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Optimization of Species-Selective Reversible Proteasome Inhibitors for the Treatment of Malaria
Abstract Malaria remains a critical global health challenge, with increasing resistance to frontline therapies necessitating novel drug targets. The proteasome has emerged as a promising target for antimalarial drug discovery. This study describes efforts to optimize a series of species-selective reversible inhibitors targeting the Plasmodium falciparum 20S proteasome. Starting from the carboxypiperidine scaffold identified through a high-throughput viability screen, we conducted iterative structure–activity relationship studies, leading to the development of highly potent and selective inhibitors with good oral bioavailability. Lead compounds demonstrated nanomolar potency against P. falciparum blood-stage parasites and selective inhibition of the parasite proteasome over the human counterpart. Cryo-EM structural studies confirmed binding at the β5 subunit, while in vivo pharmacokinetic studies identified promising candidates for further development. These findings support proteasome inhibition as a viable strategy for novel antimalarial drug development.
Sensor Impacts Evaluation and Verification: Expert Interview Responses
The sensor configuration/deployment method has critical impacts on energy efficient building control and thermal comfort. However, traditional sensor techniques for building operation and fault detection and diagnostics (FDD) are not necessarily optimal in terms of energy efficiency and thermal comfort, and their global effects are not thoroughly investigated. In an effort to address and overcome this limitation, a multilaboratory and multiyear project, “Sensor Impact Evaluation and Verification,” was proposed. Its purpose is to develop a framework to investigate the impacts of sensor deployment and configuration on building energy optimization, FDD, occupant thermal comfort, and potentially grid efficiency. The first project task was a literature review to establish a solid knowledge of and a background related to sensor technologies and placement. To accomplish this task, an extensive review of previous research literature was performed. A series of expert interviews were conducted to augment the findings of the literature review. This report summarizes the interview design and interview results and findings. The interview was designed and performed to (1) investigate the current status and limitations of sensor configuration, (2) identify the research gaps and expectations for potential improvements in sensor configuration and deployment, and (3) integrate expert (e.g., researcher, building operation practitioner) knowledge and experience to develop use-case scenarios.
SPECTRASAT: A concept for the collection of global directional wave spectra
The synthetic aperture radar (SAR) imagery from SEASAT revealed a rich tapestry of backscatter patterns from the surface of the ocean. Although still far from being fully understood, these patterns occurred on nearly all spatial scales accessible to the SAR, that is from its spatial resolution of 25 m to its full swath width of 100 km. Futhermore, the backscatter signature appear to reveal a large variety of atmospheric and oceanic processes that occur above, at, and below the ocean surface. Proper interpretation of these signatures of varying scales with respect to their underlying geophysical causes is a major objective of SAR ocean research. Even now, however, it is clear that SAR offers a unique means to monitor wind and waves over global scales. A properly designed, configured, and complimented orbiting SAR system should yield substantial improvements in operational forecasts vital to marine activities. Since wind and wave information is optimally extracted in the spectral domain, the name SPECTRASAT is proposed for this global collection scheme.
Brief history of agricultural systems modeling
Agricultural systems science generates knowledge that allows researchers to consider complex problems or take informed agricultural decisions. The rich history of this science exemplifies the diversity of systems and scales over which they operate and have been studied. Modeling, an essential tool in agricultural systems science, has been accomplished by scientists from a wide range of disciplines, who have contributed concepts and tools over more than six decades. As agricultural scientists now consider the "next generation" models, data, and knowledge products needed to meet the increasingly complex systems problems faced by society, it is important to take stock of this history and its lessons to ensure that we avoid re-invention and strive to consider all dimensions of associated challenges. To this end, we summarize here the history of agricultural systems modeling and identify lessons learned that can help guide the design and development of next generation of agricultural system tools and methods. A number of past events combined with overall technological progress in other fields have strongly contributed to the evolution of agricultural system modeling, including development of process-based bio-physical models of crops and livestock, statistical models based on historical observations, and economic optimization and simulation models at household and regional to global scales. Characteristics of agricultural systems models have varied widely depending on the systems involved, their scales, and the wide range of purposes that motivated their development and use by researchers in different disciplines. Recent trends in broader collaboration across institutions, across disciplines, and between the public and private sectors suggest that the stage is set for the major advances in agricultural systems science that are needed for the next generation of models, databases, knowledge products and decision support systems. Furthermore, the lessons from history should be considered to help avoid roadblocks and pitfalls as the community develops this next generation of agricultural systems models.
