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At least 937 records · Page 52
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Disc dichotomy signature in the vertical distribution of [Mg/Fe] and the delayed gas infall scenario

Context. Analysis of the Apache Point Observatory Galactic Evolution Experiment project (APOGEE) data suggests the existence of a clear distinction between two sequences of disc stars in the [α/Fe] versus [Fe/H] abundance ratio space, known as the high- and low-α sequence, respectively. This dichotomy also emerges from an analysis of the vertical distribution of the [α/Fe] abundance ratio. Aims. We aim to test whether the revised two-infall chemical evolution models designed to reproduce the low- and high-α sequences in the [α/Fe] versus [Fe/H] ratios in the solar neighbourhood are also capable of predicting the disc bimodality observed in the vertical distribution of [Mg/Fe] in APOGEE DR16 data. Methods. Along with the chemical composition of the simple stellar populations born at different Galactic times predicted by our reference chemical evolution models in the solar vicinity, we provide their maximum vertical height above the Galactic plane |zmax| computed assuming the relation between the vertical action and stellar age in APOGEE thin-disc stars. Result. The vertical distribution of the [Mg/Fe] abundance ratio predicted by the reference chemical evolution models is in agreement with that observed when combining the APOGEE DR16 data (chemical abundances) with the astroNN catalogue (stellar ages, orbital parameters) for stars younger than 8 Gyr (only low-α sequence stars). Including the high-α disc component, the dichotomy in the vertical [Mg/Fe] abundance distribution is reproduced considering the observational cut in the Galactic height of |z|< 2 kpc. However, our model predicts an overly flat (almost constant) growth of the maximum vertical height |zmax| quantity as a function of [Mg/Fe] for high-α objects in contrast with the median values from APOGEE data. Possible explanations for such a tension are that: (i) the APOGEE sample with |z|< 2 kpc is more likely than ours to be contaminated by halo stars, causing the median values to be kinematically hotter, and (ii) external perturbations – such as minor mergers – that the Milky Way experienced in the past could have heated up the disc, and the heating of the orbits cannot be modeled by only scattering processes. Assuming a disc dissection based on chemistry for APOGEE-DR16 stars (|z|< 2 kpc), the observed |zmax| distributions for high-α and low-α sequences are in good agreement with our model predictions if we consider the errors in the vertical action estimates in the calculation. Moreover, a better agreement between predicted and observed stellar distributions at different Galactic vertical heights is achieved if asteroseismic ages are included as a constraint in the best-fit model calculations. Conclusions. The signature of a delayed gas infall episode, which gives rise to a hiatus in the star formation history of the Galaxy, are imprinted both in the [Mg/Fe] versus [Fe/H] relation and in vertical distribution of [Mg/Fe] abundances in the solar vicinity.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae

Advances in sequencing technology have unveiled examples of nucleus-encoded polycistrons, once considered rare. Exclusively polycistronic transcripts are prevalent in green algae, although the mechanism by which multiple polypeptides are translated from a single transcript is unknown. Here, we used bioinformatic and in vivo mutational analyses to evaluate competing mechanistic models for translation of bicistronic mRNAs in green algae. High-confidence manually curated datasets of bicistronic loci from two divergent green algae, Chlamydomonas reinhardtii and Auxenochlorella protothecoides, revealed a preference for weak Kozak-like sequences for ORF 1 and an underrepresentation of potential initiation codons before the ORF 2 start codon, which are suitable conditions for leaky ribosome scanning to allow ORF 2 translation. We used mutational analysis in A. protothecoides to test the mechanism. In vivo manipulation of the ORF 1 Kozak-like sequence and start codon altered reporter expression at ORF 2, with a weaker Kozak-like sequence enhancing expression and a stronger one diminishing it. A synthetic bicistronic dual reporter demonstrated inversely adjustable activity of green fluorescent protein expressed from ORF 1 and luciferase from ORF 2, depending on the strength of the ORF 1 Kozak-like sequence. Our findings demonstrate that translation of multiple ORFs in green algal bicistronic transcripts is consistent with episodic leaky scanning of ORF 1 to allow translation at ORF 2. This work has implications for the potential functionality of upstream open reading frames (uORFs) found across eukaryotic genomes and for transgene expression in synthetic biology applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structure-based group A streptococcal vaccine design: Helical wheel homology predicts antibody cross-reactivity among streptococcal M protein–derived peptides

