtures of Populus have the potential to significantly increase productivity, but results vary by mixture and by site. To capitalize on positive biodiversity effects on yield in production systems, targeted mixtures based on divergent functional traits linked to different use and acquisition strategies for site‐specific limiting resources are most likely to be successful.
BEF↗
CRISPR/Cas9-based gene activation and base editing in Populus
The genus Populus has long been used for environmental, agroforestry and industrial applications worldwide. Today Populus is also recognized as a desirable crop for biofuel production and a model tree for physiological and ecological research. As such, various modern biotechnologies, including CRISPR/Cas9-based techniques, have been actively applied to Populus for genetic and genomic improvements for traits such as increased growth rate and tailored lignin composition. However, CRISPR/Cas9 has been primarily used as the active Cas9 form to create knockouts in the hybrid poplar clone “717-1B4” (P. tremula x P. alba clone INRA 717-1B4). Alternative CRISPR/Cas9-based technologies, e.g. those involving modified Cas9 for gene activation and base editing, have not been evaluated in most Populus species for their efficacy. Here we employed a deactivated Cas9 (dCas9)-based CRISPR activation (CRISPRa) technique to fine-tune the expression of two target genes, TPX2 and LecRLK-G which play important roles in plant growth and defense response, in hybrid poplar clone “717-1B4” and poplar clone “WV94” (P. deltoides “WV94”), respectively. We observed that CRISPRa resulted in 1.2-fold to 7.0-fold increase in target gene expression through transient expression in protoplasts and Agrobacterium-mediated stable transformation, demonstrating the effectiveness of dCas9-based CRISPRa system in Populus. In addition, we applied Cas9 nickase (nCas9)-based cytosine base editor (CBE) to precisely introduce premature stop codons via C-to-T conversion, with an efficiency of 13%–14%, in the target gene PLATZ which encodes a transcription factor involved in plant fungal pathogen response in hybrid poplar clone “717-1B4”. Overall, we showcase the successful application of CRISPR/Cas-based technologies in gene expression regulation and precise gene engineering in two Populus species, facilitating the adoption of emerging genome editing tools in woody species.
59 BASIC BIOLOGICAL SCIENCES↗
Overcoming environmental constraints to high-yielding eastern cottonwood productivity in the southeastern United States
The global demand for biomass is rising, and Populus species are among the most productive temperate woody plants. This 6-year study, conducted in Sumter County, South Carolina, USA evaluated the effects of supplemental irrigation and fertilization on crown and leaf traits, dry weight productivity, and clonal variation in Populus deltoides. Eight commercially available clones (‘ST148’, ‘S2C20’, ‘3167’, ‘ST72’, ‘20WV’, ‘S7C1’, ‘ST70’, and ‘S7C15’) were assessed. Drip irrigation was applied to maintain soil tension at either 33 kPa (15% volumetric soil moisture) or 1500 kPa (10%). Nutrient treatments via weekly fertigation applications consisted of two levels: a high annual rate (initially 85 kg elemental nitrogen ha−1 year−1, increasing to 182 kg ha−1 year−1 at Year 3, then reduced to 135 kg ha−1 year−1 thereafter) and a low rate at 50% of the high treatment. Dry weight yields were estimated using standing tree measurements. Results revealed significant clonal differences in leaf area index (LAI) that peaked in Year 3, with the fastest-growing clones exhibiting lower LAI values. At Ages 2 and 3, these clones also showed higher concentrations of K, Ca, B, Cu, and Mn in leaves, along with lower Mg and Zn concentrations. Both annual height and diameter growth varied significantly by treatment and clone, with the largest height increases observed in the low fertilizer treatments from Year 3 onward. Biomass production in all irrigated plots exceeded that of non-irrigated plots across all biomass components at Ages 4, 5, and 6. Furthermore, stem-to-root dry weight ratios increased more rapidly in the best-performing treatment–clone combinations compared to non-irrigated plots. Notably, P. deltoides plots receiving fertilizer had higher soil carbon concentrations (i.e., percent C) compared to adjacent sweetgum, sycamore, and agricultural plots. These findings highlight the potential of targeted irrigation strategies to enhance biomass productivity in P. deltoides plantations.
