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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 1,081 records · Page 60
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Photoisomerization transition state manipulation by entangled two-photon absorption

Significance Entangled two-photon absorption has attracted considerable interest due to its potential applications for low–photon flux spectroscopy and microscopy. The entanglement parameters in the twin-photon state can be exploited to control two-photon excitation processes. Here we demonstrate that photon entanglement provides a powerful novel control knob for the nuclear wave packets in an optically dark electronic state. We show that the transition states in the trans–cis photoisomerization of azobenzene, initiated by an entangled two-photon absorption process, can be manipulated significantly by entangled light. These effects can be monitored experimentally by coherent stimulated X-ray Raman signals which reveal electronic coherences during the passage through conical intersections.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Structural insights reveal interplay between LAG-3 homodimerization, ligand binding, and function

Lymphocyte activation gene-3 (LAG-3) is an inhibitory receptor expressed on activated T cells and an emerging immunotherapy target. Domain 1 (D1) of LAG-3, which has been purported to directly interact with major histocompatibility complex class II (MHCII) and fibrinogen-like protein 1 (FGL1), has been the major focus for the development of therapeutic antibodies that inhibit LAG-3 receptor-ligand interactions and restore T cell function. Here, we present a high-resolution structure of glycosylated mouse LAG-3 ectodomain, identifying that cis-homodimerization, mediated through a network of hydrophobic residues within domain 2 (D2), is critically required for LAG-3 function. Additionally, we found a previously unidentified key protein-glycan interaction in the dimer interface that affects the spatial orientation of the neighboring D1 domain. Mutation of LAG-3 D2 residues reduced dimer formation, dramatically abolished LAG-3 binding to both MHCII and FGL1 ligands, and consequentially inhibited the role of LAG-3 in suppressing T cell responses. Intriguingly, we showed that antibodies directed against D1, D2, and D3 domains are all capable of blocking LAG-3 dimer formation and MHCII and FGL-1 ligand binding, suggesting a potential allosteric model of LAG-3 function tightly regulated by dimerization. Furthermore, our work reveals unique epitopes, in addition to D1, that can be targeted for immunotherapy of cancer and other human diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Solution Structure of the HIV-1 Intron Splicing Silencer and Its Interactions with the UP1 Domain of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) A1

Splicing patterns in human immunodeficiency virus type 1 (HIV-1) are maintained through cis regulatory elements that recruit antagonistic host RNA-binding proteins. The activity of the 3' acceptor site A7 is tightly regulated through a complex network of an intronic splicing silencer (ISS), a bipartite exonic splicing silencer (ESS3a/b), and an exonic splicing enhancer (ESE3). Because HIV-1 splicing depends on protein-RNA interactions, it is important to know the tertiary structures surrounding the splice sites. Herein, we present the NMR solution structure of the phylogenetically conserved ISS stem loop. ISS adopts a stable structure consisting of conserved UG wobble pairs, a folded 2X2 (GU/UA) internal loop, a UU bulge, and a flexible AGUGA apical loop. Calorimetric and biochemical titrations indicate that the UP1 domain of heterogeneous nuclear ribonucleoprotein A1 binds the ISS apical loop site-specifically and with nanomolar affinity. Atogether, this work provides additional insights into how HIV-1 uses a conserved RNA structure to commandeer a host RNA-binding protein.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

A global view of structure–function relationships in the tautomerase superfamily

The tautomerase superfamily (TSF) consists of more than 11,000 nonredundant sequences present throughout the biosphere. Characterized members have attracted much attention because of the unusual and key catalytic role of an N-terminal proline. These few characterized members catalyze a diverse range of chemical reactions, but the full scale of their chemical capabilities and biological functions remains unknown. To gain new insight into TSF structure–function relationships, we performed a global analysis of similarities across the entire superfamily and computed a sequence similarity network to guide classification into distinct subgroups. Our results indicate that TSF members are found in all domains of life, with most being present in bacteria. The eukaryotic members of the cis-3-chloroacrylic acid dehalogenase subgroup are limited to fungal species, whereas the macrophage migration inhibitory factor subgroup has wide eukaryotic representation (including mammals). Unexpectedly, we found that 346 TSF sequences lack Pro-1, of which 85% are present in the malonate semialdehyde decarboxylase subgroup. The computed network also enabled the identification of similarity paths, namely sequences that link functionally diverse subgroups and exhibit transitional structural features that may help explain reaction divergence. A structure-guided comparison of these linker proteins identified conserved transitions between them, and kinetic analysis paralleled these observations. Phylogenetic reconstruction of the linker set was consistent with these findings. Our results also suggest that contemporary TSF members may have evolved from a short 4-oxalocrotonate tautomerase–like ancestor followed by gene duplication and fusion. Our new linker-guided strategy can be used to enrich the discovery of sequence/structure/function transitions in other enzyme superfamilies.

