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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A Fast and Scalable Genetic Algorithm-Based Approach for Planning of Microgrids in Distribution Networks

As a result of climate change, extreme weather events are occurring more frequently and with increasing impact. This trend poses a significant challenge for distribution utilities and system operators to ensure that there is uninterrupted power supply to critical loads in their networks; thus, the level of proactive preparation of the distribution system to be able to handle severe impacts of extreme weather events represents the system's resilience. One method that distribution system planners can use to prepare for future extreme events is to plan multiple microgrids which can use local generation as much as possible to supply critical loads. But partitioning an existing distribution system such that multiple feasible islands are planned and which are capable of supporting critical loads is still challenging for distribution systems - first, because of the size of the network graph partitioning problem and, second, because of the difficulty in properly formulating the desired attributes of such islands or microgrids. Therefore, this paper presents a genetic algorithm based approach that facilitates incorporating multiple objectives for grid partitioning by formulating two types of problems - node allocation and edge elimination - and it considers multiple topological and resilience-enhancing objectives. The performance of the proposed genetic algorithm-based approach is numerically evaluated on multiple test systems as well as on a real distribution feeder in Colorado, United States.

genetic algorithm↗
DOE OSTI2016

Identification of a classical mutant in the industrial host Aspergillus niger by systems genetics: LaeA is required for citric acid production and regulates the formation of some secondary metabolites

Rapid acidification of the culture medium by the production of organic acids and the production of acid-induced proteases are key characteristics of the filamentous fungus Aspergillus niger. The D15 mutant of A. niger is non-acidifying mutant and used often for the expression of recombinant proteins in A. niger, because of its reduced production of extracellular proteases under non-acidic conditions. In this study, the D15 mutant is characterized in detail. Strongly reduced levels of citric and oxalic acid were observed in the D15 mutant both in shake flask cultures and in controlled batch cultivations. To identify the mutation in the D15 mutant, we successfully combined high-throughput sequencing (Illumina) with bulk segregant analysis. Because of the lack of a sexual cycle for A. niger, the parasexual cycle was used to generate a pool of segregants. From the 52 single nucleotide polymorphisms (SNPs) between the parental strains, three SNPs were homozygous in the genomic DNA of pool of segregants. These three SNPs mapped to all the right arm of chromosome II, indicating that this region contains the genetic locus affecting the phenotype related to acid production. Of the three SNPs, one mutation resulted in a missense mutation in the gene encoding the A. niger homologue of the A. nidulans methyltransferase gene laeA. Complementation analysis of the original mutant with the laeA gene and targeted disruption of laeA further confirmed that LaeA is involved in citric acid production in A. niger lab (N402) and citric acid production strains (ATCC 11414). Analysis of the secondary metabolite (SM) profile of the laeA mutants indicate that LaeA is required for the production of several SMs (asperrubrol, atromentin and JBIR86), but deletion of laeA also resulted in the presence of SMs (aspernigrin A/B and BMS-192548) that were not detected in the wild-type strain. The levels of ten other SMs were not strongly affected as a result of laeA deletion indicating that only a limited number of SM gene clusters are controlled by LaeA activity.

Aspergillus niger↗
DOE OSTI2023

Genetics of varicose veins reveals polygenic architecture and genetic overlap with arterial and venous disease

Varicose veins represent a common cause of cardiovascular morbidity, with limited available medical therapies. Although varicose veins are heritable and epidemiologic studies have identified several candidate varicose vein risk factors, the molecular and genetic basis remains uncertain. Here we analyzed the contribution of common genetic variants to varicose veins using data from the Veterans Affairs Million Veteran Program and four other large biobanks. Among 49,765 individuals with varicose veins and 1,334,301 disease-free controls, we identified 139 risk loci. We identified genetic overlap between varicose veins, other vascular diseases and dozens of anthropometric factors. Using Mendelian randomization, we prioritized therapeutic targets via integration of proteomic and transcriptomic data. Finally, topological enrichment analyses confirmed the biologic roles of endothelial shear flow disruption, inflammation, vascular remodeling and angiogenesis. Further, these findings may facilitate future efforts to develop nonsurgical therapies for varicose veins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