Group A streptococcus (Strep A) surface M protein, an α-helical coiled-coil dimer, is a vaccine target and a major determinant of streptococcal virulence. The sequence-variable N-terminal region of the M protein defines the M type and also contains epitopes that promote opsonophagocytic killing of streptococci. Recent reports have reported considerable cross-reactivity among different M types, suggesting the prospect of identifying cross-protective epitopes that would constitute a broadly protective multivalent vaccine against Strep A isolates. In this work, we have used a combination of immunological assays, structural biology, and cheminformatics to construct a recombinant M protein–based vaccine that included six Strep A M peptides that were predicted to elicit antisera that would cross-react with an additional 15 nonvaccine M types of Strep A. Rabbit antisera against this recombinant vaccine cross-reacted with 10 of the 15 nonvaccine M peptides. Two of the five nonvaccine M peptides that did not cross-react shared high sequence identity (≥50%) with the vaccine peptides, implying that high sequence identity alone was insufficient for cross-reactivity among the M peptides. Additional structural analyses revealed that the sequence identity at corresponding polar helical-wheel heptad sites between vaccine and nonvaccine peptides accurately distinguishes cross-reactive from non–cross-reactive peptides. On the basis of these observations, we developed a scoring algorithm based on the sequence identity at polar heptad sites. When applied to all epidemiologically important M types, this algorithm should enable the selection of a minimal number of M peptide–based vaccine candidates that elicit broadly protective immunity against Strep A.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Robust atom optics for Bragg atom interferometry

Multi-photon Bragg diffraction is a powerful method for fast, coherent momentum transfer of atom waves. However, laser noise, Doppler detunings, and cloud expansion limit its efficiency in large momentum transfer (LMT) pulse sequences. We present simulation studies of robust Bragg pulses developed through numerical quantum optimal control. Optimized pulse performance under noise and cloud inhomogeneities is analyzed and compared to analogous Gaussian and adiabatic rapid passage pulses in simulated LMT Mach–Zehnder interferometry sequences. The optimized pulses maintain robust population transfer and phase response over a broader range of noise, resulting in superior contrast in LMT sequences with thermal atom clouds and intensity inhomogeneities. Large optimized LMT sequences use lower pulse area than Gaussian pulses, making them less susceptible to spontaneous emission loss. The optimized sequences maintain over five times better contrast with tens of momentum separation and offer more improvement with greater LMT. Such pulses could allow operation of Bragg atom interferometers with unprecedented sensitivity, improved contrast, and hotter atom sources.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Gauges, loops, and polynomials for partition functions of graphical models

Graphical models represent multivariate and generally not normalized probability distributions. Computing the normalization factor, called the partition function, is the main inference challenge relevant to multiple statistical and optimization applications. The problem is #P-hard that is of an exponential complexity with respect to the number of variables. Here, aimed at approximating the partition function, we consider multi-graph models where binary variables and multivariable factors are associated with edges and nodes, respectively, of an undirected multi-graph. We suggest a new methodology for analysis and computations that combines the Gauge function technique from Chertkov and Chernyak with the technique developed in Anari and Oveis Gharan 2017 arXiv:1702.02937; Gurvits 2011 arXiv:1106.2844; Straszak and Vishnoi 2017 55th Annual Allerton Conf. on Communication, Control, and Computing, based on the recent progress in the field of real stable polynomials. We show that the Gauge function, representing a single-out term in a finite sum expression for the partition function which achieves extremum at the so-called belief-propagation gauge, has a natural polynomial representation in terms of gauges/variables associated with edges of the multi-graph. Moreover, Gauge function can be used to recover the partition function through a sequence of transformations allowing appealing algebraic and graphical interpretations. Algebraically, one step in the sequence consists of the application of a differential operator over gauges associated with an edge. Graphically, the sequence is interpreted as a repetitive elimination/contraction of edges resulting in multi-graph models on decreasing in size (number of edges) graphs with the same partition function as in the original multi-graph model. Even though the complexity of computing factors in the sequence of the derived multi-graph models and respective Gauge functions grow exponentially with the number of eliminated edges, polynomials associated with the new factors remain bi-stable if the original factors have this property. Moreover, we show that BP estimations in the sequence do not decrease, each low-bounding the partition function.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Sensitive and error-tolerant annotation of protein-coding DNA with BATH