Biochemistry & Molecular Biology↗
DOE OSTI2019

Structural determinants for accurate dephosphorylation of RNA polymerase II by its cognate C-terminal domain (CTD) phosphatase during eukaryotic transcription

The C-terminal domain (CTD) of RNA polymerase II contains a repetitive heptad sequence (YSPTSPS) whose phosphorylation states coordinate eukaryotic transcription by recruiting protein regulators. The precise placement and removal of phosphate groups on specific residues of the CTD are critical for the fidelity and effectiveness of RNA polymerase II–mediated transcription. During transcriptional elongation, phosphoryl-Ser 5 (pSer 5 ) is gradually dephosphorylated by CTD phosphatases, whereas Ser 2 phosphorylation accumulates. Using MS, X-ray crystallography, protein engineering, and immunoblotting analyses, in this work we investigated the structure and function of SSU72 homolog, RNA polymerase II CTD phosphatase (Ssu72, from Drosophila melanogaster ), an essential CTD phosphatase that dephosphorylates pSer 5 at the transition from elongation to termination, to determine the mechanism by which Ssu72 distinguishes the highly similar pSer 2 and pSer 5 CTDs. We found that Ssu72 dephosphorylates pSer 5 effectively but only has low activities toward pSer 7 and pSer 2 . The structural analysis revealed that Ssu72 requires that the proline residue in the substrate's SP motif is in the cis configuration, forming a tight β-turn for recognition by Ssu72. We also noted that residues flanking the SP motif, such as the bulky Tyr 1 next to Ser 2 , prevent the formation of such configuration and enable Ssu72 to distinguish among the different SP motifs. The phosphorylation of Tyr 1 further prohibited Ssu72 binding to pSer 2 and thereby prevented untimely Ser 2 dephosphorylation. Our results reveal critical roles for Tyr 1 in differentiating the phosphorylation states of Ser 2 /Ser 5 of CTD in RNA polymerase II that occur at different stages of transcription.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

A fatty acid-binding protein of Streptococcus pneumoniae facilitates the acquisition of host polyunsaturated fatty acids

Streptococcus pneumoniae is responsible for the majority of pneumonia, motivating ongoing searches for insights into its physiology that could enable new treatments. S. pneumoniae responds to exogenous fatty acids by suppressing its de novo biosynthetic pathway and exclusively utilizing extracellular fatty acids for membrane phospholipid synthesis. The first step in exogenous fatty acid assimilation is phosphorylation by fatty acid kinase (FakA), whereas bound by a fatty acid-binding protein (FakB). Staphylococcus aureus has two binding proteins, whereas S. pneumoniae expresses three. The functions of these binding proteins were not clear. Here, we determined the SpFakB1- and SpFakB2-binding proteins were bioinformatically related to the two binding proteins of Staphylococcus aureus, and biochemical and X-ray crystallographic analysis showed that SpFakB1 selectively bound saturates, whereas SpFakB2 allows the activation of monounsaturates akin to their S. aureus counterparts. The distinct SpFakB3 enables the utilization of polyunsaturates. The SpFakB3 crystal structure in complex with linoleic acid reveals an expanded fatty acid-binding pocket within the hydrophobic interior of SpFakB3 that explains its ability to accommodate multiple cis double bonds. SpFakB3 also utilizes a different hydrogen bond network than other FakBs to anchor the fatty acid carbonyl and stabilize the protein. S. pneumoniae strain JMG1 (ΔfakB3) was deficient in incorporation of linoleate from human serum verifying the role of FakB3 in this process. Thus, the multiple FakBs of S. pneumoniae permit the utilization of the entire spectrum of mammalian fatty acid structures to construct its membrane.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

One-colour (~220 nm) resonance-enhanced (S 1 –S 0 ) multi-photon dissociation of acetylene: probe of the C 2 A 1 Π u – X 1 Σ + g band by frequency-modulation spectroscopy

