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At least 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Exploring the Potential of ASHRAE Guideline 36 in District Cooling Systems: Preprint

ASHRAE Guideline 36-2021 (G36) provides high-performance control sequences for all-air and hydronic HVAC systems, and it has proven effective at reducing energy use for single building all-air equipment. The most recent version of G36 included control sequences for water-cooled chiller plants, which can be used in district cooling systems (DCSs). Despite not being a traditional application of G36 controls, DCSs could benefit from energy savings that G36 control sequences have demonstrated in single building systems. We therefore investigate the possibility to extend G36 chiller plant control from a single building to district cooling using a real-world district cooling system in Boulder, Colorado as a case study. Four timeframes representing low to peak loads are simulated and analyzed to compare energy use of the district cooling system for three control sequences. Results show that although G36 chiller plant sequences can be applied to DCSs, further analysis and potentially control optimization is needed to ensure energy savings compared to default controls.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding

Microbial split-pool ligation transcriptomics (microSPLiT) is a high-throughput single-cell RNA sequencing method for bacteria. With four combinatorial barcoding rounds, microSPLiT can profile transcriptional states in hundreds of thousands of Gram-negative and Gram-positive bacteria in a single experiment without specialized equipment. As bacterial samples are fixed and permeabilized before barcoding, they can be collected and stored ahead of time. During the first barcoding round, the fixed and permeabilized bacteria are distributed into a 96-well plate, where their transcripts are reverse transcribed into cDNA and labeled with the first well-specific barcode inside the cells. The cells are mixed and redistributed two more times into new 96-well plates, where the second and third barcodes are appended to the cDNA via in-cell ligation reactions. Finally, the cells are mixed and divided into aliquot sub-libraries, which can be stored until future use or prepared for sequencing with the addition of a fourth barcode. It takes 4 days to generate sequencing-ready libraries, including 1 day for collection and overnight fixation of samples. Here, the standard plate setup enables single-cell transcriptional profiling of up to 1 million bacterial cells and up to 96 samples in a single barcoding experiment, with the possibility of expansion by adding barcoding rounds. The protocol requires experience in basic molecular biology techniques, handling of bacterial samples and preparation of DNA libraries for next-generation sequencing. It can be performed by experienced undergraduate or graduate students. Data analysis requires access to computing resources, familiarity with Unix command line and basic experience with Python or R.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering

Abstract Replication initiator proteins (Reps) from the HUH-endonuclease superfamily process specific single-stranded DNA (ssDNA) sequences to initiate rolling circle/hairpin replication in viruses, such as crop ravaging geminiviruses and human disease causing parvoviruses. In biotechnology contexts, Reps are the basis for HUH-tag bioconjugation and a critical adeno-associated virus genome integration tool. We solved the first co-crystal structures of Reps complexed to ssDNA, revealing a key motif for conferring sequence specificity and for anchoring a bent DNA architecture. In combination, we developed a deep sequencing cleavage assay, termed HUH-seq, to interrogate subtleties in Rep specificity and demonstrate how differences can be exploited for multiplexed HUH-tagging. Together, our insights allowed engineering of only four amino acids in a Rep chimera to predictably alter sequence specificity. These results have important implications for modulating viral infections, developing Rep-based genomic integration tools, and enabling massively parallel HUH-tag barcoding and bioconjugation applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genomic analysis of 1710 surveillance-based Neisseria gonorrhoeae isolates from the USA in 2019 identifies predominant strain types and chromosomal antimicrobial-resistance determinants