Tuskan, Gerald [ORNL] (ORCID:0000000301061289)↗
DeepClone: Lightweight State Replication of Deep Learning Models for Data Parallel Training
Training modern deep neural network (DNN) models involves complex workflows triggered by model exploration, sensitivity analysis, explainability, etc. A key primitive in this context is the ability to clone a model training instance, i.e. “fork” the training process in a potentially different direction, which enables comparisons of different evolution paths using variations of training data and model parameters. However, in a quest improve the training throughput, a mix of data parallel, model parallel, pipeline parallel and layer-wise parallel approaches are making the problem of cloning highly complex. In this paper, we explore the problem of efficient cloning under such circumstances. To this end, we leverage several properties of data-parallel training and layer-wise parallelism to design DeepClone, a cloning approach based on augmenting the execution graph to gain direct access to tensors, which are then sharded and reconstructed asynchronously in order to minimize runtime overhead, standby duration, readiness duration. Compared with state-of-art approaches, DeepClone shows orders of magnitude improvement for several classes of DNN models.
data-parallel training↗
Pre- and post-coppice production and biomass chemistry of eastern cottonwood and hybrid poplars in the southeastern US
Sustainably grown feedstocks for bioenergy and bioproducts are important tools to fight climate change, provide ecosystem services, and sequester carbon. Populus species including hybrid poplars have been utilized around the world, and in the southeastern US native eastern cottonwood (P. deltoides) is often favored due to its resistance to stem cankers. However, P. deltoides has historically been grown in single stem production and its relative performance in short rotation coppice production, prevalent in Europe, is not well documented. Therefore, this study's goals were to evaluate eastern cottonwood (D × D) and hybrid poplar (P. deltoides × P. maximowiczii (D × M) and P. deltoides × P. trichocarpa (D × T) taxa) productivity under a two-year establishment and two-year coppice cycle, analyze biomass chemistry properties, identify drivers of productivity, and select clones suited for marginal vs. optimal sites. We found that D × M and D × D grew best in both establishment and coppice rotation with production increasing after coppice. Taxa and clones exhibited few differences in select biomass chemistry properties despite differences in growth rate and stem size. Across years and sites, production was correlated with the soil's carbon to nitrogen ratio, percentage of sand, and shrink-swell potential of the soil. A D × M clone ‘9709’ tended to perform better than other tested clones on marginal sites and had the highest survival rate after four years. Overall, this research suggests that Populus species can be grown in coppice rotation in the southeastern US with the potential for hybrid poplars to be successful on certain sites in the region although longer term studies are necessary to confirm these results.
54 ENVIRONMENTAL SCIENCES↗
Impact of crowding on the diversity of expanding populations
Crowding effects critically impact the self-organization of densely packed cellular assemblies, such as biofilms, solid tumors, and developing tissues. When cells grow and divide, they push each other apart, remodeling the structure and extent of the population’s range. Recent work has shown that crowding has a strong impact on the strength of natural selection. However, the impact of crowding on neutral processes, which controls the fate of new variants as long as they are rare, remains unclear. Here, we quantify the genetic diversity of expanding microbial colonies and uncover signatures of crowding in the site frequency spectrum. By combining Luria–Delbrück fluctuation tests, lineage tracing in a novel microfluidic incubator, cell-based simulations, and theoretical modeling, we find that the majority of mutations arise behind the expanding frontier, giving rise to clones that are mechanically “pushed out” of the growing region by the proliferating cells in front. These excluded-volume interactions result in a clone-size distribution that solely depends on where the mutation first arose relative to the front and is characterized by a simple power law for low-frequency clones. Our model predicts that the distribution depends on a single parameter—the characteristic growth layer thickness—and hence allows estimation of the mutation rate in a variety of crowded cellular populations. Combined with previous studies on high-frequency mutations, our finding provides a unified picture of the genetic diversity in expanding populations over the whole frequency range and suggests a practical method to assess growth dynamics by sequencing populations across spatial scales.
59 BASIC BIOLOGICAL SCIENCES↗
Single Amino Acid Mutations Affect Zika Virus Replication In Vitro and Virulence In Vivo
The 2014–2016 Zika virus (ZIKV) epidemic in the Americas resulted in large deposits of next-generation sequencing data from clinical samples. This resource was mined to identify emerging mutations and trends in mutations as the outbreak progressed over time. Information on transmission dynamics, prevalence, and persistence of intra-host mutants, and the position of a mutation on a protein were then used to prioritize 544 reported mutations based on their ability to impact ZIKV phenotype. Using this criteria, six mutants (representing naturally occurring mutations) were generated as synthetic infectious clones using a 2015 Puerto Rican epidemic strain PRVABC59 as the parental backbone. The phenotypes of these naturally occurring variants were examined using both cell culture and murine model systems. Mutants had distinct phenotypes, including changes in replication rate, embryo death, and decreased head size. In particular, a NS2B mutant previously detected during in vivo studies in rhesus macaques was found to cause lethal infections in adult mice, abortions in pregnant females, and increased viral genome copies in both brain tissue and blood of female mice. Additionally, mutants with changes in the region of NS3 that interfaces with NS5 during replication displayed reduced replication in the blood of adult mice. This analytical pathway, integrating both bioinformatic and wet lab experiments, provides a foundation for understanding how naturally occurring single mutations affect disease outcome and can be used to predict the of severity of future ZIKV outbreaks. To determine if naturally occurring individual mutations in the Zika virus epidemic genotype affect viral virulence or replication rate in vitro or in vivo, we generated an infectious clone representing the epidemic genotype of stain Puerto Rico, 2015. Using this clone, six mutants were created by changing nucleotides in the genome to cause one to two amino acid substitutions in the encoded proteins. The six mutants we generated represent mutations that differentiated the early epidemic genotype from genotypes that were either ancestral or that occurred later in the epidemic. We assayed each mutant for changes in growth rate, and for virulence in adult mice and pregnant mice. Three of the mutants caused catastrophic embryo effects including increased embryonic death or significant decrease in head diameter. Three other mutants that had mutations in a genome region associated with replication resulted in changes in in vitro and in vivo replication rates. These results illustrate the potential impact of individual mutations in viral phenotype.
