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Results for “negative selection”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Genomic Features and Pervasive Negative Selection in Rhodanobacter Strains Isolated from Nitrate and Heavy Metal Contaminated Aquifer

Despite the dominance of Rhodanobacter species in the subsurface of the contaminated Oak Ridge Reservation (ORR) site, very little is known about the mechanisms underlying their adaptions to the various stressors present at ORR. Recently, multiple Rhodanobacter strains have been isolated from the ORR groundwater samples from several wells with varying geochemical properties.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Selected Negative Linear Compressibilities in the Metal–Organic Framework of [Cu(4,4'-bpy) 2 (H 2 O) 2 ]·SiF 6

Negative linear compressibility (NLC) is a rare high-pressure observation that lattice contraction is accompanied by the structural expansion along a specific direction. Generally, this counterintuitive phenomenon only derives from the intrinsic structural characteristics of materials and cannot be tuned by external perturbations. Searching for an effective method to control NLC effect is still a challenge in both chemical and material science. In this work, we successfully discover and select the NLC behaviors in the metal-organic framework (MOF) of [Cu(4,4'-bpy) 2 (H 2 O) 2 ]·SiF 6 (Cu(bpy)·SiF) through controlling the pressure conditions therein. The NLC effect of Cu(bpy)·SiF originates from the wine-rack mechanism that quasi-square grids transfer to rhombic ones with the structural expansion along the diagonal direction at high pressure. Meanwhile, both of the pressure range and magnitude of the NLC responses are enlarged with optimized pressure conditions. This study not only presents the intriguing selected NLC behaviors of a MOF but also proves the effects of pressure conditions on NLC, which offers promising strategies for further design and applications of NLC materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Is the exquisite specificity of lymphocytes generated by thymic selection or due to evolution?

We have previously argued that the antigen receptors of T and B lymphocytes evolved to be sufficiently specific to avoid massive deletion of clonotypes by negative selection. Their optimal ‘specificity’ level, i.e., probability of binding any particular epitope, was shown to be inversely related to the number of self-antigens that the cells have to be tolerant to. Experiments have demonstrated that T lymphocytes also become more specific during negative selection in the thymus, because cells expressing the most crossreactive receptors have the highest likelihood of binding a self-antigen, and hence to be tolerized (i.e., deleted, anergized, or diverted into a regulatory T cell phenotype). Thus, there are two —not mutually exclusive— explanations for the exquisite specificity of T cells, one involving evolution and the other thymic selection. To better understand the impact of both, we extend a previously developed mathematical model by allowing for T cells with very different binding probabilities in the pre-selection repertoire. We confirm that negative selection tends to tolerize the most crossreactive clonotypes. As a result, the average level of specificity in the functional post-selection repertoire depends on the number of self-antigens, even if there is no evolutionary optimization of binding probabilities. However, the evolutionary optimal range of binding probabilities in the pre-selection repertoire also depends on the number of self-antigens. Species with more self antigens need more specific pre-selection repertoires to avoid excessive loss of T cells during thymic selection, and hence mount protective immune responses. We conclude that both evolution and negative selection are responsible for the high level of specificity of lymphocytes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A Genetic Study of Nif -Associated Genes in a Hyperthermophilic Methanogen

Methanocaldococcus has been considered a model genus, but genetic tools have not been forthcoming until recently. Here, we develop and illustrate the utility of positive selection with either of two selective agents (simvastatin and neomycin), negative selection, generation of markerless in-frame deletion mutations, and genetic complementation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Engineering sensitivity and specificity of AraC-based biosensors responsive to triacetic acid lactone and orsellinic acid

Abstract We previously described the design of triacetic acid lactone (TAL) biosensor ‘AraC-TAL1’, based on the AraC regulatory protein. Although useful as a tool to screen for enhanced TAL biosynthesis, this variant shows elevated background (leaky) expression, poor sensitivity and relaxed inducer specificity, including responsiveness to orsellinic acid (OA). More sensitive biosensors specific to either TAL or OA can aid in the study and engineering of polyketide synthases that produce these and similar compounds. In this work, we employed a TetA-based dual-selection to isolate new TAL-responsive AraC variants showing reduced background expression and improved TAL sensitivity. To improve TAL specificity, OA was included as a ‘decoy’ ligand during negative selection, resulting in the isolation of a TAL biosensor that is inhibited by OA. Finally, to engineer OA-specific AraC variants, the iterative protein redesign and optimization computational framework was employed, followed by 2 rounds of directed evolution, resulting in a biosensor with 24-fold improved OA/TAL specificity, relative to AraC-TAL1.