This study characterized high-quality whole-genome sequences of a sentinel, surveillance-based collection of 1710 Neisseria gonorrhoeae (GC) isolates from 2019 collected in the USA as part of the Gonococcal Isolate Surveillance Project (GISP). It aims to provide a detailed report of strain diversity, phylogenetic relationships and resistance determinant profiles associated with reduced susceptibilities to antibiotics of concern. The 1710 isolates represented 164 multilocus sequence types and 21 predominant phylogenetic clades. Common genomic determinants defined most strains’ phenotypic, reduced susceptibility to current and historic antibiotics (e.g. bla TEM plasmid for penicillin, tetM plasmid for tetracycline, gyrA for ciprofloxacin, 23S rRNA and/or mosaic mtr operon for azithromycin, and mosaic penA for cefixime and ceftriaxone). The most predominant phylogenetic clade accounted for 21 % of the isolates, included a majority of the isolates with low-level elevated MICs to azithromycin (2.0 µg ml –1 ), carried a mosaic mtr operon and variants in PorB, and showed expansion with respect to data previously reported from 2018. The second largest clade predominantly carried the GyrA S91F variant, was largely ciprofloxacin resistant (MIC ≥1.0 µg ml –1 ), and showed significant expansion with respect to 2018. Overall, a low proportion of isolates had medium- to high-level elevated MIC to azithromycin ((≥4.0 µg ml –1 ), based on C2611T or A2059G 23S rRNA variants). One isolate carried the penA 60.001 allele resulting in elevated MICs to cefixime and ceftriaxone of 1.0 µg ml –1 . This high-resolution snapshot of genetic profiles of 1710 GC sequences, through a comparison with 2018 data (1479 GC sequences) within the sentinel system, highlights change in proportions and expansion of select GC strains and the associated genetic mechanisms of resistance. The knowledge gained through molecular surveillance may support rapid identification of outbreaks of concern. Continued monitoring may inform public health responses to limit the development and spread of antibiotic-resistant gonorrhoea.

(3-6) antimicrobial resistance↗
DOE OSTI2023

Targeted metagenomic assessment reflects critical colonization in battlefield injuries

Current diagnostics and clinical management strategies for combat wounds are based on decisions made by expert clinicians. However, even in the hands of experienced surgeons, wounds from combat injuries can exhibit failed healing and complications related to limitations in the rapid and comprehensive generation of diagnostic information. Previous studies have demonstrated the possible use of genomic sequencing approaches to detect microbial signatures involved in combat casualty care. While effective, whole metagenome sequencing is limited by the depth required to confidently detect all relevant signatures. To address this, we developed a targeted capture sequencing panel to detect microbial signatures relevant to wound healing. These targets include known microbial nosocomial pathogens, wound colonizers, and genes involved in virulence and antimicrobial resistance. A bioinformatics pipeline was built to identify genomic regions of interest and over 8,000 oligonucleotide probes were designed for capture. The panel was synthesized and validated using control reference genomes in human background and on wound-effluent samples from a cohort of combat-injured U.S. service members. Our panel was sensitive against wound-colonizing species, Acinetobacter baumannii and Pseudomonas aeruginosa, and was specific in detecting corresponding virulence and antimicrobial-resistance genes as well as other pathogenic species present in microflora mixtures. Random forest feature permutation confirmed the prevalence of Acinetobacter and Pseudomonas in critically colonized wounds and wounds that failed to heal, respectively. Our results demonstrate the capability of targeted sequencing tools and analysis platforms to profile and deliver information on pathogenic factors influencing wound progression, thereby guiding therapeutic intervention.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Short-wavelength-sensitive 2 (Sws2) visual photopigment models combined with atomistic molecular simulations to predict spectral peaks of absorbance

For many species, vision is one of the most important sensory modalities for mediating essential tasks that include navigation, predation and foraging, predator avoidance, and numerous social behaviors. The vertebrate visual process begins when photons of the light interact with rod and cone photoreceptors that are present in the neural retina. Vertebrate visual photopigments are housed within these photoreceptor cells and are sensitive to a wide range of wavelengths that peak within the light spectrum, the latter of which is a function of the type of chromophore used and how it interacts with specific amino acid residues found within the opsin protein sequence. Minor differences in the amino acid sequences of the opsins are known to lead to large differences in the spectral peak of absorbance (i.e. the λ max value). In our prior studies, we developed a new approach that combined homology modeling and molecular dynamics simulations to gather structural information associated with chromophore conformation, then used it to generate statistical models for the accurate prediction of λ max values for photopigments derived from Rh1 and Rh2 amino acid sequences. In the present study, we test our novel approach to predict the λ max of phylogenetically distant Sws2 cone opsins. To build a model that can predict the λ max using our approach presented in our prior studies, we selected a spectrally-diverse set of 11 teleost Sws2 photopigments for which both amino acid sequence information and experimentally measured λ max values are known. The final first-order regression model, consisting of three terms associated with chromophore conformation, was sufficient to predict the λ max of Sws2 photopigments with high accuracy. This study further highlights the breadth of our approach in reliably predicting λ max values of Sws2 cone photopigments, evolutionary-more distant from template bovine RH1, and provided mechanistic insights into the role of known spectral tuning sites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