In a recent paper, we demonstrated that one-colour (~220 nm), resonance-enhanced (S 1 –S 0 ), photodissociation of acetylene generates strong $C_2$ Swan band ($d^3Π_g–a^3Π_u$) and $C_2$ Deslandres-d'Azambuja band ($C^1Π_g–A^1Π_u$) fluorescence, and long-lived (>3 µs) fluorescence from an electronically-excited $C_2$H * species. It was not known whether the $C_2A^1Π_u$ and $X^1Σ^+_g$ states are also directly populated in this process. In this paper, multiple vibration-rotation transitions between the $C_2A$-state v = 2 and the X-state v = 0 level are examined by time-resolved frequency-modulation (FM) spectroscopy. The photolysis laser wavelength is tuned into resonance at the one-photon level with S 1 –S 0 transitions that populate individual rotational levels of the S 1 $_{trans}$-conformer $3^2,3^3,$ and $3^4$ vibrational states. By comparing the phase of the FM signals from the $C_2A–X$ transitions with that from the Rb D 1 -line absorption transition, we determine that, for all of the probed A–X transitions, the X-state level is more populated than the A-state level. We propose that the acetylene S 1 level is excited by the second photon to an acetylene dissociation precursor state, which undergoes sequential C-H bond-breaking to produce the $C_2X$ state. The dissociation precursor is assigned as the $1^1B_g(trans-bent)/1^1B_1(cis-bent)$ valence state, which correlates to a doubly-excited configuration, $(1π_u)^2(1π_g)^2$, at linear geometry. Based on the rotational distributions of the $C_2X$-state fragments, we believe that at least one of the transition states involved in the photolysis via S 1 $3^4$ has a larger CC-H bend-angle for the departing H-atom than that involved in the S 1 $3^2$ and $3^3$ photolysis.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

New reactions of diazene and related species for modelling combustion of amine fuels

Potential energy surfaces for reactions involving N 2 H 2 isomers of diazene (diimide) have been explored using density functional theory, with energies based on coupled-cluster theory. A focus is on processes that create or consume these species, and isomerisation between the E (trans) and Z (cis) forms of HNNH. Furthermore, these include isomerisation and dissociation pathways for HNNH, addition of H atoms to form N 2 H 3 , abstraction by H atoms yielding short-lived NNH, and abstraction reactions of H with N 2 H 3 . Transition state and capture theories are applied for high-pressure-limiting behaviour, while low-pressure and falloff regions are characterised via the methods of Troe and coworkers. Rate constants and thermochemistry are provided to improve models of diamine chemistry, relevant to the combustion of NH 3 especially at high concentrations, high pressures or under reducing conditions. Results indicate that amine radical recombination mainly yields the E HNNH isomer, while H-abstraction from N 2 H 3 results in E HNNH and H 2 NN. However, at elevated temperature E → Z isomerisation becomes competitive, and Z HNNH, being more reactive, acts to enhance the diazene consumption rate.

10 SYNTHETIC FUELS↗
DOE OSTI2013

GYROSURFING ACCELERATION OF IONS IN FRONT OF EARTH's QUASI-PARALLEL BOW SHOCK

It is well known that shocks in space plasmas can accelerate particles to high energies. However, many details of the shock acceleration mechanism are still unknown. A critical element of shock acceleration is the injection problem; i.e., the presence of the so called seed particle population that is needed for the acceleration to work efficiently. In our case study, we present for the first time observational evidence of gyroresonant surfing acceleration in front of Earth's quasi-parallel bow shock resulting in the appearance of the long-suspected seed particle population. For our analysis, we use simultaneous multi-spacecraft measurements provided by the Cluster spacecraft ion (CIS), magnetic (FGM), and electric field and wave instrument (EFW) during a time period of large inter-spacecraft separation distance. The spacecraft were moving toward the bow shock and were situated in the foreshock region. The results show that the gyroresonance surfing acceleration takes place as a consequence of interaction between circularly polarized monochromatic (or quasi-monochromatic) transversal electromagnetic plasma waves and short large amplitude magnetic structures (SLAMSs). The magnetic mirror force of the SLAMS provides the resonant conditions for the ions trapped by the waves and results in the acceleration of ions. Since wave packets with circular polarization and different kinds of magnetic structures are very commonly observed in front of Earth's quasi-parallel bow shock, the gyroresonant surfing acceleration proves to be an important particle injection mechanism. We also show that seed ions are accelerated directly from the solar wind ion population.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Weak maser emission of methyl formate toward Sagittarius B2(N) in the green bank telescope PRIMOS survey