A new surrogate modeling technique combining Kriging and polynomial chaos expansions – Application to uncertainty analysis in computational dosimetry
In numerical dosimetry, the recent advances in high performance computing led to a strong reduction of the required computational time to assess the specific absorption rate (SAR) characterizing the human exposure to electromagnetic waves. However, this procedure remains time-consuming and a single simulation can request several hours. As a consequence, the influence of uncertain input parameters on the SAR cannot be analyzed using crude Monte Carlo simulation. The solution presented here to perform such an analysis is surrogate modeling. This paper proposes a novel approach to build such a surrogate model from a design of experiments. Considering a sparse representation of the polynomial chaos expansions using least-angle regression as a selection algorithm to retain the most influential polynomials, this paper proposes to use the selected polynomials as regression functions for the universal Kriging model. The leave-one-out cross validation is used to select the optimal number of polynomials in the deterministic part of the Kriging model. The proposed approach, called LARS-Kriging-PC modeling, is applied to three benchmark examples and then to a full-scale metamodeling problem involving the exposure of a numerical fetus model to a femtocell device. The performances of the LARS-Kriging-PC are compared to an ordinary Kriging model and to a classical sparse polynomial chaos expansion. The LARS-Kriging-PC appears to have better performances than the two other approaches. A significant accuracy improvement is observed compared to the ordinary Kriging or to the sparse polynomial chaos depending on the studied case. This approach seems to be an optimal solution between the two other classical approaches. A global sensitivity analysis is finally performed on the LARS-Kriging-PC model of the fetus exposure problem.
A constitutive model incorporating grain refinement strengthening on metallic alloys
Surface nano-crystallization techniques have been recently developed as one of the most efficient ways to optimize materials’ structure, and therefore develop the local and global mechanical behavior as to increase strength without compromising ductility. Here, in this work, we present a constitutive model incorporating grain refinement hardening to simulate the nano-crystallization technique, specifically, surface mechanical attrition treatment. The computation is implemented using user-defined VUMAT subroutines. As an example of its application, a geometry model with full coverage of random impacts are employed. The results show that the model has rather precise predictability of grain size evolution during plastic deformation. The readily embedded with a computational code of material dynamics enables this novel model to be a promising tool to study the dynamic evolution of microstructures under plastic deformation.
The constrained architecture of mammalian Hox gene clusters
In many animal species with a bilateral symmetry, Hox genes are clustered either at one or at several genomic loci. This organization has a functional relevance, as the transcriptional control applied to each gene depends upon its relative position within the gene cluster. It was previously noted that vertebrate Hox clusters display a much higher level of genomic organization than their invertebrate counterparts. The former are always more compact than the latter, they are generally devoid of repeats and of interspersed genes, and all genes are transcribed by the same DNA strand, suggesting that particular factors constrained these clusters toward a tighter structure during the evolution of the vertebrate lineage. Here, we investigate the importance of uniform transcriptional orientation by engineering several alleles within the HoxD cluster, such as to invert one or several transcription units, with or without a neighboring CTCF site. We observe that the association between the tight structure of mammalian Hox clusters and their regulation makes inversions likely detrimental to the proper implementation of this complex genetic system. We propose that the consolidation of Hox clusters in vertebrates, including transcriptional polarity, evolved in conjunction with the emergence of global gene regulation via the flanking regulatory landscapes, to optimize a coordinated response of selected subsets of target genes in cis .
Polyyne production is regulated by the transcriptional regulators PgnC and GacA in Pseudomonas protegens Pf-5
ABSTRACT Polyynes produced by bacteria have promising applications in agriculture and medicine due to their potent antimicrobial activities. Polyyne biosynthetic genes have been identified inPseudomonasandBurkholderia. However, the molecular mechanisms underlying the regulation of polyyne biosynthesis remain largely unknown. In this study, we used a soil bacteriumPseudomonas protegensPf-5, which was recently reported to produce polyyne called protegenin, as a model to investigate the regulation of bacterial polyyne production. Our results show that Pf-5 controls polyyne production at both the pathway-specific level and a higher global level. Mutation ofpgnC, a transcriptional regulatory gene located in the polyyne biosynthetic gene cluster, abolished polyyne production. Gene expression analysis revealed that PgnC directly activates the promoter of polyyne biosynthetic genes. The production of polyyne also requires a global regulator GacA. Mutation ofgacAdecreased the translation of PgnC, which is consistent with the result thatpgnCleader mRNA bound directly to RsmE, an RNA-binding protein negatively regulated by GacA. These results suggest that GacA induces the expression of the PgnC regulator, which in turn activates polyyne biosynthesis. Additionally, the polyyne-producing strain of Pf-5, but not the polyyne-nonproducing strain, could inhibit a broad spectrum of bacteria including both Gram-negative and Gram-positive bacteria. IMPORTANCE Antimicrobial metabolites produced by bacteria are widely used in agriculture and medicine to control plant, animal, and human pathogens. Although bacteria-derived polyynes have been identified as potent antimicrobials for decades, the molecular mechanisms by which bacteria regulate polyyne biosynthesis remain understudied. In this study, we found that polyyne biosynthesis is directly activated by a pathway-specific regulator PgnC, which is induced by a global regulator GacA through the RNA-binding protein RsmE inPseudomonas protegens. To our knowledge, this work is the first comprehensive study of the regulatory mechanisms of bacterial polyyne biosynthesis at both pathway-specific level and global level. The discovered molecular mechanisms can help us optimize polyyne production for agricultural or medical applications.