LCOE Design Optimization Using Genetic Algorithm with Improved Component Models for Medium-Voltage Transformerless PV Inverters

For real-world installations of photovoltaic and other renewable energy resources, the critical design metric is the levelized cost of energy (LCOE); however, many power electronics design optimizations are performed with efficiency and power density as the primary design goals. Recent work has shown that a new LCOE-focused optimization approach can yield improved system designs balancing cost and energy generation. This paper expands the LCOE optimization approach by considering comprehensive optimization parameters, adding new modeling of inductor cost, extending the semiconductor model to include effects of losses on housing cost, and implementing a genetic algorithm to improve computation efficiency.

41 EE - Solar Energy Technologies Office (EE-4S)↗
DOE OSTI2015

Genetic analysis of inflorescence and plant height components in sorghum (Panicoidae) and comparative genetics with rice (Oryzoidae)

Domestication has played an important role in shaping characteristics of the inflorescence and plant height in cultivated cereals. Taking advantage of meta-analysis of QTLs, phylogenetic analyses in 502 diverse sorghum accessions, GWAS in a sorghum association panel (n = 354) and comparative data, we provide insight into the genetic basis of the domestication traits in sorghum and rice. We performed genome-wide association studies (GWAS) on 6 traits related to inflorescence morphology and 6 traits related to plant height in sorghum, comparing the genomic regions implicated in these traits by GWAS and QTL mapping, respectively. In a search for signatures of selection, we identify genomic regions that may contribute to sorghum domestication regarding plant height, flowering time and pericarp color. Comparative studies across taxa show functionally conserved ‘hotspots’ in sorghum and rice for awn presence and pericarp color that do not appear to reflect corresponding single genes but may indicate co-regulated clusters of genes. We also reveal homoeologous regions retaining similar functions for plant height and flowering time since genome duplication an estimated 70 million years ago or more in a common ancestor of cereals. In most such homoeologous QTL pairs, only one QTL interval exhibits strong selection signals in modern sorghum. Intersections among QTL, GWAS and comparative data advance knowledge of genetic determinants of inflorescence and plant height components in sorghum, and add new dimensions to comparisons between sorghum and rice.

09 BIOMASS FUELS↗
DOE OSTI2014

Discovery of a meta-stable Al-Sm phase with unknown stoichiometry using a genetic algorithm

Unknown crystalline phases observed during the devitrification process of glassy metal alloys significantly limit our ability to understand and control phase selection in these systems driven far from equilibrium. Here, we report a new meta-stable Al 5 Sm phase identified by simultaneously searching Al-rich compositions of the Al–Sm system, using an efficient genetic algorithm. The excellent match between calculated and experimental X-ray diffraction patterns confirms that this new phase appeared in the crystallization of melt-spun Al 90 Sm 10 alloys.

Zhang, Feng↗
DOE OSTI2018

Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide‐rich de novo designed peptides

Abstract Disulfide‐rich peptides represent an important protein family with broad pharmacological potential. Recent advances in computational methods have made it possible to design new peptides which adopt a stable conformation de novo. Here, we describe a system to produce disulfide‐rich de novo peptides using Escherichia coli as the expression host. The advantage of this system is that it enables production of uniformly 13 C‐ and 15 N‐labeled peptides for solution nuclear magnetic resonance (NMR) studies. This expression system was used to isotopically label two previously reported de novo designed peptides, and to determine their solution structures using NMR. The ensemble of NMR structures calculated for both peptides agreed well with the design models, further confirming the accuracy of the design protocol. Collection of NMR data on the peptides under reducing conditions revealed a dependency on disulfide bonds to maintain stability. Furthermore, we performed long‐time molecular dynamics (MD) simulations with tempering to assess the stability of two families of de novo designed peptides. Initial designs which exhibited a stable structure during simulations were more likely to adopt a stable structure in vitro , but attempts to utilize this method to redesign unstable peptides to fold into a stable state were unsuccessful. Further work is therefore needed to assess the utility of MD simulation techniques for de novo protein design.