A non-LTE radiative transfer treatment of cis-methyl formate (HCOOCH{sub 3}) rotational lines is presented for the first time using a set of theoretical collisional rate coefficients. These coefficients have been computed in the temperature range 5-30 K by combining coupled-channel scattering calculations with a high accuracy potential energy surface for HCOOCH{sub 3}-He. The results are compared to observations toward the Sagittarius B2(N) molecular cloud using the publicly available PRIMOS survey from the Green Bank Telescope. A total of 49 low-lying transitions of methyl formate, with upper levels below 25 K, are identified. These lines are found to probe a presumably cold (∼30 K), moderately dense (∼10{sup 4} cm{sup –3}), and extended region surrounding Sgr B2(N). The derived column density of ∼4 × 10{sup 14} cm{sup –2} is only a factor of ∼10 larger than the column density of the trans conformer in the same source. Provided that the two conformers have the same spatial distribution, this result suggests that strongly non-equilibrium processes must be involved in their synthesis. Finally, our calculations show that all detected emission lines with a frequency below 30 GHz are (collisionally pumped) weak masers amplifying the continuum of Sgr B2(N). This result demonstrates the importance and generality of non-LTE effects in the rotational spectra of complex organic molecules at centimeter wavelengths.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

THE MICROWAVE SPECTROSCOPY OF METHYL FORMATE IN THE SECOND TORSIONAL EXCITED STATE

The cis-methyl formate molecule is a well known molecule found in interstellar space. Recently, rotational lines of methyl formate in the first CH{sub 3} torsional excited state were observed in Orion KL and W51e2. It is quite natural to observe methyl formate in even higher vibrational states considering the temperature estimated in Orion KL and W51e2. Maeda et al. reported results on the laboratory spectroscopy of methyl formate including the spectral analysis in its second CH{sub 3} torsional state. Their assignments were limited to a series of a-type R-branch lines and low K{sub a} b-type R-branch transitions, and many assigned lines are excluded in the least-squares analysis. In the present study, we extended the line assignments of both the A- and E-species transitions in the second CH{sub 3} torsional state especially in the frequency region below the 120 GHz region. By combining the present assignments and those made by Maeda et al., 1951 transitions in total for the second CH{sub 3} torsional state, 1096 A-species transitions up to J = 39, and K{sub a} = 15 and 855 E-species transitions up to J = 35 and K{sub a} = 13, were least-squares analyzed by using the pseudo-principal-axis-method Hamiltonian with 42 parameters consisting of rotational, centrifugal distortion, and internal rotational constants in the second CH{sub 3} torsional state. In addition, 1012 transitions out of 1096 A-species transitions could also be least-squares analyzed by using Watson's A-reduced Hamiltonian with 43 parameters, which can serve to calculate the energy levels of the A-species lines of molecules with the CH{sub 3} internal rotation conveniently.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2015

COMPREHENSIVE ANALYSIS OF PREBIOTIC PROPENAL UP TO 660 GHz

Since interstellar detection of propenal is only based on two rotational transitions in the centimeter wave region, its high resolution rotational spectrum has been measured up to 660 GHz and fully characterized by assignment of more than 12,000 transitions to provide direct laboratory data to the astronomical community. Spectral assignments and analysis include transitions from the ground state of the trans and cis isomers, three trans-{sup 13}C isotopologues, and ten excited vibrational states of the trans form. Combining new millimeter and submillimeter data with those from the far-infrared region has yielded the most precise set of spectroscopic constants of trans-propenal obtained to date. Newly determined rotational constants, centrifugal distortion constants, vibrational energies, and Coriolis and Fermi interaction constants are given with high accuracy and were used to predict transition frequencies and intensities over a wide frequency range. Results of this work should facilitate astronomers further observation of propenal in the interstellar medium.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2018