Engineering well-expressed, V2-immunofocusing HIV-1 envelope glycoprotein membrane trimers for use in heterologous prime-boost vaccine regimens
HIV-1 vaccine immunofocusing strategies may be able to induce broadly-reactive neutralizing antibodies (NAbs). Here, we engineered a panel of diverse, membrane-resident native HIV-1 trimers vulnerable to two broad targets—the V2 apex and fusion peptide (FP). Selection criteria included i) high expression and ii) infectious function, so that trimer neutralization sensitivity can be profiled in pseudovirus (PV) assays. Initially, we boosted the expression of 17 candidate trimers by truncating gp41 and introducing a gp120-gp41 SOS disulfide to prevent gp120 shedding. "Repairs" were made to fill glycan holes and eliminate other strain-specific aberrations. A new neutralization assay allowed PV infection when our standard assay was insufficient. Trimers with exposed V3 loops, a target of non-NAbs, were discarded. To try to increase V2-sensitivity, we removed clashing glycans and modified the C-strand. Notably, a D167N mutation improved V2-sensitivity in several cases. Glycopeptide analysis of JR-FL trimers revealed near complete sequon occupation and that filling the N197 glycan hole was well-tolerated. In contrast, sequon optimization and inserting/removing glycans at other positions frequently had global "ripple" effects on glycan maturation and sequon occupation throughout the gp120 outer domain and gp41. V2 MAb CH01 selectively bound to trimers with small high mannose glycans near the base of the V1 loop, thereby avoiding clashes. Knocking in a rare N49 glycan was found to perturb gp41 glycans, increasing FP NAb sensitivity—and sometimes improving expression. Finally, a biophysical analysis of VLPs revealed that i) ~25% of particles bear Env spikes, ii) spontaneous particle budding is high and only increases 4-fold upon Gag transfection, and iii) Env+ particles express ~30–40 spikes. Taken together, we identified 7 diverse trimers with a range of sensitivities to two targets to allow rigorous testing of immunofocusing vaccine concepts.
Initial Assessment for a Generic Horizontal Fissile Solution Vessel with an Electron Beam-based Neutron Generator
The LANL NA-23 program office has provided an extensive design study for a medical isotope (i.e. Molybdenum-99) production facility based on a fissile solution vessel with various accelerator technologies. These concept designs and associated R&D have provided affordable pathways for system optimization for industry counter partner such as SHINE and Global Medial Isotope Supply (GMIS). A horizontal fissile solution vessel design with an electron beam (E-beam) accelerator is proposed and studied with modeling capabilities developed for previous concepts (i.e. a generic vertical fissile solution vessel with a deuterium-tritium (DT) accelerator). An initial system assessment is performed by estimating theoretical Molybdenum-99 production yield with MCNP6.2. A baseline system configuration is constructed based on early design discussions between LANL and GMIS. Since only an initial design concept is available at this stage, all associated system design parameters can be adjusted to fit the best system performance characteristics. In this work, unlike previous vertical system studies, the cooling configuration of the horizontal fissile solution vessel is not considered, and only fission reactions are used to quantify the theoretical product yield. Five parametric design studies are proposed, preliminary results are briefly reported, and extended design studies beyond what is proposed here are also discussed. It is concluded that a comprehensive system analysis via multiphysics coupled calculation developed by LANL should be further conducted for the final design.