We present BATH, a tool for highly sensitive annotation of protein-coding DNA based on direct alignment of that DNA to a database of protein sequences or profile hidden Markov models (pHMMs). BATH is built on top of the HMMER3 code base, and simplifies the annotation workflow for pHMM-based translated sequence annotation by providing a straightforward input interface and easy-to-interpret output. BATH also introduces novel frameshift-aware algorithms to detect frameshift-inducing nucleotide insertions and deletions (indels). BATH matches the accuracy of HMMER3 for annotation of sequences containing no errors, and produces superior accuracy to all tested tools for annotation of sequences containing nucleotide indels. These results suggest that BATH should be used when high annotation sensitivity is required, particularly when frameshift errors are expected to interrupt protein-coding regions, as is true with long-read sequencing data and in the context of pseudogenes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

TreeSAPP: the Tree-based Sensitive and Accurate Phylogenetic Profiler

Microbial communities drive matter and energy transformations integral to global biogeochemical cycles, yet many taxonomic groups facilitating these processes remain poorly represented in biological sequence databases. Due to this missing information, taxonomic assignment of sequences from environmental genomes remains inaccurate. We present the Tree-based Sensitive and Accurate Phylogenetic Profiler (TreeSAPP) software for functionally and taxonomically classifying genes, reactions and pathways from genomes of cultivated and uncultivated microorganisms using reference packages representing coding sequences mediating multiple globally relevant biogeochemical cycles. TreeSAPP uses linear regression of evolutionary distance on taxonomic rank to improve classifications, assigning both closely related and divergent query sequences at the appropriate taxonomic rank. TreeSAPP is able to provide quantitative functional and taxonomic classifications for both assembled and unassembled sequences and files supporting interactive tree of life visualizations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

DNABERT-S: pioneering species differentiation with species-aware DNA embeddings

SUMMARY: We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space. Differentiating species from genomic sequences (i.e. DNA and RNA) is vital yet challenging, since many real-world species remain uncharacterized, lacking known genomes for reference. Embedding-based methods are therefore used to differentiate species in an unsupervised manner. DNABERT-S builds upon a pre-trained genome foundation model named DNABERT-2. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C2LR) strategy. Empirical results on 28 diverse datasets show DNABERT-S's effectiveness, especially in realistic label-scarce scenarios. For example, it identifies twice more species from a mixture of unlabeled genomic sequences, doubles the Adjusted Rand Index (ARI) in species clustering, and outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training. AVAILABILITY AND IMPLEMENTATION: Model, codes, and data are publically available at https://github.com/MAGICS-LAB/DNABERT_S.