Calibration and performance of the ATLAS Tile Calorimeter during the LHC Run 2

The Tile Calorimeter (TileCal) is the hadronic sampling calorimeter of the ATLAS experiment at the Large Hadron Collider (LHC). TileCal uses iron absorbers and scintillators as active material and it covers the central region | η| < 1.7. Jointly with the other sub-detectors it is designed for measurements of hadrons, jets, tau-particles and missing transverse energy. It also assists in muon identification. TileCal is regularly monitored and calibrated by several different calibration systems: a Cs radioactive source, a laser light system to check the PMT response, and a charge injection system (CIS) to check the front-end electronics. These calibration systems, in conjunction with data collected during proton-proton collisions, Minimum Bias (MB) events, provide extensive monitoring of the instrument and a means for equalizing the calorimeter response at each stage of the signal propagation. The performance of the calorimeter has been established with cosmic ray muons and the large sample of the proton-proton collisions and compared to Monte Carlo (MC) simulations. The response of high momentum isolated muons is also used to study the energy response at the electromagnetic scale, isolated hadrons are used as a probe of the hadronic response. The calorimeter time resolution is studied with multijet events. A description of the different TileCal calibration systems and the results on the calorimeter performance during the LHC Run 2 are introduced. The findings on the pile-up noise and response uniformity studies are also reported on.

47 OTHER INSTRUMENTATION↗
DOE OSTI2026

Pixel response characterization of the ARCADIA fully depleted MAPS

Monolithic Active Pixel Sensors (MAPS) achieved widespread use in several scientific applications, thanks to their properties, such as low material budget and high granularity. The ARCADIA INFN project developed a Fully-Depleted MAPS (FD-MAPS), using a modified LFoundry 110 nm CIS process. This work presents the first laboratory characterization of the ARCADIA MD3 prototype. Measurements include threshold uniformity studies using both test-pulse injection and a 55 Fe source, as well as threshold and noise calibration achieved thanks to monochromatic X-ray sources. Ultimately, charge-collection efficiency is evaluated using an infrared laser setup.

Particle tracking detectors↗
DOE OSTI2020

Shifting agricultural practices to produce sustainable, low carbon intensity feedstocks for biofuel production

The carbon intensity (CI) of biofuel's well-to-pump life cycle is calculated by life cycle analysis (LCA) to account for the energy/material inputs of the feedstock production and fuel conversion stages and the associated greenhouse gas (GHG) emissions during these stages. The LCA is used by the California Air Resources Board's Low Carbon Fuel Standard (LCFS) program to calculate CI and monetary credits are issued based on the difference between a given fuel's CI and a reference fuel's CI. Through the Tier 2 certification program under which individual fuel production facilities can submit their own CIs with their facility input data, the LCFS has driven innovative technologies to biofuel conversion facilities, resulting in substantial reductions in GHG emissions as compared to the baseline gasoline or diesel. A similar approach can be taken to allow feedstock petition in the LCFS so that lower-CI feedstock can be rewarded. Here we examined the potential for various agronomic practices to improve the GHG profiles of corn ethanol by performing feedstock-level CI analysis for the Midwestern United States. Our system boundary covers GHG emissions from the cradle-to-farm-gate activities (i.e. farm input manufacturing and feedstock production), along with the potential impacts of soil organic carbon change during feedstock production. We conducted scenario-based CI analysis of ethanol, coupled with regionalized inventory data, for various farming practices to manage corn fields, and identified key parameters affecting cradle-to-farm-gate GHG emissions. The results demonstrate large spatial variations in CI of ethanol due to farm input use and land management practices. In particular, adopting conservation tillage, reducing nitrogen fertilizer use, and implementing cover crops has the potential to reduce GHG emissions per unit corn produced when compared to a baseline scenario of corn–soybean rotation. This work shows a large potential emission offset opportunity by allowing feedstock producers a path to Tier 2 petitions that reward low-CI feedstocks and further reduce biofuels' CI. The prevalence of significant acreage that has not been optimized for CI suggests that policy changes that incentivize optimization of this parameter could provide significant additionality over current trends in farm efficiency and adoption of conservation practice.