Buchko, Garry W.↗
DOE OSTI2013

Advanced genetic tools for plant biotechnology

Basic research has provided a much better understanding of the genetic networks and regulatory hierarchies in plants. To meet the challenges of agriculture, we must be able to rapidly translate this knowledge into generating improved plants. Therefore, in this Review, we discuss advanced tools that are currently available for use in plant biotechnology to produce new products in plants and to generate plants with new functions. These tools include synthetic promoters, 'tunable' transcription factors, genome-editing tools and site-specific recombinases. We also review some tools with the potential to enable crop improvement, such as methods for the assembly and synthesis of large DNA molecules, plant transformation with linked multigenes and plant artificial chromosomes. These genetic technologies should be integrated to realize their potential for applications to pressing agricultural and environmental problems.

Liu, WS↗
DOE OSTI2026

Data for "Genetics of flooding tolerance in an F2 Miscanthus sacchariflorus ssp. lutarioriparius × M. sinensis population"

This dataset contains all data and supplementary materials from "Genetics of flooding tolerance in an F2 Miscanthus sacchariflorus ssp. lutarioriparius × M. sinensis population". 1. The dataset S1 table contains the raw phenotypic data collected during the experiment. 2. The dataset S2 table contains the LSmean values for the 24 traits studied. 3. The dataset S3 table contains the TASSEL GBSv2 map, marker information, and genotype data used for mapping. 4. The dataset S4 table contains information on candidate genes found in each of the QTL intervals. 5. The dataset S5 table contains the GO annotations and KEGG enrichment analyses for those candidate genes. 6. The dataset S6 table contains information on the sequences used to classify AP2 ERF transcription factors. 7. The dataset S7 table contains information on AP2 ERF orthologs between Miscanthus and rice based on synteny. 8. Supplementary file 1 contains the ANOVA results using the raw phenotypic data collected from protocol "A". 9. Supplementary file 2 contains the ANOVA results using the raw phenotypic data collected from protocol "B". 10. Supplementary file 3 contains notes on the comparison of SNP calling methods. 11. Supplementary file 4 is a script for analyzing candidate genes found in QTL intervals.

Miscanthus, flood, partial submergence, complete s↗
DOE OSTI2016

Structural and Genetic Studies Demonstrate Neurologic Dysfunction in Triosephosphate Isomerase Deficiency Is Associated with Impaired Synaptic Vesicle Dynamics

Triosephosphate isomerase (TPI) deficiency is a poorly understood disease characterized by hemolytic anemia, cardiomyopathy, neurologic dysfunction, and early death. TPI deficiency is one of a group of diseases known as glycolytic enzymopathies, but is unique for its severe patient neuropathology and early mortality. The disease is caused by missense mutations and dysfunction in the glycolytic enzyme, TPI. Previous studies have detailed structural and catalytic changes elicited by disease-associated TPI substitutions, and samples of patient erythrocytes have yielded insight into patient hemolytic anemia; however, the neuropathophysiology of this disease remains a mystery. This study combines structural, biochemical, and genetic approaches to demonstrate that perturbations of the TPI dimer interface are sufficient to elicit TPI deficiency neuropathogenesis. The present study demonstrates that neurologic dysfunction resulting from TPI deficiency is characterized by synaptic vesicle dysfunction, and can be attenuated with catalytically inactive TPI. Collectively, our findings are the first to identify, to our knowledge, a functional synaptic defect in TPI deficiency derived from molecular changes in the TPI dimer interface.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural and genetic convergence of HIV-1 neutralizing antibodies in vaccinated non-human primates

A primary goal of HIV-1 vaccine development is the consistent elicitation of protective, neutralizing antibodies. While highly similar neutralizing antibodies (nAbs) have been isolated from multiple HIV-infected individuals, it is unclear whether vaccination can consistently elicit highly similar nAbs in genetically diverse primates. Here, we show in three outbred rhesus macaques that immunization with Env elicits a genotypically and phenotypically conserved nAb response. From these vaccinated macaques, we isolated four antibody lineages that had commonalities in immunoglobulin variable, diversity, and joining gene segment usage. Atomic-level structures of the antigen binding fragments of the two most similar antibodies showed nearly identical paratopes. The Env binding modes of each of the four vaccine-induced nAbs were distinct from previously known monoclonal HIV-1 neutralizing antibodies, but were nearly identical to each other. The similarities of these antibodies show that the immune system in outbred primates can respond to HIV-1 Env vaccination with a similar structural and genotypic solution for recognizing a particular neutralizing epitope. These results support rational vaccine design for HIV-1 that aims to reproducibly elicit, in genetically diverse primates, nAbs with specific paratope structures capable of binding conserved epitopes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Population Genetics of Invasive Brown Tree Snakes ( Boiga irregularis ) on Guam, USA