Wang, Zhiqing↗
DOE OSTI2022

Trait drift in microalgae and applications for strain improvement

Microalgae are increasingly used to generate a wide range of commercial products, and there is growing evidence that microalgae-based products can be produced sustainably. However, industrial production of microalgal biomass is not as developed as other biomanufacturing platform technologies. In addition, results of bench-scale research often fail to translate to large-scale or mass production systems. This disconnect may result from trait drift and evolution occurring, through time, in response to unique drivers in each environment, such as cultivation regimes, weather, and pests. Moreover, outdoor and indoor cultivation of microalgae has the potential to impose negative selection pressures, which makes the maintenance of desired traits a challenge. In this context, this review sheds the light on our current understanding of trait drift and evolution in microalgae. Here, we delineate the basics of phenotype plasticity and evolution, with a focus on how microalgae respond under various conditions. In addition, we review techniques that exploit phenotypic plasticity and evolution for strain improvement in view of industrial commercial applications, highlighting associated advantages and shortcomings. Finally, we suggest future research directions and recommendations to overcome unwanted trait drift and evolution in microalgae cultivation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Shaping Nanobodies and Intrabodies against Proteoforms

Proteoforms expand genomic diversity and direct developmental processes. While high-resolution mass spectrometry has accelerated characterization of proteoforms, molecular techniques working to bind, and disrupt the function of specific proteoforms have lagged behind. In this study, we worked to develop intrabodies capable of binding specific proteoforms. Herein we employed a synthetic camelid nanobody library expressed in yeast to identify nanobody binders of different SARS-CoV-2 receptor binding domain (RBD) proteoforms. Importantly, employment of the positive and negative selection mechanism inherent to the synthetic system allowed for amplification of nanobody-expressing yeast that bind to the original (Wuhan strain RBD) but not the E484K (Beta variant) mutation. Nanobodies raised against specific RBD proteoforms were validated by yeast-2-hybrid analysis and sequence comparisons. These results provide a clear framework for development of proteoform-specific nanobodies and intrabodies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Manifesting Direction-Specific Complexation in [HFIP –H ·H 2 O 2 ] – : Exclusive Formation of a High-Lying Conformation

Size-selective, negative ion photoelectron spectroscopy in conjunction with quantum chemical calculations is employed to investigate the geometric and electronic structures of a protype system in catalytic olefin epoxidation research, i.e., deprotonated hexafluoroisopropanol ([HFIP -H ] - ) complexed with hydrogen peroxide (H 2 O 2 ). Spectral assignments and molecular electrostatic surface analyses unveil a surprising prevalent existence of a high-lying isomer with asymmetric dual hydrogenbonding configuration that is preferably formed driven by influential directionspecific electrostatic interactions upon H 2 O 2 approaching [HFIP -H ] - anion. Subsequent inspections of molecular orbitals, charge and spin density distributions indicate the occurrence of partial charge transfer from [HFIP -H ] - to H 2 O 2 upon hydrogen bonding interactions. Accompanying with electron detachment, a proton transfer occurs to form the neutral complex of [HFIP•HOO • ] structure. In conclusion, this work conspicuously illustrates the importance of directionality encoded in intermolecular interactions involving asymmetric and complex molecules, while the produced hydroperoxyl radical HOO • offers a possible new pathway in olefin epoxidation chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica

Abstract Genome-wide functional genetic screens have been successful in discovering genotype-phenotype relationships and in engineering new phenotypes. While broadly applied in mammalian cell lines and in E. coli , use in non-conventional microorganisms has been limited, in part, due to the inability to accurately design high activity CRISPR guides in such species. Here, we develop an experimental-computational approach to sgRNA design that is specific to an organism of choice, in this case the oleaginous yeast Yarrowia lipolytica . A negative selection screen in the absence of non-homologous end-joining, the dominant DNA repair mechanism, was used to generate single guide RNA (sgRNA) activity profiles for both SpCas9 and LbCas12a. This genome-wide data served as input to a deep learning algorithm, DeepGuide, that is able to accurately predict guide activity. DeepGuide uses unsupervised learning to obtain a compressed representation of the genome, followed by supervised learning to map sgRNA sequence, genomic context, and epigenetic features with guide activity. Experimental validation, both genome-wide and with a subset of selected genes, confirms DeepGuide’s ability to accurately predict high activity sgRNAs. DeepGuide provides an organism specific predictor of CRISPR guide activity that with retraining could be applied to other fungal species, prokaryotes, and other non-conventional organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Identifying sequence perturbations to an intrinsically disordered protein that determine its phase-separation behavior