59 BASIC BIOLOGICAL SCIENCES↗
Predictive analytics of selections of russet potatoes
We explore the application of machine learning algorithms specifically to enhance the selection process of Russet potato (Solanum tuberosum L.) clones in breeding trials by predicting their suitability for advancement. This study addresses the challenge of efficiently identifying high-yield, disease-resistant, and climate-resilient potato varieties that meet processing industry standards. Leveraging manually collected data from trials in the state of Oregon, we investigate the potential of a wide variety of state-of-the-art binary classification models. The dataset includes 1086 clones, with data on 38 attributes recorded for each clone, focusing on yield, size, appearance, and frying characteristics, with several control varieties planted consistently across four Oregon regions from 2013 to 2021. We conduct a comprehensive analysis of the dataset that includes preprocessing, feature engineering, and imputation to address missing values. We focus on several key metrics such as accuracy, F1-score, and Matthews correlation coefficient (MCC) for model evaluation. The top-performing models, namely a feedforward neural network classifier (Neural Net), a histogram-based gradient boosting classifier (HGBC), and a support vector machine classifier (SVM), demonstrate consistent and significant results. To further validate our findings, we conducted a simulation study using the aims, data-generating mechanisms, estimands, methods, and performance measures (ADEMP) framework, simulating different data-generating scenarios to assess model robustness and performance through true positive, true negative, false positive, and false negative distributions, area under the receiver operating characteristic curve (AUC-ROC) and MCC. The simulation results highlight that non-linear models like SVM and HGBC consistently show higher AUC-ROC and MCC than logistic regression, thus outperforming the traditional linear model across various distributions, and emphasizing the importance of model selection and tuning in agricultural trials. Variable selection further enhances model performance and identifies influential features in predicting trial outcomes. The findings emphasize the potential of machine learning in streamlining the selection process for potato varieties, offering benefits such as increased efficiency, substantial cost savings, and judicious resource utilization. Our study contributes insights into precision agriculture and showcases the relevance of advanced technologies for informed decision-making in breeding programs.
60 APPLIED LIFE SCIENCES↗
An extensible vector toolkit and parts library for advanced engineering of plant genomes
Abstract Plant biotechnology is rife with new advances in transformation and genome engineering techniques. A common requirement for delivery and coordinated expression in plant cells, however, places the design and assembly of transformation constructs at a crucial juncture as desired reagent suites grow more complex. Modular cloning principles have simplified some aspects of vector design, yet many important components remain unavailable or poorly adapted for rapid implementation in biotechnology research. Here, we describe a universal Golden Gate cloning toolkit for vector construction. The toolkit chassis is compatible with the widely accepted Phytobrick standard for genetic parts, and supports assembly of arbitrarily complex T‐DNAs through improved capacity, positional flexibility, and extensibility in comparison to extant kits. We also provision a substantial library of newly adapted Phytobricks, including regulatory elements for monocot and dicot gene expression, and coding sequences for genes of interest such as reporters, developmental regulators, and site‐specific recombinases. Finally, we use a series of dual‐luciferase assays to measure contributions to expression from promoters, terminators, and from cross‐cassette interactions attributable to enhancer elements in certain promoters. Taken together, these publicly available cloning resources can greatly accelerate the testing and deployment of new tools for plant engineering.