The introduction of Brown Tree Snakes (BTS; Boiga irregularis) on Guam has had devastating impacts on native wildlife and human infrastructure, resulting in concerted efforts to control populations and prevent the spread of this invasive species to other islands. These control efforts, particularly aerial drops of acetaminophen, can eradicate BTS within target areas, but snakes can repopulate those areas via compensatory immigration. Therefore, understanding how gene flow corresponds to dispersal can add critical information for maximizing effectiveness of control efforts. To examine dispersal patterns of BTS on Guam from a genetics perspective, we genotyped 332 individual snakes at 22 microsatellite loci to test for the presence of physical barriers (e.g., roads) and spatial genetic structure associated with restricted dispersal. Brown Tree Snakes experience sufficient gene flow on Guam to resist any strong physical barriers, a likely interaction between their large population size and ability to cross physical obstacles such as roads. In addition, BTS exhibited isolation-by-distance across the entire study area, but those captured on Andersen Air Force Base in northern Guam appeared to disperse randomly regardless of sex. Overall, BTS experience high gene flow across Guam, particularly in less urbanized areas in northern Guam. Therefore, compensatory immigration will likely make complete eradication difficult without antisnake barriers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Biosensors for detecting and/or neutralizing bioavailable uranium and related U-sensitive genetic molecular components, gene cassettes, vectors, genetic circuits, compositions, methods and systems

UO 2 F 2 biosensors, and related U-sensing and/or F-sensing genetic molecular components, genetic circuits, compositions, methods and systems are described, which in several embodiments can be used to detect and/or neutralize uranium and in particular bioavailable UO 2 F 2 .

Park, Dan Mcfarland↗
DOE OSTI2023

Genetic variation and genetic complexity of nodule occupancy in soybean inoculated with USDA110 and USDA123 rhizobium strains

Abstract Background Symbiotic nitrogen fixation differs among Bradyrhizobium japonicum strains. Soybean inoculated with USDA123 has a lower yield than strains known to have high nitrogen fixation efficiency, such as USDA110. In the main soybean-producing area in the Midwest of the United States, USDA123 has a high nodule incidence in field-grown soybean and is competitive but inefficient in nitrogen fixation. In this study, a high-throughput system was developed to characterize nodule number among 1,321 Glycine max and 69 Glycine soja accessions single inoculated with USDA110 and USDA123. Results Seventy-three G. max accessions with significantly different nodule number of USDA110 and USDA123 were identified. After double inoculating 35 of the 73 accessions, it was observed that PI189939, PI317335, PI324187B, PI548461, PI562373, and PI628961 were occupied by USDA110 and double-strain nodules but not by USDA123 nodules alone. PI567624 was only occupied by USDA110 nodules, and PI507429 restricted all strains. Analysis showed that 35 loci were associated with nodule number in G. max when inoculated with strain USDA110 and 35 loci with USDA123. Twenty-three loci were identified in G. soja when inoculated with strain USDA110 and 34 with USDA123. Only four loci were common across two treatments, and each locus could only explain 0.8 to 1.5% of phenotypic variation. Conclusions High-throughput phenotyping systems to characterize nodule number and occupancy were developed, and soybean germplasm restricting rhizobium strain USDA123 but preferring USDA110 was identified. The larger number of minor effects and a small few common loci controlling the nodule number indicated trait genetic complexity and strain-dependent nodulation restriction. The information from the present study will add to the development of cultivars that limit USDA123, thereby increasing nitrogen fixation efficiency and productivity.

59 BASIC BIOLOGICAL SCIENCES↗