FUN-PROSE: A deep learning approach to predict condition-specific gene expression in fungi

mRNA levels of all genes in a genome is a critical piece of information defining the overall state of the cell in a given environmental condition. Being able to reconstruct such condition-specific expression in fungal genomes is particularly important to metabolically engineer these organisms to produce desired chemicals in industrially scalable conditions. Most previous deep learning approaches focused on predicting the average expression levels of a gene based on its promoter sequence, ignoring its variation across different conditions. Here we present FUN-PROSE—a deep learning model trained to predict differential expression of individual genes across various conditions using their promoter sequences and expression levels of all transcription factors. We train and test our model on three fungal species and get the correlation between predicted and observed condition-specific gene expression as high as 0.85. We then interpret our model to extract promoter sequence motifs responsible for variable expression of individual genes. We also carried out input feature importance analysis to connect individual transcription factors to their gene targets. A sizeable fraction of both sequence motifs and TF-gene interactions learned by our model agree with previously known biological information, while the rest corresponds to either novel biological facts or indirect correlations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Old Woman Creek Wetland Sediment and Electrochemical Sensor Microbial Community, 2023

We are developing a technique to monitor microbiological activities referred to as zero resistance ammetry, which entails the deployment of graphite electrodes in sediments. Measurement of current between electrodes of contrasting redox regimes and/or predominant terminal electron accepting processes can be used as an indicator of the extents of microbiological activity. We deployed an electrode array at depths of 2 mm, 4 mm, 76 mm, 78 mm, 152 mm, 154 mm, 227 mm, and 229 mm below the wetland sediment water interface in the Old Woman Creek National Estuarine Research Center, Huron, OH, USA (Lat. = 41.380833, Long. = -82.508889). A core was collected from adjacent sediment and subsamples were collected from depth intervals of 0 – 25 mm, 25 – 127 mm, 127 – 128 mm, and below 178 mm. To determine if the microbial communities attached to the electrodes were reflective of the adjacent sediment-associated microbial community, we conducted a 16S rRNA gene-based (V4 region) survey of these respective materials. This data package contains the results of these surveys, including metadata on the depths from which samples were collected (samples.csv), DNA extraction and sequencing information (OWC_DEPTH_AMPLICON_SEQUENCING_METADATA), sequence processing information (OWC_DEPTH_BIOINFORMATIC_METADATA.csv), an operational taxonomic unit (OTU) table (OWC_DEPTH_97OTUS_TABLE.csv), and nucleotide sequences of OTUs (OWC_DEPTH_97OTUS_SEQS.fasta). All files can be opened using a text-editing application. The fasta file is compatible with bioinformatics applications.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Study of the Protection Improvements for a Weak Grid Area With High Inverter-Based Resources (IBRs)

This project designs enhanced protection scheme for the real-world weak grid area with a high penetration of IBRs. As the existing protection schemes are originally designed for traditional synchronous machines, we first evaluate if the protection scheme will continue to operate reliably in systems with high levels of IBRs. Hardware relays are tested using a controller-hardware-in-the-loop setup. PSCAD electromagnetic transient simulation with IBR original equipment manufacturer black-box models is used to perform fault studies and generate COMTRADE data, which are replayed by a real-time digital simulator (RTDS) to feed input to the hardware relays. Three scenarios are analyzed: normal operation, an N-1 contingency, and an IBR-only scenario. The evaluation results reveal the following: 1) the protection scheme remains reliable under normal conditions and N-1 contingencies and 2) in IBR-only scenarios, differential protection (87L) continues to operate reliably, whereas local protection elements, such as distance and directional elements, fail because of the lack of regulated negative sequence current contributed by IBRs. Enhanced protection is designed to address the challenge of lack of negative sequence current from IBRs, including increased restraining factors a2 and k2 to block 32Q or using V instead QV ORDER for ground faults, enhanced mho distance element with voltage and phase angle supervision for L-L faults. The efficacy of enhanced protection logic is validated and proven to work reliably. Additionally, IEEE Std. 2800-2022 negative sequence current compliant GFL and GFM IBRs from another vendor are tested and proven to work reliably without need for enhanced logic. Therefore, this work provides valuable decision-making for utilities facing protection system challenges due to IBRs, either designing enhanced protection scheme or requesting their IBRs being IEEE Std. 2800-2022 compliant to produce regulated negative sequence current for protection relay to make correct decision.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2021