42 ENGINEERING↗
Overexpression of human ACE2 protein in mouse fibroblasts stably transfected with the intact ACE2 gene
Infection by SARS-CoV-2 is dependent on binding of the viral spike protein to angiotensin converting enzyme 2 (ACE2), a membrane glycoprotein expressed on epithelial cells in the human upper respiratory tract. Recombinant ACE2 protein has potential application for anti-viral therapy. Here we co-transfected mouse fibroblasts (A9 cells) with a cloned fragment of human genomic DNA containing the intact ACE2 gene and an unlinked neomycin phosphotransferase gene, and then selected stable neomycin-resistant transfectants. Transfectant clones expressed ACE2 protein at levels that were generally proportional to the number of ACE2 gene copies integrated in the cell genome, ranging up to approximately 50 times the level of ACE2 present of Vero-E6 cells. Cells overexpressing ACE2 were hypersensitive to infection by spike-pseudotyped vesicular stomatitis virus (VSV-S), and adsorption of VSV-S to these cells occurred at an accelerated rate compared to Vero-E6 cells. In conclusion, the transfectant cell clones described here therefore have favorable attributes as feedstocks for large-scale production of recombinant human ACE2 protein.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Mathematical model of broadly reactive plasma cell production
Strain-specific plasma cells are capable of producing neutralizing antibodies that are essential for clearance of challenging pathogens. These neutralizing antibodies also function as a main defense against disease establishment in a host. However, when a rapidly mutating pathogen infects a host, successful control of the invasion requires shifting the production of plasma cells from strain-specific to broadly reactive. In this study, we develop a mathematical model of germinal center dynamics and use it to predict the events that lead to improved breadth of the plasma cell response. We examine scenarios that lead to germinal centers that are composed of B-cells that come from a single strain-specific clone, a single broadly reactive clone or both clones. We find that the initial B-cell clonal composition, T-follicular helper cell signaling, increased rounds of productive somatic hypermutation, and B-cell selection strength are among the mechanisms differentiating between strain-specific and broadly reactive plasma cell production during infections. Understanding the contribution of these factors to emergence of breadth may assist in boosting broadly reactive plasma cells production.
59 BASIC BIOLOGICAL SCIENCES↗
Translocations are induced in hematopoietic stem cells after irradiation of fetal mice
Abstract Although mammalian fetuses have been suggested to be sensitive to radiation, an increased frequency of translocations was not observed in blood lymphocytes from atomic bomb (A-bomb) survivors who were exposed to the bomb in utero and examined as adults. Since experiments using hematopoietic cells of mice and rats confirmed this finding, it was hypothesized that either irradiated fetal hematopoietic stem cells (f-HSCs) cannot generate exchange-type chromosomal aberrations or cells bearing induced aberrations are eliminated before the animals reach adulthood. In the present study, pregnant mice (12.5–15.5 days post coitum [dpc]) were irradiated with 2 Gy of X-rays and long-term HSCs (LT-HSCs) were isolated 24 h later. Multicolor fluorescence in situ hybridization (mFISH) analysis of LT-HSC clones proliferated in vitro showed that nine out of 43 (21%) clones from fetuses and 21 out of 41 (51%) clones from mothers bore translocations. These results indicate that cells with translocations can arise in mouse f-HSCs but exist at a lower frequency than in the mothers 24 h after X-ray exposure. Thus, it seems likely that translocation-bearing f-HSCs are generated but subsequently disappear, so that the frequency of lymphocyte translocations may decrease and reach the control level by the time the animals reach adulthood.
60 APPLIED LIFE SCIENCES↗
Genetic Basis of Chromate Adaptation and the Role of the Pre-existing Genetic Divergence during an Experimental Evolution Study with Desulfovibrio vulgaris Populations
Hexavalent chromium [Cr(VI)] is a common environmental pollutant. However, little is known about the genetic basis of microbial evolution under Cr(VI) stress and the influence of the prior evolution histories on the subsequent evolution under Cr(VI) stress. In this study, Desulfovibrio vulgaris Hildenborough (DvH), a model sulfate-reducing bacterium, was experimentally evolved for 600 generations. By evolving the replicate populations of three genetically diverse DvH clones, including ancestor (AN, without prior experimental evolution history), non-stress-evolved EC3-10, and salt stress-evolved ES9-11, the contributions of adaptation, chance, and pre-existing genetic divergence to the evolution under Cr(VI) stress were able to be dissected. Significantly decreased lag phases under Cr(VI) stress were observed in most evolved populations, while increased Cr(VI) reduction rates were primarily observed in populations evolved from EC3-10 and ES9-11. The pre-existing genetic divergence in the starting clones showed strong influences on the changes in lag phases, growth rates, and Cr(VI) reduction rates. Additionally, the genomic mutation spectra in populations evolved from different starting clones were significantly different. A total of 14 newly mutated genes obtained mutations in at least two evolved populations, suggesting their importance in Cr(VI) adaptation. An in-frame deletion mutation of one of these genes, the chromate transporter gene DVU0426, demonstrated that it played an important role in Cr(VI) tolerance. Overall, our study identified potential key functional genes for Cr(VI) tolerance and demonstrated the important role of pre-existing genetic divergence in evolution under Cr(VI) stress conditions.
54 ENVIRONMENTAL SCIENCES↗