Phase separation of intrinsically disordered proteins (IDPs) commonly underlies the formation of membraneless organelles, which compartmentalize molecules intracellularly in the absence of a lipid membrane. Identifying the protein sequence features responsible for IDP phase separation is critical for understanding physiological roles and pathological consequences of biomolecular condensation, as well as for harnessing phase separation for applications in bioinspired materials design. To expand our knowledge of sequence determinants of IDP phase separation, we characterized variants of the intrinsically disordered RGG domain from LAF-1, a model protein involved in phase separation and a key component of P granules. Based on a predictive coarse-grained IDP model, we identified a region of the RGG domain that has high contact probability and is highly conserved between species; deletion of this region significantly disrupts phase separation in vitro and in vivo. We determined the effects of charge patterning on phase behavior through sequence shuffling. We designed sequences with significantly increased phase separation propensity by shuffling the wild-type sequence, which contains well-mixed charged residues, to increase charge segregation. This result indicates the natural sequence is under negative selection to moderate this mode of interaction. We measured the contributions of tyrosine and arginine residues to phase separation experimentally through mutagenesis studies and computationally through direct interrogation of different modes of interaction using all-atom simulations. Finally, we show that despite these sequence perturbations, the RGG-derived condensates remain liquid-like. Together, these studies advance our fundamental understanding of key biophysical principles and sequence features important to phase separation.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Systematic identification of cis -regulatory variants that cause gene expression differences in a yeast cross

Sequence variation in regulatory DNA alters gene expression and shapes genetically complex traits. However, the identification of individual, causal regulatory variants is challenging. Here, we used a massively parallel reporter assay to measure the cis-regulatory consequences of 5832 natural DNA variants in the promoters of 2503 genes in the yeast Saccharomyces cerevisiae. We identified 451 causal variants, which underlie genetic loci known to affect gene expression. Several promoters harbored multiple causal variants. In five promoters, pairs of variants showed non-additive, epistatic interactions. Causal variants were enriched at conserved nucleotides, tended to have low derived allele frequency, and were depleted from promoters of essential genes, which is consistent with the action of negative selection. Causal variants were also enriched for alterations in transcription factor binding sites. Models integrating these features provided modest, but statistically significant, ability to predict causal variants. This work revealed a complex molecular basis for cis-acting regulatory variation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Rationally designed negative electrode for selective CO 2 -to-CO conversion in protonic ceramic electrochemical cells

Protonic ceramic electrochemical cells (PCECs) are solid-state electrochemical devices that employ proton-conducting oxides as electrolytes, which offer a promising approach for electrification of chemical manufacturing, including CO 2 reduction to produce value-added chemicals (e.g., CO). The primary advantage of PCECs is their intermediate operating temperatures (300–600 °C), which thermodynamically and kinetically favor the CO 2 reduction chemistry at the negative electrode. However, the conventional negative electrodes of PCECs, such as BaZr 0.8–x Ce x Y 0.2 O 3-δ -Ni or BaZr 0.8–x Ce x Y 0.1 Yb 0.1 O 3-δ -Ni, cannot reduce CO 2 to either CH 4 or CO with a selectivity of >99 %, leading to the production of a CO and CH 4 mixture. Herein, an oxide-supported in-situ exsolved Ni-Fe alloyed nanoparticle electrocatalyst, Sr 2 Fe 1.4 Mo 0.5 O 6-δ -Ni0.175 (SFM-Ni0.175), is first employed as the negative electrode of PCECs. The PCECs equipped with this new negative electrode selectively favor the CO 2 -to-CO conversion. A selectivity of ~100 % toward CO has been demonstrated over a wide range of operating temperatures (400–600 °C) and applied potentials/current densities. The negative electrode demonstrated in this work fully suppresses the CH 4 production. In situ diffuse reflectance infrared spectroscopy (DRIFTS) was performed to probe the CO 2 reduction mechanisms over both SFM-Ni0.175 and the traditional negative electrode (BCZYYb7111 +Ni), which indicates SFM-Ni0.175 inhibits the formation of formate species, leading to selective production of CO. Finally, this work validates that PCECs equipped with the rationally designed negative electrode can selectively manufacture chemicals.