Microbial Community Field Surveys Reveal Abundant Pseudomonas Population in Sorghum Rhizosphere Composed of Many Closely Related Phylotypes

While the root-associated microbiome is typically less diverse than the surrounding soil due to both plant selection and microbial competition for plant derived resources, it typically retains considerable complexity, harboring many hundreds of distinct bacterial species. Here, we report a time-dependent deviation from this trend in the rhizospheres of field grown sorghum. In this study, 16S rRNA amplicon sequencing was used to determine the impact of nitrogen fertilization on the development of the root-associated microbiomes of 10 sorghum genotypes grown in eastern Nebraska. We observed that early rhizosphere samples exhibit a significant reduction in overall diversity due to a high abundance of the bacterial genus Pseudomonas that occurred independent of host genotype in both high and low nitrogen fields and was not observed in the surrounding soil or associated root endosphere samples. When clustered at 97% identity, nearly all the Pseudomonas reads in this dataset were assigned to a single operational taxonomic unit (OTU); however, exact sequence variant (ESV)-level resolution demonstrated that this population comprised a large number of distinct Pseudomonas lineages. Furthermore, single-molecule long-read sequencing enabled high-resolution taxonomic profiling revealing further heterogeneity in the Pseudomonas lineages that was further confirmed using shotgun metagenomic sequencing. Finally, field soil enriched with specific carbon compounds recapitulated the increase in Pseudomonas, suggesting a possible connection between the enrichment of these Pseudomonas species and a plant-driven exudate profile.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Understanding the Origin of Structural Diversity of DNA Double Helix

Deciphering the contribution of DNA subunits to the variability of its 3D structure represents an important step toward the elucidation of DNA functions at the atomic level. In the pursuit of that goal, our previous studies revealed that the essential conformational characteristics of the most populated “canonic” BI and AI conformational families of Watson–Crick duplexes, including the sequence dependence of their 3D structure, preexist in the local energy minima of the elemental single-chain fragments, deoxydinucleoside monophosphates (dDMPs). Those computations have uncovered important sequence-dependent regularity in the superposition of neighbor bases. The present work expands our studies to new minimal fragments of DNA with Watson–Crick nucleoside pairs that differ from canonic families in the torsion angles of the sugar-phosphate backbone (SPB). To address this objective, computations have been performed on dDMPs, cdDMPs (complementary dDMPs), and minimal fragments of SPBs of respective systems by using methods of molecular and quantum mechanics. These computations reveal that the conformations of dDMPs and cdDMPs having torsion angles of SPB corresponding to the local energy minima of separate minimal units of SPB exhibit sequence-dependent characteristics representative of canonic families. In contrast, conformations of dDMP and cdDMP with SPB torsions being far from the local minima of separate SPB units exhibit more complex sequence dependence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Identification and Characterization of ten Escherichia coli Strains Encoding Novel Shiga Toxin 2 Subtypes, Stx2n as Well as Stx2j, Stx2m, and Stx2o, in the United States