Zhou, Zhihan↗
DOE OSTI2025

NEAR: Neural Embeddings for Amino acid Relationships

Protein language models (PLMs) have recently demonstrated potential to supplant classical protein database search methods based on sequence alignment, but are slower than common alignment-based tools and appear to be prone to a high rate of false labeling. Here, we present NEAR, a method based on neural representation learning that is designed to improve both speed and accuracy of search for likely homologs in a large protein sequence database. NEAR’s ResNet embedding model is trained using contrastive learning guided by trusted sequence alignments. It computes per-residue embeddings for target and query protein sequences, and identifies alignment candidates with a pipeline consisting of residue-level k-NN search and a simple neighbor aggregation scheme. Tests on a benchmark consisting of trusted remote homologs and randomly shuffled decoy sequences reveal that NEAR substantially improves accuracy relative to state-of-the-art PLMs, with lower memory requirements and faster embedding and search speed. While these results suggest that the NEAR model may be useful for standalone homology detection with increased sensitivity over standard alignment-based methods, in this manuscript we focus on a more straightforward analysis of the model’s value as a high-speed pre-filter for sensitive annotation. In that context, NEAR is at least 5x faster than the pre-filter currently used in the widely-used profile hidden Markov model (pHMM) search tool HMMER3, and also outperforms the pre-filter used in our fast pHMM tool, nail.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

CUT&RUN identifies centromeric DNA regions of Rhodotorula toruloides IFO0880

ABSTRACT Rhodotorula toruloides has been increasingly explored as a host for bioproduction of lipids, fatty acid derivatives and terpenoids. Various genetic tools have been developed, but neither a centromere nor an autonomously replicating sequence (ARS), both necessary elements for stable episomal plasmid maintenance, has yet been reported. In this study, cleavage under targets and release using nuclease (CUT&RUN), a method used for genome-wide mapping of DNA–protein interactions, was used to identify R. toruloides IFO0880 genomic regions associated with the centromeric histone H3 protein Cse4, a marker of centromeric DNA. Fifteen putative centromeres ranging from 8 to 19 kb in length were identified and analyzed, and four were tested for, but did not show, ARS activity. These centromeric sequences contained below average GC content, corresponded to transcriptional cold spots, were primarily nonrepetitive and shared some vestigial transposon-related sequences but otherwise did not show significant sequence conservation. Future efforts to identify an ARS in this yeast can utilize these centromeric DNA sequences to improve the stability of episomal plasmids derived from putative ARS elements.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The hTERT core promoter forms three parallel G-quadruplexes

The structure of the 68 nt sequence with G-quadruplex forming potential within the hTERT promoter is disputed. One model features a structure with three stacked parallel G-quadruplex units, while another features an unusual duplex hairpin structure adjoined to two stacked parallel and antiparallel quadruplexes. We report here the results of an integrated structural biology study designed to distinguish between these possibilities. As part of our study, we designed a sequence with an optimized hairpin structure and show that its biophysical and biochemical properties are inconsistent with the structure formed by the hTERT wild-type sequence. By using circular dichroism, thermal denaturation, nuclear magnetic resonance spectroscopy, analytical ultracentrifugation, small-angle X-ray scattering, molecular dynamics simulations and a DNase I cleavage assay we found that the wild type hTERT core promoter folds into a stacked, three-parallel G-quadruplex structure. The hairpin structure is inconsistent with all of our experimental data obtained with the wild-type sequence. All-atom models for both structures were constructed using molecular dynamics simulations. These models accurately predicted the experimental hydrodynamic properties measured for each structure. We found with certainty that the wild-type hTERT promoter sequence does not form a hairpin structure in solution, but rather folds into a compact stacked three-G-quadruplex conformation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters

Secondary metabolites are small molecules produced by all corners of life, often with specialized bioactive functions with clinical and environmental relevance. Secondary metabolite biosynthetic gene clusters (BGCs) can often be identified within DNA sequences by various sequence similarity tools, but determining the exact functions of genes in the pathway and predicting their chemical products can often only be done by careful, manual comparative analysis. To facilitate this, we report the first release of the secondary metabolism collaboratory (SMC), which aims to provide a comprehensive, tool-agnostic repository of BGC sequence data drawn from all publicly available and user-submitted bacterial and archaeal genome and contig sources. On the website, users are provided a searchable catalog of putative BGCs identified from each source, along with visualizations of gene and domain annotations derived from multiple sequence analysis tools. SMC’s data is also available through publicly-accessible application programming interface (API) endpoints to facilitate programmatic access. Users are encouraged to share their findings (and search for others’) through comment posts on BGC and source pages. At the time of writing, SMC is the largest repository of BGC information, holding 13.1M BGC regions from 1.3M source sequences and growing, and can be found at https://smc.jgi.doe.gov.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Distant-acting Enhancers in Development and Disease