Integrating the Design of Desalination Technologies into Produced Water Network Optimization
The oil and gas energy sector uses billions of gallons of water for hydraulic fracturing each year to extract oil and gas. The water injected into the ground for fracturing along with naturally occurring formation water from oil wells surfaces back in the form of produced water. Produced water can contain high concentrations of total dissolved solids and is unfit for reuse outside the oil and gas industry without desalination. In semi-arid shale plays, produced water desalination for beneficial reuse could play a crucial role in alleviating water shortages and addressing extreme drought conditions. In this poster we co-optimize the design and operation of desalination technologies along with operational decisions across produced water networks. A multi-period produced water network model with simplified split-fraction-based desalination nodes is developed. Rigorous steady-state desalination mathematical models based on mechanical vapor recompression are developed and embedded at the desalination sites in the network model. An optimal common design across all periods is ensured using global capacity constraints. The solution approach is demonstrated for multi-period planning problems on networks from the PARETO open-source library. Model formulation and challenges associated with scalability are discussed.
Integrating the Design of Desalination Technologies into Produced Water Network Optimization
The oil and gas energy sector uses billions of gallons of water for hydraulic fracturing each year to extract oil and gas. The water injected into the ground for fracturing along with naturally occur-ring formation water from the oil wells surfaces back in the form of produced water. Produced water can contain high concentrations of total dissolved solids and is unfit for reuse outside the oil and gas industry without desalination. In semi-arid shale plays, produced water desalination for beneficial reuse could play a crucial role in alleviating water shortages and addressing extreme drought conditions. In this paper we co-optimize the design and operation of desalination technologies along with operational decisions across produced water networks. A multi-period produced water network model with simplified split-fraction-based desalination nodes is developed. Rigorous steady-state desalination mathematical models based on mechanical vapor recompression are developed and embedded at the desalination sites in the network model. An optimal common design is ensured across all periods using global capacity constraints. The solution approach is demonstrated for multi-period planning problems on networks from the PARETO open-source library. Model formulation and challenges associated with scalability are discussed.
Electromagnetic deep-probing (100-1000 KMS) of the Earth's interior from artificial satellites: Constraints on the regional emplacement of crustal resources
The applicability of electromagnetic deep sounding experiments using natural sources in the magnetosphere by incorporating Magsat data with other geophysical data was evaluated. Magsat satellite data, ground based magnetic observations, appropriate reference field models, and other satellite data was analyzed. The optimal combination of observations which lead first to a global and then to a regional characterization of the conductivity of the Earth's upper mantle is sought.
Integrated Task And Data Parallel Programming: Language Design
his research investigates the combination of task and data parallel language constructs within a single programming language. There are an number of applications that exhibit properties which would be well served by such an integrated language. Examples include global climate models, aircraft design problems, and multidisciplinary design optimization problems. Our approach incorporates data parallel language constructs into an existing, object oriented, task parallel language. The language will support creation and manipulation of parallel classes and objects of both types (task parallel and data parallel). Ultimately, the language will allow data parallel and task parallel classes to be used either as building blocks or managers of parallel objects of either type, thus allowing the development of single and multi-paradigm parallel applications. 1995 Research Accomplishments In February I presented a paper at Frontiers '95 describing the design of the data parallel language subset. During the spring I wrote and defended my dissertation proposal. Since that time I have developed a runtime model for the language subset. I have begun implementing the model and hand-coding simple examples which demonstrate the language subset. I have identified an astrophysical fluid flow application which will validate the data parallel language subset. 1996 Research Agenda Milestones for the coming year include implementing a significant portion of the data parallel language subset over the Legion system. Using simple hand-coded methods, I plan to demonstrate (1) concurrent task and data parallel objects and (2) task parallel objects managing both task and data parallel objects. My next steps will focus on constructing a compiler and implementing the fluid flow application with the language. Concurrently, I will conduct a search for a real-world application exhibiting both task and data parallelism within the same program m. Additional 1995 Activities During the fall I collaborated with Andrew Grimshaw and Adam Ferrari to write a book chapter which will be included in Parallel Processing in C++ edited by Gregory Wilson. I also finished two courses, Compilers and Advanced Compilers, in 1995. These courses complete my class requirements at the University of Virginia. I have only my dissertation research and defense to complete.