The sharing of genome sequences in online data repositories allows for large scale analyses of specific genes or gene families. This can result in the detection of novel gene subtypes as well as the development of improved detection methods. Here, we used publicly available WGS data to detect a novel Stx subtype, Stx2n in two clinical E. coli strains isolated in the USA. During this process, additional Stx2 subtypes were detected; six Stx2j, one Stx2m strain, and one Stx2o, were all analyzed for variability from the originally described subtypes. Complete genome sequences were assembled from short- or long-read sequencing and analyzed for serotype, and ST types. The WGS data from Stx2n- and Stx2o-producing STEC strains were further analyzed for virulence genes pro-phage analysis and phage insertion sites. Nucleotide and amino acid maximum parsimony trees showed expected clustering of the previously described subtypes and a clear separation of the novel Stx2n subtype. WGS data were used to design OMNI PCR primers for the detection of all known stx1 (283 bp amplicon), stx2 (400 bp amplicon), intimin encoded by eae (221 bp amplicon), and stx2f (438 bp amplicon) subtypes. These primers were tested in three different laboratories, using standard reference strains. An analysis of the complete genome sequence showed variability in serogroup, virulence genes, and ST type, and Stx2 pro-phages showed variability in size, gene composition, and phage insertion sites. The strains with Stx2j, Stx2m, Stx2n, and Stx2o showed toxicity to Vero cells. Stx2j carrying strain, 2012C-4221, was induced when grown with sub-inhibitory concentrations of ciprofloxacin, and toxicity was detected. Taken together, these data highlight the need to reinforce genomic surveillance to identify the emergence of potential new Stx2 or Stx1 variants. The importance of this surveillance has a paramount impact on public health. Per our description in this study, we suggest that 2017C-4317 be designated as the Stx2n type-strain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Developing Asparagaceae1726: An Asparagaceae‐specific probe set targeting 1726 loci for Hyb‐Seq and phylogenomics in the family

Abstract Premise Target sequence capture (Hyb‐Seq) is a cost‐effective sequencing strategy that employs RNA probes to enrich for specific genomic sequences. By targeting conserved low‐copy orthologs, Hyb‐Seq enables efficient phylogenomic investigations. Here, we present Asparagaceae1726—a Hyb‐Seq probe set targeting 1726 low‐copy nuclear genes for phylogenomics in the angiosperm family Asparagaceae—which will aid the often‐challenging delineation and resolution of evolutionary relationships within Asparagaceae. Methods Here we describe and validate the Asparagaceae1726 probe set (https://github.com/bentzpc/Asparagaceae1726) in six of the seven subfamilies of Asparagaceae. We perform phylogenomic analyses with these 1726 loci and evaluate how inclusion of paralogs and bycatch plastome sequences can enhance phylogenomic inference with target‐enriched data sets. Results We recovered at least 82% of target orthologs from all sampled taxa, and phylogenomic analyses resulted in strong support for all subfamilial relationships. Additionally, topology and branch support were congruent between analyses with and without inclusion of target paralogs, suggesting that paralogs had limited effect on phylogenomic inference. Discussion Asparagaceae1726 is effective across the family and enables the generation of robust data sets for phylogenomics of any Asparagaceae taxon. Asparagaceae1726 establishes a standardized set of loci for phylogenomic analysis in Asparagaceae, which we hope will be widely used for extensible and reproducible investigations of diversification in the family.

Plant Sciences↗
DOE OSTI2020

HIV-1 transmitted drug resistance surveillance: shifting trends in study design and prevalence estimates

HIV-1 transmitted drug resistance (TDR) prevalence increased during the initial years of the antiretroviral therapy (ART) global scale-up. Few studies have examined recent trends in TDR prevalence using published genetic sequences and described the characteristics of ART-naïve persons from whom these published sequences have been obtained. We identified 125 studies published between 2014 and 2019 for which HIV-1 reverse transcriptase (RT) with or without protease from ≥50 ART-naïve adult persons were submitted to the GenBank sequence database. The population characteristics and TDR prevalence were compared to those in 122 studies published in the preceding five years between 2009 and 2013. TDR prevalence was analysed using median study-level and person-level data. The 2009 to 2013 and 2014 to 2019 studies reported sequence data from 32,866 and 41,724 ART-naïve persons respectively. Studies from the low- and middle-income country (LMIC) regions in sub-Saharan Africa, South/Southeast Asia and Latin America/Caribbean accounted for approximately two-thirds of the studies during each period. Between the two periods, the proportion of studies from sub-Saharan Africa and from South/Southeast Asia countries other than China decreased from 43% to 32% and the proportion of studies performed at sentinel sites for recent HIV-1 infection decreased from 33% to 22%. Between 2014 and 2019, median study-level TDR prevalence was 4.1% in South/Southeast Asia, 6.0% in sub-Saharan Africa, 9.1% in Latin America/Caribbean, 8.5% in Europe and 14.2% in North America. In the person-level analysis, there was an increase in overall, NNRTI and two-class NRTI/NNRTI resistance in sub-Saharan Africa; an increase in NNRTI resistance in Latin America/Caribbean, and an increase in overall, NNRTI and PI resistance in North America. Overall, NNRTI and dual NRTI/NNRTI-associated TDR prevalence was significantly higher in sub-Saharan Africa studies published between 2014 and 2019 compared with those published between 2009 and 2013. The decreasing proportion of studies from the hardest hit LMIC regions and the shift away from sentinel sites for recent infection suggests that global TDR surveillance efforts and publication of findings require renewed emphasis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