Multiple converging lines of evidence from experimental and human genetic studies indicate that both common and rare sequence variants involving enhancers play major roles in Mendelian and complex human disease phenotypes. We use a combination of sequence-based molecular approaches including chromatin mapping and synthesis-enabled modification of enhancer sequences, large-scale transgenic mouse studies (http://enhancer.lbl.gov), and CRISPR genome editing in the mouse model to study the in vivofunction of enhancers in developmental, evolutionary, and disease-related processes. Using examples from our ongoing work, I will illustrate how these methods provide insight into the function and evolution of distant-acting regulatory sequences and offer a starting point for understanding their role in human disease. I will discuss how improved in vivo mouse assays can be used to study candidate pathogenic human mutations in enhancers at scale, revealing the extent to which human genetic studies alone can be insufficient to identify truly causal mutations in enhancers. I will also show how such assays can be used to explore the sensitivity of enhancers that are extremely conserved ("ultraconserved") in evolution to mutations, revealing a remarkable functional robustness to sequence changes that contrasts with apparent evolutionary constraints.

Visel, A↗
DOE OSTI2023

An HMM approach expands the landscape of sesquiterpene cyclases across the kingdom Fungi

Sesquiterpene cyclases (STC) catalyse the cyclization of the C15 molecule farnesyl diphosphate into a vast variety of mono- or polycyclic hydrocarbons and, for a few enzymes, oxygenated structures, with diverse stereogenic centres. The huge diversity in sesquiterpene skeleton structures in nature is primarily the result of the type of cyclization driven by the STC. Despite the phenomenal impact of fungal sesquiterpenes on the ecology of fungi and their potentials for applications, the fungal sesquiterpenome is largely untapped. The identification of fungal STC is generally based on protein sequence similarity with characterized enzymes. This approach has improved our knowledge on STC in a few fungal species, but it has limited success for the discovery of distant sequences. Besides, the tools based on secondary metabolite biosynthesis gene clusters have shown poor performance for terpene cyclases. Here, we used four sets of sequences of fungal STC that catalyse four types of cyclization, and specific amino acid motives to identify phylogenetically related sequences in the genomes of basidiomycetes fungi from the order Polyporales. We validated that four STC genes newly identified from the genome sequence of Leiotrametes menziesii, each classified in a different phylogenetic clade, catalysed a predicted cyclization of farnesyl diphosphate. We built HMM models and searched STC genes in 656 fungal genomes genomes. We identified 5605 STC genes, which were classified in one of the four clades and had a predicted cyclization mechanism. We noticed that the HMM models were more accurate for the prediction of the type of cyclization catalysed by basidiomycete STC than for ascomycete STC.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Improved Control Strategy of Grid-Forming Inverters for Fault Ride-Through in a Microgrid System

This paper develops an improved control strategy of grid-forming (GFM) inverters with fault ride-through capabilities to guarantee the stable operation of microgrids under fault conditions, especially islanded microgrids and asymmetrical faults. The proposed control strategy includes the dual control of positive-sequence and negative-sequence control as well as the adaptive virtual impedance (VI) control. Unlike existing works, the proposed strategy applies the VI control for only the d component of the positive-sequence control and leaves the q component of the positive-sequence control and the dq component of the negative-sequence control as zero, thus achieving improved stability and balanced three-phase voltages under asymmetrical faults. The adaptive feature of the VI control guarantees the stability of the GFM inverter under severe faults, which could cause the saturation of the inner current loop and instability if the VI is not adaptive. Simulation results of various unbalanced faults with high- and low-fault impedances show that the proposed control strategy improves the stability of the GFM inverter and achieves stable and balanced output voltages in islanded microgrids. And the algorithm also improves the stability of GFM inverters under balanced faults with high- and low-fault impedances.