Integrated Task and Data Parallel Programming
This research investigates the combination of task and data parallel language constructs within a single programming language. There are an number of applications that exhibit properties which would be well served by such an integrated language. Examples include global climate models, aircraft design problems, and multidisciplinary design optimization problems. Our approach incorporates data parallel language constructs into an existing, object oriented, task parallel language. The language will support creation and manipulation of parallel classes and objects of both types (task parallel and data parallel). Ultimately, the language will allow data parallel and task parallel classes to be used either as building blocks or managers of parallel objects of either type, thus allowing the development of single and multi-paradigm parallel applications. 1995 Research Accomplishments In February I presented a paper at Frontiers 1995 describing the design of the data parallel language subset. During the spring I wrote and defended my dissertation proposal. Since that time I have developed a runtime model for the language subset. I have begun implementing the model and hand-coding simple examples which demonstrate the language subset. I have identified an astrophysical fluid flow application which will validate the data parallel language subset. 1996 Research Agenda Milestones for the coming year include implementing a significant portion of the data parallel language subset over the Legion system. Using simple hand-coded methods, I plan to demonstrate (1) concurrent task and data parallel objects and (2) task parallel objects managing both task and data parallel objects. My next steps will focus on constructing a compiler and implementing the fluid flow application with the language. Concurrently, I will conduct a search for a real-world application exhibiting both task and data parallelism within the same program. Additional 1995 Activities During the fall I collaborated with Andrew Grimshaw and Adam Ferrari to write a book chapter which will be included in Parallel Processing in C++ edited by Gregory Wilson. I also finished two courses, Compilers and Advanced Compilers, in 1995. These courses complete my class requirements at the University of Virginia. I have only my dissertation research and defense to complete.
Power System Optimization Codes Modified
A major modification of and addition to existing Closed Brayton Cycle (CBC) space power system optimization codes was completed. These modifications relate to the global minimum mass search driver programs containing three nested iteration loops comprising iterations on cycle temperature ratio, and three separate pressure ratio iteration loops--one loop for maximizing thermodynamic efficiency, one for minimizing radiator area, and a final loop for minimizing overall power system mass. Using the method of steepest ascent, the code sweeps through the pressure ratio space repeatedly, each time with smaller iteration step sizes, so that the three optimum pressure ratios can be obtained to any desired accuracy for each of the objective functions referred to above (i.e., maximum thermodynamic efficiency, minimum radiator area, and minimum system mass). Two separate options for the power system heat source are available: 1. A nuclear fission reactor can be used. It is provided with a radiation shield 1. (composed of a lithium hydride (LiH) neutron shield and tungsten (W) gamma shield). Suboptions can be used to select the type of reactor (i.e., fast spectrum liquid metal cooled or epithermal high-temperature gas reactor (HTGR)). 2. A solar heat source can be used. This option includes a parabolic concentrator and heat receiver for raising the temperature of the recirculating working fluid. A useful feature of the code modifications is that key cycle parameters are displayed, including the overall system specific mass in kilograms per kilowatt and the system specific power in watts per kilogram, as the results for each temperature ratio are computed. As the minimum mass temperature ratio is encountered, a message is printed out. Several levels of detailed information on cycle state points, subsystem mass results, and radiator temperature profiles are stored for this temperature ratio condition and can be displayed or printed by users.
Brief History of Agricultural Systems Modeling
Agricultural systems science generates knowledge that allows researchers to consider complex problems or take informed agricultural decisions. The rich history of this science exemplifies the diversity of systems and scales over which they operate and have been studied. Modeling, an essential tool in agricultural systems science, has been accomplished by scientists from a wide range of disciplines, who have contributed concepts and tools over more than six decades. As agricultural scientists now consider the next generation models, data, and knowledge products needed to meet the increasingly complex systems problems faced by society, it is important to take stock of this history and its lessons to ensure that we avoid re-invention and strive to consider all dimensions of associated challenges. To this end, we summarize here the history of agricultural systems modeling and identify lessons learned that can help guide the design and development of next generation of agricultural system tools and methods. A number of past events combined with overall technological progress in other fields have strongly contributed to the evolution of agricultural system modeling, including development of process-based bio-physical models of crops and livestock, statistical models based on historical observations, and economic optimization and simulation models at household and regional to global scales. Characteristics of agricultural systems models have varied widely depending on the systems involved, their scales, and the wide range of purposes that motivated their development and use by researchers in different disciplines. Recent trends in broader collaboration across institutions, across disciplines, and between the public and private sectors suggest that the stage is set for the major advances in agricultural systems science that are needed for the next generation of models, databases, knowledge products and decision support systems. The lessons from history should be considered to help avoid roadblocks and pitfalls as the community develops this next generation of agricultural systems models.