A new primer set for Clade I nosZ that recovers genes from a broader range of taxa

Denitrification is an important global N cycle process. The gene encoding NosZ that converts nitrous oxide (N 2 O) to N 2 has been widely used as a biomarker to study denitrifying communities. However, conventional PCR primers target a limited range of the genetically diverse Clade I nosZ, and the amplicons are too long for sequencing on current NGS platforms. To address these issues, here we developed a new PCR primer set that amplifies a 355-bp region of Clade I nosZ and captures broader taxonomic coverage than conventional primers in in silico tests. When compared with the widely used nosZF_nosZR_Rich_2003 set using the same soil samples and the same sequencing depth, the new set retrieved genes from four times more unique species, with consistently higher general diversity-based metrics. The new primer set performed well with different sequencing platforms (Ion Torrent and Illumina), and among a wide variety of soils from polar to tropical, desert to agricultural, and surface to a very low biomass subsoil, with significant differences in denitrifying community diversity and composition. This new primer set for Clade I together with the primers recently reported for Clade II by Chee-Sanford et al. provides a more comprehensive assessment of denitrifier gene hosts, their ecological patterns, and the degree of novelty in retrieved gene sequences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Large-scale harmonic balance simulations with Krylov subspace and preconditioner recycling

The multi-harmonic balance method combined with numerical continuation provides an efficient framework to compute a family of time-periodic solutions, or response curves, for large-scale, nonlinear mechanical systems. The predictor and corrector steps repeatedly solve a sequence of linear systems that scale by the model size and number of harmonics in the assumed Fourier series approximation. In this paper, a novel Newton–Krylov iterative method is embedded within the multi-harmonic balance and continuation algorithm to efficiently compute the approximate solutions from the sequence of linear systems that arise during the prediction and correction steps. Further, the method recycles, or reuses, both the preconditioner and the Krylov subspace generated by previous linear systems in the solution sequence. A delayed frequency preconditioner refactorizes the preconditioner only when the performance of the iterative solver deteriorates. The GCRO-DR iterative solver recycles a subset of harmonic Ritz vectors to initialize the solution subspace for the next linear system in the sequence. The performance of the iterative solver is demonstrated on two exemplars with contact-type nonlinearities and benchmarked against a direct solver with traditional Newton–Raphson iterations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Image Processing Pipeline for Fluoroelastomer Crystallite Detection in Atomic Force Microscopy Images

Phase transformations in materials systems can be tracked using atomic force microscopy (AFM), enabling the examination of surface properties and macroscale morphologies. In situ measurements investigating phase transformations generate large datasets of time-lapse image sequences. The interpretation of the resulting image sequences, guided by domain-knowledge, requires manual image processing using handcrafted masks. Here this approach is time-consuming and restricts the number of images that can be processed. Her in this study, we developed an automated image processing pipeline which integrates image detection and segmentation methods. We examine five time-series AFM videos of various fluoroelastomer phase transformations. The number of image sequences per video ranges from a hundred to a thousand image sequences. The resulting image processing pipeline aims to automatically classify and analyze images to enable batch processing. Using this pipeline, the growth of each individual fluoroelastomer crystallite can be tracked through time. We incorporated statistical analysis into the pipeline to investigate trends in phase transformations between different fluoroelastomer batches. Understanding these phase transformations is crucial, as it can provide valuable insights into manufacturing processes, improve product quality, and possibly lead to the development of more advanced fluoroelastomer formulations.

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↗