adaptive virtual impedance control↗
DOE OSTI2023

Energy-Centric Cooperative Onramp Merging Strategy: An Analytical Solution

Cooperative highway onramp merging plays an important role in mitigating highway traffic congestion. A crucial component of a cooperative merging system is the merging sequence strategy, which determines each merging participant's order to reach the merging point. Existing merging sequence strategies can be classified into rule-based and optimization-based approaches. The rule-based strategies can be effortlessly implemented with a light online computational burden. However, they may not achieve the optimal energy efficiency. In contrast, the optimization-based strategies can yield the optimal merging sequence to minimize fuel consumption, but typically involve computationally expensive numerical optimization. To leverage the advantages from both sides, we propose a novel merging sequence strategy that can minimize fuel consumption while avoiding online numerical optimization. The key idea is to analytically formulate the expected fuel consumption of each merging participant. Using a realistic highway onramp scenario based on the NGSIM dataset, we validate the performance and the computational efficiency of the proposed merging sequence strategy via SUMO/SIMULINK joint simulation.

Wang, Zejiang↗
DOE OSTI2023

Targeted synthesis of predicted metastable compounds using modulated elemental reactants

Three metastable compounds predicted to be kinetically stable using an “island” approach were successfully synthesized from designed modulated elemental reactants. Fe0.8V0.2Se2 was synthesized by depositing ultrathin elemental layers in a V|Fe|Se sequence to control the local composition. An alloyed rock salt structured Pb3Mn2Se5 constituent layer, which does not exist as a bulk compound, was synthesized in the heterostructure (Pb3Mn2Se5)0.6VSe2 by depositing a precursor with a V|Se|Pb|Se|Mn|Se|Pb|Se|Mn|Se|Pb|Se sequence of elemental layers that mimicked the compositional profile of the targeted heterostructure. The heterostructure (PbSe)1+δ(FeSe2)2 was prepared by depositing a precursor with a repeating layering sequence of Fe|Pb|Fe|Se, where each sequence contains the number of atoms required to form a single unit cell. In all three systems, the local compositions in the layer sequence kinetically favored the nucleation and growth of the targeted products during the deposition. The diffusion lengths to form the targeted compounds were short, and the diffusion was limited by postdeposition low temperature annealing to favor the growth of the targeted compounds and avoid the decomposition into a mixture of thermodynamically stable compounds.

Lemon, Mellie (ORCID:0000000328705881)↗
DOE OSTI2023

Understanding the transient large amplitude oscillatory shear behavior of yield stress fluids

A full understanding of the sequence of processes exhibited by yield stress fluids under large amplitude oscillatory shearing is developed using multiple experimental and analytical approaches. A novel component rate Lissajous curve, where the rates at which strain is acquired unrecoverably and recoverably are plotted against each other, is introduced and its utility is demonstrated by application to the analytical responses of four simple viscoelastic models. Using the component rate space, yielding and unyielding are identified by changes in the way strain is acquired, from recoverably to unrecoverably and back again. The behaviors are investigated by comparing the experimental results with predictions from the elastic Bingham model that is constructed using the Oldroyd–Prager formalism and the recently proposed continuous model by Kamani, Donley, and Rogers in which yielding is enhanced by rapid acquisition of elastic strain. The physical interpretation gained from the transient large amplitude oscillatory shear (LAOS) data is compared to the results from the analytical sequence of physical processes framework and a novel time-resolved Pipkin space. The component rate figures, therefore, provide an independent test of the interpretations of the sequence of physical processes analysis that can also be applied to other LAOS analysis frameworks. Each of these methods, the component rates, the sequence of physical processes analysis, and the time-resolved Pipkin diagrams, unambigiously identifies the same material physics, showing that yield stress fluids go through a sequence of physical processes that includes elastic deformation, gradual yielding, plastic flow, and gradual unyielding.

Kamani, Krutarth M. (ORCID:0000000338975420)↗