25 ENERGY STORAGE↗
DOE OSTI2022

A reverse-selective ion exchange membrane for the selective transport of phosphates via an outer-sphere complexation–diffusion pathway

Specific-ion selectivity is a highly desirable feature for the next generation of membranes. However, existing membranes rely on differences in charge, size and hydration energy, which limits their ability to target individual ion species. Here we demonstrate a nanocomposite ion-exchange membrane material that enables a reverse-selective transport mechanism that can selectively pass a single ion species. Here we demonstrate this transport mechanism with phosphate ions selectively transporting across negatively charged cation exchange membranes. Selective transport is enabled by the in situ growth of hydrous manganese oxide nanoparticles throughout a cation exchange membrane that provide a diffusion pathway via phosphate-specific, reversible outer-sphere interactions. On incorporating the hydrous manganese oxide nanoparticles, the membrane’s phosphate flux increased by a factor of 27 over an unmodified cation exchange membrane, and the selectivity of phosphorous over sulfate, nitrate and chloride reaches 47,100 and 20, respectively. By pairing ion-specific outer-sphere interactions between the target ions and appropriate nanoparticles, these nanocomposite ion-exchange materials can, in principle, achieve selective transport for a range of ions.

42 ENGINEERING↗
DOE OSTI2023

REC protein family expansion by the emergence of a new signaling pathway

This report presents multi-genome evidence that REC protein family expansion occurs when the emergence of new pathways gives rise to functional discordance. Specificity between residues in REC domain containing response regulators with paired histidine kinases is under negative purifying selection, constrained by the presence of other bacterial two-component systems signaling cascades that share sequence and structural identity. Presuming that the two-component systems can evolve by neutral amino acid changes (neutral drift) when purifying evolutionary constraints are relaxed, how might the REC protein family expand by amino acid changes when these constraints remain intact? Using an unsupervised machine learning approach to observe the sequence landscape of REC domains across long phylogenetic distances, we find that within-gene recombination, a subcategory of gene conversion, switched the effector domain and, consequently, the regulatory context of a duplicated response regulator from transcriptional regulation by σ54 to that by σ70. We determined that the recombined response regulator diverged from its parent by episodic diversifying selection and neutral drift. Functional experiments of the parent of recombined response regulators in a model Pseudomonas putida KT2440 model system revealed that the parent and recombined response regulators sense and respond to different carboxylic acids. Finally, a residue-switching experiment using structural predictions and functional characterization suggests that the new residues in the recombined regulator could form a new interaction interface and mediate condition-specific phosphotransfer. Overall, our study finds that genetic perturbations can create conditions of functional discordance, whereby the REC protein family can evolve by episodic diversifying selection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Properties of Gaseous Deprotonated L-Cysteine S-Sulfate Anion [cysS-SO3]−: Intramolecular H-Bond Network, Electron Affinity, Chemically Active Site, and Vibrational Fingerprints

L-cysteine S-sulfate, Cys-SSO3H, and their derivatives play essential roles in biological chemistry and pharmaceutical synthesis, yet their intrinsic molecular properties have not been studied to date. In this contribution, the deprotonated anion [cysS-SO3]− was introduced in the gas phase by electrospray and characterized by size-selected, cryogenic, negative ion photoelectron spectroscopy. The electron affinity of the [cysS-SO3]• radical was determined to be 4.95 ± 0.10 eV. In combination with theoretical calculations, it was found that the most stable structure of [cysS-SO3]− (S1) is stabilized via three intramolecular hydrogen bonds (HBs); i.e., one O-H……N between the -COOH and -NH2 groups, and two N-H……O HBs between -NH2 and -SO3, in which the amino group serves as both HB acceptor and donor. In addition, a nearly iso-energetic conformer (S2) with the formation of an O-H……N-H……O-S chain-type binding motif competes with S1 in the source. The most reactive site of the molecule susceptible for electrophilic attacks is the linkage S atom. Theoretically predicted infrared spectra indicate that O-H and N-H stretching modes are the fingerprint region (2800 to 3600 cm−1) to distinguish different isomers. The obtained information lays out a foundation to better understand the transformation and structure–reactivity correlation of Cys-SSO3H in biologic settings.

74 ATOMIC AND MOLECULAR PHYSICS↗