09 BIOMASS FUELS↗
DOE OSTI2012

A GAS-PHASE FORMATION ROUTE TO INTERSTELLAR TRANS-METHYL FORMATE

The abundance of methyl formate in the interstellar medium has previously been underpredicted by chemical models. Additionally, grain surface chemistry cannot account for the relative abundance of the cis- and trans-conformers of methyl formate, and the trans-conformer is not even formed at detectable abundance on these surfaces. This highlights the importance of studying formation pathways to methyl formate in the gas phase. The rate constant and branching fractions are reported for the gas-phase reaction between protonated methanol and formic acid to form protonated trans-methyl formate and water as well as adduct ion: Rate constants were experimentally determined using a flowing afterglow-selected ion flow tube apparatus at 300 K and a pressure of 530 mTorr helium. The results indicate a moderate overall rate constant of (3.19 {+-} 0.39) Multiplication-Sign 10{sup -10} cm{sup 3} s{sup -1} ({+-} 1{sigma}) and an average branching fraction of 0.05 {+-} 0.04 for protonated trans-methyl formate and 0.95 {+-} 0.04 for the adduct ion. These experimental results are reinforced by ab initio calculations at the MP2(full)/aug-cc-pVTZ level of theory to examine the reaction coordinate and complement previous density functional theory calculations. This study underscores the need for continued observational studies of trans-methyl formate and for the exploration of other gas-phase formation routes to complex organic molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Symptoms and Systemic Drug Reactions in Persons Receiving Weekly Rifapentine Plus Isoniazid (3HP) Treatment for Latent Tuberculosis Infection

Abstract Background Three months of weekly rifapentine plus isoniazid (3HP) therapy for latent tuberculosis infection (LTBI) is recommended worldwide. The development of symptoms and systemic drug reactions (SDRs) on 3HP have not been fully characterized. We aimed to determine the patterns of symptom development and identify SDRs and associated factors in patients taking 3HP. Methods We analyzed symptoms data in participants receiving 3HP in the Tuberculosis Trials Consortium's iAdhere study (Study 33). We examined the patterns of symptom reporting across participants from baseline and 4 monthly visits. Bivariate analyses and multivariable regression models were used to identify factors associated with SDRs. Risk ratios (RRs) and 95% confidence intervals (CIs) were calculated. Results Among 1002 participants receiving 3HP, 768 (77%) reported at least 1 symptom; 97% of these symptoms were grade 1 (79%) or grade 2 (18%). Most symptoms developed in the first month and resolved. A total of 111 (11%) participants had symptoms that met criteria for SDRs; however, 53 (48%) of these participants completed therapy. Factors associated with SDRs and discontinuation included female sex (RR: 2.05; 95% CI: 1.19–3.54), age ≥45 years (RR: 1.99; 95% CI: 1.19–3.31), and use of concomitant medications (RR: 2.26; 95% CI: 1.15–4.42). Conclusions Although most patients receiving 3HP reported symptoms, most were mild, occurred early, and resolved without stopping treatment. Among patients experiencing SDRs, nearly half were able to complete therapy. Patient and provider education should focus on differentiating severe reactions where 3HP should be stopped from minor symptoms that will resolve. Clinical Trials Registration. NCT01582711.

Immunology↗
DOE OSTI2021

The Ancient Salicoid Genome Duplication Event: A Platform for Reconstruction of De Novo Gene Evolution in Populus trichocarpa

Orphan genes are characteristic genomic features that have no detectable homology to genes in any other species and represent an important attribute of genome evolution as sources of novel genetic functions. Here, we identified 445 genes specific to Populus trichocarpa. Of these, we performed deeper reconstruction of 13 orphan genes to provide evidence of de novo gene evolution. Populus and its sister genera Salix are particularly well suited for the study of orphan gene evolution because of the Salicoid whole-genome duplication event which resulted in highly syntenic sister chromosomal segments across the Salicaceae. We leveraged this genomic feature to reconstruct de novo gene evolution from intergenera, interspecies, and intragenomic perspectives by comparing the syntenic regions within the P. trichocarpa reference, then P. deltoides, and finally Salix purpurea. Furthermore, we demonstrated that 86.5% of the putative orphan genes had evidence of transcription. Additionally, we also utilized the Populus genome-wide association mapping panel, a collection of 1,084 undomesticated P. trichocarpa genotypes to further determine putative regulatory networks of orphan genes using expression quantitative trait loci (eQTL) mapping. Functional enrichment of these eQTL subnetworks identified common biological themes associated with orphan genes such as response to stress and defense response. We also identify a putative cis-element for a de novo gene and leverage conserved synteny to describe evolution of a putative transcription factor binding site. Overall, 45% of orphan genes were captured in trans-eQTL networks.

59 BASIC BIOLOGICAL SCIENCES↗